Research Centres and Instituteshttps://hdl.handle.net/10023/392024-03-28T06:09:49Z2024-03-28T06:09:49ZCommunicating Lutheranism : church building in an age of orthodoxy, 1555-1618Schofield, Neale Denishttps://hdl.handle.net/10023/292192024-02-13T09:53:37Z2022-06-16T00:00:00ZMartin Luther’s preaching and books transformed the small town of Wittenberg into the home of the Protestant Reformation. Yet, Wittenberg’s dependence on Luther has prompted scholarship to question the town’s world-historical significance after his death. This thesis discusses the role of Wittenberg’s print trade in shaping the Protestant church between 1555 and 1618. It describes a changing book market and identifies the factors contributing to its commercial success and the city’s ongoing religious influence. We focus on the careers of printers, publishers and booksellers who helped embed the teachings of the Reformation by working with university theologians and political leaders to publish Lutheran books. The results were remarkable. Wittenberg became the leading German publishing city, nearly doubling its annual output of new editions compared to the Reformation period. Discoveries from research in German archives and libraries shed new light on Wittenberg’s printing history and the contribution of different occupational groups within the book trades. This study examines the role of printing and printers in the confessional battles between German universities. Wittenberg’s books, especially academic dissertations, became the spearhead for establishing Lutheran orthodoxy in the early seventeenth century. The book’s preface was used polemically, leaving the contents of the book to express the tenets of faith. Each chapter introduces significant figures in the development of Wittenberg’s book trades: Samuel Selfisch, Hans Lufft, Christoph Walther, Johann Krafft, Conrad Ruhel and Johann Gormann. The outcome of this study is that the essential role of Wittenberg’s print trade in building the church is recognised for a crucial era of Wittenberg’s Reformation history that, to this point, has been relatively neglected. The book industry played an important part in ensuring that Wittenberg retained its position as the intellectual home of Lutheranism after the death of its talismanic leader.
2022-06-16T00:00:00ZSchofield, Neale DenisMartin Luther’s preaching and books transformed the small town of Wittenberg into the home of the Protestant Reformation. Yet, Wittenberg’s dependence on Luther has prompted scholarship to question the town’s world-historical significance after his death. This thesis discusses the role of Wittenberg’s print trade in shaping the Protestant church between 1555 and 1618. It describes a changing book market and identifies the factors contributing to its commercial success and the city’s ongoing religious influence. We focus on the careers of printers, publishers and booksellers who helped embed the teachings of the Reformation by working with university theologians and political leaders to publish Lutheran books. The results were remarkable. Wittenberg became the leading German publishing city, nearly doubling its annual output of new editions compared to the Reformation period. Discoveries from research in German archives and libraries shed new light on Wittenberg’s printing history and the contribution of different occupational groups within the book trades. This study examines the role of printing and printers in the confessional battles between German universities. Wittenberg’s books, especially academic dissertations, became the spearhead for establishing Lutheran orthodoxy in the early seventeenth century. The book’s preface was used polemically, leaving the contents of the book to express the tenets of faith. Each chapter introduces significant figures in the development of Wittenberg’s book trades: Samuel Selfisch, Hans Lufft, Christoph Walther, Johann Krafft, Conrad Ruhel and Johann Gormann. The outcome of this study is that the essential role of Wittenberg’s print trade in building the church is recognised for a crucial era of Wittenberg’s Reformation history that, to this point, has been relatively neglected. The book industry played an important part in ensuring that Wittenberg retained its position as the intellectual home of Lutheranism after the death of its talismanic leader.Women as book producers : the case of NurembergFarrell-Jobst, Jessica Jadehttps://hdl.handle.net/10023/292112024-02-13T03:01:21Z2022-06-16T00:00:00ZThis thesis explores the multifaceted roles in which women participated in the early modern book trade. Focusing on Nuremberg, home to many successful bookwomen, it examines how they crafted work identities and exercised agency in the printing trades, emphasizing the centrality of the family unit. This thesis reveals that not only were women involved in the book trade more frequently than hitherto acknowledged but that their participation was varied and often invisible. Locality is key to understanding the multitude of factors that both promoted and restricted women’s work. The thesis begins by reconstructing the Nuremberg print trade, looking at the local market, censorship, and patron demands that shaped it. These considerations dictated the occupational experiences and business practises of the bookmen and bookwomen working in the trade. Chapter two explores the specific gendered and legal realities women faced while engaged in this trade. Regional marriage customs, inheritance law and guild organizations defined women’s rights to property, work and legal sovereignty. The second half of the thesis presents two case studies. Drawing on a previously unexamined collection of archival sources, the first study explores the sixteenth-century careers of Katherine Gerlachin and Catherine Dietrichin, and how they actively forged work identities separate to that of wife or widow. The second case, from the seventeenth century, inspects the Endter family business, revealing that, even when not listed on imprints, women served crucial roles in larger familial enterprises. Taken together, these chapters demonstrate that women’s work can only be fully revealed by understanding that the early modern book trade was composed of family units in which women operated as vital members. As mother, wife and daughter, women took on the jobs of craftsmen, office managers, business leaders, shareholders, investors, or a combination of these tasks to play major roles in their familial businesses.
2022-06-16T00:00:00ZFarrell-Jobst, Jessica JadeThis thesis explores the multifaceted roles in which women participated in the early modern book trade. Focusing on Nuremberg, home to many successful bookwomen, it examines how they crafted work identities and exercised agency in the printing trades, emphasizing the centrality of the family unit. This thesis reveals that not only were women involved in the book trade more frequently than hitherto acknowledged but that their participation was varied and often invisible. Locality is key to understanding the multitude of factors that both promoted and restricted women’s work. The thesis begins by reconstructing the Nuremberg print trade, looking at the local market, censorship, and patron demands that shaped it. These considerations dictated the occupational experiences and business practises of the bookmen and bookwomen working in the trade. Chapter two explores the specific gendered and legal realities women faced while engaged in this trade. Regional marriage customs, inheritance law and guild organizations defined women’s rights to property, work and legal sovereignty. The second half of the thesis presents two case studies. Drawing on a previously unexamined collection of archival sources, the first study explores the sixteenth-century careers of Katherine Gerlachin and Catherine Dietrichin, and how they actively forged work identities separate to that of wife or widow. The second case, from the seventeenth century, inspects the Endter family business, revealing that, even when not listed on imprints, women served crucial roles in larger familial enterprises. Taken together, these chapters demonstrate that women’s work can only be fully revealed by understanding that the early modern book trade was composed of family units in which women operated as vital members. As mother, wife and daughter, women took on the jobs of craftsmen, office managers, business leaders, shareholders, investors, or a combination of these tasks to play major roles in their familial businesses.Quantifying costs and rewards in optimal foraging models of the marine environment. Using bulk feeding mysticete whales as an exampleSwift, René Jameshttps://hdl.handle.net/10023/291972024-02-09T11:30:19Z2021-06-30T00:00:00ZAnimals feed to maintain body condition and maximise fitness. Feeding is a multi-stage behaviour that encapsulates aspects of an animals' sensory and foraging ecology, and that can be divided into the following broad functional categories; prey detection, capture, and handling (assimilation of acquired energy stores). The evolutionary consequences of foraging have the potential to shape predator-prey dynamics, influence community and ecosystem structure; and to drive the evolution of physiological and morphological adaptations that minimise energetic costs and maximise energy uptake. Excess energy can be converted to fat (lipids) and stored to enhance reproductive potential or to protect against temporary (voluntary) starvation associated often with long distance migration or changes in prey distribution. Understanding how an animal balances these conflicting forces, and makes key foraging decisions is an important aspect to understanding their ecology. Simple questions such as how, when, where, why and what an animal chooses to feed on are difficult to answer without the development and application of new technologies. The development of new tools and analytical approaches is particularly important in the marine environment where these key life history decisions occur offshore and or at depth. Bulk feeding rorqual whales are amongst the largest species to have lived on Earth, and are major consumers of schooling krill and forage fish. Because of their size and ability to consume significant quantities of fish and krill they have an important role in structuring ecological communities. Lunge feeding is an energetically costly bulk feeding behaviour that is practised by all members of this super-family. To understand how energy fluxes pass through the consumer to be expressed as body condition it is first necessary to have reliable proxies of the energetic costs and gains associated with feeding. In this thesis methods for estimating these energy fluxes were explored using data from summer feeding (Balaenoptera physalus) and humpback whales (Megaptera novaeangliae) in Canada, and winter feeding humpback whales in northern Norway. Calibrated speed measurements were used as a proxy for the energetic costs associated with bulk feeding (lunge) and transport in baleen whales (chapter 2). Speed measurements were used to develop a lunge detector (chapter 3). Lunge speed and other kinematic variables associated with bulk feeding were used to identify species-specific signatures in feeding behaviour as a potential method for identifying prey type, and thus their caloric value as a proxy for energy uptake (chapter 4)). The feasibility of using new sensors, (i) sonar to measure prey density and dynamics from the perspective of the feeding whale (chapter 5), and (ii) an ultrasound to measure blubber depth in wild marine mammals as a proxy of body condition (chapter 6) were tested.
2021-06-30T00:00:00ZSwift, René JamesAnimals feed to maintain body condition and maximise fitness. Feeding is a multi-stage behaviour that encapsulates aspects of an animals' sensory and foraging ecology, and that can be divided into the following broad functional categories; prey detection, capture, and handling (assimilation of acquired energy stores). The evolutionary consequences of foraging have the potential to shape predator-prey dynamics, influence community and ecosystem structure; and to drive the evolution of physiological and morphological adaptations that minimise energetic costs and maximise energy uptake. Excess energy can be converted to fat (lipids) and stored to enhance reproductive potential or to protect against temporary (voluntary) starvation associated often with long distance migration or changes in prey distribution. Understanding how an animal balances these conflicting forces, and makes key foraging decisions is an important aspect to understanding their ecology. Simple questions such as how, when, where, why and what an animal chooses to feed on are difficult to answer without the development and application of new technologies. The development of new tools and analytical approaches is particularly important in the marine environment where these key life history decisions occur offshore and or at depth. Bulk feeding rorqual whales are amongst the largest species to have lived on Earth, and are major consumers of schooling krill and forage fish. Because of their size and ability to consume significant quantities of fish and krill they have an important role in structuring ecological communities. Lunge feeding is an energetically costly bulk feeding behaviour that is practised by all members of this super-family. To understand how energy fluxes pass through the consumer to be expressed as body condition it is first necessary to have reliable proxies of the energetic costs and gains associated with feeding. In this thesis methods for estimating these energy fluxes were explored using data from summer feeding (Balaenoptera physalus) and humpback whales (Megaptera novaeangliae) in Canada, and winter feeding humpback whales in northern Norway. Calibrated speed measurements were used as a proxy for the energetic costs associated with bulk feeding (lunge) and transport in baleen whales (chapter 2). Speed measurements were used to develop a lunge detector (chapter 3). Lunge speed and other kinematic variables associated with bulk feeding were used to identify species-specific signatures in feeding behaviour as a potential method for identifying prey type, and thus their caloric value as a proxy for energy uptake (chapter 4)). The feasibility of using new sensors, (i) sonar to measure prey density and dynamics from the perspective of the feeding whale (chapter 5), and (ii) an ultrasound to measure blubber depth in wild marine mammals as a proxy of body condition (chapter 6) were tested.Visual commonplacing : the transmission and reception of printed devotional images in Reformed EnglandEpstein, Norahttps://hdl.handle.net/10023/291772024-03-05T09:48:45Z2023-06-15T00:00:00ZThis thesis introduces the framework of ‘visual commonplacing’ as a way of analysing the
repeating illustrations printed in early modern English books and ephemera. This research
focuses on religious relief-cut images printed in the post-Reformation Tudor years and the
printers, publishers and readers who copied and reused illustrations. By situating this practice
within material, print and religious history we discover that copying was not uninspired or
derivative but functioned within a wider memory culture, where imitation was a function of
invention. Moreover, in a period marked by flashpoints of iconoclasm, repeating a religious
image already circulating in state-authorised print was a prudent choice for book producers.
This study begins by exploring the economic motivations for recycling images and traces
the most highly copied illustrations of the period from the earliest days of the Reformation to the
end of the Tudor period. The next chapter examines the alteration of woodcuts in the print shop,
showing how blocks were not fixed, but mutable surfaces where images could be reused while
replacing aspects of the iconography no longer acceptable in the current climate. Moving away
from workshop practices, the third chapter unpacks how repeating images served the mnemonic
aims of the book, by building specific meaning and associations through repetition. This is
followed by an investigation into how publishers exploited the echo chamber of early modern
print to circulate polemic images, furthering divisive religious strategies. Finally, we consider
how readers used the images printed in their books and broadsides in their own visual
commonplacing, by examining manuscript and embroidered copies and illustrations cut from one
work and repurposed in another. This thesis challenges past critiques that derided copying by
centring recycling on agents, detailing the creative and cognitive flexibility exhibited by visual
commonplacers.
2023-06-15T00:00:00ZEpstein, NoraThis thesis introduces the framework of ‘visual commonplacing’ as a way of analysing the
repeating illustrations printed in early modern English books and ephemera. This research
focuses on religious relief-cut images printed in the post-Reformation Tudor years and the
printers, publishers and readers who copied and reused illustrations. By situating this practice
within material, print and religious history we discover that copying was not uninspired or
derivative but functioned within a wider memory culture, where imitation was a function of
invention. Moreover, in a period marked by flashpoints of iconoclasm, repeating a religious
image already circulating in state-authorised print was a prudent choice for book producers.
This study begins by exploring the economic motivations for recycling images and traces
the most highly copied illustrations of the period from the earliest days of the Reformation to the
end of the Tudor period. The next chapter examines the alteration of woodcuts in the print shop,
showing how blocks were not fixed, but mutable surfaces where images could be reused while
replacing aspects of the iconography no longer acceptable in the current climate. Moving away
from workshop practices, the third chapter unpacks how repeating images served the mnemonic
aims of the book, by building specific meaning and associations through repetition. This is
followed by an investigation into how publishers exploited the echo chamber of early modern
print to circulate polemic images, furthering divisive religious strategies. Finally, we consider
how readers used the images printed in their books and broadsides in their own visual
commonplacing, by examining manuscript and embroidered copies and illustrations cut from one
work and repurposed in another. This thesis challenges past critiques that derided copying by
centring recycling on agents, detailing the creative and cognitive flexibility exhibited by visual
commonplacers.The "no-go" areas in Northern Ireland 1969-1972Turner, Robert Cormack Johnhttps://hdl.handle.net/10023/291082024-02-10T03:07:16Z2022-06-14T00:00:00ZThe purpose behind the thesis is to explore a little studied (and indeed little known) phenomenon of
grassroots popular politics that took place in Northern Ireland between the years 1969-1972, during
the early years of the conflict there. In several working-class communities on both sides of the
communal divide, barricades were erected and the state was effectively excluded. These communities
took political and social control of their own districts. It was, in many respects, albeit non-ideological, “an accidental experiment in anarchism”. How this worked out in the no-go areas, and
what they have to tell us about the relationship of people to the state, are the subjects of this thesis.
In the introduction I shall ask why the study of the no-go areas is relevant to us; and what, if anything,
it has to tell us about popular politics, and people's relationship with the state. Due to the fact that
this is in many ways a very little known subject I will be looking in some detail at its narrative history:
looking at the first phase of the no-go areas of 1969, and the conditions between 1969-1971 that
were to lead to the second phase of the no-go areas in August 1971 in Chapter One. In Chapter Two
I take up the narrative again to look at the development of the far more revolutionary nationalist
second phase of the no-go areas from 1971-1972, and their loyalist counter parts in the summer of
1972. In Chapter Three I look at how: the no-go areas were actually run; their internal politics; what
ideologies underpinned them; and what tensions existed within them. This is also the chapter in which
I explore comparative events from other periods in history, both international and Irish. In Chapter
Four I see how in the absence of the state the no-go areas dealt with crime and kept order. In Chapter
Five I look at the military aspects of the no-go areas; the role of the paramilitaries within them; and
how the British state and army viewed them from a military perspective. In the Conclusion I bring
the story together and see what can be learned from the political and experiment that was the no-go areas: a unique event in the western Europe of the last half of the twentieth century, when people
expelled the state and initiated an experiment in direct democracy.
Overall, I conclude that the no-go areas drew upon local traditions of self-reliance and were the
products of the prevalent fear of the time. But they both represented, and worsened, the destabilisation
of Northern Ireland: and the nationalist no-go areas allowed a republican insurgency to gather
momentum. Internally, nationalist and loyalist no-go areas differed substantially. Nationalist no-go
areas were – at least, initially – strikingly liberal in their own administration of ‘law and order’: and
showed a capacity for informal self-organisation that was robust. The second Free Derry survived for
about a year with no overall organised governing structure to speak of. By contrast, loyalist areas
were firmly under the control of the UDA.
2022-06-14T00:00:00ZTurner, Robert Cormack JohnThe purpose behind the thesis is to explore a little studied (and indeed little known) phenomenon of
grassroots popular politics that took place in Northern Ireland between the years 1969-1972, during
the early years of the conflict there. In several working-class communities on both sides of the
communal divide, barricades were erected and the state was effectively excluded. These communities
took political and social control of their own districts. It was, in many respects, albeit non-ideological, “an accidental experiment in anarchism”. How this worked out in the no-go areas, and
what they have to tell us about the relationship of people to the state, are the subjects of this thesis.
In the introduction I shall ask why the study of the no-go areas is relevant to us; and what, if anything,
it has to tell us about popular politics, and people's relationship with the state. Due to the fact that
this is in many ways a very little known subject I will be looking in some detail at its narrative history:
looking at the first phase of the no-go areas of 1969, and the conditions between 1969-1971 that
were to lead to the second phase of the no-go areas in August 1971 in Chapter One. In Chapter Two
I take up the narrative again to look at the development of the far more revolutionary nationalist
second phase of the no-go areas from 1971-1972, and their loyalist counter parts in the summer of
1972. In Chapter Three I look at how: the no-go areas were actually run; their internal politics; what
ideologies underpinned them; and what tensions existed within them. This is also the chapter in which
I explore comparative events from other periods in history, both international and Irish. In Chapter
Four I see how in the absence of the state the no-go areas dealt with crime and kept order. In Chapter
Five I look at the military aspects of the no-go areas; the role of the paramilitaries within them; and
how the British state and army viewed them from a military perspective. In the Conclusion I bring
the story together and see what can be learned from the political and experiment that was the no-go areas: a unique event in the western Europe of the last half of the twentieth century, when people
expelled the state and initiated an experiment in direct democracy.
Overall, I conclude that the no-go areas drew upon local traditions of self-reliance and were the
products of the prevalent fear of the time. But they both represented, and worsened, the destabilisation
of Northern Ireland: and the nationalist no-go areas allowed a republican insurgency to gather
momentum. Internally, nationalist and loyalist no-go areas differed substantially. Nationalist no-go
areas were – at least, initially – strikingly liberal in their own administration of ‘law and order’: and
showed a capacity for informal self-organisation that was robust. The second Free Derry survived for
about a year with no overall organised governing structure to speak of. By contrast, loyalist areas
were firmly under the control of the UDA.Navigating to the Island of Hope - a Pacific response to globalisation, environmental degradation and climate changeGard, Rowan A.https://hdl.handle.net/10023/290832024-03-07T16:59:03Z2020-07-27T00:00:00ZNavigating to the Island of Hope - A Pacific Response to Climate Change, Environmental Degradation and Economic Globalisation in Oceania explores and seeks to understand indigenous responses to the powerful forces of globalisation and climate change through ethnographic research and cultural analysis spanning more than eight years in totality, and the Pacific renaissance concept of the Island of Hope. The Island of Hope serves as a lens, and is of interest both from a scholarly perspective and a praxis perspective, as the Island of Hope is a complex amalgamation and synthesis of Pacific ethics elements, economic justice, communal interconnectedness, cosmology and the Christian idea of heaven on Earth. This dissertation, just as the Island of Hope itself does, aims to critique and offer a unique perspective on a motivating and unifying principle in Oceania, which extends from the personal to international in scope, and explores the political and economic, the religious and spiritual, the local and global, as well as nature conservation and climate change activism. Global connections dictate global obligations.
2020-07-27T00:00:00ZGard, Rowan A.Navigating to the Island of Hope - A Pacific Response to Climate Change, Environmental Degradation and Economic Globalisation in Oceania explores and seeks to understand indigenous responses to the powerful forces of globalisation and climate change through ethnographic research and cultural analysis spanning more than eight years in totality, and the Pacific renaissance concept of the Island of Hope. The Island of Hope serves as a lens, and is of interest both from a scholarly perspective and a praxis perspective, as the Island of Hope is a complex amalgamation and synthesis of Pacific ethics elements, economic justice, communal interconnectedness, cosmology and the Christian idea of heaven on Earth. This dissertation, just as the Island of Hope itself does, aims to critique and offer a unique perspective on a motivating and unifying principle in Oceania, which extends from the personal to international in scope, and explores the political and economic, the religious and spiritual, the local and global, as well as nature conservation and climate change activism. Global connections dictate global obligations.Articulating life-itself : growth, place and movement on Mugaba (Rennell) in the Solomon IslandsBrowne, Mia Kimberlyhttps://hdl.handle.net/10023/290822024-02-15T03:06:41Z2020-12-02T00:00:00ZMugaba (Rennell) and Mugiki (Bellona) in the Solomon Islands, is the site of multiple stories, to which different values are given through different registers of 'life-itself'. Research expeditions that renamed Mugaba's life forms would later provide the compelling qualities to merit East Rennell as a UNESCO World Heritage Site (and later as World Heritage in Danger). Earlier ethnographic accounts that endeavoured to capture the last glimpses of a pre-Christian culture, represented both Euro-American genetic legacies, and Rennellese and Bellonese descriptions of people 'coming out of place'. Fieldwork on East Rennell spanned over two years, exploring how Rennellese people have folded these converging stories into their analyses of historical becoming, creating novel articulations of life and its processes. Under the research theme 'Life Itself in the Pacific' at the Centre for Pacific Studies, this work takes Rennellese descriptions of life (human and non-human others) and its contingencies as its starting point. It explores Rennellese articulations of Life-Itself, how people's growth is also enabled by different kinds of movements and flows - those that have elsewhere been qualified as 'history', 'kinship', 'gender', and even 'ecology' - to examine what is at risk in an 'endangered' World Heritage Site.
2020-12-02T00:00:00ZBrowne, Mia KimberlyMugaba (Rennell) and Mugiki (Bellona) in the Solomon Islands, is the site of multiple stories, to which different values are given through different registers of 'life-itself'. Research expeditions that renamed Mugaba's life forms would later provide the compelling qualities to merit East Rennell as a UNESCO World Heritage Site (and later as World Heritage in Danger). Earlier ethnographic accounts that endeavoured to capture the last glimpses of a pre-Christian culture, represented both Euro-American genetic legacies, and Rennellese and Bellonese descriptions of people 'coming out of place'. Fieldwork on East Rennell spanned over two years, exploring how Rennellese people have folded these converging stories into their analyses of historical becoming, creating novel articulations of life and its processes. Under the research theme 'Life Itself in the Pacific' at the Centre for Pacific Studies, this work takes Rennellese descriptions of life (human and non-human others) and its contingencies as its starting point. It explores Rennellese articulations of Life-Itself, how people's growth is also enabled by different kinds of movements and flows - those that have elsewhere been qualified as 'history', 'kinship', 'gender', and even 'ecology' - to examine what is at risk in an 'endangered' World Heritage Site.Infrastructure in Melanesia : imaginaries, experiences and practices of road making in Buka IslandRosolowsky, Marlit Felizitashttps://hdl.handle.net/10023/290812024-01-29T10:45:27Z2021-06-28T00:00:00ZThis thesis explores Melanesian concepts of roads based on multilocal ethnographic research on different kinds of roads in Buka Island, the northern island of the Autonomous Region of Bougainville, Papua New Guinea. It explores how different modes of socialities, politics, and future imaginaries have to be negotiated in the context of infrastructural transformation and varying degrees of infrastructural fragility. Taking the idioms for roads like maroro in Haku dialect and rot in Tok Pisin as an analytical vantage point, my thesis analyses how people in Buka conceptualize, build, maintain, and move along different types of roads, including garden roads (beaten footpaths), coral roads, and sealed sections of a highway. It compares the different socialities, politics, and imaginaries these roads generate and the ways in which they intersect and mutually inform each other. Inspired by the anthropology of roads and infrastructure, I argue that Melanesian socialities and politics and their continuously changing articulations can be addressed particularly well by looking at infrastructural transformations, specifically of roads. In addition, this thesis contributes a Melanesian perspective to the anthroplogy of roads and infrastructure by experimenting with the question of what practices and imaginaries create roads and what makes them infrastructural in Buka. It demonstrates the importance of taking other concepts of roads and types of roads into account when seeking to understand the changes large-scale public infrastructure projects like highway construction bring about for people.
2021-06-28T00:00:00ZRosolowsky, Marlit FelizitasThis thesis explores Melanesian concepts of roads based on multilocal ethnographic research on different kinds of roads in Buka Island, the northern island of the Autonomous Region of Bougainville, Papua New Guinea. It explores how different modes of socialities, politics, and future imaginaries have to be negotiated in the context of infrastructural transformation and varying degrees of infrastructural fragility. Taking the idioms for roads like maroro in Haku dialect and rot in Tok Pisin as an analytical vantage point, my thesis analyses how people in Buka conceptualize, build, maintain, and move along different types of roads, including garden roads (beaten footpaths), coral roads, and sealed sections of a highway. It compares the different socialities, politics, and imaginaries these roads generate and the ways in which they intersect and mutually inform each other. Inspired by the anthropology of roads and infrastructure, I argue that Melanesian socialities and politics and their continuously changing articulations can be addressed particularly well by looking at infrastructural transformations, specifically of roads. In addition, this thesis contributes a Melanesian perspective to the anthroplogy of roads and infrastructure by experimenting with the question of what practices and imaginaries create roads and what makes them infrastructural in Buka. It demonstrates the importance of taking other concepts of roads and types of roads into account when seeking to understand the changes large-scale public infrastructure projects like highway construction bring about for people.Unravelling the complex reproductive tactics of male humpback whales : an integrative analysis of paternity, age, testosterone, and genetic diversityEichenberger, Francahttps://hdl.handle.net/10023/290702024-02-15T03:07:58Z2024-06-12T00:00:00ZHow the underlying forces of sexual selection impact reproductive tactics including elaborate acoustic displays in cetaceans remains poorly understood. Here, I combined 26 years (1995-2020) of photo-identification, behavioural, (epi)genetic, and endocrine data from an endangered population of humpback whales (New Caledonia), to explore male reproductive success, age, physiology, and population dynamics over almost a third of the lifespan of a humpback whale. First, I conducted a paternity analysis on 177 known mother-offspring pairs and confirmed previous findings of low variation in reproductive success in male humpback whales. Second, epigenetic age estimates of 485 males revealed a left-skewed population age structure in the first half of the study period that became more balanced in the second half. Further, older males (> 23 years) more often engaged in certain reproductive tactics (singing and escorting) and were more successful in siring offspring once the population age structure stabilised, suggesting reproductive tactics and reproductive success in male humpback whales may be age-dependent. Third, using enzyme immunoassays on 457 blubber samples, I observed a seasonal decline in male testosterone in the population over the breeding season. Testosterone levels appeared highest during puberty, then decreased and levelled off at the onset of maturity, yet were highly variable at any point during the breeding season and across males of all ages. Lastly, I investigated the influence of genetic diversity at the major histocompatibility complex (MHC) class I and class IIa (DQB and DRB-a) on patterns of male reproductive success in humpback whales. Mating pairs shared fewer alleles than expected under random mating at MHC class I and IIa, thus, providing evidence of an MHC-mediated female mate choice in humpback whales. This thesis provides novel, critical insights into the evolutionary consequences of commercial whaling on the demography, patterns of reproduction and sexual selection of exploited populations of baleen whales.
2024-06-12T00:00:00ZEichenberger, FrancaHow the underlying forces of sexual selection impact reproductive tactics including elaborate acoustic displays in cetaceans remains poorly understood. Here, I combined 26 years (1995-2020) of photo-identification, behavioural, (epi)genetic, and endocrine data from an endangered population of humpback whales (New Caledonia), to explore male reproductive success, age, physiology, and population dynamics over almost a third of the lifespan of a humpback whale. First, I conducted a paternity analysis on 177 known mother-offspring pairs and confirmed previous findings of low variation in reproductive success in male humpback whales. Second, epigenetic age estimates of 485 males revealed a left-skewed population age structure in the first half of the study period that became more balanced in the second half. Further, older males (> 23 years) more often engaged in certain reproductive tactics (singing and escorting) and were more successful in siring offspring once the population age structure stabilised, suggesting reproductive tactics and reproductive success in male humpback whales may be age-dependent. Third, using enzyme immunoassays on 457 blubber samples, I observed a seasonal decline in male testosterone in the population over the breeding season. Testosterone levels appeared highest during puberty, then decreased and levelled off at the onset of maturity, yet were highly variable at any point during the breeding season and across males of all ages. Lastly, I investigated the influence of genetic diversity at the major histocompatibility complex (MHC) class I and class IIa (DQB and DRB-a) on patterns of male reproductive success in humpback whales. Mating pairs shared fewer alleles than expected under random mating at MHC class I and IIa, thus, providing evidence of an MHC-mediated female mate choice in humpback whales. This thesis provides novel, critical insights into the evolutionary consequences of commercial whaling on the demography, patterns of reproduction and sexual selection of exploited populations of baleen whales."That glorious sight" : theological aesthetics in the poetry of Edmund Spenser and John MiltonMorley, David Jacobhttps://hdl.handle.net/10023/287672024-02-13T03:03:32Z2022-06-16T00:00:00ZThis thesis explores how the Protestant poets Edmund Spenser and John Milton utilize the beautiful as a theological category, and it sets their concerns as Protestant poets in constructive dialogue with the insights of Hans Urs von Balthasar’s theological aesthetics. In Part I, I demonstrate important similarities between the experiential rhythm of Balthasar’s aesthetics and the typical justifications of poetry in Protestant literary theory of the sixteenth and seventeenth centuries: the interrelationship of theological form, attraction, and response (Chapter 1); I also show how Balthasar’s aesthetics provide an account of the connection between the forms of Christ, the Christian, and Christian art which offers a theological grounding for the conception of the Christian poet in such Protestant poetics (Chapter 2). In light of this theological approach, I explore four poems across the careers of Spenser and Milton. In Part II, I examine the power and function of Una’s beauty in Spenser’s narrative of holiness in Book 1 of The Faerie Queene (Chapter 3), and I argue that the climactic, beautiful figure of Sapience in his An Hymne of Heavenly Beautie should be interpreted Christologically rather than philosophically (Chapter 4). In Part III, I consider the beauty of the Christian form in Milton’s Mask Presented at Ludlow Castle, arguing that the Lady’s beauty manifests a paradoxical “strong weakness” central to Milton’s understanding of Christianity (Chapter 5), and I positively reappraise the oft maligned figure of Christ in Paradise Regained in light of Balthasar’s theological retrieval of the concept of Ignatian indifference, while maintaining some fundamental differences between Balthasar and Milton’s doctrines of God such that Milton’s Christ cannot aesthetically manifest the glory of the Father (Chapter 6). The thesis contributes to a revaluation of the history of Protestant theological aesthetics in English literature by illustrating how two of England’s major Protestant poets frequently portray Christian theological realities as beautiful and attractive. It also contributes ecumenically to Balthasar studies by demonstrating how such canonical Protestant poetry can both nuance and be illuminated by Balthasar’s aesthetic insights about the Christian faith.
2022-06-16T00:00:00ZMorley, David JacobThis thesis explores how the Protestant poets Edmund Spenser and John Milton utilize the beautiful as a theological category, and it sets their concerns as Protestant poets in constructive dialogue with the insights of Hans Urs von Balthasar’s theological aesthetics. In Part I, I demonstrate important similarities between the experiential rhythm of Balthasar’s aesthetics and the typical justifications of poetry in Protestant literary theory of the sixteenth and seventeenth centuries: the interrelationship of theological form, attraction, and response (Chapter 1); I also show how Balthasar’s aesthetics provide an account of the connection between the forms of Christ, the Christian, and Christian art which offers a theological grounding for the conception of the Christian poet in such Protestant poetics (Chapter 2). In light of this theological approach, I explore four poems across the careers of Spenser and Milton. In Part II, I examine the power and function of Una’s beauty in Spenser’s narrative of holiness in Book 1 of The Faerie Queene (Chapter 3), and I argue that the climactic, beautiful figure of Sapience in his An Hymne of Heavenly Beautie should be interpreted Christologically rather than philosophically (Chapter 4). In Part III, I consider the beauty of the Christian form in Milton’s Mask Presented at Ludlow Castle, arguing that the Lady’s beauty manifests a paradoxical “strong weakness” central to Milton’s understanding of Christianity (Chapter 5), and I positively reappraise the oft maligned figure of Christ in Paradise Regained in light of Balthasar’s theological retrieval of the concept of Ignatian indifference, while maintaining some fundamental differences between Balthasar and Milton’s doctrines of God such that Milton’s Christ cannot aesthetically manifest the glory of the Father (Chapter 6). The thesis contributes to a revaluation of the history of Protestant theological aesthetics in English literature by illustrating how two of England’s major Protestant poets frequently portray Christian theological realities as beautiful and attractive. It also contributes ecumenically to Balthasar studies by demonstrating how such canonical Protestant poetry can both nuance and be illuminated by Balthasar’s aesthetic insights about the Christian faith.Look at the Sky : the bird Simurgh in text and image in Iran (1010-1650)Castro Royo, Laurahttps://hdl.handle.net/10023/285682023-10-26T08:11:13Z2023-11-29T00:00:00ZThis research focuses on the mythological bird Sīmurgh and her representations in literature and art in the Persianate world from 1010 to 1650. Sīmurgh is generally overlooked in both art and literature, and she has not been the subject of monographic study. This dissertation proposes a combination of approaches from literary and art historical analyses to offer a complete picture of the importance of this bird for the arts and culture of the Persianate world. The results of the research show that Sīmurgh is a multifaceted subject: she is a narrative character, a mystical symbol, and a decorative motif. There is no division between these aspects; rather, they coexist.
The dissertation is divided in two parts. The first five chapters are dedicated to the study of the role of Sīmurgh in literature. The chapters are divided by genre: epic poetry, encyclopaedic works, and Sufi-mystical poetry. The following four chapters that form the second part of this dissertation analyse the iconography of Sīmurgh. They first investigate the possible origins of her visual representation up until c. 1300s. Following, a chapter is dedicated to the critical stage in which text and image became related and a recognisable iconography was established for the literary character of Sīmurgh. The dissertation ends with a chapter that discusses a following stage in which the iconography of Sīmurgh detached itself from the narrative text and started to function as decoration.
2023-11-29T00:00:00ZCastro Royo, LauraThis research focuses on the mythological bird Sīmurgh and her representations in literature and art in the Persianate world from 1010 to 1650. Sīmurgh is generally overlooked in both art and literature, and she has not been the subject of monographic study. This dissertation proposes a combination of approaches from literary and art historical analyses to offer a complete picture of the importance of this bird for the arts and culture of the Persianate world. The results of the research show that Sīmurgh is a multifaceted subject: she is a narrative character, a mystical symbol, and a decorative motif. There is no division between these aspects; rather, they coexist.
The dissertation is divided in two parts. The first five chapters are dedicated to the study of the role of Sīmurgh in literature. The chapters are divided by genre: epic poetry, encyclopaedic works, and Sufi-mystical poetry. The following four chapters that form the second part of this dissertation analyse the iconography of Sīmurgh. They first investigate the possible origins of her visual representation up until c. 1300s. Following, a chapter is dedicated to the critical stage in which text and image became related and a recognisable iconography was established for the literary character of Sīmurgh. The dissertation ends with a chapter that discusses a following stage in which the iconography of Sīmurgh detached itself from the narrative text and started to function as decoration.Sounds beneath the surface : a multiple-approach study of bottlenose dolphin acoustic communicationCasoli, Marcohttps://hdl.handle.net/10023/284292023-09-21T10:43:26Z2023-11-28T00:00:00ZBottlenose dolphins (Tursiops truncatus) live in complex individualized societies that combine stable social units with fluid groups, and they largely rely on sound to interact with one another. This thesis applies a suite of approaches to study their acoustic communication. I studied the wild population of Sarasota, which offers long-term behavioural data and opportunities to deploy sound-and-movement recording tags. Bottlenose dolphins display a wide call repertoire, including graded sounds challenging to classify. I use dolphin social interactions to present a novel tag-based approach for studying communicative roles of call parameters changes. Applying continuously-sampled parameters, this approach examines how individuals change movements as a function of signal features. I focus then on signature whistles, sounds encoding identity information that in Sarasota are documented for most individuals. Signature whistles function as individually-distinctive contact calls, for instance between closely-bonded animals during separation, but their function between groups is poorly documented. Analysing Dtag data from instances of group encounters, I show that dolphins did not regularly produce signature whistles upon detecting another group, nor systematically before joining; instead, signatures appeared to be used strategically depending on the encountered individuals. Dolphins sometimes imitate the signature whistle of others, which is thought to function for addressing known individuals. Performing first-ever playbacks of natural signature whistle copies, I show that free-ranging subjects turned more frequently towards the playback upon hearing copies of their signature vs signature whistles of others, supporting the addressing function of copies. Signature whistle copies are often produced right after the subject’s signature, in so-called vocal matching interactions. Using playbacks with temporarily-captured subjects, I test whether signature whistle matching, or vocal matching per se, has an addressing signalling role. Subjects turned more times and produced their signature more frequently in response to signature whistle matching vs matching of other calls, supporting the former hypothesis.
2023-11-28T00:00:00ZCasoli, MarcoBottlenose dolphins (Tursiops truncatus) live in complex individualized societies that combine stable social units with fluid groups, and they largely rely on sound to interact with one another. This thesis applies a suite of approaches to study their acoustic communication. I studied the wild population of Sarasota, which offers long-term behavioural data and opportunities to deploy sound-and-movement recording tags. Bottlenose dolphins display a wide call repertoire, including graded sounds challenging to classify. I use dolphin social interactions to present a novel tag-based approach for studying communicative roles of call parameters changes. Applying continuously-sampled parameters, this approach examines how individuals change movements as a function of signal features. I focus then on signature whistles, sounds encoding identity information that in Sarasota are documented for most individuals. Signature whistles function as individually-distinctive contact calls, for instance between closely-bonded animals during separation, but their function between groups is poorly documented. Analysing Dtag data from instances of group encounters, I show that dolphins did not regularly produce signature whistles upon detecting another group, nor systematically before joining; instead, signatures appeared to be used strategically depending on the encountered individuals. Dolphins sometimes imitate the signature whistle of others, which is thought to function for addressing known individuals. Performing first-ever playbacks of natural signature whistle copies, I show that free-ranging subjects turned more frequently towards the playback upon hearing copies of their signature vs signature whistles of others, supporting the addressing function of copies. Signature whistle copies are often produced right after the subject’s signature, in so-called vocal matching interactions. Using playbacks with temporarily-captured subjects, I test whether signature whistle matching, or vocal matching per se, has an addressing signalling role. Subjects turned more times and produced their signature more frequently in response to signature whistle matching vs matching of other calls, supporting the former hypothesis.Title redactedO'Harrow, Haileyhttps://hdl.handle.net/10023/284282023-10-17T02:06:57Z2023-11-29T00:00:00ZAbstract redacted
2023-11-29T00:00:00ZO'Harrow, HaileyAbstract redactedA call to action : crafting inclusive digital museum objects, networks and ecologiesMeehan, Nicôle Paulahttps://hdl.handle.net/10023/281482024-02-01T22:25:53Z2023-11-29T00:00:00ZIn this thesis, I examine the omnipresent digital museum object, seeking to understand what it is, what it does, and what it could be. I explore the lack of consensus surrounding the definition of the digital museum object, offering a new conceptualisation of an object that exists and is valuable in its own right. In isolating the generative potential of the digital museum object, I suggest that it offers inclusive and polyvocal opportunities to museums. By placing the digital museum object in a complex relational network of interactions, analysed through nuanced application of actor-network theory (ANT), I expose the asymmetrical power structures embedded between museum and audience in the postdigital landscape.
Finally, this research places digital museum objects and networks within a dynamic, evolving transnational and transcultural digital ecology. This ecology is rooted in the colonial practices of physical environments, replicated in the digital sphere. Thus, I trouble general claims that the digital landscape has democratised access, stating that instead, many of the issues encountered in physical museum spaces are replicated (or even heightened) in the postdigital environment. The creation of inclusive polyvocal digital museum objects is one positive step in an effort that seeks to counter exclusive structures and to create digital spaces that are more welcoming to all. Moreover, based on my analysis, I suggest practical steps that might be taken in beginning a journey towards creating digital museum objects that speak with, and for many, people.
2023-11-29T00:00:00ZMeehan, Nicôle PaulaIn this thesis, I examine the omnipresent digital museum object, seeking to understand what it is, what it does, and what it could be. I explore the lack of consensus surrounding the definition of the digital museum object, offering a new conceptualisation of an object that exists and is valuable in its own right. In isolating the generative potential of the digital museum object, I suggest that it offers inclusive and polyvocal opportunities to museums. By placing the digital museum object in a complex relational network of interactions, analysed through nuanced application of actor-network theory (ANT), I expose the asymmetrical power structures embedded between museum and audience in the postdigital landscape.
Finally, this research places digital museum objects and networks within a dynamic, evolving transnational and transcultural digital ecology. This ecology is rooted in the colonial practices of physical environments, replicated in the digital sphere. Thus, I trouble general claims that the digital landscape has democratised access, stating that instead, many of the issues encountered in physical museum spaces are replicated (or even heightened) in the postdigital environment. The creation of inclusive polyvocal digital museum objects is one positive step in an effort that seeks to counter exclusive structures and to create digital spaces that are more welcoming to all. Moreover, based on my analysis, I suggest practical steps that might be taken in beginning a journey towards creating digital museum objects that speak with, and for many, people.Narratives of grievance and victimisation in Iranian foreign policy under Shah Mohammad Reza Pahlavi, Prime Minister Mohammad Mosaddeq, Ayatollah Ruhollah Khomeini and President Manhood AhmadinejadMoinian, Mahnazhttps://hdl.handle.net/10023/275272023-05-12T20:32:51Z2023-06-15T00:00:00ZThis thesis investigates one of Iran’s grand narratives, the myth of victimisation, as a tool of the Iranian political elite to achieve foreign policy goals. It studies the leadership of Shah Mohammad Reza Pahlavi (1941-1979), Prime Minister Mohammad Mosaddeq (1951-1953), Ayatollah Ruhollah Khomeini (1979-1989), and President Mahmood Ahmadinejad (2005-2013) to argue that the sense of grievance of justice denied has had a cultural provenance, rooted in historical, literary and religious references spanning centuries. Accordingly Iranian leaders have been able to pursue and perpetuate narratives that have served to cast Iranians as victims of foreign intrigue, thus relieving themselves from accountability and inaction.
The narrative of grievance has had a resurgence with the rise of populism around the world, but as an ideational catalyst in Iranian politics, where it has been at play for decades, it has received scant attention. The leaders studied in this thesis have each employed this narrative to varying degrees and effects, to cast the world as a battleground between victim and victimizer. This process was most evident in the lead up to and in the aftermath of the Islamic Revolution, when Ayatollah Khomeini and President Ahmadinejad repurposed the myth of victimisation to launch and export the revolution. While the Shah and Prime Minister Mosaddeq disseminated such myths to extract favourable concessions from foreign powers, mainly the United States and Great Britain.
As a result, the grounding of Iran’s most exigent foreign policy issues in myths and populist narratives has led to an incongruity between its potential and its current standing in the community of nations.
2023-06-15T00:00:00ZMoinian, MahnazThis thesis investigates one of Iran’s grand narratives, the myth of victimisation, as a tool of the Iranian political elite to achieve foreign policy goals. It studies the leadership of Shah Mohammad Reza Pahlavi (1941-1979), Prime Minister Mohammad Mosaddeq (1951-1953), Ayatollah Ruhollah Khomeini (1979-1989), and President Mahmood Ahmadinejad (2005-2013) to argue that the sense of grievance of justice denied has had a cultural provenance, rooted in historical, literary and religious references spanning centuries. Accordingly Iranian leaders have been able to pursue and perpetuate narratives that have served to cast Iranians as victims of foreign intrigue, thus relieving themselves from accountability and inaction.
The narrative of grievance has had a resurgence with the rise of populism around the world, but as an ideational catalyst in Iranian politics, where it has been at play for decades, it has received scant attention. The leaders studied in this thesis have each employed this narrative to varying degrees and effects, to cast the world as a battleground between victim and victimizer. This process was most evident in the lead up to and in the aftermath of the Islamic Revolution, when Ayatollah Khomeini and President Ahmadinejad repurposed the myth of victimisation to launch and export the revolution. While the Shah and Prime Minister Mosaddeq disseminated such myths to extract favourable concessions from foreign powers, mainly the United States and Great Britain.
As a result, the grounding of Iran’s most exigent foreign policy issues in myths and populist narratives has led to an incongruity between its potential and its current standing in the community of nations.Early English genealogies : the evolution of their content, form, and functionEddington, Christopher Markhttps://hdl.handle.net/10023/272932023-11-11T03:08:30Z2022-11-30T00:00:00ZThis thesis traces, for the first time in detail, the evolution of early English genealogical literary forms in pre-Conquest texts, from the short pedigrees written in Latin in Historia ecclesiastica gentis Anglorum in the early eighth century to the extensive pedigree of Æthelwulf in the Anglo-Saxon Chronicle in the late ninth. It argues that early English genealogies were modelled on those in the Bible, and influenced by theological number symbolism and chronological frameworks, which were based on biblical genealogy. Key characteristics of English genealogy are discussed including: descent from Woden; the use of ethnonyms and dynastic eponyms; the alliteration of names, and the formal properties of structures and patterns in genealogies. A central argument of this thesis is that many of the variations between the content of different versions of shared or similar genealogical materials result from the increasing importance to writers of their structural, alliterative, and metrical forms, the development of which reflects, or even affects, the changing priorities or ideologies of the genealogists. As almost all of the genealogies are incorporated into other texts, the purposes of those texts are considered and the use the genealogies are put to. A second key argument of this thesis is that genealogy performs ideological work within narrative and other literary texts
2022-11-30T00:00:00ZEddington, Christopher MarkThis thesis traces, for the first time in detail, the evolution of early English genealogical literary forms in pre-Conquest texts, from the short pedigrees written in Latin in Historia ecclesiastica gentis Anglorum in the early eighth century to the extensive pedigree of Æthelwulf in the Anglo-Saxon Chronicle in the late ninth. It argues that early English genealogies were modelled on those in the Bible, and influenced by theological number symbolism and chronological frameworks, which were based on biblical genealogy. Key characteristics of English genealogy are discussed including: descent from Woden; the use of ethnonyms and dynastic eponyms; the alliteration of names, and the formal properties of structures and patterns in genealogies. A central argument of this thesis is that many of the variations between the content of different versions of shared or similar genealogical materials result from the increasing importance to writers of their structural, alliterative, and metrical forms, the development of which reflects, or even affects, the changing priorities or ideologies of the genealogists. As almost all of the genealogies are incorporated into other texts, the purposes of those texts are considered and the use the genealogies are put to. A second key argument of this thesis is that genealogy performs ideological work within narrative and other literary textsPatterns of commemoration in central Italy : manuscript calendars and social time in Perugia, Assisi and Gubbio, c. 1100–1500Kaasik, Holgerhttps://hdl.handle.net/10023/269462023-11-30T03:07:39Z2022-11-30T00:00:00ZThis thesis examines the use of medieval calendars as commemorative devices. Medieval calendars were practical and open-ended texts that could remain in use for several generations, accumulating layers of modification according to the needs and preferences of their users. Composed to regulate social time and annual collective commemoration, calendars bridged past, present and future action and synchronised individuals and communities within urban centres, on a regional level and across vast distances throughout Latin Christendom. Scholarly interest has typically focused on individual manuscripts and key calendar traditions, such as that of the Roman Curia, aiming to reconstruct seminal liturgies. This thesis instead repositions calendars in their social context and compares the calendars of three neighbouring towns and diocesan centres of distinct size, political, economic and religious influence in Central Italy – Perugia, Assisi and Gubbio – set against an extended corpus of Central and Northern Italian calendars. Altogether, the material comprises eighty manuscripts and 21354 calendar entries. By revealing how calendars served differing functions between the centres of this geographically compact area, and how these practices evolved following divergent trajectories, the comparative approach allows for the identification of trends and patterns of commemoration that would otherwise remain hidden.
The thesis argues that while the primary functions of medieval calendars – sustaining communal memory and structuring the liturgical year – are widely recognised, a great variety of practices can be uncovered considering sufficient comparative context. The thesis demonstrates that although commemorations of patron saints remained a staple of calendars, to the point of seeming almost detached from surrounding socio-religious and political developments, there are fundamental and systematic differences between the centres examined in how calendars were used to perpetuate minor local commemorations, reconcile local patterns of commemorations with those of transregional religious orders and to construct and maintain connections with neighbouring regions. Such differences go well beyond the appearance of individual saints in particular manuscripts and reflect the varying needs and preferences of the communities producing and using the manuscripts, affected by the scale, centrality and geographical orientation of the urban centres examined, as well as by broader developments such as the expansion of the Franciscan order and the Papal Curia’s presence in the region over the thirteenth century.
2022-11-30T00:00:00ZKaasik, HolgerThis thesis examines the use of medieval calendars as commemorative devices. Medieval calendars were practical and open-ended texts that could remain in use for several generations, accumulating layers of modification according to the needs and preferences of their users. Composed to regulate social time and annual collective commemoration, calendars bridged past, present and future action and synchronised individuals and communities within urban centres, on a regional level and across vast distances throughout Latin Christendom. Scholarly interest has typically focused on individual manuscripts and key calendar traditions, such as that of the Roman Curia, aiming to reconstruct seminal liturgies. This thesis instead repositions calendars in their social context and compares the calendars of three neighbouring towns and diocesan centres of distinct size, political, economic and religious influence in Central Italy – Perugia, Assisi and Gubbio – set against an extended corpus of Central and Northern Italian calendars. Altogether, the material comprises eighty manuscripts and 21354 calendar entries. By revealing how calendars served differing functions between the centres of this geographically compact area, and how these practices evolved following divergent trajectories, the comparative approach allows for the identification of trends and patterns of commemoration that would otherwise remain hidden.
The thesis argues that while the primary functions of medieval calendars – sustaining communal memory and structuring the liturgical year – are widely recognised, a great variety of practices can be uncovered considering sufficient comparative context. The thesis demonstrates that although commemorations of patron saints remained a staple of calendars, to the point of seeming almost detached from surrounding socio-religious and political developments, there are fundamental and systematic differences between the centres examined in how calendars were used to perpetuate minor local commemorations, reconcile local patterns of commemorations with those of transregional religious orders and to construct and maintain connections with neighbouring regions. Such differences go well beyond the appearance of individual saints in particular manuscripts and reflect the varying needs and preferences of the communities producing and using the manuscripts, affected by the scale, centrality and geographical orientation of the urban centres examined, as well as by broader developments such as the expansion of the Franciscan order and the Papal Curia’s presence in the region over the thirteenth century.Behavioural responses by seals to offshore energy activitiesWhyte, Katherine Faehttps://hdl.handle.net/10023/263972022-11-16T03:03:58Z2022-06-15T00:00:00ZTo effectively manage interactions between industrial activities and wildlife populations in increasingly urbanised environments, it is essential to understand how animals may be affected by different anthropogenic activities. In this thesis, I used biologging devices to investigate the potential effects of sound disturbance on seals. By simulation study, I evaluated the use of statistical tools (Mahalanobis distance) to detect unusual instances of movement and dive behaviour in seal biologging data. The results of these simulations were used to produce recommendations for future studies aiming to detect behavioural changes in animal movement data. Building on the findings of this work, I examined the movement and dive behaviour of 24 harbour seals (Phoca vitulina) during pile driving construction at an offshore wind farm in the UK. Using GPS location data collected on animal-borne tags, I identified statistically unusual horizontal movement events during pile driving, typically consisting of increases in speed, the cessation of horizontal movement, or the sudden initiation of travel. Using dive data from animal-borne tags, I identified statistically unusual groups of dives, and also characterised the effect of pile driving activity on behaviour-switching between different dive types (by hidden Markov models). Seals were found to switch dive behaviours more often during pile driving (compared to baseline periods), and the identified unusual dives were typically shorter and shallower, with longer post-dive surface intervals. For both horizontal and diving responses, dose-response curves were produced to estimate the relationship between the received sound level of pile driving and the probability of a behavioural change. By examining behaviour at the individual-level, improved insights of at-sea seal behaviour during disturbance events were gained. The results of this thesis also inform future offshore activities, enabling the renewable energy industry to develop in a timely and environmentally-responsible manner.
2022-06-15T00:00:00ZWhyte, Katherine FaeTo effectively manage interactions between industrial activities and wildlife populations in increasingly urbanised environments, it is essential to understand how animals may be affected by different anthropogenic activities. In this thesis, I used biologging devices to investigate the potential effects of sound disturbance on seals. By simulation study, I evaluated the use of statistical tools (Mahalanobis distance) to detect unusual instances of movement and dive behaviour in seal biologging data. The results of these simulations were used to produce recommendations for future studies aiming to detect behavioural changes in animal movement data. Building on the findings of this work, I examined the movement and dive behaviour of 24 harbour seals (Phoca vitulina) during pile driving construction at an offshore wind farm in the UK. Using GPS location data collected on animal-borne tags, I identified statistically unusual horizontal movement events during pile driving, typically consisting of increases in speed, the cessation of horizontal movement, or the sudden initiation of travel. Using dive data from animal-borne tags, I identified statistically unusual groups of dives, and also characterised the effect of pile driving activity on behaviour-switching between different dive types (by hidden Markov models). Seals were found to switch dive behaviours more often during pile driving (compared to baseline periods), and the identified unusual dives were typically shorter and shallower, with longer post-dive surface intervals. For both horizontal and diving responses, dose-response curves were produced to estimate the relationship between the received sound level of pile driving and the probability of a behavioural change. By examining behaviour at the individual-level, improved insights of at-sea seal behaviour during disturbance events were gained. The results of this thesis also inform future offshore activities, enabling the renewable energy industry to develop in a timely and environmentally-responsible manner.Resurrecting empire : Iranian imperial nationalism in 1919Grobien, Philip Henninghttps://hdl.handle.net/10023/253912023-07-14T02:06:22Z2022-06-16T00:00:00ZNarratives of the late Qajar period have considered Iran a country in decline, unable to engage effectively with British and Russian modernity, spearheaded by imperial practices. Yet, in truth, this account requires a re-appraisal. This thesis examines the dialectic between a pre-modern Iran and the modern forces Iran faced and will show how Iran engaged with and applied western achievements which were eventually used in an Iranian paradigm.
This thesis focuses on Iran’s diplomacy after the First World War and, in particular, Iran’s attendance at the Peace of Paris in 1919. It will show that Iran followed a persistent and lengthy pursuit to reclaim territory and was to put forward a nationalist programme which sought a sovereign and independent Iran. This nuanced nationalism, an imperial nationalism, used modern methods and sought integration into the post-war world order.
Using previously unused primary sources, this thesis will interrogate Iran’s loss of territory and examine how this informed Iran’s post-war diplomacy. In doing so it will highlight an under-researched area and show that Iran espoused a far more consolidated nationalistic approach in 1919 which included an increasingly modern and professional diplomatic approach. Modernity and imperialism helped to precipitate the loss of territory, however, the loss of territory informed Iran’s distinct nationalism in 1919. An imperial nationalism, which was founded on a framework of empire locked into ideas of sovereignty.
2022-06-16T00:00:00ZGrobien, Philip HenningNarratives of the late Qajar period have considered Iran a country in decline, unable to engage effectively with British and Russian modernity, spearheaded by imperial practices. Yet, in truth, this account requires a re-appraisal. This thesis examines the dialectic between a pre-modern Iran and the modern forces Iran faced and will show how Iran engaged with and applied western achievements which were eventually used in an Iranian paradigm.
This thesis focuses on Iran’s diplomacy after the First World War and, in particular, Iran’s attendance at the Peace of Paris in 1919. It will show that Iran followed a persistent and lengthy pursuit to reclaim territory and was to put forward a nationalist programme which sought a sovereign and independent Iran. This nuanced nationalism, an imperial nationalism, used modern methods and sought integration into the post-war world order.
Using previously unused primary sources, this thesis will interrogate Iran’s loss of territory and examine how this informed Iran’s post-war diplomacy. In doing so it will highlight an under-researched area and show that Iran espoused a far more consolidated nationalistic approach in 1919 which included an increasingly modern and professional diplomatic approach. Modernity and imperialism helped to precipitate the loss of territory, however, the loss of territory informed Iran’s distinct nationalism in 1919. An imperial nationalism, which was founded on a framework of empire locked into ideas of sovereignty.Fantastic feasts and where to find them : using biologging to investigate foraging behaviour of marine megafauna across a range of spatiotemporal scalesVance, Heather Margarethttps://hdl.handle.net/10023/238352021-08-25T11:30:31Z2021-12-01T00:00:00ZUnderstanding the strategies animals use to locate, select, and capture prey can guide more robust conservation efforts. In marine megafauna, foraging is often inferred from infrequent surface positions using biotelemetry tags. In this thesis I argue that finer-scale measurements of predator movements, prey availability and behaviour are critical to understanding foraging decisions. To explore this I used multi-sensor, high-resolution biologging tags on three megafauna species and compared optimal foraging predictions to actual behaviour over a hierarchy of spatiotemporal scales. At the landscape scale, I studied a central-place forager, the harbour seal, which accesses distant and nearshore prey although the relative importance of these resources is poorly understood. I found that prey encounter rates were similar for the two resources but while prey were distributed extensively offshore, inshore foraging was concentrated in just a few discrete patches. I suggest that the trade-off between accessibility and conspecific competition may influence site selection. At the patch scale, I studied a bulk-filter feeder, whale sharks, which are presumed to be highly-selective to offset the energetic cost of this strategy. Using novel sonar tags to record fine-scale behaviour and prey densities, I found that sharks did not selectively harvest rare dense patches. Instead, a less-selective strategy with continual-patch assessment may be advantageous when prey density is highly heterogenous. At the scale of prey captures, I studied the sensory and locomotor responses of an echolocating predator to evasive prey. Results revealed rapid responses to prey movements which scale with the acceleration of prey, enabling this energetically constrained mammal to reliably capture high-energy prey. Within each study, detailed biologging measurements were critical to understanding factors influencing foraging choices and capabilities. Such data help define the plasticity with which predators can respond to changing prey distribution, density, and performance, and provide critical insights to focus effective conservation actions.
2021-12-01T00:00:00ZVance, Heather MargaretUnderstanding the strategies animals use to locate, select, and capture prey can guide more robust conservation efforts. In marine megafauna, foraging is often inferred from infrequent surface positions using biotelemetry tags. In this thesis I argue that finer-scale measurements of predator movements, prey availability and behaviour are critical to understanding foraging decisions. To explore this I used multi-sensor, high-resolution biologging tags on three megafauna species and compared optimal foraging predictions to actual behaviour over a hierarchy of spatiotemporal scales. At the landscape scale, I studied a central-place forager, the harbour seal, which accesses distant and nearshore prey although the relative importance of these resources is poorly understood. I found that prey encounter rates were similar for the two resources but while prey were distributed extensively offshore, inshore foraging was concentrated in just a few discrete patches. I suggest that the trade-off between accessibility and conspecific competition may influence site selection. At the patch scale, I studied a bulk-filter feeder, whale sharks, which are presumed to be highly-selective to offset the energetic cost of this strategy. Using novel sonar tags to record fine-scale behaviour and prey densities, I found that sharks did not selectively harvest rare dense patches. Instead, a less-selective strategy with continual-patch assessment may be advantageous when prey density is highly heterogenous. At the scale of prey captures, I studied the sensory and locomotor responses of an echolocating predator to evasive prey. Results revealed rapid responses to prey movements which scale with the acceleration of prey, enabling this energetically constrained mammal to reliably capture high-energy prey. Within each study, detailed biologging measurements were critical to understanding factors influencing foraging choices and capabilities. Such data help define the plasticity with which predators can respond to changing prey distribution, density, and performance, and provide critical insights to focus effective conservation actions.Feeling forsaken : Christ's descent into hell in the theology of John CalvinHill, Preston McDanielhttps://hdl.handle.net/10023/235522023-06-19T13:12:18Z2021-07-01T00:00:00ZThere currently exists a substantial lacuna in scholarship on the place of Christ’s descent into hell in the theology of John Calvin. Although Calvin devoted five times more space in his ‘Institutes’ to Christ’s descent into hell than to any other clause of the Apostles’ Creed—an exposition which was nearly sextupled in length throughout the course of his career—the secondary literature on this theme is virtually non-existent and only passingly treated in Calvin scholarship to date. The impression given by this scarcity is that Calvin had little to say about the descensus or that what he did have to say is so obvious as to require only minimal secondary exposition. However, a mere glance beyond the ‘Institutes’ to Calvin’s other writings significantly unsettles such an opinion. From as early as age 25 in his first treatise ‘Psychopannychia’ to his later commentaries, sermons, and final draft of the ‘Institutes’, Calvin vehemently espoused an innovative descensus interpretation that remained virtually unchanged throughout his life. Moreover, despite longstanding popular opinion, all the major themes of Calvin’s interpretation can be found in prominent medieval, Renaissance, and late modern forerunners predating Calvin, demonstrating that his interpretation was far from novel. The disparity between Calvin’s detailed interpretation and the oversight of Calvin research on these important points calls for a fresh look at the place of Christ’s descent into hell in his theology. This thesis reconstructs Calvin’s descensus theology by tracing its development from the ‘Psychopannychia’ to the successive editions of Calvin’s ‘Institutes’, strategically comparing the major elements uncovered to significant forerunners of Calvin’s interpretation. This study puts forward the thesis that Calvin’s descensus theology cannot be referred exclusively to the events of the crucifixion without significant detriment to its other substantial manifestations in Calvin’s exposition, including the Gethsemane narrative, the intermediate state, the body/soul distinction of Christ’s suffering, and Christ’s beloved relation with the Father. Christ’s descent into hell clearly exceeds a mere metaphorical reference to the cross in Calvin’s theology.
2021-07-01T00:00:00ZHill, Preston McDanielThere currently exists a substantial lacuna in scholarship on the place of Christ’s descent into hell in the theology of John Calvin. Although Calvin devoted five times more space in his ‘Institutes’ to Christ’s descent into hell than to any other clause of the Apostles’ Creed—an exposition which was nearly sextupled in length throughout the course of his career—the secondary literature on this theme is virtually non-existent and only passingly treated in Calvin scholarship to date. The impression given by this scarcity is that Calvin had little to say about the descensus or that what he did have to say is so obvious as to require only minimal secondary exposition. However, a mere glance beyond the ‘Institutes’ to Calvin’s other writings significantly unsettles such an opinion. From as early as age 25 in his first treatise ‘Psychopannychia’ to his later commentaries, sermons, and final draft of the ‘Institutes’, Calvin vehemently espoused an innovative descensus interpretation that remained virtually unchanged throughout his life. Moreover, despite longstanding popular opinion, all the major themes of Calvin’s interpretation can be found in prominent medieval, Renaissance, and late modern forerunners predating Calvin, demonstrating that his interpretation was far from novel. The disparity between Calvin’s detailed interpretation and the oversight of Calvin research on these important points calls for a fresh look at the place of Christ’s descent into hell in his theology. This thesis reconstructs Calvin’s descensus theology by tracing its development from the ‘Psychopannychia’ to the successive editions of Calvin’s ‘Institutes’, strategically comparing the major elements uncovered to significant forerunners of Calvin’s interpretation. This study puts forward the thesis that Calvin’s descensus theology cannot be referred exclusively to the events of the crucifixion without significant detriment to its other substantial manifestations in Calvin’s exposition, including the Gethsemane narrative, the intermediate state, the body/soul distinction of Christ’s suffering, and Christ’s beloved relation with the Father. Christ’s descent into hell clearly exceeds a mere metaphorical reference to the cross in Calvin’s theology.Livery and dule : dressing life and death in the late medieval Scottish royal householdWesterhof Nyman, Perin Joyhttps://hdl.handle.net/10023/231742021-07-21T14:49:00Z2021-07-01T00:00:00ZThis thesis examines the use of meaningful and symbolic dress at the late medieval Scottish royal court, arguing that group displays of colour-coded clothing, exemplified by livery and mourning dress, played key political roles both in the day-to-day functioning of the court and royal household and at large-scale ceremonial events. The discussion takes an interdisciplinary approach to a wide body of source types, and considers evidence from the fourteenth to the mid-sixteenth centuries, concluding with the funeral of James V in 1543. Although a number of Scottish historians have considered the political implications of individual sixteenth-century monarchs’ wardrobes, there has been little focused discussion of the dress of the wider household and court before the mid-sixteenth century. This thesis shows that dress was employed throughout the late medieval period and the early sixteenth century as a means of visually defining the structures of the household and parts of the court, the roles of the people within them, and their relationships to each other and to the monarch. It argues that clothing’s ability to express constructed meaning and identity made it a powerful and versatile tool. Examinations of livery and heraldic dress, funereal dress and textile displays, and mourning dress are used to explore the employment of clothing by the Scottish crown, nobility, and household officials. These discussions culminate in three case studies of the finely-tuned displays of liveries and mourning that were organised for the funerals of Scottish monarchs Madeleine de Valois, Margaret Tudor, and James V. By showing that meaningful dress was a core element in the expression of interpersonal and political discourse at all levels of court life, and by making the technical definitions, forms, functions, and associated meanings of late medieval Scottish dress more accessible, this thesis seeks to facilitate the wider integration of dress evidence into Scottish historical research.
2021-07-01T00:00:00ZWesterhof Nyman, Perin JoyThis thesis examines the use of meaningful and symbolic dress at the late medieval Scottish royal court, arguing that group displays of colour-coded clothing, exemplified by livery and mourning dress, played key political roles both in the day-to-day functioning of the court and royal household and at large-scale ceremonial events. The discussion takes an interdisciplinary approach to a wide body of source types, and considers evidence from the fourteenth to the mid-sixteenth centuries, concluding with the funeral of James V in 1543. Although a number of Scottish historians have considered the political implications of individual sixteenth-century monarchs’ wardrobes, there has been little focused discussion of the dress of the wider household and court before the mid-sixteenth century. This thesis shows that dress was employed throughout the late medieval period and the early sixteenth century as a means of visually defining the structures of the household and parts of the court, the roles of the people within them, and their relationships to each other and to the monarch. It argues that clothing’s ability to express constructed meaning and identity made it a powerful and versatile tool. Examinations of livery and heraldic dress, funereal dress and textile displays, and mourning dress are used to explore the employment of clothing by the Scottish crown, nobility, and household officials. These discussions culminate in three case studies of the finely-tuned displays of liveries and mourning that were organised for the funerals of Scottish monarchs Madeleine de Valois, Margaret Tudor, and James V. By showing that meaningful dress was a core element in the expression of interpersonal and political discourse at all levels of court life, and by making the technical definitions, forms, functions, and associated meanings of late medieval Scottish dress more accessible, this thesis seeks to facilitate the wider integration of dress evidence into Scottish historical research.Translating identities : 'being a missionary' in Papua New GuineaRoberts, E. Mei-Lihttps://hdl.handle.net/10023/221342024-01-30T03:06:52Z2006-01-01T00:00:00ZMany studies of missionaries have taken an historical perspective,
looking particularly at missionaries’ role in colonialism. However,
missionaries are still very much part of contemporary Papua New
Guinea (PNG), with a significant number of expatriate missionary
groups working in PNG. This thesis is a study of a present day
mission in PNG, SIL International, formerly known as the Summer
Institute of Linguistics (SIL). It examines the way in which the
mission community is constructed and the boundaries and divisions
within the community itself. It attempts to challenge some of the
stereotypes of missionaries and show that there are different views of
what it is to ‘be a missionary’ even within the missionary community
itself. I focus particularly on what it means to ‘be a missionary’ and
the ambiguities and ambivalences between the ideals and realities of
mission work.
The focus of the study was on SIL members themselves and their
identities as missionaries rather than the effect of their missionising
on others. This is examined through a number of different themes.
Debates about the fence surrounding the mission station highlighted
the way in which it created both a physical and a symbolic boundary
between those living inside the fence and the people living outside of
it. Related to this were debates regarding the mission station,
Ukarumpa and how SIL members should ‘communicate the gospel’.
SIL’s main goal is Bible translation and the thesis explores the
challenges and problems of translation, both the practical aspects of
Bible translation and translating between cultures. Literacy work is
also an important part of SIL’s goal and is shown to be especially
significant in maintaining a good relationship with the PNG
government. Finally, notions of ‘home’ and ‘belonging’, particularly
in relation to the children of missionaries, and the notion of ‘citizens
of heaven’ is shown to help shape SIL members’ identities as
‘missionaries’.
2006-01-01T00:00:00ZRoberts, E. Mei-LiMany studies of missionaries have taken an historical perspective,
looking particularly at missionaries’ role in colonialism. However,
missionaries are still very much part of contemporary Papua New
Guinea (PNG), with a significant number of expatriate missionary
groups working in PNG. This thesis is a study of a present day
mission in PNG, SIL International, formerly known as the Summer
Institute of Linguistics (SIL). It examines the way in which the
mission community is constructed and the boundaries and divisions
within the community itself. It attempts to challenge some of the
stereotypes of missionaries and show that there are different views of
what it is to ‘be a missionary’ even within the missionary community
itself. I focus particularly on what it means to ‘be a missionary’ and
the ambiguities and ambivalences between the ideals and realities of
mission work.
The focus of the study was on SIL members themselves and their
identities as missionaries rather than the effect of their missionising
on others. This is examined through a number of different themes.
Debates about the fence surrounding the mission station highlighted
the way in which it created both a physical and a symbolic boundary
between those living inside the fence and the people living outside of
it. Related to this were debates regarding the mission station,
Ukarumpa and how SIL members should ‘communicate the gospel’.
SIL’s main goal is Bible translation and the thesis explores the
challenges and problems of translation, both the practical aspects of
Bible translation and translating between cultures. Literacy work is
also an important part of SIL’s goal and is shown to be especially
significant in maintaining a good relationship with the PNG
government. Finally, notions of ‘home’ and ‘belonging’, particularly
in relation to the children of missionaries, and the notion of ‘citizens
of heaven’ is shown to help shape SIL members’ identities as
‘missionaries’.Rousham, Oxfordshire - preserving its place in historyMason, Clairehttps://hdl.handle.net/10023/219952022-03-10T17:01:04Z1991-01-01T00:00:00ZThe development of the English Landscape Garden was a direct result of the political, social and cultural climate of 18th c. Britain. Rousham, Oxfordshire, as created by Charles Bridgeman and William Kent, may be seen as a transitional garden, included in that short phase of natural wilderness landscapes which lies between French and Dutch influenced formality and 'Capability' Brown's ruthless clearance and 'improvements'. Rousham, as Kent's only unaltered work, is of unique importance; for it is often said that it was with the advent of Kent's informality that British landscape gardening began to lead the world. Charles Bridgeman was also an important figure in the move towards a less formal garden and it has not been fully established how great a part he played; therefore a detailed survey is made of the work at Rousham to assess his contribution. Bridgeman's Rousham was still relatively 'formal', with straight lines and geometric shapes. Kent created a small but varied and relaxed garden with major plays of light, shade and perspective. Much of Kent's construction is reminiscent of Italian garden theatre scenes; Rousham is evocative, with ethereal concepts. A wide range of influences were apparent in the design of Rousham; these, their representation and survival are discussed on the basis of fieldwork and contemporary sources which are listed at the beginning of Chapter Three. In conclusion; Rousham's importance within the field of garden history is established, and an examination made of protection and maintenance to ensure survival of the features and mood of this historic survival.
1991-01-01T00:00:00ZMason, ClaireThe development of the English Landscape Garden was a direct result of the political, social and cultural climate of 18th c. Britain. Rousham, Oxfordshire, as created by Charles Bridgeman and William Kent, may be seen as a transitional garden, included in that short phase of natural wilderness landscapes which lies between French and Dutch influenced formality and 'Capability' Brown's ruthless clearance and 'improvements'. Rousham, as Kent's only unaltered work, is of unique importance; for it is often said that it was with the advent of Kent's informality that British landscape gardening began to lead the world. Charles Bridgeman was also an important figure in the move towards a less formal garden and it has not been fully established how great a part he played; therefore a detailed survey is made of the work at Rousham to assess his contribution. Bridgeman's Rousham was still relatively 'formal', with straight lines and geometric shapes. Kent created a small but varied and relaxed garden with major plays of light, shade and perspective. Much of Kent's construction is reminiscent of Italian garden theatre scenes; Rousham is evocative, with ethereal concepts. A wide range of influences were apparent in the design of Rousham; these, their representation and survival are discussed on the basis of fieldwork and contemporary sources which are listed at the beginning of Chapter Three. In conclusion; Rousham's importance within the field of garden history is established, and an examination made of protection and maintenance to ensure survival of the features and mood of this historic survival.Museological criticism and museum practice : how far can museum practice be informed by museological criticism? : (with reference to the National Galleries of Scotland and the Royal Museums of Scotland)Okeke, Chidihttps://hdl.handle.net/10023/219752022-03-08T12:43:11Z1992-01-01T00:00:00ZIn this dissertation I will be looking at a selective range of museological criticism that has been applied to the educative purpose and functions of museums and more specifically to galleries from the mid-nineteenth century to the present. I will give an outline of these criticisms, their development, the basis of their arguments and the implications they have had for museum and gallery educational practice. This will, it is hoped, illustrate some of the social, cultural and economic developments which have affected both museological criticism and museum practice. In conclusion I will evaluate the extent to which museum and gallery practice can be informed by museological criticism by looking at the current educational practices of two institutions whose collections incorporate the subject areas of the museological criticisms that I have selected.
1992-01-01T00:00:00ZOkeke, ChidiIn this dissertation I will be looking at a selective range of museological criticism that has been applied to the educative purpose and functions of museums and more specifically to galleries from the mid-nineteenth century to the present. I will give an outline of these criticisms, their development, the basis of their arguments and the implications they have had for museum and gallery educational practice. This will, it is hoped, illustrate some of the social, cultural and economic developments which have affected both museological criticism and museum practice. In conclusion I will evaluate the extent to which museum and gallery practice can be informed by museological criticism by looking at the current educational practices of two institutions whose collections incorporate the subject areas of the museological criticisms that I have selected.A brief history of the North American ethnographic collections in six Scottish museumsCraw-Eismont, Beverley J.https://hdl.handle.net/10023/219252022-02-01T10:46:59Z1993-01-01T00:00:00ZStarting in the late 18th century, when Captain Cook's crews numbered many Scots among them, and throughout the 19th century, when trade and exploration between the "Old" and" New" World particularly flourished, strong ties between Scotland and North America were formed. Scholars, explorers, fur-traders, surveyors and map-makers, artists, missionaries, adventurers and "tourists" were keen, when they returned home, to share the fascinating items and "artificial curiosities" which they had discovered amongst the Native American peoples. Most of the North American and Inuit objects collected, therefore, and which have been subsequently donated to museums, were acquired in a casual and unplanned way with a few notable exceptions. Most of this material derives from the whaling and fur trading activities in the 19th century and early 20th century. Now, over a hundred years later, a variety of interest, use, emphasis, and type of display, was discovered in the museums visited which seemed to reflect trends in historical and anthropological views and those of current "museology". This ranges from the "Cabinets of Curiosities", through Pitt Rivers typology to the modern thematic approach. The concerns of this dissertation are to investigate the collections of North American Ethnographic Material in Six Scottish Museums in the following categories: one national museum, one city corporation, two university museums, and two district councils and briefly to describe their history.
1993-01-01T00:00:00ZCraw-Eismont, Beverley J.Starting in the late 18th century, when Captain Cook's crews numbered many Scots among them, and throughout the 19th century, when trade and exploration between the "Old" and" New" World particularly flourished, strong ties between Scotland and North America were formed. Scholars, explorers, fur-traders, surveyors and map-makers, artists, missionaries, adventurers and "tourists" were keen, when they returned home, to share the fascinating items and "artificial curiosities" which they had discovered amongst the Native American peoples. Most of the North American and Inuit objects collected, therefore, and which have been subsequently donated to museums, were acquired in a casual and unplanned way with a few notable exceptions. Most of this material derives from the whaling and fur trading activities in the 19th century and early 20th century. Now, over a hundred years later, a variety of interest, use, emphasis, and type of display, was discovered in the museums visited which seemed to reflect trends in historical and anthropological views and those of current "museology". This ranges from the "Cabinets of Curiosities", through Pitt Rivers typology to the modern thematic approach. The concerns of this dissertation are to investigate the collections of North American Ethnographic Material in Six Scottish Museums in the following categories: one national museum, one city corporation, two university museums, and two district councils and briefly to describe their history.Causes of individual variation in fasting fuel allocation and consequences for diving behaviour in grey seal pups (Halichoerus grypus)Bennett, Kimberley A.https://hdl.handle.net/10023/208232020-10-27T03:03:39Z2005-06-24T00:00:00ZGrey seal pups are weaned abruptly after a short, intensive nursing period, during
which
they lay down fat and protein. Fat stores are crucial for insulation when they
first go to sea and protein is essential for muscle and oxygen store development. Both
components also provide them with energy to sustain them during an extended
postweaning fast and their first days and weeks at sea until they can forage
effectively. There is thus a trade off between the requirements for fat and protein in
metabolism and for other functions. It is crucial for the survival of grey seal pups that
they begin to feed before these reserves become critically depleted. The ability to do
so
depends on the size of their fat and protein stores at weaning, energy partitioning
during the postweaning fast and the development of adequate diving and foraging
capabilities. The management of fat and protein stores through energy partitioning
and
appropriate timing of departure are key to survival but the mechanism by which
this management is achieved is unknown.
To
investigate the mechanism that controls energy partitioning and timing of
departure from the colony, changes in body mass and composition and levels of
hormones that are involved in energy balance in other mammals were measured
during the postweaning fast of wild grey seal pups. The impact of initial energy
reserves and hormone levels on
energy use and departure was investigated directly, by
manipulation of energy reserves and hormone levels, using supplementary feeding
and hormone treatment. This is the first time such intervention studies have been
performed in wild fasting pups. The impact of the stress of repeated handling on
hormone levels and energy utilisation was also examined. The movement patterns and
development of maximum diving capabilities of pups after departure were
investigated using satellite telemetry.
Leptin was present in grey seal serum but could not be measured accurately using two
currently available immunoassays. Prolactin was not detected in postweaned pup
serum and was eliminated as a
potential candidate for control of fuel use and timing
of
departure from the colony. Cortisol and thyroid hormones (TH) were measured in
serum but Cortisol could not be measured in grey seal saliva.
Cortisol and TH are
potentially involved in energy expenditure and fuel partitioning
during fasting. Cortisol and total thyroxine levels decreased from weaning to midway through the fast. Both hormones increased in response to both natural and artificially
induced
changes in fuel availability. Dexamethasone, a potent Cortisol analogue,
caused a short-term increase in mass
loss, and induced reversible and short-lived
changes in Cortisol levels and immune function, but its impact on energy partitioning
was unclear. The effects of the
drug were not mediated through TH. There were no
changes in TH or Cortisol consistently associated with the timing of departure and
dexamethasone did not induce
departure. Neither hormone therefore seemed likely to
be involved
directly in the cue to leave the breeding colony. Handling regime did not
impact significantly on Cortisol secretion, TH levels or long-term fuel use in grey seal
pups.
Fatter animals, or those provided with additional food, relied more heavily on
fat to meet
energetic requirements than leaner pups. There was no difference in
energy partitioning between the sexes. Grey seal pups had a greater tolerance to
protein depletion than terrestrial mammals but may have reached critical protein
levels soon after
departure from the colony. They were therefore under considerable
pressure to begin to feed very soon after they have gone to sea, despite their extensive
fat reserves.
Pups showed marked inter-individual differences in movement patterns, which
were
very different from those of adults. Initially they undertook coastal movement,
but showed wide
dispersal from the colony within their first few months at sea. They
began to exhibit adult-like repeated trips from known haul-outs to discrete offshore
areas 4-5 months after
departure. They were able to reach almost all areas and depths
available in the North Sea, but were constrained in their ability to remain submerged,
in terms of dive duration, post-dive surface interval and percentage of time spent
diving over extended periods, compared with adults. Their maximum ability to remain
submerged when they first went to sea was related to the duration of the postweaning
fast and thus the
degree of development on land. In contrast, maximum diving
capabilities achieved during the first three months at sea did not vary substantially
between animals and increased with time since
departure, and were thus likely to be a
product of diving-induced development of oxygen stores and cardiovascular control.
Overall, larger body size and longer fast duration conferred increased diving
capabilities, which may present one mechanism for increased survivorship in bigger
animals.
2005-06-24T00:00:00ZBennett, Kimberley A.Grey seal pups are weaned abruptly after a short, intensive nursing period, during
which
they lay down fat and protein. Fat stores are crucial for insulation when they
first go to sea and protein is essential for muscle and oxygen store development. Both
components also provide them with energy to sustain them during an extended
postweaning fast and their first days and weeks at sea until they can forage
effectively. There is thus a trade off between the requirements for fat and protein in
metabolism and for other functions. It is crucial for the survival of grey seal pups that
they begin to feed before these reserves become critically depleted. The ability to do
so
depends on the size of their fat and protein stores at weaning, energy partitioning
during the postweaning fast and the development of adequate diving and foraging
capabilities. The management of fat and protein stores through energy partitioning
and
appropriate timing of departure are key to survival but the mechanism by which
this management is achieved is unknown.
To
investigate the mechanism that controls energy partitioning and timing of
departure from the colony, changes in body mass and composition and levels of
hormones that are involved in energy balance in other mammals were measured
during the postweaning fast of wild grey seal pups. The impact of initial energy
reserves and hormone levels on
energy use and departure was investigated directly, by
manipulation of energy reserves and hormone levels, using supplementary feeding
and hormone treatment. This is the first time such intervention studies have been
performed in wild fasting pups. The impact of the stress of repeated handling on
hormone levels and energy utilisation was also examined. The movement patterns and
development of maximum diving capabilities of pups after departure were
investigated using satellite telemetry.
Leptin was present in grey seal serum but could not be measured accurately using two
currently available immunoassays. Prolactin was not detected in postweaned pup
serum and was eliminated as a
potential candidate for control of fuel use and timing
of
departure from the colony. Cortisol and thyroid hormones (TH) were measured in
serum but Cortisol could not be measured in grey seal saliva.
Cortisol and TH are
potentially involved in energy expenditure and fuel partitioning
during fasting. Cortisol and total thyroxine levels decreased from weaning to midway through the fast. Both hormones increased in response to both natural and artificially
induced
changes in fuel availability. Dexamethasone, a potent Cortisol analogue,
caused a short-term increase in mass
loss, and induced reversible and short-lived
changes in Cortisol levels and immune function, but its impact on energy partitioning
was unclear. The effects of the
drug were not mediated through TH. There were no
changes in TH or Cortisol consistently associated with the timing of departure and
dexamethasone did not induce
departure. Neither hormone therefore seemed likely to
be involved
directly in the cue to leave the breeding colony. Handling regime did not
impact significantly on Cortisol secretion, TH levels or long-term fuel use in grey seal
pups.
Fatter animals, or those provided with additional food, relied more heavily on
fat to meet
energetic requirements than leaner pups. There was no difference in
energy partitioning between the sexes. Grey seal pups had a greater tolerance to
protein depletion than terrestrial mammals but may have reached critical protein
levels soon after
departure from the colony. They were therefore under considerable
pressure to begin to feed very soon after they have gone to sea, despite their extensive
fat reserves.
Pups showed marked inter-individual differences in movement patterns, which
were
very different from those of adults. Initially they undertook coastal movement,
but showed wide
dispersal from the colony within their first few months at sea. They
began to exhibit adult-like repeated trips from known haul-outs to discrete offshore
areas 4-5 months after
departure. They were able to reach almost all areas and depths
available in the North Sea, but were constrained in their ability to remain submerged,
in terms of dive duration, post-dive surface interval and percentage of time spent
diving over extended periods, compared with adults. Their maximum ability to remain
submerged when they first went to sea was related to the duration of the postweaning
fast and thus the
degree of development on land. In contrast, maximum diving
capabilities achieved during the first three months at sea did not vary substantially
between animals and increased with time since
departure, and were thus likely to be a
product of diving-induced development of oxygen stores and cardiovascular control.
Overall, larger body size and longer fast duration conferred increased diving
capabilities, which may present one mechanism for increased survivorship in bigger
animals.The United Nations and terrorism : a long term assessment of changes and continuitiesMüller, Johannes-Alexanderhttps://hdl.handle.net/10023/202772024-01-13T03:02:17Z2020-07-28T00:00:00ZAlthough terrorism continues to retain its localised nature in some respects, the threat has taken on an international character for some time now. Consequently, national efforts to curb terrorism are not sufficient in dealing with the threat, underscoring the importance of multilateral counterterrorism cooperation. The United Nations (UN) is perhaps the most visible and predominant international organisation for security issues and has thus built the prime case study for this research endeavour. The aim of this thesis has been to examine how the UN’s response to terrorism has changed since the 1970s. In doing so, the project has provided an empirical overview of 50 years of UN counterterrorism efforts and has analysed the empirical data to identify patterns, continuities, and disruptions in the UN’s response. The findings suggest that the United Nations has seen both change and continuity in its efforts to quell terrorist violence and it has been demonstrated that, while multilateral counterterrorism cooperation is possible at the UN, it is cumbersome and progress is best done away from the political limelight. The obstacles that have prevented swift action when the UN General Assembly first took up the issue in 1972 have remained remarkably consistent and are unlikely to be solved quickly. The step-by-step criminalisation of certain offences through treaty-making has however allowed the Assembly to make some progress. Following the Cold War, the Security Council has — although not spared from definitional short-comings — responded to terrorism in a more assertive (e.g. sanctions) and at times forceful manner. Finally, it has been highlighted that the politised nature of terrorism can greatly limit counterterrorism responses. Therefore, it has been suggested that future academic inquiry must explore the extent to which less politised organisations, those that are technical and regional in nature, might be better suited to address terrorism within their framework.
2020-07-28T00:00:00ZMüller, Johannes-AlexanderAlthough terrorism continues to retain its localised nature in some respects, the threat has taken on an international character for some time now. Consequently, national efforts to curb terrorism are not sufficient in dealing with the threat, underscoring the importance of multilateral counterterrorism cooperation. The United Nations (UN) is perhaps the most visible and predominant international organisation for security issues and has thus built the prime case study for this research endeavour. The aim of this thesis has been to examine how the UN’s response to terrorism has changed since the 1970s. In doing so, the project has provided an empirical overview of 50 years of UN counterterrorism efforts and has analysed the empirical data to identify patterns, continuities, and disruptions in the UN’s response. The findings suggest that the United Nations has seen both change and continuity in its efforts to quell terrorist violence and it has been demonstrated that, while multilateral counterterrorism cooperation is possible at the UN, it is cumbersome and progress is best done away from the political limelight. The obstacles that have prevented swift action when the UN General Assembly first took up the issue in 1972 have remained remarkably consistent and are unlikely to be solved quickly. The step-by-step criminalisation of certain offences through treaty-making has however allowed the Assembly to make some progress. Following the Cold War, the Security Council has — although not spared from definitional short-comings — responded to terrorism in a more assertive (e.g. sanctions) and at times forceful manner. Finally, it has been highlighted that the politised nature of terrorism can greatly limit counterterrorism responses. Therefore, it has been suggested that future academic inquiry must explore the extent to which less politised organisations, those that are technical and regional in nature, might be better suited to address terrorism within their framework.Simulating cetacean responses to sonar exposure within a Bayesian hierarchical modelling framework : technical reportBouchet, PhilHarris, Catriona MThomas, Lenhttps://hdl.handle.net/10023/199092024-03-24T00:46:50Z2020-04-21T00:00:00ZIn this report, we present a framework for simulating responses of cetaceans to various military sonar exposure contexts using Bayesian hierarchical modelling. This work was motivated by the need to assess the utility of different types of animal-attached biotelemetry tags in improving our understanding of dose–response relationships. Specifically, we used a Monte Carlo approach to conduct a sensitivity analysis of the effects of uncertainty in acoustic dose measurements (i.e. received sound levels) on the probability of behavioural response. Accompanying R code is available and fully described in a sister document.
Funding: The research reported here was financially supported by the US Navy Living Marine Resources Programme (LMR) Contract No. N3943018C2080.
2020-04-21T00:00:00ZBouchet, PhilHarris, Catriona MThomas, LenIn this report, we present a framework for simulating responses of cetaceans to various military sonar exposure contexts using Bayesian hierarchical modelling. This work was motivated by the need to assess the utility of different types of animal-attached biotelemetry tags in improving our understanding of dose–response relationships. Specifically, we used a Monte Carlo approach to conduct a sensitivity analysis of the effects of uncertainty in acoustic dose measurements (i.e. received sound levels) on the probability of behavioural response. Accompanying R code is available and fully described in a sister document.C. S. Lewis and the neurotic imagination : a Horneyan analysisVaughan, Simonhttps://hdl.handle.net/10023/198522021-07-26T17:06:21Z2020-06-01T00:00:00ZStandard accounts of C. S. Lewis’s life and work have typically struggled to explain the complexity of the data and its apparent contradictions, and reduce his conversion to an inscrutable metaphysical event of unquestioned validity. Such treatments of Lewis are often constrained by the shared evangelical intent of the scholars concerned. This thesis argues, sympathetically but critically, that sense can more easily be made of Lewis’s life and work in general, and of his conversion and poetry in particular, if they are understood as the outworking of a dynamic psychological process, one bound up with his failure in early manhood to achieve success (in terms of either recognition or creative potency) as a poet. It argues further that after his conversion his creativity was hampered by the metaphysical constraints he placed on it, which were themselves partly an expression of neurotic demands he made on himself as a consequence of the earlier failure. In giving such an account, the thesis avoids the pitfalls of a Freudian analysis (the only kind to which Lewis has so far been subjected). Instead, the methodology used draws on the psychoanalytical theories of Karen Horney as applied within a broader humanist framework.
Horney’s theory posits the imaginative creation in the neurotic person’s mind of an idealized self as a substitute for the real self, which is despised (Chapter 2). The idealized self must then be defended from the incursions of reality by the adoption of various defensive postures (Chapters 3 and 4). These postures, however, offer only partial solutions to the neurotic conflict and are inherently unstable, providing a spurious sense of integration (Chapter 5), as evidenced by the shifting from one solution to another in moments of crisis. Lewis is shown both to have undergone this self-idealization and, to some degree, to have intuited it, without extricating himself entirely from the process (Chapter 6).
2020-06-01T00:00:00ZVaughan, SimonStandard accounts of C. S. Lewis’s life and work have typically struggled to explain the complexity of the data and its apparent contradictions, and reduce his conversion to an inscrutable metaphysical event of unquestioned validity. Such treatments of Lewis are often constrained by the shared evangelical intent of the scholars concerned. This thesis argues, sympathetically but critically, that sense can more easily be made of Lewis’s life and work in general, and of his conversion and poetry in particular, if they are understood as the outworking of a dynamic psychological process, one bound up with his failure in early manhood to achieve success (in terms of either recognition or creative potency) as a poet. It argues further that after his conversion his creativity was hampered by the metaphysical constraints he placed on it, which were themselves partly an expression of neurotic demands he made on himself as a consequence of the earlier failure. In giving such an account, the thesis avoids the pitfalls of a Freudian analysis (the only kind to which Lewis has so far been subjected). Instead, the methodology used draws on the psychoanalytical theories of Karen Horney as applied within a broader humanist framework.
Horney’s theory posits the imaginative creation in the neurotic person’s mind of an idealized self as a substitute for the real self, which is despised (Chapter 2). The idealized self must then be defended from the incursions of reality by the adoption of various defensive postures (Chapters 3 and 4). These postures, however, offer only partial solutions to the neurotic conflict and are inherently unstable, providing a spurious sense of integration (Chapter 5), as evidenced by the shifting from one solution to another in moments of crisis. Lewis is shown both to have undergone this self-idealization and, to some degree, to have intuited it, without extricating himself entirely from the process (Chapter 6).‘This distressing malady’ : childbirth and mental illness in Scotland 1820 – 1930Campbell, Morag Allanhttps://hdl.handle.net/10023/195342021-07-23T10:50:53Z2020-06-25T00:00:00ZMy thesis explores the experiences of women who suffered from mental disorder related to childbirth and pregnancy, looking in particular at Dundee, Fife and Forfarshire in the north-east of Scotland, during the period 1820 to 1930. This study offers a new perspective on women’s lives, wellbeing and healthcare in this region by examining at a local level the ideas surrounding postpartum mental illness.
By the mid-nineteenth century, the term ‘puerperal insanity’ was widely known and much discussed and deliberated in medical literature. However, the day-to-day care and treatment of postpartum women suffering from mental disorder was not straightforward. My findings demonstrate that the diagnosis and treatment of postpartum mental illness in nineteenth- and early twentieth-century Scotland was a complex issue influenced as much by social and economic factors as by medical ideas.
Using records from the chartered asylums at Montrose and Dundee, court and prison records, and newspaper accounts, I have uncovered how childbearing-related mental illness was recognised, accepted and supported by families, neighbours, friends and authorities. Within the asylum, I have revealed how physicians assessed their patients’ characters and status as much as their physical conditions, but nevertheless in many cases provided positive medical care and much-needed rest and nourishment. In criminal cases, my study has looked beyond legislation and verdicts to reveal a positive and constructive approach to the care and custody of women who had committed child murder.
Awareness of postpartum mental illness in the community was developed through a collaboration of medical and lay knowledge, acquired through interactions between physicians, families and communities, and filtered through pre-existing understandings and ideas. I have identified a lay understanding and accepted discourse which guided the ideas and actions of friends, family and community in dealing with the problems associated with mental illness among postpartum women.
2020-06-25T00:00:00ZCampbell, Morag AllanMy thesis explores the experiences of women who suffered from mental disorder related to childbirth and pregnancy, looking in particular at Dundee, Fife and Forfarshire in the north-east of Scotland, during the period 1820 to 1930. This study offers a new perspective on women’s lives, wellbeing and healthcare in this region by examining at a local level the ideas surrounding postpartum mental illness.
By the mid-nineteenth century, the term ‘puerperal insanity’ was widely known and much discussed and deliberated in medical literature. However, the day-to-day care and treatment of postpartum women suffering from mental disorder was not straightforward. My findings demonstrate that the diagnosis and treatment of postpartum mental illness in nineteenth- and early twentieth-century Scotland was a complex issue influenced as much by social and economic factors as by medical ideas.
Using records from the chartered asylums at Montrose and Dundee, court and prison records, and newspaper accounts, I have uncovered how childbearing-related mental illness was recognised, accepted and supported by families, neighbours, friends and authorities. Within the asylum, I have revealed how physicians assessed their patients’ characters and status as much as their physical conditions, but nevertheless in many cases provided positive medical care and much-needed rest and nourishment. In criminal cases, my study has looked beyond legislation and verdicts to reveal a positive and constructive approach to the care and custody of women who had committed child murder.
Awareness of postpartum mental illness in the community was developed through a collaboration of medical and lay knowledge, acquired through interactions between physicians, families and communities, and filtered through pre-existing understandings and ideas. I have identified a lay understanding and accepted discourse which guided the ideas and actions of friends, family and community in dealing with the problems associated with mental illness among postpartum women.Energetics of moulting in phocid sealsPaterson, William Davidhttps://hdl.handle.net/10023/191112021-03-23T17:20:08Z2019-06-26T00:00:00ZThe moult in phocid seals is a distinct period when behavioural and physiological
changes occur. During this key stage in the annual life cycle animals elevate skin
temperature to facilitate proliferation of hair follicle cells as they shed and renew their
entire pelage. Due to the physiological constraints of raising skin temperature while in
the water animals must haul out on land with increasing duration as the moult proceeds.
The overall aim of this thesis was to provide insight into the physiology of moulting in
phocid seals and to determine the physiological consequences associated with changes
in haulout behaviour caused by anthropogenic disturbance. In harbour seals, metabolic
rate was higher during the moult compared to when the moult had finished, particularly
during the first 40 minutes after hauling out. Subcutaneous temperature increased at a
faster rate and reached a higher asymptote when seals were moulting. High skin
temperatures were also recorded in moulting southern elephant seals resulting in
increased heat flux to the surrounding environment. Heat loss values equated to animals
having a metabolic rate of up to 2.3 x Kleiber. Disturbance trials of harbour seals showed
that individuals were highly site faithful to haulout locations despite repeated
disturbance. The impact of disturbance is therefore not to cause animals to transition to
another site but to increase the frequency with which animals enter the water and the
duration of time spent at sea. Similar levels of disturbance may have thermoregulatory
consequences when seals are in a moulting state. These results demonstrate physiological changes during the moult that incur an increased metabolic demand.
Anthropogenic disturbance that causes seals to enter the water at a higher frequency
than normal when moulting may incur a cumulative energetic cost. Mitigation to protect
seals at haulout sites during the moult are supported by these findings.
2019-06-26T00:00:00ZPaterson, William DavidThe moult in phocid seals is a distinct period when behavioural and physiological
changes occur. During this key stage in the annual life cycle animals elevate skin
temperature to facilitate proliferation of hair follicle cells as they shed and renew their
entire pelage. Due to the physiological constraints of raising skin temperature while in
the water animals must haul out on land with increasing duration as the moult proceeds.
The overall aim of this thesis was to provide insight into the physiology of moulting in
phocid seals and to determine the physiological consequences associated with changes
in haulout behaviour caused by anthropogenic disturbance. In harbour seals, metabolic
rate was higher during the moult compared to when the moult had finished, particularly
during the first 40 minutes after hauling out. Subcutaneous temperature increased at a
faster rate and reached a higher asymptote when seals were moulting. High skin
temperatures were also recorded in moulting southern elephant seals resulting in
increased heat flux to the surrounding environment. Heat loss values equated to animals
having a metabolic rate of up to 2.3 x Kleiber. Disturbance trials of harbour seals showed
that individuals were highly site faithful to haulout locations despite repeated
disturbance. The impact of disturbance is therefore not to cause animals to transition to
another site but to increase the frequency with which animals enter the water and the
duration of time spent at sea. Similar levels of disturbance may have thermoregulatory
consequences when seals are in a moulting state. These results demonstrate physiological changes during the moult that incur an increased metabolic demand.
Anthropogenic disturbance that causes seals to enter the water at a higher frequency
than normal when moulting may incur a cumulative energetic cost. Mitigation to protect
seals at haulout sites during the moult are supported by these findings.Humpback whales in Brazil : distribution, abundance and human impactsBortolotto, Guilherme Augustohttps://hdl.handle.net/10023/189322021-04-12T15:55:01Z2019-12-03T00:00:00ZThe humpback whale population breeding in Brazilian waters has greatly increased, after near extinction due to whaling in the twentieth century. Today, these animals are under pressure from human activities in the area. In this thesis, habitat use, distribution, abundance, population status and potential threat from oil spills were investigated to improve knowledge of the population’s ecology and provide useful information for conservation and management. Distribution and habitat use were investigated through spatial models applied to line transect data and to tracking data. Line transect data were also used to estimate abundance. Distribution maps from both data types were used with a simulation of oil dispersion to evaluate risk of impact from oil spills. The new abundance estimates, together with information on population increase from another study, were used to update a Bayesian population dynamics model to re-assess population status. Modelling of line transect data indicated whale density to be higher in slower currents, at shorter distances to both the coastline and shelf edge, and at sea surface temperatures between 24 and 25°C, and to be related to shelter. A higher concentration of animals was predicted in the southern portion of Abrolhos bank, an enlargement of the continental shelf. Modelling of tracking data agreed with those findings, despite differences in the nature of the data and analytical methods. Risk maps of oil spill impact indicated that areas in the south of the breeding range present highest risks to the animals. Abundance estimates (14,264, CV = 0.084, in 2008; 20,389, CV = 0.071, in 2012) provide further evidence that the population is increasing, and contributed to improved precision in the population status assessment. New information provided here will inform conservation of the humpback whale population breeding in Brazilian waters and the need for, and implementation of, any necessary management action.
2019-12-03T00:00:00ZBortolotto, Guilherme AugustoThe humpback whale population breeding in Brazilian waters has greatly increased, after near extinction due to whaling in the twentieth century. Today, these animals are under pressure from human activities in the area. In this thesis, habitat use, distribution, abundance, population status and potential threat from oil spills were investigated to improve knowledge of the population’s ecology and provide useful information for conservation and management. Distribution and habitat use were investigated through spatial models applied to line transect data and to tracking data. Line transect data were also used to estimate abundance. Distribution maps from both data types were used with a simulation of oil dispersion to evaluate risk of impact from oil spills. The new abundance estimates, together with information on population increase from another study, were used to update a Bayesian population dynamics model to re-assess population status. Modelling of line transect data indicated whale density to be higher in slower currents, at shorter distances to both the coastline and shelf edge, and at sea surface temperatures between 24 and 25°C, and to be related to shelter. A higher concentration of animals was predicted in the southern portion of Abrolhos bank, an enlargement of the continental shelf. Modelling of tracking data agreed with those findings, despite differences in the nature of the data and analytical methods. Risk maps of oil spill impact indicated that areas in the south of the breeding range present highest risks to the animals. Abundance estimates (14,264, CV = 0.084, in 2008; 20,389, CV = 0.071, in 2012) provide further evidence that the population is increasing, and contributed to improved precision in the population status assessment. New information provided here will inform conservation of the humpback whale population breeding in Brazilian waters and the need for, and implementation of, any necessary management action.The role of individual behaviour in the collective cultural evolution of humpback whale songsLamoni, Luca Ubaldohttps://hdl.handle.net/10023/186212019-10-08T02:06:03Z2018-12-06T00:00:00ZFor more than forty years, the complex songs emitted by humpback whales have
fascinated the scientific community as well as the general public. These songs are
produced by males during the breeding season, and are hierarchically structured and
population specific. Within a population, males tend to conform to the same song type,
but songs undergo gradual unidirectional change. Instances of more rapid song changes
have also been recorded, where the song sung by a population has been replaced by the
song of an adjacent population. The learning mechanisms that concurrently drive song
conformity, and simultaneously allow gradual (evolution) and rapid (revolution) song
change are not currently understood. This thesis aims to address this gap by using
innovative theoretical models as well as more established empirical methods.
Chapter 1 provides a general introduction to the thesis topics. In chapter 2 I
introduce a spatially explicit agent-based modelling approach to investigate humpback
whale song evolution and transmission. I found that shared feeding grounds promote
inter-population song transmission, song conformity emerges as a function of breeding
ground geographical segregation, and production errors facilitate gradual evolution of
songs. In chapter 3, the same modelling approach is extended to simulate song
revolutions using a new learning bias in combination with different movement
scenarios. I found that the consistent emergence of song revolutions is dependent on
cognitive (song memory), behavioural (singing probability) and spatial (agent density)
factors. Finally, in chapter 4, I analyse intra- and inter- individual song variability at
different hierarchical levels of organisation in songs recorded off eastern Australia. I
found that variability is not homogeneously distributed across the different song levels.
Furthermore, I identified consistent and distinctive individual patterns of song
production consistent with the theory that songs could represent mate quality
advertisements for females.
2018-12-06T00:00:00ZLamoni, Luca UbaldoFor more than forty years, the complex songs emitted by humpback whales have
fascinated the scientific community as well as the general public. These songs are
produced by males during the breeding season, and are hierarchically structured and
population specific. Within a population, males tend to conform to the same song type,
but songs undergo gradual unidirectional change. Instances of more rapid song changes
have also been recorded, where the song sung by a population has been replaced by the
song of an adjacent population. The learning mechanisms that concurrently drive song
conformity, and simultaneously allow gradual (evolution) and rapid (revolution) song
change are not currently understood. This thesis aims to address this gap by using
innovative theoretical models as well as more established empirical methods.
Chapter 1 provides a general introduction to the thesis topics. In chapter 2 I
introduce a spatially explicit agent-based modelling approach to investigate humpback
whale song evolution and transmission. I found that shared feeding grounds promote
inter-population song transmission, song conformity emerges as a function of breeding
ground geographical segregation, and production errors facilitate gradual evolution of
songs. In chapter 3, the same modelling approach is extended to simulate song
revolutions using a new learning bias in combination with different movement
scenarios. I found that the consistent emergence of song revolutions is dependent on
cognitive (song memory), behavioural (singing probability) and spatial (agent density)
factors. Finally, in chapter 4, I analyse intra- and inter- individual song variability at
different hierarchical levels of organisation in songs recorded off eastern Australia. I
found that variability is not homogeneously distributed across the different song levels.
Furthermore, I identified consistent and distinctive individual patterns of song
production consistent with the theory that songs could represent mate quality
advertisements for females.From here and now to there and then : practical recommendations for extrapolating cetacean density surface models to novel conditionsBouchet, Philippe Jean-FrancoisMiller, David LawrenceRoberts, JasonMannocci, LauraHarris, Catriona MThomas, Lenhttps://hdl.handle.net/10023/185092024-03-28T00:47:09Z2019-09-04T00:00:00ZDensity surface models (DSMs) are clearly established as a method of choice for the analysis of cetacean line transect survey data, and are increasingly used to inform risk assessments in remote marine areas subject to rising anthropogenic impacts (e.g. the high seas). However, despite persistent skepticism about the validity of extrapolated models, more and more DSMs are being applied well beyond the boundaries of the study regions where field sampling originally took place. This leads to potentially uncertain and error-prone model predictions that may mislead on-the-ground management interventions and undermine conservation decision-making. In addition, no consensus currently exists on the best way to define and measure extrapolation when it occurs, leaving users without the tools they require to audit models projected into novel conditions. Consequently, a transparent and consistent protocol for identifying scenarios under which extrapolation may be appropriate (or conversely, ill-advised) is urgently needed to better gauge how models behave outside the boundaries of sample data and to know how much faith can be placed in their outputs. This report aims to address this gap by synthesising recent advances in extrapolation detection, and presenting recommendations for a minimum standard for measuring extrapolation in novel environmental space. Such guidelines are essential to promoting transparency, replicability, and quality control, and will help marine scientists, managers and policy agencies to (i) better interpret density surfaces and their associated uncertainty; (ii) refine model development and selection approaches; and (iii) optimise the allocation of future survey effort by identifying priority knowledge gaps, e.g. by delineating areas where model predictions are the least supported by data. Our review is accompanied by supplementary R code offering a user-friendly framework for quantifying, summarising and visualising various forms of extrapolation in multivariate environmental space a priori (ahead of model fitting). We illustrate its application with case studies designed to revisit previously published predictions of sperm whale (Physeter macrocephalus) and beaked whale (Ziphiidae spp.) densities in the Northwest Atlantic, and evaluate them in light of several extrapolation metrics. Very early in their training, ecologists are given strong warnings against extrapolating, as model predictions made in data-deficient contexts rely heavily on assumptions that may not hold outside the range of sampled conditions. Navigating the ‘uncharted waters’ of extrapolation, however, is critical to scientific progress, and will be best achieved with a clear understanding of the mechanics, benefits, and limitations of extrapolated models.
2019-09-04T00:00:00ZBouchet, Philippe Jean-FrancoisMiller, David LawrenceRoberts, JasonMannocci, LauraHarris, Catriona MThomas, LenDensity surface models (DSMs) are clearly established as a method of choice for the analysis of cetacean line transect survey data, and are increasingly used to inform risk assessments in remote marine areas subject to rising anthropogenic impacts (e.g. the high seas). However, despite persistent skepticism about the validity of extrapolated models, more and more DSMs are being applied well beyond the boundaries of the study regions where field sampling originally took place. This leads to potentially uncertain and error-prone model predictions that may mislead on-the-ground management interventions and undermine conservation decision-making. In addition, no consensus currently exists on the best way to define and measure extrapolation when it occurs, leaving users without the tools they require to audit models projected into novel conditions. Consequently, a transparent and consistent protocol for identifying scenarios under which extrapolation may be appropriate (or conversely, ill-advised) is urgently needed to better gauge how models behave outside the boundaries of sample data and to know how much faith can be placed in their outputs. This report aims to address this gap by synthesising recent advances in extrapolation detection, and presenting recommendations for a minimum standard for measuring extrapolation in novel environmental space. Such guidelines are essential to promoting transparency, replicability, and quality control, and will help marine scientists, managers and policy agencies to (i) better interpret density surfaces and their associated uncertainty; (ii) refine model development and selection approaches; and (iii) optimise the allocation of future survey effort by identifying priority knowledge gaps, e.g. by delineating areas where model predictions are the least supported by data. Our review is accompanied by supplementary R code offering a user-friendly framework for quantifying, summarising and visualising various forms of extrapolation in multivariate environmental space a priori (ahead of model fitting). We illustrate its application with case studies designed to revisit previously published predictions of sperm whale (Physeter macrocephalus) and beaked whale (Ziphiidae spp.) densities in the Northwest Atlantic, and evaluate them in light of several extrapolation metrics. Very early in their training, ecologists are given strong warnings against extrapolating, as model predictions made in data-deficient contexts rely heavily on assumptions that may not hold outside the range of sampled conditions. Navigating the ‘uncharted waters’ of extrapolation, however, is critical to scientific progress, and will be best achieved with a clear understanding of the mechanics, benefits, and limitations of extrapolated models.Title redactedMaple, Sarah Elizabethhttps://hdl.handle.net/10023/179902019-06-27T14:55:39Z2017-06-20T00:00:00Z2017-06-20T00:00:00ZMaple, Sarah ElizabethNot just fat : investigating novel physiological state biomarkers in cetacean blubberKershaw, Joannahttps://hdl.handle.net/10023/179772021-03-19T12:05:21Z2019-06-26T00:00:00ZDespite its importance as a predictor of fitness, no consensus has been reached about how to
assess the nutritive body condition of free-ranging cetaceans. Standard indices of condition
used in terrestrial ecology were assessed in cetaceans using data and samples from stranded
animals. The most appropriate morphometric indices were identified as mass/length2 and
girth/length (where mass data were unavailable). Blubber thickness, and blubber lipid content
were poor indicators of condition. Variation in lipid content suggested that there may be tradeoffs
occurring between different blubber functions involved in energy storage, controlling
buoyancy, and preserving thermoregulatory properties in species with different life-history
strategies.
Novel blubber biomarkers of physiological state were investigated as objective and widely
applicable tools for estimating body condition. Blubber cortisol concentrations were negatively
correlated with morphometric indices of condition in stranded animals from two cetacean
families. Blubber cortisol concentrations were thus identified as a candidate biomarker. When
applied to a 13-year dataset of biopsy samples from female humpback whales (Megaptera
novaeangliae), cortisol concentrations showed significant inter-annual variation.
Concentrations were weakly correlated with annual pregnancy rates. High individual
variability in blubber cortisol concentrations was likely a result of the multi-functional nature
of cortisol. Cortisol concentrations thus probably provide a ‘snap shot’ of the metabolic state
of the tissue when sampled.
A proteomic approach was developed to extract and identify proteins in blubber. A range of
proteins involved in numerous metabolic processes and pathways were identified. These
proteins likely capture the range of physiological processes experienced by individuals at the
time of sampling. This new proteomic approach will help to assign novel functions to marine
mammal blubber in keeping with current understanding of the multi-functional role of adipose
tissue as an endocrine organ in mammals. It will also allow the future development of protein
biomarkers of health and physiological state.
2019-06-26T00:00:00ZKershaw, JoannaDespite its importance as a predictor of fitness, no consensus has been reached about how to
assess the nutritive body condition of free-ranging cetaceans. Standard indices of condition
used in terrestrial ecology were assessed in cetaceans using data and samples from stranded
animals. The most appropriate morphometric indices were identified as mass/length2 and
girth/length (where mass data were unavailable). Blubber thickness, and blubber lipid content
were poor indicators of condition. Variation in lipid content suggested that there may be tradeoffs
occurring between different blubber functions involved in energy storage, controlling
buoyancy, and preserving thermoregulatory properties in species with different life-history
strategies.
Novel blubber biomarkers of physiological state were investigated as objective and widely
applicable tools for estimating body condition. Blubber cortisol concentrations were negatively
correlated with morphometric indices of condition in stranded animals from two cetacean
families. Blubber cortisol concentrations were thus identified as a candidate biomarker. When
applied to a 13-year dataset of biopsy samples from female humpback whales (Megaptera
novaeangliae), cortisol concentrations showed significant inter-annual variation.
Concentrations were weakly correlated with annual pregnancy rates. High individual
variability in blubber cortisol concentrations was likely a result of the multi-functional nature
of cortisol. Cortisol concentrations thus probably provide a ‘snap shot’ of the metabolic state
of the tissue when sampled.
A proteomic approach was developed to extract and identify proteins in blubber. A range of
proteins involved in numerous metabolic processes and pathways were identified. These
proteins likely capture the range of physiological processes experienced by individuals at the
time of sampling. This new proteomic approach will help to assign novel functions to marine
mammal blubber in keeping with current understanding of the multi-functional role of adipose
tissue as an endocrine organ in mammals. It will also allow the future development of protein
biomarkers of health and physiological state.Can I play with madness : American missionaries in Iran during the 1960s and 1970sHopkins, Philip Ohttps://hdl.handle.net/10023/178862021-03-24T15:49:58Z2019-06-27T00:00:00ZThis thesis studied the interaction of American Protestant missionaries with Iranians during
the 1960s and 1970s. It focused on the missionary activities of four American Protestant
groups: Presbyterians, Assemblies of God, International Missions, and Southern Baptists.
It argued that American missionaries’ predisposition toward their own culture confused
their message of the gospel and added to the negative perception of Christianity among
Iranians. This bias was seen primarily in the American missionaries’ desire to modernise
Iran through education and healthcare, and between the missionaries’ relationship with
Iranian Christians. Iranian attitudes towards missionary involvement in these areas were
investigated, as was the changing American missionary strategy from a traditional method
where missionaries had final say on most matters related to American and Iranian Christian
interaction to the beginnings of an indigenous system where a partnership developed
between the missionary and the Iranian Christian. Freedoms that American missionaries
were given under Mohammed Reza Shah to be overt in their evangelistic and discipleship
activities, and details of the amount of Christian material propagated, were investigated. As
missionaries eventually withdrew from Iran’s education and healthcare systems, more
opportunities to be involved in Christian and Western activities were given to Iranian
Christians. Finally, the state of the Iranian Church after 1979, when American missionaries
were expelled from the country, was contrasted with the Iranian Church during the Pahlavi
era. This section explained that while Iranian Christians were thankful for American
missionaries, they were also resentful because Iranian Christians wanted Christianity to fit
better within Iranian accepted norms and practices.
2019-06-27T00:00:00ZHopkins, Philip OThis thesis studied the interaction of American Protestant missionaries with Iranians during
the 1960s and 1970s. It focused on the missionary activities of four American Protestant
groups: Presbyterians, Assemblies of God, International Missions, and Southern Baptists.
It argued that American missionaries’ predisposition toward their own culture confused
their message of the gospel and added to the negative perception of Christianity among
Iranians. This bias was seen primarily in the American missionaries’ desire to modernise
Iran through education and healthcare, and between the missionaries’ relationship with
Iranian Christians. Iranian attitudes towards missionary involvement in these areas were
investigated, as was the changing American missionary strategy from a traditional method
where missionaries had final say on most matters related to American and Iranian Christian
interaction to the beginnings of an indigenous system where a partnership developed
between the missionary and the Iranian Christian. Freedoms that American missionaries
were given under Mohammed Reza Shah to be overt in their evangelistic and discipleship
activities, and details of the amount of Christian material propagated, were investigated. As
missionaries eventually withdrew from Iran’s education and healthcare systems, more
opportunities to be involved in Christian and Western activities were given to Iranian
Christians. Finally, the state of the Iranian Church after 1979, when American missionaries
were expelled from the country, was contrasted with the Iranian Church during the Pahlavi
era. This section explained that while Iranian Christians were thankful for American
missionaries, they were also resentful because Iranian Christians wanted Christianity to fit
better within Iranian accepted norms and practices.Communication accommodation theory : a dolphin perspectiveJones, Brittanyhttps://hdl.handle.net/10023/178602021-03-16T11:09:05Z2019-06-26T00:00:00ZFor humans, there is a well-established theory, which explains much of the variation in human verbal dyadic speech behavior, the “communication accommodation theory (CAT)”. In its most basic form, CAT predicts that as two conversation partners become more similar in their speech patterns, the more likely they are to perceive the interaction, and/or the other person favorably. In this exploration of CAT in a non-human mammal, I look for the cornerstones of the theory in bottlenose dolphin communication. Dolphins depend largely on acoustic communication to maintain ever-changing social interactions in a marine environment. Dolphins have individually specific signature whistles that allow them to broadcast their identity, and also are able to encode additional information across those whistle emissions. They often use these whistles in antiphonal exchanges with other dolphins. In Chapter 2, I show that dolphins use signature whistles more often when conspecifics are present, suggesting a socially mediated system for signature whistle use. I find that male allies do not converge their signature whistles from pre-alliance to alliance formation, as previously suggested, nor over the course of alliance (Chapter 3). I do find that allies have more similar signature whistles to their male partner than to non-allies and in Chapter 4, find that male allies subtly accommodate during antiphonal signature whistle exchanges. During experimental playbacks of manipulated whistles to a bottlenose dolphin, I recorded subtle parameter accommodation in the frequency pitch shifts from one unit of a signature whistle playback to the next, suggesting that even when there is no difference in reinforcement, dolphins have the propensity for accommodation during signature whistle interactions. This thesis presents the first suggestion that the CAT may be a good model for the study for animal communication systems moving forward.
2019-06-26T00:00:00ZJones, BrittanyFor humans, there is a well-established theory, which explains much of the variation in human verbal dyadic speech behavior, the “communication accommodation theory (CAT)”. In its most basic form, CAT predicts that as two conversation partners become more similar in their speech patterns, the more likely they are to perceive the interaction, and/or the other person favorably. In this exploration of CAT in a non-human mammal, I look for the cornerstones of the theory in bottlenose dolphin communication. Dolphins depend largely on acoustic communication to maintain ever-changing social interactions in a marine environment. Dolphins have individually specific signature whistles that allow them to broadcast their identity, and also are able to encode additional information across those whistle emissions. They often use these whistles in antiphonal exchanges with other dolphins. In Chapter 2, I show that dolphins use signature whistles more often when conspecifics are present, suggesting a socially mediated system for signature whistle use. I find that male allies do not converge their signature whistles from pre-alliance to alliance formation, as previously suggested, nor over the course of alliance (Chapter 3). I do find that allies have more similar signature whistles to their male partner than to non-allies and in Chapter 4, find that male allies subtly accommodate during antiphonal signature whistle exchanges. During experimental playbacks of manipulated whistles to a bottlenose dolphin, I recorded subtle parameter accommodation in the frequency pitch shifts from one unit of a signature whistle playback to the next, suggesting that even when there is no difference in reinforcement, dolphins have the propensity for accommodation during signature whistle interactions. This thesis presents the first suggestion that the CAT may be a good model for the study for animal communication systems moving forward.Contrasting examples of liturgical installation art in Christian worship in England and Scotland from the 1980s to the present dayMarples, Carolhttps://hdl.handle.net/10023/178192021-03-04T10:25:29Z2019-06-25T00:00:00ZThis dissertation argues that liturgical installation is a sub-genre of installation art. Liturgical installation encompasses many of the same key characteristics as installation art but with the distinction that its main focus is to ‘serve the liturgy.’ I intend to demonstrate that liturgical installation, albeit in very different forms, has existed in Christian worship in Scotland and England since the early 1980s. This was initially on the fringes but latterly also within the institution of the Church.
Despite its presence in worship for nearly forty years, to date, only a very limited amount has been published on the subject of liturgical installation either by academics, ministers or artists. In support of my key claim that liturgical installation is a sub-genre of installation art, Chapter One will explore the history, development and nature of secular installation art. Contemporary secular art installations, in particular the work of Ann Hamilton and Paul Thek, will be examined in detail. This body of work will be drawn upon throughout the dissertation by way of comparison with the liturgical installations under discussion. This will enable exploration of the parallels and differences between installations created for the purely secular art world and those with a liturgical focus.
Chapters Two, Three and Four of the thesis investigate a series of liturgical installations in three different worship expressions: The worship of Wild Goose (1982 - Present Day), the Alternative Worship Movement, with particular focus on the Nine O’ Clock Service (1985-1995), the Late Late Service (ca. 1991-2000) and Soul Circus (2011 - Present Day) and specific instances where liturgical installation has been employed in institutional worship: that of the Presbyterian Parish Church of Renfield St. Stephen’s, Glasgow and the Scottish Episcopal of St. James the Less, Leith, Edinburgh. In addition, in order to compare and contrast liturgical worship with installations made for exhibitional purposes in ecclesial spaces, I examine three case studies of exhibitions at Sheffield, Salisbury and Birmingham Cathedrals. Throughout the thesis, I will explore what this new genre of liturgical installation has brought to the worship of the Church and what it can bring in the future. I will investigate where and for what reasons it has been employed albeit in diverse ways in these very different expressions of contemporary worship. I will conclude by offering some important questions and considerations for the enhanced practice of liturgical installation in the Church.
2019-06-25T00:00:00ZMarples, CarolThis dissertation argues that liturgical installation is a sub-genre of installation art. Liturgical installation encompasses many of the same key characteristics as installation art but with the distinction that its main focus is to ‘serve the liturgy.’ I intend to demonstrate that liturgical installation, albeit in very different forms, has existed in Christian worship in Scotland and England since the early 1980s. This was initially on the fringes but latterly also within the institution of the Church.
Despite its presence in worship for nearly forty years, to date, only a very limited amount has been published on the subject of liturgical installation either by academics, ministers or artists. In support of my key claim that liturgical installation is a sub-genre of installation art, Chapter One will explore the history, development and nature of secular installation art. Contemporary secular art installations, in particular the work of Ann Hamilton and Paul Thek, will be examined in detail. This body of work will be drawn upon throughout the dissertation by way of comparison with the liturgical installations under discussion. This will enable exploration of the parallels and differences between installations created for the purely secular art world and those with a liturgical focus.
Chapters Two, Three and Four of the thesis investigate a series of liturgical installations in three different worship expressions: The worship of Wild Goose (1982 - Present Day), the Alternative Worship Movement, with particular focus on the Nine O’ Clock Service (1985-1995), the Late Late Service (ca. 1991-2000) and Soul Circus (2011 - Present Day) and specific instances where liturgical installation has been employed in institutional worship: that of the Presbyterian Parish Church of Renfield St. Stephen’s, Glasgow and the Scottish Episcopal of St. James the Less, Leith, Edinburgh. In addition, in order to compare and contrast liturgical worship with installations made for exhibitional purposes in ecclesial spaces, I examine three case studies of exhibitions at Sheffield, Salisbury and Birmingham Cathedrals. Throughout the thesis, I will explore what this new genre of liturgical installation has brought to the worship of the Church and what it can bring in the future. I will investigate where and for what reasons it has been employed albeit in diverse ways in these very different expressions of contemporary worship. I will conclude by offering some important questions and considerations for the enhanced practice of liturgical installation in the Church.The impact of the modernisation of Iran on Kurdish society : modernity, modernisation and social change (1920-1979)Cabi, Maroufhttps://hdl.handle.net/10023/178172021-03-05T12:49:26Z2019-06-27T00:00:00ZThis PhD study examines the consequences of modernity and modernisation for Kurdish-Iranian society in the twentieth century. It identifies a dual process of socio-economic transformation and homogenisation of culture and identity, the dialectics of which (re)formed the economic, social, political and cultural structures of modern Kurdish society in Iran. As a result, socio-economically, Kurdish society became integrated in modern Iran, whereas it vigorously resisted homogenisation of identity and culture; at the same time, it maintained porous cultural borders with other societies in Iran, and continued to be shaped by mechanisms of modern cultural encounters. The socio-economic transformation of Iran strengthened and created new bonds between societies in Iran, while at the same time resistance and struggle for political and cultural rights became permanent characteristics of Kurdish-Iranian society. During the modernisation of Iran, the era of the ‘White Revolution’ is distinguished for the profound transformation of Iran it entailed. Therefore, an interpretation of the era constitutes the main concern of this thesis because, building on previous attempts to modernise Iran, the era of the White Revolution was crucial in engendering profound changes in Kurdish society.
The theoretical framework of this study is informed by theories of social change and transformation against modernisation theories, and by theories of nation and nationalism which theoretically enable this research to distance itself from national narratives. Significantly, this framework includes a range of cultural critiques, benefits from studies of homogenisation and state formation, and relies on rich scholarly works on the formation of modern Iran, which, when combined, accentuate the cultural, political and social dimensions of modern nation-building in Iran. The result is a multi-dimensional approach to social change in Kurdish society. It is the dynamics of the dual process which continue to (re)form the foundations of Kurdish society in Iran; and it is this approach which I regard as a crucial contribution to both Kurdish and Iranian studies.
2019-06-27T00:00:00ZCabi, MaroufThis PhD study examines the consequences of modernity and modernisation for Kurdish-Iranian society in the twentieth century. It identifies a dual process of socio-economic transformation and homogenisation of culture and identity, the dialectics of which (re)formed the economic, social, political and cultural structures of modern Kurdish society in Iran. As a result, socio-economically, Kurdish society became integrated in modern Iran, whereas it vigorously resisted homogenisation of identity and culture; at the same time, it maintained porous cultural borders with other societies in Iran, and continued to be shaped by mechanisms of modern cultural encounters. The socio-economic transformation of Iran strengthened and created new bonds between societies in Iran, while at the same time resistance and struggle for political and cultural rights became permanent characteristics of Kurdish-Iranian society. During the modernisation of Iran, the era of the ‘White Revolution’ is distinguished for the profound transformation of Iran it entailed. Therefore, an interpretation of the era constitutes the main concern of this thesis because, building on previous attempts to modernise Iran, the era of the White Revolution was crucial in engendering profound changes in Kurdish society.
The theoretical framework of this study is informed by theories of social change and transformation against modernisation theories, and by theories of nation and nationalism which theoretically enable this research to distance itself from national narratives. Significantly, this framework includes a range of cultural critiques, benefits from studies of homogenisation and state formation, and relies on rich scholarly works on the formation of modern Iran, which, when combined, accentuate the cultural, political and social dimensions of modern nation-building in Iran. The result is a multi-dimensional approach to social change in Kurdish society. It is the dynamics of the dual process which continue to (re)form the foundations of Kurdish society in Iran; and it is this approach which I regard as a crucial contribution to both Kurdish and Iranian studies.The reform of zeal: François de Sales and militant French CatholicismDonlan, Thomas A.https://hdl.handle.net/10023/174152019-04-22T08:53:07Z2018-12-01T00:00:00ZThe Reform of Zeal explores the origins, nature, and impact of François de Sales’s vision of Catholic douceur (gentleness) in the era of the French Wars of Religion. Since Natalie Zemon Davis’s pioneering work on the ‘rites of violence’, scholarship has focused on the militant Catholic cultures of early modern France. Taking a fresh approach to de Sales’s work as a missionary, spiritual director, and founder of the Order of Visitation, this volume documents the evolution of de Sales’s spirituality and his championing of religious cultures of nonviolence within French Catholicism. The Reform of Zeal argues that Salesian douceur not only constituted one of the most effective critiques of French Catholic militancy in the period, but also a unique source of religious renewal in the seventeenth century, independent of Leaguer and early dévot fervour.
2018-12-01T00:00:00ZDonlan, Thomas A.The Reform of Zeal explores the origins, nature, and impact of François de Sales’s vision of Catholic douceur (gentleness) in the era of the French Wars of Religion. Since Natalie Zemon Davis’s pioneering work on the ‘rites of violence’, scholarship has focused on the militant Catholic cultures of early modern France. Taking a fresh approach to de Sales’s work as a missionary, spiritual director, and founder of the Order of Visitation, this volume documents the evolution of de Sales’s spirituality and his championing of religious cultures of nonviolence within French Catholicism. The Reform of Zeal argues that Salesian douceur not only constituted one of the most effective critiques of French Catholic militancy in the period, but also a unique source of religious renewal in the seventeenth century, independent of Leaguer and early dévot fervour.Statistical analysis of SAMBAH survey and associated dataThomas, LenBurt, M Louisehttps://hdl.handle.net/10023/173282023-04-18T09:37:47Z2016-03-01T00:00:00ZSAMBAH (Static Acoustic Monitoring of the Baltic Sea Harbour Porpoise) was an international project involving all EU countries around the Baltic Sea, funded by those countries and by the EU Life program (Project Number LIFE08 NAT/S/000261). It ran from 1/1/2010 to 30/9/2015. One major goal of the project was to estimate the abundance of Baltic Sea harbour porpoise, by designing and implementing a large-scale multi-year passive acoustic survey. CREEM was contracted to collaborate on the survey design, and provide statistical analysis of resulting data. A number of internal reports were produced and circulated to the project team, detailing aspects of the analysis. In this CREEM technical report, we collate the most recent version of each of these internal reports as a means of making them publicly available.
2016-03-01T00:00:00ZThomas, LenBurt, M LouiseSAMBAH (Static Acoustic Monitoring of the Baltic Sea Harbour Porpoise) was an international project involving all EU countries around the Baltic Sea, funded by those countries and by the EU Life program (Project Number LIFE08 NAT/S/000261). It ran from 1/1/2010 to 30/9/2015. One major goal of the project was to estimate the abundance of Baltic Sea harbour porpoise, by designing and implementing a large-scale multi-year passive acoustic survey. CREEM was contracted to collaborate on the survey design, and provide statistical analysis of resulting data. A number of internal reports were produced and circulated to the project team, detailing aspects of the analysis. In this CREEM technical report, we collate the most recent version of each of these internal reports as a means of making them publicly available.Title redactedHope, Julie Annehttps://hdl.handle.net/10023/171492019-05-28T08:57:11Z2016-06-22T00:00:00Z2016-06-22T00:00:00ZHope, Julie AnnePathways and practice : the general practitioner in nineteenth-century DundeeCampbell, Morag Allanhttps://hdl.handle.net/10023/171222023-04-18T23:50:57Z2018-08-17T00:00:00ZAlthough the care of the basic medical needs of much of the population, or what might be termed general medicine, accounted by the mid nineteenth century for the work of the majority of medical men in Britain, those who practiced within this field were an irregular group of practitioners who had evolved from the surgeon- apothecaries and man midwives of the eighteenth century, and who formed an unspecific mix of medical men with different qualifications, training and experiences. Increasing legislation forced the radical development of the medical profession by the end of the century and, in a changing climate of education and opportunity, medical men competed for professional survival. This they did through the cultivation and exploitation of ‘community niches’ to gain professional recognition (Digby, 1999, p. 261). The medical establishment in mid-nineteenth-century Dundee was made up of a diverse group of practitioners, in terms of education, qualification and experience, much of which still reflected the pathways and practices of the late eighteenth century. Dominated by leading medical families and intricate social networks, the medical community increasingly established itself in a distinct quarter within the city, and entrenched itself in the wider community through public appointments and civic office. This paper will explore the landscape of medical practice in this local ‘niche’, examining the ways in which the resident medical men created themselves both as individual practitioners with status and influence – the newly emerging ‘general practitioners’ – and as a distinct and respected professional community.
2018-08-17T00:00:00ZCampbell, Morag AllanAlthough the care of the basic medical needs of much of the population, or what might be termed general medicine, accounted by the mid nineteenth century for the work of the majority of medical men in Britain, those who practiced within this field were an irregular group of practitioners who had evolved from the surgeon- apothecaries and man midwives of the eighteenth century, and who formed an unspecific mix of medical men with different qualifications, training and experiences. Increasing legislation forced the radical development of the medical profession by the end of the century and, in a changing climate of education and opportunity, medical men competed for professional survival. This they did through the cultivation and exploitation of ‘community niches’ to gain professional recognition (Digby, 1999, p. 261). The medical establishment in mid-nineteenth-century Dundee was made up of a diverse group of practitioners, in terms of education, qualification and experience, much of which still reflected the pathways and practices of the late eighteenth century. Dominated by leading medical families and intricate social networks, the medical community increasingly established itself in a distinct quarter within the city, and entrenched itself in the wider community through public appointments and civic office. This paper will explore the landscape of medical practice in this local ‘niche’, examining the ways in which the resident medical men created themselves both as individual practitioners with status and influence – the newly emerging ‘general practitioners’ – and as a distinct and respected professional community.Maximal subsemigroups of finite transformation and diagram monoidsEast, JamesKumar, JitenderMitchell, James D.Wilson, Wilf A.https://hdl.handle.net/10023/171102024-02-17T00:42:18Z2018-06-15T00:00:00ZWe describe and count the maximal subsemigroups of many well-known transformation monoids, and diagram monoids, using a new unified framework that allows the treatment of several classes of monoids simultaneously. The problem of determining the maximal subsemigroups of a finite monoid of transformations has been extensively studied in the literature. To our knowledge, every existing result in the literature is a special case of the approach we present. In particular, our technique can be used to determine the maximal subsemigroups of the full spectrum of monoids of order- or orientation-preserving transformations and partial permutations considered by I. Dimitrova, V. H. Fernandes, and co-authors. We only present details for the transformation monoids whose maximal subsemigroups were not previously known; and for certain diagram monoids, such as the partition, Brauer, Jones, and Motzkin monoids. The technique we present is based on a specialised version of an algorithm for determining the maximal subsemigroups of any finite semigroup, developed by the third and fourth authors, and available in the Semigroups package for GAP, an open source computer algebra system. This allows us to concisely present the descriptions of the maximal subsemigroups, and to clearly see their common features.
The first author gratefully acknowledges the support of the Glasgow Learning, Teaching, and Research Fund in partially funding his visit to the third author in July, 2014. The second author wishes to acknowledge the support of research initiation grant [0076|2016] provided by BITS Pilani, Pilani. The fourth author wishes to acknowledge the support of his Carnegie Ph.D. Scholarship from the Carnegie Trust for the Universities of Scotland.
2018-06-15T00:00:00ZEast, JamesKumar, JitenderMitchell, James D.Wilson, Wilf A.We describe and count the maximal subsemigroups of many well-known transformation monoids, and diagram monoids, using a new unified framework that allows the treatment of several classes of monoids simultaneously. The problem of determining the maximal subsemigroups of a finite monoid of transformations has been extensively studied in the literature. To our knowledge, every existing result in the literature is a special case of the approach we present. In particular, our technique can be used to determine the maximal subsemigroups of the full spectrum of monoids of order- or orientation-preserving transformations and partial permutations considered by I. Dimitrova, V. H. Fernandes, and co-authors. We only present details for the transformation monoids whose maximal subsemigroups were not previously known; and for certain diagram monoids, such as the partition, Brauer, Jones, and Motzkin monoids. The technique we present is based on a specialised version of an algorithm for determining the maximal subsemigroups of any finite semigroup, developed by the third and fourth authors, and available in the Semigroups package for GAP, an open source computer algebra system. This allows us to concisely present the descriptions of the maximal subsemigroups, and to clearly see their common features.Computing maximal subsemigroups of a finite semigroupDonoven, C. R.Mitchell, J. D.Wilson, W. A.https://hdl.handle.net/10023/170722024-02-15T00:46:30Z2018-07-01T00:00:00ZA proper subsemigroup of a semigroup is maximal if it is not contained in any other proper subsemigroup. A maximal subsemigroup of a finite semigroup has one of a small number of forms, as described in a paper of Graham, Graham, and Rhodes. Determining which of these forms arise in a given finite semigroup is difficult, and no practical mechanism for doing so appears in the literature. We present an algorithm for computing the maximal subsemigroups of a finite semigroup S given knowledge of the Green's structure of S, and the ability to determine maximal subgroups of certain subgroups of S, namely its group H-classes. In the case of a finite semigroup S represented by a generating set X, in many examples, if it is practical to compute the Green's structure of S from X, then it is also practical to find the maximal subsemigroups of S using the algorithm we present. In such examples, the time taken to determine the Green's structure of S is comparable to that taken to find the maximal subsemigroups. The generating set X for S may consist, for example, of transformations, or partial permutations, of a finite set, or of matrices over a semiring. Algorithms for computing the Green's structure of S from X include the Froidure–Pin Algorithm, and an algorithm of the second author based on the Schreier–Sims algorithm for permutation groups. The worst case complexity of these algorithms is polynomial in |S|, which for, say, transformation semigroups is exponential in the number of points on which they act. Certain aspects of the problem of finding maximal subsemigroups reduce to other well-known computational problems, such as finding all maximal cliques in a graph and computing the maximal subgroups in a group. The algorithm presented comprises two parts. One part relates to computing the maximal subsemigroups of a special class of semigroups, known as Rees 0-matrix semigroups. The other part involves a careful analysis of certain graphs associated to the semigroup S, which, roughly speaking, capture the essential information about the action of S on its J-classes.
The third author wishes to acknowledge the support of his Carnegie Ph.D. Scholarship from the Carnegie Trust for the Universities of Scotland.
2018-07-01T00:00:00ZDonoven, C. R.Mitchell, J. D.Wilson, W. A.A proper subsemigroup of a semigroup is maximal if it is not contained in any other proper subsemigroup. A maximal subsemigroup of a finite semigroup has one of a small number of forms, as described in a paper of Graham, Graham, and Rhodes. Determining which of these forms arise in a given finite semigroup is difficult, and no practical mechanism for doing so appears in the literature. We present an algorithm for computing the maximal subsemigroups of a finite semigroup S given knowledge of the Green's structure of S, and the ability to determine maximal subgroups of certain subgroups of S, namely its group H-classes. In the case of a finite semigroup S represented by a generating set X, in many examples, if it is practical to compute the Green's structure of S from X, then it is also practical to find the maximal subsemigroups of S using the algorithm we present. In such examples, the time taken to determine the Green's structure of S is comparable to that taken to find the maximal subsemigroups. The generating set X for S may consist, for example, of transformations, or partial permutations, of a finite set, or of matrices over a semiring. Algorithms for computing the Green's structure of S from X include the Froidure–Pin Algorithm, and an algorithm of the second author based on the Schreier–Sims algorithm for permutation groups. The worst case complexity of these algorithms is polynomial in |S|, which for, say, transformation semigroups is exponential in the number of points on which they act. Certain aspects of the problem of finding maximal subsemigroups reduce to other well-known computational problems, such as finding all maximal cliques in a graph and computing the maximal subgroups in a group. The algorithm presented comprises two parts. One part relates to computing the maximal subsemigroups of a special class of semigroups, known as Rees 0-matrix semigroups. The other part involves a careful analysis of certain graphs associated to the semigroup S, which, roughly speaking, capture the essential information about the action of S on its J-classes.Lipidomic investigations into the phospholipid content and metabolism of various kinetoplastidsRoberts, Matthew D.https://hdl.handle.net/10023/169832019-07-01T10:15:15Z2017-06-21T00:00:00ZThis work expands the knowledge on phospholipid metabolism in the kinetoplastid
parasites: T. brucei, T. cruzi, Leishmania spp. that cause neglected tropical diseases
and the related non-human pathogenic Crithidia fasiculata.
As a close relative of parasitic kinetoplasts, specifically Leishmania, it is hypothesised
that Crithidia fasiculata possesses a similar lipid biosynthetic capability and therefore
represent an attractive model organism. Database mining the Crithidia genome
revealed the ability to biosynthesise all of the main phospholipid species. Utilising
various lipidomic techniques, a high level of an ω-6 18:3 fatty acid was observed,
alongside an uncommon Δ19:0 fatty acid that was later identified to be exclusive
attributed to PE species. Sphingolipid metabolism was shown to resemble that of
Leishmania and T. cruzi, given the exclusive production of inositol-phosphoceramide
species and no sphingomyelin species being observed. Using labelled precursors,
Crithidia were seen to uptake and incorporate extracellular inositol into both
phosphatidylinositol and inositol-phosphoceramide species. Crithidia were also
shown to utilise both the Kennedy pathway and methylation of
phosphatidylethanolamine to form phosphatidylcholine.
The phospholipidome of T. cruzi revealed several phosphatidylserine species for the
first time, suggesting a functional phosphatidylserine synthase. Current knowledge
of T.cruzi sphingolipid biosynthesis was also confirmed as only inositol
xxxi
phosphoceramide species were observed. The identification and subsequent
characterisation of novel phosphonolipid species are reported for the first time.
Utilising lipidomic methodologies and labelled precursors, the relative contribution
of the intracellular inositol pools within bloodstream and procyclic T. brucei towards
PI biosynthesis was examined. This highlighted that the synthesis/turnover rates for
specific phosphatidylinositol and inositol-phosphoceramide species are unequal.
Efforts to optimise media conditions highlighted that under reduced levels of
serum/glucose/inositol, bloodstream T. brucei unexpectedly adjusts its inositol
metabolism. The procyclic parasite exemplifies this fact, as under inositol/glucose
deficient media conditions they appear to have adapted to utilising glucogenesis and
inositol de-novo synthesis.
This work highlights that these parasites are rapidly dividing, their unique features of
lipid metabolism may be exploitable for drug discovery purposes.
2017-06-21T00:00:00ZRoberts, Matthew D.This work expands the knowledge on phospholipid metabolism in the kinetoplastid
parasites: T. brucei, T. cruzi, Leishmania spp. that cause neglected tropical diseases
and the related non-human pathogenic Crithidia fasiculata.
As a close relative of parasitic kinetoplasts, specifically Leishmania, it is hypothesised
that Crithidia fasiculata possesses a similar lipid biosynthetic capability and therefore
represent an attractive model organism. Database mining the Crithidia genome
revealed the ability to biosynthesise all of the main phospholipid species. Utilising
various lipidomic techniques, a high level of an ω-6 18:3 fatty acid was observed,
alongside an uncommon Δ19:0 fatty acid that was later identified to be exclusive
attributed to PE species. Sphingolipid metabolism was shown to resemble that of
Leishmania and T. cruzi, given the exclusive production of inositol-phosphoceramide
species and no sphingomyelin species being observed. Using labelled precursors,
Crithidia were seen to uptake and incorporate extracellular inositol into both
phosphatidylinositol and inositol-phosphoceramide species. Crithidia were also
shown to utilise both the Kennedy pathway and methylation of
phosphatidylethanolamine to form phosphatidylcholine.
The phospholipidome of T. cruzi revealed several phosphatidylserine species for the
first time, suggesting a functional phosphatidylserine synthase. Current knowledge
of T.cruzi sphingolipid biosynthesis was also confirmed as only inositol
xxxi
phosphoceramide species were observed. The identification and subsequent
characterisation of novel phosphonolipid species are reported for the first time.
Utilising lipidomic methodologies and labelled precursors, the relative contribution
of the intracellular inositol pools within bloodstream and procyclic T. brucei towards
PI biosynthesis was examined. This highlighted that the synthesis/turnover rates for
specific phosphatidylinositol and inositol-phosphoceramide species are unequal.
Efforts to optimise media conditions highlighted that under reduced levels of
serum/glucose/inositol, bloodstream T. brucei unexpectedly adjusts its inositol
metabolism. The procyclic parasite exemplifies this fact, as under inositol/glucose
deficient media conditions they appear to have adapted to utilising glucogenesis and
inositol de-novo synthesis.
This work highlights that these parasites are rapidly dividing, their unique features of
lipid metabolism may be exploitable for drug discovery purposes.Title redactedSugasawa, Shokohttps://hdl.handle.net/10023/169582019-01-30T09:31:31Z2016-06-01T00:00:00Z2016-06-01T00:00:00ZSugasawa, ShokoProof-carrying plansSchwaab, Christopher JosephKomendantskaya, EkaterinaHill, AlisdairFarka, FrantišekPetrick, RonaldWells, JoeHammond, Kevinhttps://hdl.handle.net/10023/168552023-04-19T00:43:25Z2019-01-01T00:00:00ZIt is becoming increasingly important to verify safety and security of AI applications. While declarative languages (of the kind found in automated planners and model checkers) are traditionally used for verifying AI systems, a big challenge is to design methods that generate verified executable programs. A good example of such a “verification to implementation” cycle is given by automated planning languages like PDDL, where plans are found via a model search in a declarative language, but then interpreted or compiled into executable code in an imperative language. In this paper, we show that this method can itself be verified. We present a formal framework and a prototype Agda implementation that represent PDDL plans as executable functions that inhabit types that are given by formulae describing planning problems. By exploiting the well-known Curry-Howard correspondence, type-checking then automatically ensures that the generated program corresponds precisely to the specification of the planning problem.
2019-01-01T00:00:00ZSchwaab, Christopher JosephKomendantskaya, EkaterinaHill, AlisdairFarka, FrantišekPetrick, RonaldWells, JoeHammond, KevinIt is becoming increasingly important to verify safety and security of AI applications. While declarative languages (of the kind found in automated planners and model checkers) are traditionally used for verifying AI systems, a big challenge is to design methods that generate verified executable programs. A good example of such a “verification to implementation” cycle is given by automated planning languages like PDDL, where plans are found via a model search in a declarative language, but then interpreted or compiled into executable code in an imperative language. In this paper, we show that this method can itself be verified. We present a formal framework and a prototype Agda implementation that represent PDDL plans as executable functions that inhabit types that are given by formulae describing planning problems. By exploiting the well-known Curry-Howard correspondence, type-checking then automatically ensures that the generated program corresponds precisely to the specification of the planning problem.The impact of multiple stressors on coastal biodiversity and associated ecosystem servicesWatson, Stephen C. L.https://hdl.handle.net/10023/168172019-03-29T10:39:56Z2017-06-21T00:00:00ZMarine and coastal ecosystems are subject to diverse and increasingly intensive anthropogenic
activities, making understanding cumulative effects critically important. However, accurately
accounting for the cumulative effects of human impacts can be difficult, with the possibility of multiple
stressors interacting and having greater impacts than expected, compounding direct and indirect
effects on individuals, populations, communities and ecosystems. Assessment of multiple stressors
therefore requires extensive scientific research that directly tests how single or multiple ecological
components are affected by stressors, both singly and when combined, and as a consequence,
cumulative effects assessments are now increasingly included in environmental assessments.
Currently, there is a need to assess these at larger spatial scales, with additional research also urgently
needed on the responses of ecological components, processes and functions to single and cumulative
stressors. As cumulative environmental impacts could be better addressed by regional stressor effects
assessments that combine methods for predicting multiple pressures on ecosystem recovery
alongside degradation, this study used several separate approaches that can be used in parallel to give
support for local management measures. I tested four completely different methods – a range of
multi-metric indices, a food web model (Ecopath), a predictive model (Ecosim) and a Bayesian Belief
Network model. Each approach was tested and compared in two shallow water estuarine systems, in
Scotland and England, initially concerning the impact of nutrient enrichment and subsequent recovery
and was followed by an investigation of how the addition of multiple stressors (nutrient levels,
temperature and river-flow rates) would impact the future state of each system. The response to
stressors was highly context dependent, varying between and within geographic locations. Overall,
each of the four different approaches complemented each other and gave strong support for the need
to make big reductions in the pressures and to consider trade-offs between impacting pressures. The
models and tools also indicate that in order to reach an improved overall environmental state of each
ecosystem, a focus on nutrient reductions are likely to be the most effective of the controls on
stressors explored and that cumulative effects of the management of nutrient inputs and increased
water temperatures and river-flow are likely to exist.
2017-06-21T00:00:00ZWatson, Stephen C. L.Marine and coastal ecosystems are subject to diverse and increasingly intensive anthropogenic
activities, making understanding cumulative effects critically important. However, accurately
accounting for the cumulative effects of human impacts can be difficult, with the possibility of multiple
stressors interacting and having greater impacts than expected, compounding direct and indirect
effects on individuals, populations, communities and ecosystems. Assessment of multiple stressors
therefore requires extensive scientific research that directly tests how single or multiple ecological
components are affected by stressors, both singly and when combined, and as a consequence,
cumulative effects assessments are now increasingly included in environmental assessments.
Currently, there is a need to assess these at larger spatial scales, with additional research also urgently
needed on the responses of ecological components, processes and functions to single and cumulative
stressors. As cumulative environmental impacts could be better addressed by regional stressor effects
assessments that combine methods for predicting multiple pressures on ecosystem recovery
alongside degradation, this study used several separate approaches that can be used in parallel to give
support for local management measures. I tested four completely different methods – a range of
multi-metric indices, a food web model (Ecopath), a predictive model (Ecosim) and a Bayesian Belief
Network model. Each approach was tested and compared in two shallow water estuarine systems, in
Scotland and England, initially concerning the impact of nutrient enrichment and subsequent recovery
and was followed by an investigation of how the addition of multiple stressors (nutrient levels,
temperature and river-flow rates) would impact the future state of each system. The response to
stressors was highly context dependent, varying between and within geographic locations. Overall,
each of the four different approaches complemented each other and gave strong support for the need
to make big reductions in the pressures and to consider trade-offs between impacting pressures. The
models and tools also indicate that in order to reach an improved overall environmental state of each
ecosystem, a focus on nutrient reductions are likely to be the most effective of the controls on
stressors explored and that cumulative effects of the management of nutrient inputs and increased
water temperatures and river-flow are likely to exist.Gift-giving and inheritance strategies in late Roman law and legal practiceHumfress, Carolinehttps://hdl.handle.net/10023/166412023-11-08T18:30:01Z2017-06-07T00:00:00ZIn Roman law, an inheritance could be passed on according to the rules of intestate or testate succession. The Roman law of succession presents people with an enormous display of legal ingenuity. This chapter analyses some of the legal instruments and rules by which late Roman testators and donors were able to pursue making over bequests and inheritances to the institutional Christian church. It presents an overview of Roman family law and inheritance structures, paying particular attention to post-classical legal developments. The chapter explores donation and inheritance law in the specific context of the institutional Christian church from the age of Constantine onwards. It expands on this analysis via a focus on specific examples of strategic behaviour relating to Christian gift-giving and inheritance in the later fourth, fifth and sixth centuries AD. It shows that Roman legislators themselves engaged in strategic behaviour, attempting to use the Roman law of donation and inheritance as a means of socio-religious control.
2017-06-07T00:00:00ZHumfress, CarolineIn Roman law, an inheritance could be passed on according to the rules of intestate or testate succession. The Roman law of succession presents people with an enormous display of legal ingenuity. This chapter analyses some of the legal instruments and rules by which late Roman testators and donors were able to pursue making over bequests and inheritances to the institutional Christian church. It presents an overview of Roman family law and inheritance structures, paying particular attention to post-classical legal developments. The chapter explores donation and inheritance law in the specific context of the institutional Christian church from the age of Constantine onwards. It expands on this analysis via a focus on specific examples of strategic behaviour relating to Christian gift-giving and inheritance in the later fourth, fifth and sixth centuries AD. It shows that Roman legislators themselves engaged in strategic behaviour, attempting to use the Roman law of donation and inheritance as a means of socio-religious control.BayesPiles : visualisation support for Bayesian network structure learningVogogias, AthanasiosKennedy, JessieArchambault, DanielBach, BenjaminSmith, V AnneCurrant, Hannahhttps://hdl.handle.net/10023/166362023-04-18T23:47:32Z2018-11-01T00:00:00ZWe address the problem of exploring, combining, and comparing large collections of scored, directed networks for understanding inferred Bayesian networks used in biology. In this field, heuristic algorithms explore the space of possible network solutions, sampling this space based on algorithm parameters and a network score that encodes the statistical fit to the data. The goal of the analyst is to guide the heuristic search and decide how to determine a final consensus network structure, usually by selecting the top-scoring network or constructing the consensus network from a collection of high-scoring networks. BayesPiles, our visualisation tool, helps with understanding the structure of the solution space and supporting the construction of a final consensus network that is representative of the underlying dataset. BayesPiles builds upon and extends MultiPiles to meet our domain requirements. We developed BayesPiles in conjunction with computational biologists who have used this tool on datasets used in their research. The biologists found our solution provides them with new insights and helps them achieve results that are representative of the underlying data.
2018-11-01T00:00:00ZVogogias, AthanasiosKennedy, JessieArchambault, DanielBach, BenjaminSmith, V AnneCurrant, HannahWe address the problem of exploring, combining, and comparing large collections of scored, directed networks for understanding inferred Bayesian networks used in biology. In this field, heuristic algorithms explore the space of possible network solutions, sampling this space based on algorithm parameters and a network score that encodes the statistical fit to the data. The goal of the analyst is to guide the heuristic search and decide how to determine a final consensus network structure, usually by selecting the top-scoring network or constructing the consensus network from a collection of high-scoring networks. BayesPiles, our visualisation tool, helps with understanding the structure of the solution space and supporting the construction of a final consensus network that is representative of the underlying dataset. BayesPiles builds upon and extends MultiPiles to meet our domain requirements. We developed BayesPiles in conjunction with computational biologists who have used this tool on datasets used in their research. The biologists found our solution provides them with new insights and helps them achieve results that are representative of the underlying data.Theatrical living : responsive lives which manifest God's loving presence and waysReinhardt, David Leehttps://hdl.handle.net/10023/165792018-11-30T12:05:34Z2018-06-26T00:00:00ZGod is revealed through Scripture and the Incarnation as desiring to establish loving relationships with others beyond the Trinity. In the beginning he did so by creating human beings, and making himself, his desires, and his ways known to them. He chose to do so through particular actions and encounters in history which involved various forms of embodied manifestation, and led up to the supreme manifestation: the enfleshing of Jesus. Following on from the acts of Jesus which perfectly manifested God and his ways to the world in the flesh, human creatures created in the image of God and united to Christ are also called and gifted by God to manifest God’s presence, activity, and ways in this world by using their bodies to live faithfully and responsively to the leading of the Spirit.
In order to investigate and demonstrate these claims, Part I of the thesis examines a selection of precedent-setting events chronicled in the Old Testament in which God manifested his presence and ways to people in a variety of circumstances. Part II is concerned with a theological examination of God’s manifestations and the roles people can and should play in these manifestations. It begins by engaging with reflections on the subject from the early church fathers Irenaeus, Athanasius, and Augustine; and, in keeping with the Reformed approach taken in the thesis generally, this is followed by in-depth treatments of Reformer John Calvin and Reformed theologian Karl Barth on the revelation, manifestation, and proclamation of God by people in this world.
Having substantiated the claim that how people live is significant and of concern to God as it can impinge upon his ongoing desire to make himself and his ways known, Part III is designed to provide a fuller understanding of some of the meaning and significance conveyed by bodily expressions in human interactions with an eye towards seeking ways to live more faithfully to God. It identifies the theatre, particularly improvisational theatre, as a laboratory for understanding human living, and so explores the insights of theatre practitioners into everyday living; while also considering the work of philosophers of language and sociologists who do the same. Through this spotlight on the theatricality of life the case is made for attempting to live responsively, in keeping with improvisational actors, in ways that are faithful to God and which can serve to aid those united to Christ as they seek to make God known to others.
2018-06-26T00:00:00ZReinhardt, David LeeGod is revealed through Scripture and the Incarnation as desiring to establish loving relationships with others beyond the Trinity. In the beginning he did so by creating human beings, and making himself, his desires, and his ways known to them. He chose to do so through particular actions and encounters in history which involved various forms of embodied manifestation, and led up to the supreme manifestation: the enfleshing of Jesus. Following on from the acts of Jesus which perfectly manifested God and his ways to the world in the flesh, human creatures created in the image of God and united to Christ are also called and gifted by God to manifest God’s presence, activity, and ways in this world by using their bodies to live faithfully and responsively to the leading of the Spirit.
In order to investigate and demonstrate these claims, Part I of the thesis examines a selection of precedent-setting events chronicled in the Old Testament in which God manifested his presence and ways to people in a variety of circumstances. Part II is concerned with a theological examination of God’s manifestations and the roles people can and should play in these manifestations. It begins by engaging with reflections on the subject from the early church fathers Irenaeus, Athanasius, and Augustine; and, in keeping with the Reformed approach taken in the thesis generally, this is followed by in-depth treatments of Reformer John Calvin and Reformed theologian Karl Barth on the revelation, manifestation, and proclamation of God by people in this world.
Having substantiated the claim that how people live is significant and of concern to God as it can impinge upon his ongoing desire to make himself and his ways known, Part III is designed to provide a fuller understanding of some of the meaning and significance conveyed by bodily expressions in human interactions with an eye towards seeking ways to live more faithfully to God. It identifies the theatre, particularly improvisational theatre, as a laboratory for understanding human living, and so explores the insights of theatre practitioners into everyday living; while also considering the work of philosophers of language and sociologists who do the same. Through this spotlight on the theatricality of life the case is made for attempting to live responsively, in keeping with improvisational actors, in ways that are faithful to God and which can serve to aid those united to Christ as they seek to make God known to others.Indiscriminate violence against civilians : an inquiry into the nature and the effects of group-selective violenceBrandsch, Jürgenhttps://hdl.handle.net/10023/165592019-08-16T08:33:47Z2018-06-26T00:00:00ZIndiscriminate violence against civilians is a recurrent problem in armed conflicts of all sorts. However, from a social science perspective this type of violence poses a puzzle. The literature on government and non-government violence mostly assumes that indiscriminate violence has counter-productive effect and is ultimately self-defeating. Yet, this begs the question as to why an actor should use indiscriminate violence at all?
This dissertation tries to solve at least part of the puzzle. First, it critically reviews the literature and points to some misunderstandings that have made progress in comprehending indiscriminate violence more difficult. Second, the dissertation provides a theory on the effects of indiscriminate violence that targets groups, i.e. group-selective violence. While most of the literature assumes that violence against groups seeks to coerce the groups that are attacked, this dissertation widens the view and includes non-targeted groups in the calculation as well. It thereby demonstrates that group-selective violence can be able to produce coercive effects among those groups that are not targeted while generating only limited counter-productive effects.
Empirically, this dissertation provides two types of supporting evidence. First, it will provide several case studies as a plausibility probe. These cases are designed to highlight that group-selective violence is used in the way proposed by the theory and has the hypothesized effects. Second, the dissertation will test the hypotheses of the theory of group-selective violence with data on violence against civilians in ethnic wars. Here quantitative methods are used to investigate the patterns and the consequences of violence. Both empirical investigations provide support for the notion that group-selective violence can be beneficial for the perpetrator and that it is used to achieve those benefits. In sum, this dissertation puts forth the theoretical background and empirical support for the effectiveness of group-selective violence.
2018-06-26T00:00:00ZBrandsch, JürgenIndiscriminate violence against civilians is a recurrent problem in armed conflicts of all sorts. However, from a social science perspective this type of violence poses a puzzle. The literature on government and non-government violence mostly assumes that indiscriminate violence has counter-productive effect and is ultimately self-defeating. Yet, this begs the question as to why an actor should use indiscriminate violence at all?
This dissertation tries to solve at least part of the puzzle. First, it critically reviews the literature and points to some misunderstandings that have made progress in comprehending indiscriminate violence more difficult. Second, the dissertation provides a theory on the effects of indiscriminate violence that targets groups, i.e. group-selective violence. While most of the literature assumes that violence against groups seeks to coerce the groups that are attacked, this dissertation widens the view and includes non-targeted groups in the calculation as well. It thereby demonstrates that group-selective violence can be able to produce coercive effects among those groups that are not targeted while generating only limited counter-productive effects.
Empirically, this dissertation provides two types of supporting evidence. First, it will provide several case studies as a plausibility probe. These cases are designed to highlight that group-selective violence is used in the way proposed by the theory and has the hypothesized effects. Second, the dissertation will test the hypotheses of the theory of group-selective violence with data on violence against civilians in ethnic wars. Here quantitative methods are used to investigate the patterns and the consequences of violence. Both empirical investigations provide support for the notion that group-selective violence can be beneficial for the perpetrator and that it is used to achieve those benefits. In sum, this dissertation puts forth the theoretical background and empirical support for the effectiveness of group-selective violence.Rules, power and constitutions : following OnufLang, Anthonyhttps://hdl.handle.net/10023/165292023-07-24T14:30:28Z2017-05-23T00:00:00ZThis chapter explores the role of power in the theory of global constitutionalism. It draws on the work of Nicholas Onuf, whose launched constructivist IR theory. It borrows from Onuf the idea of rules and rule making, but critiques his work for failing to devvelop the idea of power in constitutional theory. It concludes with an analysis of global constitutent power.
2017-05-23T00:00:00ZLang, AnthonyThis chapter explores the role of power in the theory of global constitutionalism. It draws on the work of Nicholas Onuf, whose launched constructivist IR theory. It borrows from Onuf the idea of rules and rule making, but critiques his work for failing to devvelop the idea of power in constitutional theory. It concludes with an analysis of global constitutent power.Multivalence, liminality, and the theological imagination : contextualising the image of fire for contemporary Christian practiceDyer, Rebekah Maryhttps://hdl.handle.net/10023/164522019-07-16T14:17:50Z2018-12-07T00:00:00ZThis thesis contends that the image of fire is a multivalent and theologically valuable image for application in British Christian communities. My research offers an original contribution by contextualising the image of fire for Christian practice in Britain, and combining critical observation of several contemporary fire rites with theological analysis. In addition, I conduct original case studies of three Scottish fire rituals: the Stonehaven Fireball Ceremony, the Beltane Fire Festival, and Up-Helly-Aa in Lerwick, Shetland.
The potential contribution of fire imagery to Christian practice has been overlooked by modern theological scholarship, social anthropologists, and Christian practitioners. Since the multivalence of the image has not been fully recognised, fire imagery has often been reduced to a binary of ‘positive’ and ‘negative’ associations. Through my study of non-faith fire rituals and existing Christian fire practices, I explore the interplay between multivalence, multiplicity, and liminality in fire imagery. I demonstrate that deeper theological engagement with the image of fire can enhance participation, transformation, and reflection in transitional ritual experience.
I argue that engaging with the multivalence of the image of fire could allow faith communities to move beyond dominant interpretive frameworks and apply the image within their own specific context. First, I orientate the discussion by examining the multivalence of biblical fire imagery and establishing the character of fire within the British social imagination. Second, I use critical observation of community fire practices in non-faith contexts to build a new contextual framework for the analysis of fire imagery. Finally, I apply my findings to a contextual analysis of existing Christian fire practices in Britain. Throughout, I argue that sensory and imaginative interaction with the image of fire provides a way to communicate and interact with theological ideas; experience personal and communal change; and mediate experience of the sacred.
2018-12-07T00:00:00ZDyer, Rebekah MaryThis thesis contends that the image of fire is a multivalent and theologically valuable image for application in British Christian communities. My research offers an original contribution by contextualising the image of fire for Christian practice in Britain, and combining critical observation of several contemporary fire rites with theological analysis. In addition, I conduct original case studies of three Scottish fire rituals: the Stonehaven Fireball Ceremony, the Beltane Fire Festival, and Up-Helly-Aa in Lerwick, Shetland.
The potential contribution of fire imagery to Christian practice has been overlooked by modern theological scholarship, social anthropologists, and Christian practitioners. Since the multivalence of the image has not been fully recognised, fire imagery has often been reduced to a binary of ‘positive’ and ‘negative’ associations. Through my study of non-faith fire rituals and existing Christian fire practices, I explore the interplay between multivalence, multiplicity, and liminality in fire imagery. I demonstrate that deeper theological engagement with the image of fire can enhance participation, transformation, and reflection in transitional ritual experience.
I argue that engaging with the multivalence of the image of fire could allow faith communities to move beyond dominant interpretive frameworks and apply the image within their own specific context. First, I orientate the discussion by examining the multivalence of biblical fire imagery and establishing the character of fire within the British social imagination. Second, I use critical observation of community fire practices in non-faith contexts to build a new contextual framework for the analysis of fire imagery. Finally, I apply my findings to a contextual analysis of existing Christian fire practices in Britain. Throughout, I argue that sensory and imaginative interaction with the image of fire provides a way to communicate and interact with theological ideas; experience personal and communal change; and mediate experience of the sacred.Dealing with nationalism in view of a human need to belong: the feasibility of narrative transformation in Northern IrelandEnglberger, Florianhttps://hdl.handle.net/10023/164012023-12-05T03:02:32Z2018-12-07T00:00:00ZThis thesis seeks to delineate what change in divided societies such as Northern Ireland is possible. Two steps are necessary to answer this question: first, to explain the potency of nationalism. I contend that taking the evolutionary history of humans and a human need to belong into account is essential for an understanding of A.D. Smith’s ethno-symbolist approach to nationalism. We need to acknowledge that human beings emerged from small-scale settings and are therefore conservative beings who seek those patterns of familiarity that make up the ordinary ‘everyday’. They are also prejudiced beings, as prejudice helps to break down a complex world into digestible pieces. The ethnic state excluding an ethnic ‘other’ is an answer to these calls for simplicity. By establishing an apparent terra firma, a habitus, symbols of an ethnic past and national present speak of nationalist narratives that provide a sense of ontological security. In (Northern) Ireland, ethno-national communities based on prejudiced understandings of history have long been established. In this second step I maintain that change that violates the core potent national narratives cannot be achieved. The Provisional IRA’s change from insurrection to parliament became feasible because a radical break with republican dogmas was avoided. Sinn Féin, despite a rhetorical move towards ‘reconciliation’, still seek to outmanoeuvre the unionist ‘other’. The history of Irish socialism, on the other hand, has been a failure, as it embodied a radical attempt to banish the ‘other’ from the national narrative. Regarding ‘post-conflict’ Northern Ireland, I argue for a peacebuilding approach that leaves the confinements of hostile identity politics, as these mass guarantors of ontological security possess only limited potential for relationship transformation. We need to appreciate those almost invisible acts of empathy and peace that could be found even in Northern Ireland’s darkest hours.
2018-12-07T00:00:00ZEnglberger, FlorianThis thesis seeks to delineate what change in divided societies such as Northern Ireland is possible. Two steps are necessary to answer this question: first, to explain the potency of nationalism. I contend that taking the evolutionary history of humans and a human need to belong into account is essential for an understanding of A.D. Smith’s ethno-symbolist approach to nationalism. We need to acknowledge that human beings emerged from small-scale settings and are therefore conservative beings who seek those patterns of familiarity that make up the ordinary ‘everyday’. They are also prejudiced beings, as prejudice helps to break down a complex world into digestible pieces. The ethnic state excluding an ethnic ‘other’ is an answer to these calls for simplicity. By establishing an apparent terra firma, a habitus, symbols of an ethnic past and national present speak of nationalist narratives that provide a sense of ontological security. In (Northern) Ireland, ethno-national communities based on prejudiced understandings of history have long been established. In this second step I maintain that change that violates the core potent national narratives cannot be achieved. The Provisional IRA’s change from insurrection to parliament became feasible because a radical break with republican dogmas was avoided. Sinn Féin, despite a rhetorical move towards ‘reconciliation’, still seek to outmanoeuvre the unionist ‘other’. The history of Irish socialism, on the other hand, has been a failure, as it embodied a radical attempt to banish the ‘other’ from the national narrative. Regarding ‘post-conflict’ Northern Ireland, I argue for a peacebuilding approach that leaves the confinements of hostile identity politics, as these mass guarantors of ontological security possess only limited potential for relationship transformation. We need to appreciate those almost invisible acts of empathy and peace that could be found even in Northern Ireland’s darkest hours.The Aurunci and SidiciniSmith, Christopher Johnhttps://hdl.handle.net/10023/163652023-04-19T00:42:48Z2017-11-01T00:00:00Z2017-11-01T00:00:00ZSmith, Christopher JohnThe role of civil society actors in peacemaking : the case of GuatemalaBrett, Roddyhttps://hdl.handle.net/10023/163042023-04-25T23:49:12Z2017-04-24T00:00:00ZThis article builds upon recent scholarship in critical peace studies that focuses on the role of civil society actors in formal peacemaking processes, in short, peace talks, and post-conflict peacebuilding. The article specifically explores the role of civil society actors in the Guatemalan peace process. The research addresses the possible tensions and potential complementarities in processes where civil society enjoys a mandated role in centralised, formal peace negotiations carried out between the state and armed actors in talks levied within the liberal peace framework. In the case of Guatemala, non-state actors participated to an unprecedented extent in the peace negotiations, and Guatemala has not relapsed into armed conflict. However, post-conflict Guatemala is a violent and unstable country. Consequently, the study challenges the assumption that peacemaking is necessarily more successful in those instances where provisions have been established to guarantee the participation of civil society.
2017-04-24T00:00:00ZBrett, RoddyThis article builds upon recent scholarship in critical peace studies that focuses on the role of civil society actors in formal peacemaking processes, in short, peace talks, and post-conflict peacebuilding. The article specifically explores the role of civil society actors in the Guatemalan peace process. The research addresses the possible tensions and potential complementarities in processes where civil society enjoys a mandated role in centralised, formal peace negotiations carried out between the state and armed actors in talks levied within the liberal peace framework. In the case of Guatemala, non-state actors participated to an unprecedented extent in the peace negotiations, and Guatemala has not relapsed into armed conflict. However, post-conflict Guatemala is a violent and unstable country. Consequently, the study challenges the assumption that peacemaking is necessarily more successful in those instances where provisions have been established to guarantee the participation of civil society.Surveying abundance and stand type associations of Formica aquilonia and F. lugubris (Hymenoptera: Formicidae) nest mounds over an extensive area : Trialing a novel methodBorkin, KerrySummers, RonThomas, Lenhttps://hdl.handle.net/10023/162602023-04-18T09:43:03Z2012-01-03T00:00:00ZRed wood ants are ecologically important members of woodland communities, and some species are of conservation concern. They occur commonly only in certain habitats in Britain, but there is limited knowledge of their numbers and distribution. This study provided baseline information at a key locality (Abernethy Forest, 37 km2) in the central Highlands of Scotland and trialed a new method of surveying red wood ant density and stand type associations: a distance sampling line transect survey of nests. This method is efficient because it allows an observer to quickly survey a large area either side of transect lines, without having to assume that all nests are detected. Instead, data collected on the distance of nests from the line are used to estimate probability of detection and the effective transect width, using the free software "Distance". Surveys took place in August and September 2003 along a total of 71.2 km of parallel, equally-spaced transects. One hundred and forty-four red wood ant nests were located, comprising 89 F. aquilonia (Yarrow, 1955) and 55 F. lugubris (Zetterstedt, 1838) nests. Estimated densities were 1.13 nests per hectare (95% CI 0.74-1.73) for F. aquilonia and 0.83 nests per hectare (95% CI 0.32-2.17) for F. lugubris. These translated to total estimated nest numbers of 4,200 (95% CI 2,700-6,400) and 3,100 (95% CI 1,200-8,100), respectively, for the whole forest. Indices of stand selection indicated that F. aquilonia had some positive association with old-growth and F. lugubris with younger stands (stem exclusion stage). No nests were found in areas that had been clear-felled, and ploughed and planted in the 1970s-1990s. The pattern of stand type association and hence distribution of F. aquilonia and F. lugubris may be due to the differing ability to disperse (F. lugubris is the faster disperser) and compete (F. aquilonia is competitively superior). We recommend using line transect sampling for extensive surveys of ants that construct nest mounds to estimate abundance and stand type association.
2012-01-03T00:00:00ZBorkin, KerrySummers, RonThomas, LenRed wood ants are ecologically important members of woodland communities, and some species are of conservation concern. They occur commonly only in certain habitats in Britain, but there is limited knowledge of their numbers and distribution. This study provided baseline information at a key locality (Abernethy Forest, 37 km2) in the central Highlands of Scotland and trialed a new method of surveying red wood ant density and stand type associations: a distance sampling line transect survey of nests. This method is efficient because it allows an observer to quickly survey a large area either side of transect lines, without having to assume that all nests are detected. Instead, data collected on the distance of nests from the line are used to estimate probability of detection and the effective transect width, using the free software "Distance". Surveys took place in August and September 2003 along a total of 71.2 km of parallel, equally-spaced transects. One hundred and forty-four red wood ant nests were located, comprising 89 F. aquilonia (Yarrow, 1955) and 55 F. lugubris (Zetterstedt, 1838) nests. Estimated densities were 1.13 nests per hectare (95% CI 0.74-1.73) for F. aquilonia and 0.83 nests per hectare (95% CI 0.32-2.17) for F. lugubris. These translated to total estimated nest numbers of 4,200 (95% CI 2,700-6,400) and 3,100 (95% CI 1,200-8,100), respectively, for the whole forest. Indices of stand selection indicated that F. aquilonia had some positive association with old-growth and F. lugubris with younger stands (stem exclusion stage). No nests were found in areas that had been clear-felled, and ploughed and planted in the 1970s-1990s. The pattern of stand type association and hence distribution of F. aquilonia and F. lugubris may be due to the differing ability to disperse (F. lugubris is the faster disperser) and compete (F. aquilonia is competitively superior). We recommend using line transect sampling for extensive surveys of ants that construct nest mounds to estimate abundance and stand type association.Assessing the utility and limitations of accelerometers and machine learning approaches in classifying behaviour during lactation in a phocid sealSchuert, CourtneyPomeroy, PatrickTwiss, Seanhttps://hdl.handle.net/10023/162532024-03-09T00:43:37Z2018-10-16T00:00:00ZBackground: Classifying behaviour with animal-borne accelerometers is quickly becoming a popular tool for remotely observing behavioural states in a variety of species. Most accelerometry work in pinnipeds has focused on classifying behaviour at sea often quantifying behavioural trade-offs associated with foraging and diving in income breeders. Very little work to date has been done to resolve behaviour during the critical period of lactation in a capital breeder. Capital breeding phocids possess finite reserves that they must allocate appropriately to maintain themselves and their new offspring during their brief nursing period. Within this short time, fine-scale behavioural trade-offs can have significant fitness consequences for mother and offspring and must be carefully managed. Here, we present a case study in extracting and classifying lactation behaviours in a wild, breeding pinniped, the grey seal (Halichoerus grypus). Results: Using random forest models, we were able to resolve 4 behavioural states that constitute the majority of a female grey seals’ activity budget during lactation. Resting, alert, nursing, and a form of pup interaction were extracted and classified reliably. For the first time, we quantified the potential confounding variance associated with individual differences in a wild context as well as differences due to sampling location in a largely inactive model species. Conclusions: At this stage, the majority of a female grey seal’s activity budget was classified well using accelerometers, but some rare and context-dependent behaviours were not well captured. While we did find significant variation between individuals in behavioural mechanics, individuals did not differ significantly within themselves; inter-individual variability should be an important consideration in future efforts. These methods can be extended to other efforts to study grey seals and other pinnipeds who exhibit a capital breeding system. Using accelerometers to classify behaviour during lactation allows for fine-scale assessments of time and energy trade-offs for species with fixed stores.
Funding for this work was provided by the Durham Doctoral Studentship scheme at Durham University and supported by Natural Environment Research Council’s core funding to the Sea Mammal Research Unit at the University of St. Andrews.
2018-10-16T00:00:00ZSchuert, CourtneyPomeroy, PatrickTwiss, SeanBackground: Classifying behaviour with animal-borne accelerometers is quickly becoming a popular tool for remotely observing behavioural states in a variety of species. Most accelerometry work in pinnipeds has focused on classifying behaviour at sea often quantifying behavioural trade-offs associated with foraging and diving in income breeders. Very little work to date has been done to resolve behaviour during the critical period of lactation in a capital breeder. Capital breeding phocids possess finite reserves that they must allocate appropriately to maintain themselves and their new offspring during their brief nursing period. Within this short time, fine-scale behavioural trade-offs can have significant fitness consequences for mother and offspring and must be carefully managed. Here, we present a case study in extracting and classifying lactation behaviours in a wild, breeding pinniped, the grey seal (Halichoerus grypus). Results: Using random forest models, we were able to resolve 4 behavioural states that constitute the majority of a female grey seals’ activity budget during lactation. Resting, alert, nursing, and a form of pup interaction were extracted and classified reliably. For the first time, we quantified the potential confounding variance associated with individual differences in a wild context as well as differences due to sampling location in a largely inactive model species. Conclusions: At this stage, the majority of a female grey seal’s activity budget was classified well using accelerometers, but some rare and context-dependent behaviours were not well captured. While we did find significant variation between individuals in behavioural mechanics, individuals did not differ significantly within themselves; inter-individual variability should be an important consideration in future efforts. These methods can be extended to other efforts to study grey seals and other pinnipeds who exhibit a capital breeding system. Using accelerometers to classify behaviour during lactation allows for fine-scale assessments of time and energy trade-offs for species with fixed stores.Evolution of muscle regulatory genes in chordatesColl-Lladó, Clarahttps://hdl.handle.net/10023/161362018-12-12T11:18:27Z2016-11-30T00:00:00Z2016-11-30T00:00:00ZColl-Lladó, ClaraMonkeys (Sapajus apella and Macaca tonkeana) and great apes (Gorilla gorilla, Pongo pygmaeus, Pongo abelii, Pan paniscus and Pan troglodytes) play for the highest bidBroihanne, M. -H.Romain, A.Call, JosepThierry, B.Wascher, C. A. F.De Marco, A.Verrier, D.Dufour, V.https://hdl.handle.net/10023/160922024-02-20T00:42:24Z2018-12-27T00:00:00ZMany studies investigate the decisions made by animals by focussing on their individual attitudes towards risk, i.e., risk seeking, risk neutrality or risk aversion. However, little attention has been paid to how far individuals understand the different odds of outcomes. In a previous gambling task involving up to 18 different lotteries (Pelé et al., 2014), non-human primates used probabilities of gains and losses to make their decision. Although the use of complex mathematical calculation for decision-making seemed unlikely, we applied a gradual decrease in the chances to win throughout the experiment. This probably facilitated the extraction of information about odds. Here, we investigated whether individuals would still make efficient decisions if this facilitating factor was removed. To do so, we randomized the order of presentation of the 18 lotteries. Individuals from four ape and two monkey species were tested. Only capuchin monkeys differed in their gambling behaviour, playing even when there was nothing to win. Randomising the lottery presentation order leads all species to predominantly use a maximax heuristic in which individuals gamble as soon as there is at least one chance to win more than they already possess, whatever the risk. Most species also gambled more as the frequency of larger rewards increased. These results suggest the occurrence of optimistic behaviour. The maximax heuristic is sometimes observed in human managerial and financial decision-making, where risk is ignored for potential gains, however low they may be. Our results suggest a shared and strong propensity in primates to rely on heuristics whenever complexity in evaluation of outcome odds arises.
This work was supported by grants from the Agence Nationale de la Recherche (ANR-08-412 BLAN-0042-01) and the European Science Foundation (Compcog Exchange Grant N°3648).
2018-12-27T00:00:00ZBroihanne, M. -H.Romain, A.Call, JosepThierry, B.Wascher, C. A. F.De Marco, A.Verrier, D.Dufour, V.Many studies investigate the decisions made by animals by focussing on their individual attitudes towards risk, i.e., risk seeking, risk neutrality or risk aversion. However, little attention has been paid to how far individuals understand the different odds of outcomes. In a previous gambling task involving up to 18 different lotteries (Pelé et al., 2014), non-human primates used probabilities of gains and losses to make their decision. Although the use of complex mathematical calculation for decision-making seemed unlikely, we applied a gradual decrease in the chances to win throughout the experiment. This probably facilitated the extraction of information about odds. Here, we investigated whether individuals would still make efficient decisions if this facilitating factor was removed. To do so, we randomized the order of presentation of the 18 lotteries. Individuals from four ape and two monkey species were tested. Only capuchin monkeys differed in their gambling behaviour, playing even when there was nothing to win. Randomising the lottery presentation order leads all species to predominantly use a maximax heuristic in which individuals gamble as soon as there is at least one chance to win more than they already possess, whatever the risk. Most species also gambled more as the frequency of larger rewards increased. These results suggest the occurrence of optimistic behaviour. The maximax heuristic is sometimes observed in human managerial and financial decision-making, where risk is ignored for potential gains, however low they may be. Our results suggest a shared and strong propensity in primates to rely on heuristics whenever complexity in evaluation of outcome odds arises.Automatic generation and selection of streamlined constraint models via Monte Carlo search on a model latticeSpracklen, PatrickAkgun, OzgurMiguel, Ian Jameshttps://hdl.handle.net/10023/158942024-03-27T00:38:28Z2018-01-01T00:00:00ZStreamlined constraint reasoning is the addition of uninferred constraints to a constraint model to reduce the search space, while retaining at least one solution. Previously it has been established that it is possible to generate streamliners automatically from abstract constraint specifications in Essence and that effective combinations of streamliners can allow instances of much larger scale to be solved. A shortcoming of the previous approach was the crude exploration of the power set of all combinations using depth and breadth first search. We present a new approach based on Monte Carlo search over the lattice of streamlined models, which efficiently identifies effective streamliner combinations.
Funding: EPSRC EP/P015638/1.
2018-01-01T00:00:00ZSpracklen, PatrickAkgun, OzgurMiguel, Ian JamesStreamlined constraint reasoning is the addition of uninferred constraints to a constraint model to reduce the search space, while retaining at least one solution. Previously it has been established that it is possible to generate streamliners automatically from abstract constraint specifications in Essence and that effective combinations of streamliners can allow instances of much larger scale to be solved. A shortcoming of the previous approach was the crude exploration of the power set of all combinations using depth and breadth first search. We present a new approach based on Monte Carlo search over the lattice of streamlined models, which efficiently identifies effective streamliner combinations.Forgetting the Juvenalien in our midst : literary amnesia in the satiresGeue, Tom Alexanderhttps://hdl.handle.net/10023/157422023-04-19T00:42:37Z2018-02-01T00:00:00Z2018-02-01T00:00:00ZGeue, Tom AlexanderGetting below the surface : density estimation methods for deep diving animals using slow autonomous underwater vehiclesGkikopoulou, Kalliopi Charitomenihttps://hdl.handle.net/10023/156452023-03-20T13:35:47Z2018-01-01T00:00:00ZUnderwater gliders can provide an alternative cost-effective platform for passive acoustic monitoring surveys, compared to boat surveys, for abundance estimation and to collect high resolution environmental data for habitat studies. Gliders are usually equipped with one acoustic sensor, which limits the methods available for abundance estimation from acoustic data. Estimation of parameters used in distance sampling methodology, such as the detection function and cue rates, must be estimated separately from the glider deployment. A methodology for deriving the acoustic detection function of vocal animals is demonstrated in chapter 2 with a combined biologging and passive acoustic experiment. The methodology consists of distance estimation of the clicks produced by the tagged animal and detected at acoustic receivers placed at different depths, using surface bounce detections to estimate range. In addition, different detection algorithms were tested for the detectability of Blainville’s beaked whales. Detectability was found to vary with depth for Blainville’s beaked whales in the area of El Hierro (Canary Islands). The depth dependent detectability for this species was tested further in chapter 3 with a wider dataset from two different geographic populations of Blainville’s beaked whales, those of El Hierro and the Bahamas. Differences in detectability were found using depth and animal movement data as recorded on the DTAG in a simulated network of receivers placed at different depths. In addition, sequences of clicks, called click scans, were tested as an additional “cue” for cue counting methodology. The high directionality of beaked whale regular clicks leads to reduced detection ranges for receivers close to the surface or for receivers placed much deeper than the foraging depths of the wales and this reduction translates into varying lengths and numbers of detected click clusters as a function of distance and receiver depth. Chapter 4 presents a method for estimating density of animals from underwater gliders and tests the method in a simulated glider survey using different distribution and density scenarios using clicks and click scans as cue for density estimation.
2018-01-01T00:00:00ZGkikopoulou, Kalliopi CharitomeniUnderwater gliders can provide an alternative cost-effective platform for passive acoustic monitoring surveys, compared to boat surveys, for abundance estimation and to collect high resolution environmental data for habitat studies. Gliders are usually equipped with one acoustic sensor, which limits the methods available for abundance estimation from acoustic data. Estimation of parameters used in distance sampling methodology, such as the detection function and cue rates, must be estimated separately from the glider deployment. A methodology for deriving the acoustic detection function of vocal animals is demonstrated in chapter 2 with a combined biologging and passive acoustic experiment. The methodology consists of distance estimation of the clicks produced by the tagged animal and detected at acoustic receivers placed at different depths, using surface bounce detections to estimate range. In addition, different detection algorithms were tested for the detectability of Blainville’s beaked whales. Detectability was found to vary with depth for Blainville’s beaked whales in the area of El Hierro (Canary Islands). The depth dependent detectability for this species was tested further in chapter 3 with a wider dataset from two different geographic populations of Blainville’s beaked whales, those of El Hierro and the Bahamas. Differences in detectability were found using depth and animal movement data as recorded on the DTAG in a simulated network of receivers placed at different depths. In addition, sequences of clicks, called click scans, were tested as an additional “cue” for cue counting methodology. The high directionality of beaked whale regular clicks leads to reduced detection ranges for receivers close to the surface or for receivers placed much deeper than the foraging depths of the wales and this reduction translates into varying lengths and numbers of detected click clusters as a function of distance and receiver depth. Chapter 4 presents a method for estimating density of animals from underwater gliders and tests the method in a simulated glider survey using different distribution and density scenarios using clicks and click scans as cue for density estimation.Behavioral conservatism is linked to complexity of behavior in chimpanzees (Pan troglodytes) : implications for cognition and cumulative cultureDavis, Sarah J.Schapiro, Steven J.Lambeth, Susan P.Wood, Lara A.Whiten, Andrewhttps://hdl.handle.net/10023/156102024-02-22T00:42:30Z2018-07-19T00:00:00ZCumulative culture is rare, if not altogether absent in non-human species. At the foundation of cumulative learning is the ability to modify, relinquish or build upon prior behaviors flexibly to make them more productive or efficient. Within the primate literature, a failure to optimize solutions in this way is often proposed to derive from low-fidelity copying of witnessed behaviors, sub-optimal social learning heuristics, or a lack of relevant socio-cognitive adaptations. However, humans can also be markedly inflexible in their behaviors, perseverating with, or becoming fixated on outdated or inappropriate responses. Humans show differential patterns of flexibility as a function of cognitive load, exhibiting difficulties with inhibiting sub-optimal behaviors when there are high demands on working memory. We present a series of studies on captive chimpanzees which indicate that behavioral conservatism in apes may be underlain by similar constraints: chimpanzees showed relatively little conservatism when behavioral optimization involved the inhibition of a well-established but simple solution, or the addition of a simple modification to a well-established but complex solution. In contrast, when behavioral optimization involved the inhibition of a well-established but complex solution, chimpanzees showed evidence of conservatism. We propose that conservatism is linked to behavioral complexity, potentially mediated by cognitive resource availability, and may be an important factor in the evolution of cumulative culture.
2018-07-19T00:00:00ZDavis, Sarah J.Schapiro, Steven J.Lambeth, Susan P.Wood, Lara A.Whiten, AndrewCumulative culture is rare, if not altogether absent in non-human species. At the foundation of cumulative learning is the ability to modify, relinquish or build upon prior behaviors flexibly to make them more productive or efficient. Within the primate literature, a failure to optimize solutions in this way is often proposed to derive from low-fidelity copying of witnessed behaviors, sub-optimal social learning heuristics, or a lack of relevant socio-cognitive adaptations. However, humans can also be markedly inflexible in their behaviors, perseverating with, or becoming fixated on outdated or inappropriate responses. Humans show differential patterns of flexibility as a function of cognitive load, exhibiting difficulties with inhibiting sub-optimal behaviors when there are high demands on working memory. We present a series of studies on captive chimpanzees which indicate that behavioral conservatism in apes may be underlain by similar constraints: chimpanzees showed relatively little conservatism when behavioral optimization involved the inhibition of a well-established but simple solution, or the addition of a simple modification to a well-established but complex solution. In contrast, when behavioral optimization involved the inhibition of a well-established but complex solution, chimpanzees showed evidence of conservatism. We propose that conservatism is linked to behavioral complexity, potentially mediated by cognitive resource availability, and may be an important factor in the evolution of cumulative culture.The tribes and the state: informal alliances and conflict patterns in contemporary SyriaDukhan, Haianhttps://hdl.handle.net/10023/155762021-09-21T14:33:45Z2017-01-01T00:00:00ZThroughout history and up to the present day, tribalism continues to influence many issues related to governance, conflict and stability in the Middle East and North Africa. While many civil society advocates argue that tribal affiliation in the middle East has diminished, as evidenced by the disappearance of intertribal conflicts, family loyalties continue to play a significant role in the everyday life of the Middle East from employment in the public sector to recruitment in the army and security apparatus to competition between families and clans for many of the government positions and other social services provided by the state. Most research has tended to focus on Islamism and Jihadism. Most recently, the Arab Spring was accompanied by the resurgence of sectarianism, extremism and other social phenomena which at the sub or trans-state levels have been empowered by the weakening of states yet, although tribes have also been empowered, the resurgence of tribalism was not studied deeply. Political scientists who focus their research on the political processes of the Middle East tend to focus their attention on state institutions, state policies and national parties. By contrast, anthropologists who are interested in politics limit their focus to segments of the communities and tribal affiliations. This dissertation will attempt to do both by relating the local patterns to the larger system of which they are part. The strategic objective of this research is to explore the policies of the successive Syrian governments towards the Arab tribes and their reactions to these policies and their consequences for the relationship between state and tribe from the fall of the Ottoman Empire and its withdrawal from Syria in 1916 until the eruption of the current Syrian civil war. The research will develop a new understanding of the linkages between environment, economy and government policies as the affect the tribes and their relationship with the state.
2017-01-01T00:00:00ZDukhan, HaianThroughout history and up to the present day, tribalism continues to influence many issues related to governance, conflict and stability in the Middle East and North Africa. While many civil society advocates argue that tribal affiliation in the middle East has diminished, as evidenced by the disappearance of intertribal conflicts, family loyalties continue to play a significant role in the everyday life of the Middle East from employment in the public sector to recruitment in the army and security apparatus to competition between families and clans for many of the government positions and other social services provided by the state. Most research has tended to focus on Islamism and Jihadism. Most recently, the Arab Spring was accompanied by the resurgence of sectarianism, extremism and other social phenomena which at the sub or trans-state levels have been empowered by the weakening of states yet, although tribes have also been empowered, the resurgence of tribalism was not studied deeply. Political scientists who focus their research on the political processes of the Middle East tend to focus their attention on state institutions, state policies and national parties. By contrast, anthropologists who are interested in politics limit their focus to segments of the communities and tribal affiliations. This dissertation will attempt to do both by relating the local patterns to the larger system of which they are part. The strategic objective of this research is to explore the policies of the successive Syrian governments towards the Arab tribes and their reactions to these policies and their consequences for the relationship between state and tribe from the fall of the Ottoman Empire and its withdrawal from Syria in 1916 until the eruption of the current Syrian civil war. The research will develop a new understanding of the linkages between environment, economy and government policies as the affect the tribes and their relationship with the state.Counting the cost of tagging : quanitifying and reducing the behavioural and energetic impacts of tags in a large marine vertebrateMcKnight, Joseph Christopherhttps://hdl.handle.net/10023/155602019-09-27T08:55:36Z2018-01-01T00:00:00ZDespite the invaluable contribution of animal-borne sensors to research, an underlying issue with their use is the potential to impact the behaviour and energetics of instrumented animals, which could have consequences for both animal welfare and data validity. Here I show that the presence of a SMRU GPS/GSM phone tag affects the behaviour and energetics of harbour seals (Phoca vitulina) and grey seals (halichoerus grypus). To reduce the impacts of tagging a computational fluid dynamic (CFD) modelling exercise was undertaken to quantify and describe the additional drag from a phone tag, which informed the redesign of a ‘new’ low drag phone tag. Central to the CFD modelling exercise was a biological relevant and spatially accurate geometry of a swimming harp seal (Pagophilus groenlandicus) generated by a three dimensional (3D) photogrammetrical methodology, developed and calibrated on sea carcasses. CFD modelling predicted additional drag from a phone tag on a 100kg harp seal was 16%. Tag redesign generated a more streamlined tag that reduced tag induced drag by 46%. Comparing the behaviour and energetics of juvenile grey seals carrying the ‘new’ or existing phone tag showed that despite significant reductions in drag resulting from redesign, there was limited amelioration of behavioural impacts and no reduction in the impact on energetics. To better understand the energetics of diving seals, a novel animal-borne sensor was developed. The sensor (PortaSeal) used non-invasive near-infrared spectroscopy ot measure the haemodynamics and oxygenation in the brain and blubber of juvenile harbour seals. Data from the PortaSeal provided numerous insights into the haemodynamic basis of oxygen management of phocid seals.
2018-01-01T00:00:00ZMcKnight, Joseph ChristopherDespite the invaluable contribution of animal-borne sensors to research, an underlying issue with their use is the potential to impact the behaviour and energetics of instrumented animals, which could have consequences for both animal welfare and data validity. Here I show that the presence of a SMRU GPS/GSM phone tag affects the behaviour and energetics of harbour seals (Phoca vitulina) and grey seals (halichoerus grypus). To reduce the impacts of tagging a computational fluid dynamic (CFD) modelling exercise was undertaken to quantify and describe the additional drag from a phone tag, which informed the redesign of a ‘new’ low drag phone tag. Central to the CFD modelling exercise was a biological relevant and spatially accurate geometry of a swimming harp seal (Pagophilus groenlandicus) generated by a three dimensional (3D) photogrammetrical methodology, developed and calibrated on sea carcasses. CFD modelling predicted additional drag from a phone tag on a 100kg harp seal was 16%. Tag redesign generated a more streamlined tag that reduced tag induced drag by 46%. Comparing the behaviour and energetics of juvenile grey seals carrying the ‘new’ or existing phone tag showed that despite significant reductions in drag resulting from redesign, there was limited amelioration of behavioural impacts and no reduction in the impact on energetics. To better understand the energetics of diving seals, a novel animal-borne sensor was developed. The sensor (PortaSeal) used non-invasive near-infrared spectroscopy ot measure the haemodynamics and oxygenation in the brain and blubber of juvenile harbour seals. Data from the PortaSeal provided numerous insights into the haemodynamic basis of oxygen management of phocid seals.Using metric space indexing for complete and efficient record linkageAkgün, ÖzgürDearle, AlanKirby, Graham Njal CameronChristen, Peterhttps://hdl.handle.net/10023/151812024-02-15T00:36:57Z2018-01-01T00:00:00ZRecord linkage is the process of identifying records that refer to the same real-world entities in situations where entity identifiers are unavailable. Records are linked on the basis of similarity between common attributes, with every pair being classified as a link or non-link depending on their similarity. Linkage is usually performed in a three-step process: first, groups of similar candidate records are identified using indexing, then pairs within the same group are compared in more detail, and finally classified. Even state-of-the-art indexing techniques, such as locality sensitive hashing, have potential drawbacks. They may fail to group together some true matching records with high similarity, or they may group records with low similarity, leading to high computational overhead. We propose using metric space indexing (MSI) to perform complete linkage, resulting in a parameter-free process combining indexing, comparison and classification into a single step delivering complete and efficient record linkage. An evaluation on real-world data from several domains shows that linkage using MSI can yield better quality than current indexing techniques, with similar execution cost, without the need for domain knowledge or trial and error to configure the process.
2018-01-01T00:00:00ZAkgün, ÖzgürDearle, AlanKirby, Graham Njal CameronChristen, PeterRecord linkage is the process of identifying records that refer to the same real-world entities in situations where entity identifiers are unavailable. Records are linked on the basis of similarity between common attributes, with every pair being classified as a link or non-link depending on their similarity. Linkage is usually performed in a three-step process: first, groups of similar candidate records are identified using indexing, then pairs within the same group are compared in more detail, and finally classified. Even state-of-the-art indexing techniques, such as locality sensitive hashing, have potential drawbacks. They may fail to group together some true matching records with high similarity, or they may group records with low similarity, leading to high computational overhead. We propose using metric space indexing (MSI) to perform complete linkage, resulting in a parameter-free process combining indexing, comparison and classification into a single step delivering complete and efficient record linkage. An evaluation on real-world data from several domains shows that linkage using MSI can yield better quality than current indexing techniques, with similar execution cost, without the need for domain knowledge or trial and error to configure the process.Human cytomegalovirus major immediate early 1 protein targets host chromosomes by docking to the acidic pocket on the nucleosome surfaceMücke, KatrinPaulus, ChristinaBernhardt, KatharinaGerrer, KatrinSchön, KathrinFink, AlinaSauer, Eva-MariaAsbach-Nitzsche, AlexandraHarwardt, ThomasKieninger, BärbelKremer, WernerKalbitzer, Hans RobertNevels, Michaelhttps://hdl.handle.net/10023/148712022-07-05T10:30:02Z2014-01-15T00:00:00ZThe 72-kDa immediate early 1 (IE1) protein encoded by human cytomegalovirus (hCMV) is a nuclearly localized promiscuous regulator of viral and cellular transcription. IE1 has long been known to associate with host mitotic chromatin, yet the mechanisms underlying this interaction have not been specified. In this study, we identify the cellular chromosome receptor for IE1. We demonstrate that the viral protein targets human nucleosomes by directly binding to core histones in a nucleic acid-independent manner. IE1 exhibits two separable histone-interacting regions with differential binding specificities for H2A-H2B and H3-H4. The H2A-H2B binding region was mapped to an evolutionarily conserved 10-amino-acid motif within the chromatin-tethering domain (CTD) of IE1. Results from experimental approaches combined with molecular modeling indicate that the IE1 CTD adopts a β-hairpin structure, docking with the acidic pocket formed by H2A-H2B on the nucleosome surface. IE1 binds to the acidic pocket in a way similar to that of the latency-associated nuclear antigen (LANA) of the Kaposi's sarcoma-associated herpesvirus. Consequently, the IE1 and LANA CTDs compete for binding to nucleosome cores and chromatin. Our work elucidates in detail how a key viral regulator is anchored to human chromosomes and identifies the nucleosomal acidic pocket as a joint target of proteins from distantly related viruses. Based on the striking similarities between the IE1 and LANA CTDs and the fact that nucleosome targeting by IE1 is dispensable for productive replication even in "clinical" strains of hCMV, we speculate that the two viral proteins may serve analogous functions during latency of their respective viruses.
2014-01-15T00:00:00ZMücke, KatrinPaulus, ChristinaBernhardt, KatharinaGerrer, KatrinSchön, KathrinFink, AlinaSauer, Eva-MariaAsbach-Nitzsche, AlexandraHarwardt, ThomasKieninger, BärbelKremer, WernerKalbitzer, Hans RobertNevels, MichaelThe 72-kDa immediate early 1 (IE1) protein encoded by human cytomegalovirus (hCMV) is a nuclearly localized promiscuous regulator of viral and cellular transcription. IE1 has long been known to associate with host mitotic chromatin, yet the mechanisms underlying this interaction have not been specified. In this study, we identify the cellular chromosome receptor for IE1. We demonstrate that the viral protein targets human nucleosomes by directly binding to core histones in a nucleic acid-independent manner. IE1 exhibits two separable histone-interacting regions with differential binding specificities for H2A-H2B and H3-H4. The H2A-H2B binding region was mapped to an evolutionarily conserved 10-amino-acid motif within the chromatin-tethering domain (CTD) of IE1. Results from experimental approaches combined with molecular modeling indicate that the IE1 CTD adopts a β-hairpin structure, docking with the acidic pocket formed by H2A-H2B on the nucleosome surface. IE1 binds to the acidic pocket in a way similar to that of the latency-associated nuclear antigen (LANA) of the Kaposi's sarcoma-associated herpesvirus. Consequently, the IE1 and LANA CTDs compete for binding to nucleosome cores and chromatin. Our work elucidates in detail how a key viral regulator is anchored to human chromosomes and identifies the nucleosomal acidic pocket as a joint target of proteins from distantly related viruses. Based on the striking similarities between the IE1 and LANA CTDs and the fact that nucleosome targeting by IE1 is dispensable for productive replication even in "clinical" strains of hCMV, we speculate that the two viral proteins may serve analogous functions during latency of their respective viruses.Abundance estimate, survival and site fidelity patterns of Blainville’s (Mesoplodon densirostris) and Cuvier’s (Ziphius cavirostris) beaked whales off El Hierro (Canary Islands)Reyes Suárez, Crístelhttps://hdl.handle.net/10023/141892019-03-29T10:34:23Z2018-06-27T00:00:00ZBeaked whales (Fam. Ziphiidae) comprise 22 different species, however due to their cryptic behaviour, information on these species is very limited. Beaked whales appear to be highly sensitive to anthropogenic noise, which can lead to mass strandings. The scarcity of knowledge about the abundance and population dynamics of most beaked whale species impedes the correct assessment of the effects that these impacts have on their populations. Coastal, year round populations of Blainville’s and Cuvier’s beaked whales were found in El Hierro (Canary Islands) in 2003. Long-term photo-ID studies have been conducted since then using a combination of land and at sea observations. Here I present the first results relating to site fidelity, abundance estimates and apparent survival for Blainville’s and Cuvier’s beaked whales in the Northeast Atlantic. The number of identifiable adults, i.e. animals with regular to very good photos and recognizable marks in the same area of the body, comprises 69 Blainville´s and 66 Cuvier´s beaked whales. Individuals that were captured in only one year are considered transients (T) while animals seen in multiple years are defined here as recaptured (R). Analysis of site fidelity patterns showed that 35% and 53% of the marked population on Blainville’s and Cuvier’s, respectively, were recaptured and form island-associated populations with a pattern of residence in the area. In Blainville’s, females spend longer periods in coastal waters than males and indeterminate whales (subadults or adult females never observed with calves). Males visit the area during shorter periods and there is an apparent hierarchy in individual male use of the area. Indeterminate individuals seem to emigrate after a 3 year period. These data coincide with results from Bahamas in showing a higher number of females than males with high site philopatry, and less philopatry in subadults. It has been proposed that these observations in Bahamas could be explained by males fighting for access to the female resident population for polygynous mating, and some subadults leaving the area. In Cuvier’s beaked whales, there is no apparent sexual segregation in the use of the area albeit a low number of calves challenge a robust identification of adult females. More data are needed to define social structure of the Cuvier’s beaked whale population.
Mark-recapture methods were used to calculate abundance estimate and apparent survival in both species. Data was restricted to six years (2010 to 2015) in order to apply open and also closed population models that could account for heterogeneity in the data. Results of closed model estimates (Chapman analysis of two periods pooling data biannually: 2010-2013 and 2012-2015) are robust and provide best estimates corrected by the proportion of marked individuals of 33 (95% CI: 24-46) island associated Blainville´s beaked whales for both periods, and 53 (95% CI: 38-71, for 2010-2013) and 39 (95% CI: 34-44 for 2012-2015) island associated Cuvier´s beaked whales. POPAN open model analyses of the full period provides best estimates of total abundances of 103 (95% CI: 85-125) and 87 (95% CI: 73-103) for Blainville´s and Cuvier´s beaked whales, respectively.
2018-06-27T00:00:00ZReyes Suárez, CrístelBeaked whales (Fam. Ziphiidae) comprise 22 different species, however due to their cryptic behaviour, information on these species is very limited. Beaked whales appear to be highly sensitive to anthropogenic noise, which can lead to mass strandings. The scarcity of knowledge about the abundance and population dynamics of most beaked whale species impedes the correct assessment of the effects that these impacts have on their populations. Coastal, year round populations of Blainville’s and Cuvier’s beaked whales were found in El Hierro (Canary Islands) in 2003. Long-term photo-ID studies have been conducted since then using a combination of land and at sea observations. Here I present the first results relating to site fidelity, abundance estimates and apparent survival for Blainville’s and Cuvier’s beaked whales in the Northeast Atlantic. The number of identifiable adults, i.e. animals with regular to very good photos and recognizable marks in the same area of the body, comprises 69 Blainville´s and 66 Cuvier´s beaked whales. Individuals that were captured in only one year are considered transients (T) while animals seen in multiple years are defined here as recaptured (R). Analysis of site fidelity patterns showed that 35% and 53% of the marked population on Blainville’s and Cuvier’s, respectively, were recaptured and form island-associated populations with a pattern of residence in the area. In Blainville’s, females spend longer periods in coastal waters than males and indeterminate whales (subadults or adult females never observed with calves). Males visit the area during shorter periods and there is an apparent hierarchy in individual male use of the area. Indeterminate individuals seem to emigrate after a 3 year period. These data coincide with results from Bahamas in showing a higher number of females than males with high site philopatry, and less philopatry in subadults. It has been proposed that these observations in Bahamas could be explained by males fighting for access to the female resident population for polygynous mating, and some subadults leaving the area. In Cuvier’s beaked whales, there is no apparent sexual segregation in the use of the area albeit a low number of calves challenge a robust identification of adult females. More data are needed to define social structure of the Cuvier’s beaked whale population.
Mark-recapture methods were used to calculate abundance estimate and apparent survival in both species. Data was restricted to six years (2010 to 2015) in order to apply open and also closed population models that could account for heterogeneity in the data. Results of closed model estimates (Chapman analysis of two periods pooling data biannually: 2010-2013 and 2012-2015) are robust and provide best estimates corrected by the proportion of marked individuals of 33 (95% CI: 24-46) island associated Blainville´s beaked whales for both periods, and 53 (95% CI: 38-71, for 2010-2013) and 39 (95% CI: 34-44 for 2012-2015) island associated Cuvier´s beaked whales. POPAN open model analyses of the full period provides best estimates of total abundances of 103 (95% CI: 85-125) and 87 (95% CI: 73-103) for Blainville´s and Cuvier´s beaked whales, respectively.Unrecorded copies of Middle English verse and prose in Dublin, Trinity College, MS 352Connolly, Margarethttps://hdl.handle.net/10023/141772023-04-18T23:37:58Z2018-01-01T00:00:00ZThis article gives details of otherwise unrecorded copies of extracts from Walter Hilton's 'Scale of Perfection' and from 'Dives and Pauper' which occur in a sixteenth-century manuscript commonplace book, Dublin, Trinity College, MS 352. Some of the extracts may have been copied from printed sources.
2018-01-01T00:00:00ZConnolly, MargaretThis article gives details of otherwise unrecorded copies of extracts from Walter Hilton's 'Scale of Perfection' and from 'Dives and Pauper' which occur in a sixteenth-century manuscript commonplace book, Dublin, Trinity College, MS 352. Some of the extracts may have been copied from printed sources.Firm type, feed-in tariff, and wind energy investment in Germany : An investigation of decision making factors of energy producers regarding investing in wind energy capacityWerner, LoneScholtens, Lambertus Johannes Regnerushttps://hdl.handle.net/10023/138702023-04-25T23:47:20Z2017-04-19T00:00:00ZThe development of renewable and sustainable energy is advanced by public financial support. Particularly so in the German Energiewende, which seeks to replace nuclear and fossil electricity generation with wind, sun, and biomass. We study the impact of the (changes in the) feed-in tariff policy on the investment in wind electricity generation capacity in Germany in the period 2000-2014. We estimate a generic investment model which includes this support mechanism, the cost of capital, investment risks like wind and price volatility, and manufacturing costs. We discuss specific features for different types of wind energy investors, such as the incumbents, small private investors, diversified companies, and independent power producers. We find that a change in the feed-in tariff has a negative impact on investment capacity regarding the generation of wind energy: a one monetary unit increase in the variation of the tariff is to be associated with a decrease by 0.17 MW wind capacity installed. We argue it is policy uncertainty that makes investors shy away from making real investments. We also argue that the drivers for wind energy investment can differ along different types of firms. For the traditional power producers, especially electricity price volatility, construction costs, and carbon prices seem to matter. But for the other investor types, the feed-in tariff is crucial indeed.
2017-04-19T00:00:00ZWerner, LoneScholtens, Lambertus Johannes RegnerusThe development of renewable and sustainable energy is advanced by public financial support. Particularly so in the German Energiewende, which seeks to replace nuclear and fossil electricity generation with wind, sun, and biomass. We study the impact of the (changes in the) feed-in tariff policy on the investment in wind electricity generation capacity in Germany in the period 2000-2014. We estimate a generic investment model which includes this support mechanism, the cost of capital, investment risks like wind and price volatility, and manufacturing costs. We discuss specific features for different types of wind energy investors, such as the incumbents, small private investors, diversified companies, and independent power producers. We find that a change in the feed-in tariff has a negative impact on investment capacity regarding the generation of wind energy: a one monetary unit increase in the variation of the tariff is to be associated with a decrease by 0.17 MW wind capacity installed. We argue it is policy uncertainty that makes investors shy away from making real investments. We also argue that the drivers for wind energy investment can differ along different types of firms. For the traditional power producers, especially electricity price volatility, construction costs, and carbon prices seem to matter. But for the other investor types, the feed-in tariff is crucial indeed.III - Contractarianism as a political moralitySachs, Benjamin Alanhttps://hdl.handle.net/10023/136792023-04-18T10:05:55Z2016-05-26T00:00:00ZContractarianism initially made its mark, in the seventeenth century, as a sort of theory of everything in ethics. But gradually philosophers became convinced that there were resources available outside contractarianism for settling important moral questions—for instance, ideas of human rights and the moral equality of persons. Then Rawls revived contractarianism with a more modest aim—namely, as a theory of justice. But even this agenda for contractarianism has been called into question, most notably by G.A. Cohen, who contends that we have other tools at our disposal for identifying the true conception of justice. So the question remains: how should contractarianism be construed if it is to provide answers to questions that cannot be answered in some other way? In my essay I offer a very simple answer: contractarianism should be construed as a political morality. I arrive at this answer by starting with contractarianism as a theory of everything and paring away the unappealing layers of contractarianism so understood. I begin by describing what contractarianism is. Then I dispense with contractarianism as a theory of state legitimacy, as a theory of interpersonal morality, and as a theory of justice. Finally, I distinguish political morality from the other already-mentioned areas of morality, and argue that contractarianism is a sensible theory of its grounds.
2016-05-26T00:00:00ZSachs, Benjamin AlanContractarianism initially made its mark, in the seventeenth century, as a sort of theory of everything in ethics. But gradually philosophers became convinced that there were resources available outside contractarianism for settling important moral questions—for instance, ideas of human rights and the moral equality of persons. Then Rawls revived contractarianism with a more modest aim—namely, as a theory of justice. But even this agenda for contractarianism has been called into question, most notably by G.A. Cohen, who contends that we have other tools at our disposal for identifying the true conception of justice. So the question remains: how should contractarianism be construed if it is to provide answers to questions that cannot be answered in some other way? In my essay I offer a very simple answer: contractarianism should be construed as a political morality. I arrive at this answer by starting with contractarianism as a theory of everything and paring away the unappealing layers of contractarianism so understood. I begin by describing what contractarianism is. Then I dispense with contractarianism as a theory of state legitimacy, as a theory of interpersonal morality, and as a theory of justice. Finally, I distinguish political morality from the other already-mentioned areas of morality, and argue that contractarianism is a sensible theory of its grounds.The bête noire and the noble lie : the International Criminal Court and (the disavowal of) politicsRoyer, Christofhttps://hdl.handle.net/10023/135712023-04-25T23:53:21Z2018-05-25T00:00:00ZFor the traditional legalistic discourse on the International Criminal Court (ICC), “politics” is a bête noire that compromises the independence of the Court and thus needs to be avoided and overcome. In response to this legalistic approach, a burgeoning body of literature insists that the Court does not exist and operate “beyond politics”, arguing that the ICC is an institution where law and politics are intimately connected. The present article seeks to contribute to this “non-traditional” literature by addressing two of its fundamental weaknesses: First, writers of the “non-traditional camp” often present a rather limited view of “politics”; in particular, they have shied away from taking the radical step of portraying and analysing the ICC as a “political actor”. This undermines both its critical and constructive potential. Secondly, these commentators offer a simplistic explanation as to why “traditionalists” treat politics as the ICC’s bête noire: Traditionalists, they claim, are “legalists” with scant interest in and understanding of politics. By focusing on the ICC’s nature as a political actor, this article does not only paint a more nuanced picture of the ICC but also demonstrates the constructive potential of this understanding of the ICC to shed light on the so-called “peace versus justice dilemma”. And secondly, it demonstrates that precisely because the ICC is and ought to be a prudent political actor, it must officially disavow politics. The “noble lie” of disavowing politics, therefore, is a prudential strategy to avoid dangerous moral and political consequences and, ultimately, to secure the continued existence of the ICC itself.
2018-05-25T00:00:00ZRoyer, ChristofFor the traditional legalistic discourse on the International Criminal Court (ICC), “politics” is a bête noire that compromises the independence of the Court and thus needs to be avoided and overcome. In response to this legalistic approach, a burgeoning body of literature insists that the Court does not exist and operate “beyond politics”, arguing that the ICC is an institution where law and politics are intimately connected. The present article seeks to contribute to this “non-traditional” literature by addressing two of its fundamental weaknesses: First, writers of the “non-traditional camp” often present a rather limited view of “politics”; in particular, they have shied away from taking the radical step of portraying and analysing the ICC as a “political actor”. This undermines both its critical and constructive potential. Secondly, these commentators offer a simplistic explanation as to why “traditionalists” treat politics as the ICC’s bête noire: Traditionalists, they claim, are “legalists” with scant interest in and understanding of politics. By focusing on the ICC’s nature as a political actor, this article does not only paint a more nuanced picture of the ICC but also demonstrates the constructive potential of this understanding of the ICC to shed light on the so-called “peace versus justice dilemma”. And secondly, it demonstrates that precisely because the ICC is and ought to be a prudent political actor, it must officially disavow politics. The “noble lie” of disavowing politics, therefore, is a prudential strategy to avoid dangerous moral and political consequences and, ultimately, to secure the continued existence of the ICC itself.The eponymous Jacquerie : making revolt mean some thingsFirnhaber-Baker, Justinehttps://hdl.handle.net/10023/135502023-07-24T14:30:17Z2016-11-29T00:00:00ZLabelling an activity makes it mean something. The decision to term a group of actions a ‘revolt’ or an ‘uprising’ today has profound implications for interpretation, just as calling them ‘rumours’ or ‘takehan’ went to the very heart of the perception and reception of contentious political acts 600 years ago. The word ‘jacquerie’ is no exception. In English, as in French, the word has meant ‘a peasant revolt, especially a very bloody one’ since the nineteenth century.2 But what the modern term’s medieval eponym, the French Jacquerie of May-June 1358, actually meant to its observers and participants is a curiously underexplored subject. Only one scholarly monograph, published in the nineteenth century, has ever been written, and since then fewer than a dozen articles have appeared, the most cogent of them written by Raymond Cazelles over 30 years ago
This work was undertaken with the support of a British Arts and Humanities Research Council Early Career Fellowship (grant reference AH/K006843/1).
2016-11-29T00:00:00ZFirnhaber-Baker, JustineLabelling an activity makes it mean something. The decision to term a group of actions a ‘revolt’ or an ‘uprising’ today has profound implications for interpretation, just as calling them ‘rumours’ or ‘takehan’ went to the very heart of the perception and reception of contentious political acts 600 years ago. The word ‘jacquerie’ is no exception. In English, as in French, the word has meant ‘a peasant revolt, especially a very bloody one’ since the nineteenth century.2 But what the modern term’s medieval eponym, the French Jacquerie of May-June 1358, actually meant to its observers and participants is a curiously underexplored subject. Only one scholarly monograph, published in the nineteenth century, has ever been written, and since then fewer than a dozen articles have appeared, the most cogent of them written by Raymond Cazelles over 30 years ago3-2: Invited paper: Color on Demand - Color-tunable OLEDs for lighting and displaysFröbel, MarkusSchwab, TobiasKliem, MonaLenk, SimoneLeo, KarlReineke, SebastianGather, Malte C.https://hdl.handle.net/10023/132742024-03-27T00:42:37Z2017-01-01T00:00:00ZA device concept for highly efficient OLEDs is introduced that allows to tune the emission color of the device over a broad range of the CIE color gamut. The approach exploits the different polarities of the positive and negative half-cycles of an alternating current driving signal to independently address two vertically stacked emission units with complementary color. Ultrathin metal electrodes fabricated by a wetting layer approach are used to achieve good electrical contact to each stack with minimal impact on optical performance.
2017-01-01T00:00:00ZFröbel, MarkusSchwab, TobiasKliem, MonaLenk, SimoneLeo, KarlReineke, SebastianGather, Malte C.A device concept for highly efficient OLEDs is introduced that allows to tune the emission color of the device over a broad range of the CIE color gamut. The approach exploits the different polarities of the positive and negative half-cycles of an alternating current driving signal to independently address two vertically stacked emission units with complementary color. Ultrathin metal electrodes fabricated by a wetting layer approach are used to achieve good electrical contact to each stack with minimal impact on optical performance.Evaluating the effect of measurement error in pairs of 3D bearings in point transect sampling estimates of densityMarques, Tiago A.Duarte, PedroPeixe, TelmoMoretti, DavidThomas, Lenhttps://hdl.handle.net/10023/130372023-04-18T09:37:40Z2018-03-27T00:00:00Z2018-03-27T00:00:00ZMarques, Tiago A.Duarte, PedroPeixe, TelmoMoretti, DavidThomas, LenProfessional medical writing support and the reporting quality of randomized controlled trial abstracts among high-impact general medical journalsMills, IraSheard, CatherineHays, MeredithDouglas, KevinWinchester, Christopher C.Gattrell, William T.https://hdl.handle.net/10023/129942023-04-18T23:45:54Z2017-09-23T00:00:00ZBackground : In articles reporting randomized controlled trials, professional medical writing support is associated with increased adherence to Consolidated Standards of Reporting Trials (CONSORT). We set out to determine whether professional medical writing support was also associated with improved adherence to CONSORT for Abstracts. Methods : Using data from a previously published cross-sectional study of 463 articles reporting randomized controlled trials published between 2011 and 2014 in five top medical journals, we determined the association between professional medical writing support and CONSORT for Abstracts items using a Wilcoxon rank-sum test. Results : The mean proportion of adherence to CONSORT for Abstracts items reported was similar with and without professional medical writing support (64.3% vs 66.5%, respectively; p=0.30). Professional medical writing support was associated with lower adherence to reporting study setting (relative risk [RR]; 0.40; 95% confidence interval [CI], 0.23–0.70), and higher adherence to disclosing harms/side effects (RR 2.04; 95% CI, 1.37–3.03) and funding source (RR 1.75; 95% CI, 1.18–2.60). Conclusions : Although professional medical writing support was not associated with increased overall adherence to CONSORT for Abstracts, important aspects were improved with professional medical writing support, including reporting of adverse events and funding source. This study identifies areas to consider for improvement.
2017-09-23T00:00:00ZMills, IraSheard, CatherineHays, MeredithDouglas, KevinWinchester, Christopher C.Gattrell, William T.Background : In articles reporting randomized controlled trials, professional medical writing support is associated with increased adherence to Consolidated Standards of Reporting Trials (CONSORT). We set out to determine whether professional medical writing support was also associated with improved adherence to CONSORT for Abstracts. Methods : Using data from a previously published cross-sectional study of 463 articles reporting randomized controlled trials published between 2011 and 2014 in five top medical journals, we determined the association between professional medical writing support and CONSORT for Abstracts items using a Wilcoxon rank-sum test. Results : The mean proportion of adherence to CONSORT for Abstracts items reported was similar with and without professional medical writing support (64.3% vs 66.5%, respectively; p=0.30). Professional medical writing support was associated with lower adherence to reporting study setting (relative risk [RR]; 0.40; 95% confidence interval [CI], 0.23–0.70), and higher adherence to disclosing harms/side effects (RR 2.04; 95% CI, 1.37–3.03) and funding source (RR 1.75; 95% CI, 1.18–2.60). Conclusions : Although professional medical writing support was not associated with increased overall adherence to CONSORT for Abstracts, important aspects were improved with professional medical writing support, including reporting of adverse events and funding source. This study identifies areas to consider for improvement.The potential for Assemblage thinking in population geography : assembling population, space and placeDuffy, PaulaStojanovic, Timhttps://hdl.handle.net/10023/126452023-04-18T23:37:18Z2018-04-10T00:00:00ZThis study explores ‘Assemblage’ thinking as an approach for population geography research. The paper highlights the recent prominence of Assemblage thinking in human geography, before exploring the potential opportunities for engagement by population geographers. In particular we focus on the production of place as co-constituted by the material (space) and the discursive (knowledge, process and practice). Considering the Assemblage practice of ‘Rendering Technical’, we reflect on the role that population geography plays in authorising knowledge and supporting policy. This is investigated through a critical taxonomic analysis of recent Scottish demographic data. It is argued on the one hand that this captures key economic and population characteristics of ‘place’, while on the other hand it offers a limited technical knowledge. We conclude that a reflexive approach to research using Assemblage thinking may challenge the intimate relationship between population geographers and the state.
This paper is output from an Economic and Social Research Council Award (Reference 1506438) funded in partnership with Marine Scotland, The Scottish Government.
2018-04-10T00:00:00ZDuffy, PaulaStojanovic, TimThis study explores ‘Assemblage’ thinking as an approach for population geography research. The paper highlights the recent prominence of Assemblage thinking in human geography, before exploring the potential opportunities for engagement by population geographers. In particular we focus on the production of place as co-constituted by the material (space) and the discursive (knowledge, process and practice). Considering the Assemblage practice of ‘Rendering Technical’, we reflect on the role that population geography plays in authorising knowledge and supporting policy. This is investigated through a critical taxonomic analysis of recent Scottish demographic data. It is argued on the one hand that this captures key economic and population characteristics of ‘place’, while on the other hand it offers a limited technical knowledge. We conclude that a reflexive approach to research using Assemblage thinking may challenge the intimate relationship between population geographers and the state.Knowledge-based interoperability for mathematical software systemsKohlhase, MichaelDe Feo, LucaMüller, DennisPfeiffer, Markus JohannesRabe, FlorianThiéry, NicolasVasilyev, VictorWiesing, Tomhttps://hdl.handle.net/10023/124912023-04-19T00:42:12Z2017-01-01T00:00:00ZThere is a large ecosystem of mathematical software systems. Individually, these are optimized for particular domains and functionalities, and together they cover many needs of practical and theoretical mathematics. However, each system specializes on one area, and it remains very difficult to solve problems that need to involve multiple systems. Some integrations exist, but the are ad-hoc and have scalability and maintainability issues. In particular, there is not yet an interoperability layer that combines the various systems into a virtual research environment (VRE) for mathematics. The OpenDreamKit project aims at building a toolkit for such VREs. It suggests using a central system-agnostic formalization of mathematics (Math-in-the-Middle, MitM) as the needed interoperability layer. In this paper, we conduct the first major case study that instantiates the MitM paradigm for a concrete domain as well as a concrete set of systems. Specifically, we integrate GAP, Sage, and Singular to perform computation in group and ring theory. Our work involves massive practical efforts, including a novel formalization of computational group theory, improvements to the involved software systems, and a novel mediating system that sits at the center of a star-shaped integration layout between mathematical software systems.
Funding: OpenDreamKit Horizon 2020 European Research Infrastructures project (#676541) and DFG project RA-18723-1 OAF.
2017-01-01T00:00:00ZKohlhase, MichaelDe Feo, LucaMüller, DennisPfeiffer, Markus JohannesRabe, FlorianThiéry, NicolasVasilyev, VictorWiesing, TomThere is a large ecosystem of mathematical software systems. Individually, these are optimized for particular domains and functionalities, and together they cover many needs of practical and theoretical mathematics. However, each system specializes on one area, and it remains very difficult to solve problems that need to involve multiple systems. Some integrations exist, but the are ad-hoc and have scalability and maintainability issues. In particular, there is not yet an interoperability layer that combines the various systems into a virtual research environment (VRE) for mathematics. The OpenDreamKit project aims at building a toolkit for such VREs. It suggests using a central system-agnostic formalization of mathematics (Math-in-the-Middle, MitM) as the needed interoperability layer. In this paper, we conduct the first major case study that instantiates the MitM paradigm for a concrete domain as well as a concrete set of systems. Specifically, we integrate GAP, Sage, and Singular to perform computation in group and ring theory. Our work involves massive practical efforts, including a novel formalization of computational group theory, improvements to the involved software systems, and a novel mediating system that sits at the center of a star-shaped integration layout between mathematical software systems.Behavioral, ecological, and evolutionary aspects of meat-eating by Sumatran orangutans (Pongo abelii)Hardus, Madeleine E.Lameira, Adriano R.Zulfa, AstriAtmoko, S. Suci Utamide Vries, HanWich, Serge A.https://hdl.handle.net/10023/124552022-04-20T15:50:31Z2012-04-01T00:00:00ZMeat-eating is an important aspect of human evolution, but how meat became a substantial component of the human diet is still poorly understood. Meat-eating in our closest relatives, the great apes, may provide insight into the emergence of this trait, but most existing data are for chimpanzees. We report 3 rare cases of meat-eating of slow lorises, Nycticebus coucang, by 1 Sumatran orangutan mother-infant dyad in Ketambe, Indonesia, to examine how orangutans find slow lorises and share meat. We combine these 3 cases with 2 previous ones to test the hypothesis that slow loris captures by orangutans are seasonal and dependent on fruit availability. We also provide the first (to our knowledge) quantitative data and high-definition video recordings of meat chewing rates by great apes, which we use to estimate the minimum time necessary for a female Australopithecus africanus to reach its daily energy requirements when feeding partially on raw meat. Captures seemed to be opportunistic but orangutans may have used olfactory cues to detect the prey. The mother often rejected meat sharing requests and only the infant initiated meat sharing. Slow loris captures occurred only during low ripe fruit availability, suggesting that meat may represent a filler fallback food for orangutans. Orangutans ate meat more than twice as slowly as chimpanzees (Pan troglodytes), suggesting that group living may function as a meat intake accelerator in hominoids. Using orangutan data as a model, time spent chewing per day would not require an excessive amount of time for our social ancestors (australopithecines and hominids), as long as meat represented no more than a quarter of their diet.
2012-04-01T00:00:00ZHardus, Madeleine E.Lameira, Adriano R.Zulfa, AstriAtmoko, S. Suci Utamide Vries, HanWich, Serge A.Meat-eating is an important aspect of human evolution, but how meat became a substantial component of the human diet is still poorly understood. Meat-eating in our closest relatives, the great apes, may provide insight into the emergence of this trait, but most existing data are for chimpanzees. We report 3 rare cases of meat-eating of slow lorises, Nycticebus coucang, by 1 Sumatran orangutan mother-infant dyad in Ketambe, Indonesia, to examine how orangutans find slow lorises and share meat. We combine these 3 cases with 2 previous ones to test the hypothesis that slow loris captures by orangutans are seasonal and dependent on fruit availability. We also provide the first (to our knowledge) quantitative data and high-definition video recordings of meat chewing rates by great apes, which we use to estimate the minimum time necessary for a female Australopithecus africanus to reach its daily energy requirements when feeding partially on raw meat. Captures seemed to be opportunistic but orangutans may have used olfactory cues to detect the prey. The mother often rejected meat sharing requests and only the infant initiated meat sharing. Slow loris captures occurred only during low ripe fruit availability, suggesting that meat may represent a filler fallback food for orangutans. Orangutans ate meat more than twice as slowly as chimpanzees (Pan troglodytes), suggesting that group living may function as a meat intake accelerator in hominoids. Using orangutan data as a model, time spent chewing per day would not require an excessive amount of time for our social ancestors (australopithecines and hominids), as long as meat represented no more than a quarter of their diet.TheoArtistry, and a contemporary perspective on composing sacred choral musicCorbett, Georgehttps://hdl.handle.net/10023/124162023-04-18T23:42:54Z2017-12-28T00:00:00ZThis article presents the methodology and research underpinning the TheoArtistry Composers’ Scheme, a project based in ITIA (the Institute for Theology, Imagination and the Arts), School of Divinity, University of St Andrews (2016-17). I analyse Sir James MacMillan’s theology of music, outline some practical and theoretical issues that arose in setting up theologian-composer partnerships, and reflect critically on the six new works of sacred choral music that emerged (these are printed as an appendix). The article assesses the implications of such collaboration for future work at the interface between theology and music, and between theology and the arts more generally.
2017-12-28T00:00:00ZCorbett, GeorgeThis article presents the methodology and research underpinning the TheoArtistry Composers’ Scheme, a project based in ITIA (the Institute for Theology, Imagination and the Arts), School of Divinity, University of St Andrews (2016-17). I analyse Sir James MacMillan’s theology of music, outline some practical and theoretical issues that arose in setting up theologian-composer partnerships, and reflect critically on the six new works of sacred choral music that emerged (these are printed as an appendix). The article assesses the implications of such collaboration for future work at the interface between theology and music, and between theology and the arts more generally.The Fergusson affair: Calvinism and dissimulation in the Scottish EnlightenmentKidd, Colin Craighttps://hdl.handle.net/10023/123902024-03-28T00:42:23Z2016-06-27T00:00:00Z2016-06-27T00:00:00ZKidd, Colin CraigTitle redactedJameison, Stephen A.https://hdl.handle.net/10023/122732017-12-06T14:36:30Z2017-12-07T00:00:00Z2017-12-07T00:00:00ZJameison, Stephen A.Sex-related differences in the postmolt distribution of Weddell seals (Leptonychotes weddellii) in the southern Weddell SeaLangley, IzzyFedak, MikeNicholls, KeithBoehme, Larshttps://hdl.handle.net/10023/122662022-07-31T11:30:24Z2018-04-01T00:00:00ZThe population of Weddell seals (Leptonychotes weddellii) in the southern Weddell Sea is in a unique position on the continental shelf edge, with vast shelf waters to the south, and deep Southern Ocean to the north. We describe sex-related differences in the winter distribution of this population, from data collected by 20 conductivity-temperature-depth satellite relay data loggers deployed in February 2011 at the end of the annual molt. The regional daily speed was calculated, and a state-space model was used to estimate behavioral states to positions along individuals’ tracks. GLMMs estimated that males and smaller individuals, diving in shallower water, traveled less far per day of deployment (males 14.6 ± 2.26 km/d, females 18.9 ± 2.42 km/d), and males were estimated to dive in shallower water (males 604 ± 382 m, females 1,875 ± 1,458 m). Males and smaller individuals were also estimated to be more resident; males spent an average 83.4% ± 7.7% of their time in a resident behavioral state, compared to females at 74.1% ± 7.1%. This evidence that male and female Weddell seals in the southern Weddell Sea are adopting different strategies has not been shown elsewhere along their circumpolar distribution.
Funding: NERC grants NE/G014833/1 (MF) and NE/G014086/1 (KWN).
2018-04-01T00:00:00ZLangley, IzzyFedak, MikeNicholls, KeithBoehme, LarsThe population of Weddell seals (Leptonychotes weddellii) in the southern Weddell Sea is in a unique position on the continental shelf edge, with vast shelf waters to the south, and deep Southern Ocean to the north. We describe sex-related differences in the winter distribution of this population, from data collected by 20 conductivity-temperature-depth satellite relay data loggers deployed in February 2011 at the end of the annual molt. The regional daily speed was calculated, and a state-space model was used to estimate behavioral states to positions along individuals’ tracks. GLMMs estimated that males and smaller individuals, diving in shallower water, traveled less far per day of deployment (males 14.6 ± 2.26 km/d, females 18.9 ± 2.42 km/d), and males were estimated to dive in shallower water (males 604 ± 382 m, females 1,875 ± 1,458 m). Males and smaller individuals were also estimated to be more resident; males spent an average 83.4% ± 7.7% of their time in a resident behavioral state, compared to females at 74.1% ± 7.1%. This evidence that male and female Weddell seals in the southern Weddell Sea are adopting different strategies has not been shown elsewhere along their circumpolar distribution.Carpe lucem: harnessing organic light sources for optogeneticsMorton, AndrewMurawski, CarolineGather, Malte Christianhttps://hdl.handle.net/10023/122362023-04-19T00:45:49Z2016-12-01T00:00:00ZWith the advent of optogenetics, numerous functions in cells have been rendered responsive to the experimental delivery of light. The most common implementation of this technique features neurons genetically modified to express light-sensitive ion channel proteins, which open specifically in response to pulses of blue light, triggering electrical impulses in neurons. Optogenetics now has matured to a point where in addition to answering fundamental questions about the function of the brain, scientists begin to consider clinical applications. Further progress in this field however will require new ways of delivering light. One of these involves the use of organic light-emitting diodes (OLEDs), a display technology increasingly common in modern-day smart phones, for the optical stimulation of cells.
2016-12-01T00:00:00ZMorton, AndrewMurawski, CarolineGather, Malte ChristianWith the advent of optogenetics, numerous functions in cells have been rendered responsive to the experimental delivery of light. The most common implementation of this technique features neurons genetically modified to express light-sensitive ion channel proteins, which open specifically in response to pulses of blue light, triggering electrical impulses in neurons. Optogenetics now has matured to a point where in addition to answering fundamental questions about the function of the brain, scientists begin to consider clinical applications. Further progress in this field however will require new ways of delivering light. One of these involves the use of organic light-emitting diodes (OLEDs), a display technology increasingly common in modern-day smart phones, for the optical stimulation of cells.Biodiversity change in the Cerrado following invasive pine tree establishmentRocha Kortz, Alessandrahttps://hdl.handle.net/10023/122202023-03-21T12:29:48Z2017-12-07T00:00:00ZHow do newly established species interact with existing assemblage members to alter local biodiversity? This question is especially topical given growing concerns about increased temporal turnover levels relative to background rates. My PhD thesis concerns young, isolated pines Pinus elliottii invading the Cerrado (Brazilian savanna) as a study system to test the hypothesis that the impact of newly established individuals varies across habitat layers. I sampled both vegetation layers (shrub and grass) of two distinct habitats, the shrub-dominated campo sujo and the grass-dominated campo úmido. My results show that the pine is changing α diversity in the dominant vegetation layer of each habitat: the shrub layer of campo sujo and the grass layer of campo úmido. The shape of the diversity v. establishment time relationship is habitat dependent; there is a hump shaped relationship between diversity and pine size in the grass layer but a linear one in the shrub layer. β diversity metrics – which take species composition into account - reveal marked differences in species composition between the habitats in the shrub layer, whereas the corresponding pair of invaded and control sites of the same habitat and layer is more similar than expected (in both vegetation layers). The degree of similarity between sites also changes as the invasion proceeds. In the campo sujo habitat, sites become more compositionally distinct, whereas in the grass layer of campo úmido sites get more similar. This suggests that the timing of changes in species composition is habitat-dependent and reinforces the need to remove the invader individuals from the area. My results show that, though complex, the consequences for local biodiversity of non-native species establishment are not haphazard. As such they contribute to the understanding of species coexistence and help explain why species invasion can lead to very different biodiversity outcomes.
2017-12-07T00:00:00ZRocha Kortz, AlessandraHow do newly established species interact with existing assemblage members to alter local biodiversity? This question is especially topical given growing concerns about increased temporal turnover levels relative to background rates. My PhD thesis concerns young, isolated pines Pinus elliottii invading the Cerrado (Brazilian savanna) as a study system to test the hypothesis that the impact of newly established individuals varies across habitat layers. I sampled both vegetation layers (shrub and grass) of two distinct habitats, the shrub-dominated campo sujo and the grass-dominated campo úmido. My results show that the pine is changing α diversity in the dominant vegetation layer of each habitat: the shrub layer of campo sujo and the grass layer of campo úmido. The shape of the diversity v. establishment time relationship is habitat dependent; there is a hump shaped relationship between diversity and pine size in the grass layer but a linear one in the shrub layer. β diversity metrics – which take species composition into account - reveal marked differences in species composition between the habitats in the shrub layer, whereas the corresponding pair of invaded and control sites of the same habitat and layer is more similar than expected (in both vegetation layers). The degree of similarity between sites also changes as the invasion proceeds. In the campo sujo habitat, sites become more compositionally distinct, whereas in the grass layer of campo úmido sites get more similar. This suggests that the timing of changes in species composition is habitat-dependent and reinforces the need to remove the invader individuals from the area. My results show that, though complex, the consequences for local biodiversity of non-native species establishment are not haphazard. As such they contribute to the understanding of species coexistence and help explain why species invasion can lead to very different biodiversity outcomes.Chechen demographic growth and resistance : reactions to the existential threat from RussiaIliyasov, Marathttps://hdl.handle.net/10023/121712019-08-12T11:31:54Z2017-12-08T00:00:00ZThis thesis examines the phenomenon of Chechen population growth in the context of the protracted Russo-Chechen conflict. It argues that the conflict was the main causative reason for the growth of the Chechen population.
This hypothesis was confirmed by fieldwork, which allowed for the detection of a positive correlation between the nation’s demographic growth and the perception of the own physical existence as endangered. The results of fieldwork demonstrated that the majority of the informants connected high Chechen birth rates with the necessity of physical survival, restoration of losses, and strengthening the nation numerically. The threat to Chechen ethnic identity did not show as strong correlation with demographic growth as did the threat to physical existence.
Nevertheless, Chechen ethnic identity, which favours resistance to a foreign rule, was confirmed to be the crucial variable in determining the demographic dynamics of the nation. This in turn suggested an additional correlation: in the context of an existential threat salient ethnic identity would prompt a population growth. The latter, in such cases, is considered as a way of continuing the resistance in a non-violent way. The restoration of the losses experienced and the survival of the nation is seen as a victory and at the same time as a preparation for the next outbreak of violence.
With all of this in mind, this thesis suggests considering Chechen demographic growth as the reaction (which itself was determined by ethnic identity) to the existential threat imposed by Russia.
2017-12-08T00:00:00ZIliyasov, MaratThis thesis examines the phenomenon of Chechen population growth in the context of the protracted Russo-Chechen conflict. It argues that the conflict was the main causative reason for the growth of the Chechen population.
This hypothesis was confirmed by fieldwork, which allowed for the detection of a positive correlation between the nation’s demographic growth and the perception of the own physical existence as endangered. The results of fieldwork demonstrated that the majority of the informants connected high Chechen birth rates with the necessity of physical survival, restoration of losses, and strengthening the nation numerically. The threat to Chechen ethnic identity did not show as strong correlation with demographic growth as did the threat to physical existence.
Nevertheless, Chechen ethnic identity, which favours resistance to a foreign rule, was confirmed to be the crucial variable in determining the demographic dynamics of the nation. This in turn suggested an additional correlation: in the context of an existential threat salient ethnic identity would prompt a population growth. The latter, in such cases, is considered as a way of continuing the resistance in a non-violent way. The restoration of the losses experienced and the survival of the nation is seen as a victory and at the same time as a preparation for the next outbreak of violence.
With all of this in mind, this thesis suggests considering Chechen demographic growth as the reaction (which itself was determined by ethnic identity) to the existential threat imposed by Russia.Servius, Cato the Elder and VirgilSmith, Christopher Johnhttps://hdl.handle.net/10023/121192023-04-18T23:40:43Z2017-01-01T00:00:00ZThis paper considers one of the most significant of the authors cited in the Servian tradition, Cato the Elder. He is cited more than any other historian, and looked at the other way round, Servius is a very important source for our knowledge of Cato. This paper addresses the questions of what we learn from Servius’ use of Cato, and what we learn about Virgil ?
2017-01-01T00:00:00ZSmith, Christopher JohnThis paper considers one of the most significant of the authors cited in the Servian tradition, Cato the Elder. He is cited more than any other historian, and looked at the other way round, Servius is a very important source for our knowledge of Cato. This paper addresses the questions of what we learn from Servius’ use of Cato, and what we learn about Virgil ?Into the past : nationalism and heritage in the neoliberal ageGledhill, Jameshttps://hdl.handle.net/10023/121142020-02-20T11:58:13Z2017-12-08T00:00:00ZThis thesis examines the ideological nexus of nationalism and heritage under the social conditions of neoliberalism. The investigation aims to demonstrate how neoliberal economics stimulate the irrationalism manifest in nationalist idealisation of the past. The institutionalisation of national heritage was originally a rational function of the modern state, symbolic of its political and cultural authority. With neoliberal erosion of the productive economy and public institutions, heritage and nostalgia proliferate today in all areas of social life. It is argued that this represents a social pathology linked to the neoliberal state’s inability to construct a future-orientated national project. These conditions enhance the appeal of irrational nationalist and regionalist ideologies idealising the past as a source of cultural purity. Unable to achieve social cohesion, the neoliberal state promotes multiculturalism, encouraging minorities to embrace essentialist identity politics that parallel the nativism of right-wing nationalists and regionalists. This phenomenon is contextualised within the general crisis of progressive modernisation in Western societies that has accompanied neoliberalisation and globalisation.
A new theory of activist heritage is advanced to describe autonomous, politicised heritage that appropriates forms and practices from the state heritage sector. Using this concept, the politics of irrational nationalism and regionalism are explored through fieldwork, including participant observation, interviews and photography.
The interaction of state and activist heritage is considered at the Wewelsburg 1933-1945 Memorial Museum in Germany wherein neofascists have re-signified Nazi material culture, reactivating it within contemporary political narratives. The activist heritage of Israeli Zionism, Irish Republicanism and Ulster Loyalism is analysed through studies of museums, heritage centres, archaeological sites, exhibitions, monuments and historical re-enactments. These illustrate how activist heritage represents a political strategy within irrational ideologies that interpret the past as the ethical model for the future. This work contends that irrational nationalism fundamentally challenges the Enlightenment’s assertion of reason over faith, and culture over nature, by superimposing pre-modern ideas upon the structure of modernity. An ideological product of the Enlightenment, the nation state remains the only political unit within which a rational command of time and space is possible, and thus the only viable basis for progressive modernity.
2017-12-08T00:00:00ZGledhill, JamesThis thesis examines the ideological nexus of nationalism and heritage under the social conditions of neoliberalism. The investigation aims to demonstrate how neoliberal economics stimulate the irrationalism manifest in nationalist idealisation of the past. The institutionalisation of national heritage was originally a rational function of the modern state, symbolic of its political and cultural authority. With neoliberal erosion of the productive economy and public institutions, heritage and nostalgia proliferate today in all areas of social life. It is argued that this represents a social pathology linked to the neoliberal state’s inability to construct a future-orientated national project. These conditions enhance the appeal of irrational nationalist and regionalist ideologies idealising the past as a source of cultural purity. Unable to achieve social cohesion, the neoliberal state promotes multiculturalism, encouraging minorities to embrace essentialist identity politics that parallel the nativism of right-wing nationalists and regionalists. This phenomenon is contextualised within the general crisis of progressive modernisation in Western societies that has accompanied neoliberalisation and globalisation.
A new theory of activist heritage is advanced to describe autonomous, politicised heritage that appropriates forms and practices from the state heritage sector. Using this concept, the politics of irrational nationalism and regionalism are explored through fieldwork, including participant observation, interviews and photography.
The interaction of state and activist heritage is considered at the Wewelsburg 1933-1945 Memorial Museum in Germany wherein neofascists have re-signified Nazi material culture, reactivating it within contemporary political narratives. The activist heritage of Israeli Zionism, Irish Republicanism and Ulster Loyalism is analysed through studies of museums, heritage centres, archaeological sites, exhibitions, monuments and historical re-enactments. These illustrate how activist heritage represents a political strategy within irrational ideologies that interpret the past as the ethical model for the future. This work contends that irrational nationalism fundamentally challenges the Enlightenment’s assertion of reason over faith, and culture over nature, by superimposing pre-modern ideas upon the structure of modernity. An ideological product of the Enlightenment, the nation state remains the only political unit within which a rational command of time and space is possible, and thus the only viable basis for progressive modernity.Looking beyond Guinevere : depictions of women in Chrétien de Troyes’ Arthurian romances, the cult of saints, and religious texts of the twelfth centuryHayes, Lydia Helenhttps://hdl.handle.net/10023/121002018-05-02T16:10:03Z2017-12-08T00:00:00ZThis thesis provides a reading of Chrétien de Troyes’ Arthurian romances that reflects the cultural and intellectual context of twelfth-century Christianity. The impact of this context on Chrétien’s romances is examined by identifying the influence that contemporaneous biblical expository texts, hagiography, and the material culture of the cult of saints had upon his work. Although scholars have devoted much attention to the study of Chrétien’s romances, and some have examined the potential influences of various medieval Christian beliefs, practices, and symbols on his work, none have yet to produce a thorough study of these elements while focusing specifically on the female characters.
Scholars have identified the influence of the cult of saints on the depiction of Guinevere in The Knight of the Cart, but have not examined this influence on the depictions of the ladies in the other four romances in detail. I look beyond Guinevere, examining all of the female protagonists in the Arthurian romances, comparing their attributes and actions to those of biblical women in contemporaneous biblical exposition and those of saints in hagiography. At the heart of this comparison is the relationship between the lady and her knight, a relationship that is described in similar terms to that between a biblical woman and God and that between saint and devotee.
2017-12-08T00:00:00ZHayes, Lydia HelenThis thesis provides a reading of Chrétien de Troyes’ Arthurian romances that reflects the cultural and intellectual context of twelfth-century Christianity. The impact of this context on Chrétien’s romances is examined by identifying the influence that contemporaneous biblical expository texts, hagiography, and the material culture of the cult of saints had upon his work. Although scholars have devoted much attention to the study of Chrétien’s romances, and some have examined the potential influences of various medieval Christian beliefs, practices, and symbols on his work, none have yet to produce a thorough study of these elements while focusing specifically on the female characters.
Scholars have identified the influence of the cult of saints on the depiction of Guinevere in The Knight of the Cart, but have not examined this influence on the depictions of the ladies in the other four romances in detail. I look beyond Guinevere, examining all of the female protagonists in the Arthurian romances, comparing their attributes and actions to those of biblical women in contemporaneous biblical exposition and those of saints in hagiography. At the heart of this comparison is the relationship between the lady and her knight, a relationship that is described in similar terms to that between a biblical woman and God and that between saint and devotee.The fifth-century crisisSmith, Christopher Johnhttps://hdl.handle.net/10023/120662024-03-02T00:44:53Z2017-10-26T00:00:00ZThis essay seeks to establish the parameters of our uncertainty concerning one of the most difficult periods of Roman history, the period between the traditional end of the Roman monarchy and the passing of the Licinio-Sextian legislation. In addition to some methodological observations, the essay attempts to offer a model for understanding Roman choices and decisions in a period of change and transformation.
2017-10-26T00:00:00ZSmith, Christopher JohnThis essay seeks to establish the parameters of our uncertainty concerning one of the most difficult periods of Roman history, the period between the traditional end of the Roman monarchy and the passing of the Licinio-Sextian legislation. In addition to some methodological observations, the essay attempts to offer a model for understanding Roman choices and decisions in a period of change and transformation.J.B. Ward-Perkins, the BSR and the landscape tradition in post-war Italian archaeologySmith, Christopher Johnhttps://hdl.handle.net/10023/120632023-04-18T23:41:48Z2017-10-26T00:00:00ZNothing has so characterized the British School at Rome's approach, from its inception, as the commitment to landscape archaeology in one form or another. This paper discusses the origins of this commitment in the work of Thomas Ashby, but focuses on the major contribution of J.B. Ward-Perkins and the South Etruria Survey. This survey is set in the context both of intellectual developments in landscape archaeology, and the specific circumstances of the BSR, and its Director, after the Second World War. The article traces the impact of this work on subsequent landscape archaeology.
2017-10-26T00:00:00ZSmith, Christopher JohnNothing has so characterized the British School at Rome's approach, from its inception, as the commitment to landscape archaeology in one form or another. This paper discusses the origins of this commitment in the work of Thomas Ashby, but focuses on the major contribution of J.B. Ward-Perkins and the South Etruria Survey. This survey is set in the context both of intellectual developments in landscape archaeology, and the specific circumstances of the BSR, and its Director, after the Second World War. The article traces the impact of this work on subsequent landscape archaeology.Learning from loss : eroding coastal heritage in ScotlandGraham Allsop, Elinor LouiseDawson, Thomas ChristopherHambly, Joannahttps://hdl.handle.net/10023/120422024-02-28T00:43:21Z2017-11-09T00:00:00ZHeritage sites are constantly changing due to natural processes, and this change can happen fastest at the coast. Much legislation has been enacted to protect sites of historic interest, but these do not protect sites from natural processes. Change is already happening, and climate change predictions suggest that the pace will accelerate in the future. Instead of seeing the potential destruction of heritage sites as a disaster, we should embrace the opportunity that they can provide for us to learn about the past and to plan for the future. Heritage laws often enshrine a policy of preservation in situ, meaning that our most spectacular sites are preserved in a state of equilibrium, with a default position of no permitted intervention. However, the options for threatened coastal sites mirror those of shoreline management plans, which usually recommend either the construction of a coastal defence or, more likely, a strategy of managed retreat, where erosion is allowed to take its course after appropriate mitigations strategies have been enacted. Managed retreat can lead to a range of research projects, some of which would not normally be possible at similar, unthreatened and legally protected monuments. Such research also has the potential to involve members of the public, who can help in the discovery process, and cascade what they have learned through their communities. Information shared can be about the heritage site itself, including how communities in the past coped at times of climatic stress; and also about the processes that are now threatening the monument, thus helping teach about present day climate change.
2017-11-09T00:00:00ZGraham Allsop, Elinor LouiseDawson, Thomas ChristopherHambly, JoannaHeritage sites are constantly changing due to natural processes, and this change can happen fastest at the coast. Much legislation has been enacted to protect sites of historic interest, but these do not protect sites from natural processes. Change is already happening, and climate change predictions suggest that the pace will accelerate in the future. Instead of seeing the potential destruction of heritage sites as a disaster, we should embrace the opportunity that they can provide for us to learn about the past and to plan for the future. Heritage laws often enshrine a policy of preservation in situ, meaning that our most spectacular sites are preserved in a state of equilibrium, with a default position of no permitted intervention. However, the options for threatened coastal sites mirror those of shoreline management plans, which usually recommend either the construction of a coastal defence or, more likely, a strategy of managed retreat, where erosion is allowed to take its course after appropriate mitigations strategies have been enacted. Managed retreat can lead to a range of research projects, some of which would not normally be possible at similar, unthreatened and legally protected monuments. Such research also has the potential to involve members of the public, who can help in the discovery process, and cascade what they have learned through their communities. Information shared can be about the heritage site itself, including how communities in the past coped at times of climatic stress; and also about the processes that are now threatening the monument, thus helping teach about present day climate change.Towards a eucharistic theatre : the theatrical theologies of the Reduta, the Rhapsodic Theatre, and Grotowski's LabMatson, Cole C. E.https://hdl.handle.net/10023/120062023-04-27T10:39:49Z2016-06-21T00:00:00ZThis thesis explores the use of eucharistic language in the theatre theories of three different mid-20th-century Polish theatre companies--the Reduta Theatre, the Rhapsodic Theatre, and the Laboratory Theatre--especially as expressed in the writings of their respective primary founders: Juliusz Osterwa, Mieczysław Kotlarczyk, and Jerzy Grotowski. The thesis also describes how the Rhapsodic and Laboratory Theatres inherited different elements of the Reduta tradition, and how those two diverging branches of the Reduta's legacy have affected contemporary theatre. In addition, the thesis examines how different 20th-century theatre theorists have related the eucharist to theatre, and evaluates the legitimacy of the claim that religious rituals such as the eucharist can and ought to be replaced by secular theatrical rituals. Special attention is paid to Carl Lavery's three views of the sacred: secular, theological, and a/theological. Alexander Schmemann's conception of the eucharist is used to correct Lavery's presentation of the theological sacred and to argue for the possibility of a Christian sacred theatre, or a "eucharistic theatre." The thesis defines the concept of a eucharistic theatre; demonstrates the extent to which the Reduta, Rhapsodic, and Laboratory Theatres meet this definition; and suggests some ways in which a eucharistic theatre may be created today.
2016-06-21T00:00:00ZMatson, Cole C. E.This thesis explores the use of eucharistic language in the theatre theories of three different mid-20th-century Polish theatre companies--the Reduta Theatre, the Rhapsodic Theatre, and the Laboratory Theatre--especially as expressed in the writings of their respective primary founders: Juliusz Osterwa, Mieczysław Kotlarczyk, and Jerzy Grotowski. The thesis also describes how the Rhapsodic and Laboratory Theatres inherited different elements of the Reduta tradition, and how those two diverging branches of the Reduta's legacy have affected contemporary theatre. In addition, the thesis examines how different 20th-century theatre theorists have related the eucharist to theatre, and evaluates the legitimacy of the claim that religious rituals such as the eucharist can and ought to be replaced by secular theatrical rituals. Special attention is paid to Carl Lavery's three views of the sacred: secular, theological, and a/theological. Alexander Schmemann's conception of the eucharist is used to correct Lavery's presentation of the theological sacred and to argue for the possibility of a Christian sacred theatre, or a "eucharistic theatre." The thesis defines the concept of a eucharistic theatre; demonstrates the extent to which the Reduta, Rhapsodic, and Laboratory Theatres meet this definition; and suggests some ways in which a eucharistic theatre may be created today.Understanding collective violence : the communicative and performative qualities of violence in acts of belongingMurer, Jeffrey Stevensonhttps://hdl.handle.net/10023/119982023-04-26T00:23:30Z2014-11-01T00:00:00ZThis chapter explores the motivations for joining violent groups across arange of circumstances. In particular, the chapter will explore the similarities in the role of violence as a marker of identity within groups as diverseas street gangs and ethnic communities. Frequently, membership inviolent groups is explained in terms of individual material gain or theattainment of individual fame, in very rationalist and individualistic terms.This focus on individual choice and motivation suggests the use or disinclination to use violence is an expression of individual agency. Indeed, many of studies on civil wars or other armed conflicts treat joining these violent groups and the participation in violent acts as being anti-social, as if the choice to engage in violence is one wholly against social norms or social values. However, much can be gained by seeing these groups in completely the opposite light: gangs, communal factions, militias, even terrorist organisations can be seen as highly social environments. This chapter will examine the performative qualities of violence and the role that violence plays in the experience of belonging in large groups and in collective identity formation.
2014-11-01T00:00:00ZMurer, Jeffrey StevensonThis chapter explores the motivations for joining violent groups across arange of circumstances. In particular, the chapter will explore the similarities in the role of violence as a marker of identity within groups as diverseas street gangs and ethnic communities. Frequently, membership inviolent groups is explained in terms of individual material gain or theattainment of individual fame, in very rationalist and individualistic terms.This focus on individual choice and motivation suggests the use or disinclination to use violence is an expression of individual agency. Indeed, many of studies on civil wars or other armed conflicts treat joining these violent groups and the participation in violent acts as being anti-social, as if the choice to engage in violence is one wholly against social norms or social values. However, much can be gained by seeing these groups in completely the opposite light: gangs, communal factions, militias, even terrorist organisations can be seen as highly social environments. This chapter will examine the performative qualities of violence and the role that violence plays in the experience of belonging in large groups and in collective identity formation.Two variants of the froidure-pin algorithm for finite semigroupsJonusas, JuliusMitchell, J. D.Pfeiffer, M.https://hdl.handle.net/10023/118792023-04-18T23:36:18Z2018-02-08T00:00:00ZIn this paper, we present two algorithms based on the Froidure-Pin Algorithm for computing the structure of a finite semigroup from a generating set. As was the case with the original algorithm of Froidure and Pin, the algorithms presented here produce the left and right Cayley graphs, a confluent terminating rewriting system, and a reduced word of the rewriting system for every element of the semigroup. If U is any semigroup, and A is a subset of U, then we denote by <A> the least subsemigroup of U containing A. If B is any other subset of U, then, roughly speaking, the first algorithm we present describes how to use any information about <A>, that has been found using the Froidure-Pin Algorithm, to compute the semigroup <A∪B>. More precisely, we describe the data structure for a finite semigroup S given by Froidure and Pin, and how to obtain such a data structure for <A∪B> from that for <A>. The second algorithm is a lock-free concurrent version of the Froidure-Pin Algorithm.
2018-02-08T00:00:00ZJonusas, JuliusMitchell, J. D.Pfeiffer, M.In this paper, we present two algorithms based on the Froidure-Pin Algorithm for computing the structure of a finite semigroup from a generating set. As was the case with the original algorithm of Froidure and Pin, the algorithms presented here produce the left and right Cayley graphs, a confluent terminating rewriting system, and a reduced word of the rewriting system for every element of the semigroup. If U is any semigroup, and A is a subset of U, then we denote by <A> the least subsemigroup of U containing A. If B is any other subset of U, then, roughly speaking, the first algorithm we present describes how to use any information about <A>, that has been found using the Froidure-Pin Algorithm, to compute the semigroup <A∪B>. More precisely, we describe the data structure for a finite semigroup S given by Froidure and Pin, and how to obtain such a data structure for <A∪B> from that for <A>. The second algorithm is a lock-free concurrent version of the Froidure-Pin Algorithm.The development of molecular tools and resources for selective breeding in aquacultureHolman, Luke Earlhttps://hdl.handle.net/10023/118432019-03-29T10:35:02Z2017-06-21T00:00:00ZHuman population growth is predicted to continue well into the 21st century, and beyond. The provision of selectively bred organisms will be an essential part of global food security. While the selective breeding of terrestrial animals has been essential to the human success story, the breeding of aquatic organisms has only recently received serious attention. Aquaculture research urgently needs both specific genetic resources for existing aquatic species, and generalised workflows and pipelines for the generation of resources for newly cultivated species. This study presents a stochastic simulation of a selective program for the gilthead seabream (Sparus aurata L.). The simulation models the change of a non-selective breeding program to a scheme improving growth rate by mass selection. The effect of selection on growth rate, inbreeding and projected profits are modelled explicitly. The simulation predicts a profitable and sound breeding scheme for gilthead seabream and can also be easily adapted for new traits and species. A workflow for the filtration of an optimal number genetic variants for molecular parentage assignment was also developed and validated in Atlantic salmon (Salmo salar L.). A discovery dataset of 102 Atlantic salmon from three distinct aquaculture strains were subject to restriction site associated DNA marker sequencing. The resultant single nucleotide polymorphisms were filtered according to quality, property and suitability for probe-based high-throughput genotyping technology. The final SNP panel consisted of 94 mass genotyping assays that gave 100% accurate parentage in independent samples of known pedigree. Finally, a set of standardised trait descriptors were designed for bivalve molluscs to accompany next generation sequencing submissions. These standards are needed to provide consistent trait measurements between investigators for quality control and to enable interoperability of phenotypic and genotypic data in future meta analyses.
2017-06-21T00:00:00ZHolman, Luke EarlHuman population growth is predicted to continue well into the 21st century, and beyond. The provision of selectively bred organisms will be an essential part of global food security. While the selective breeding of terrestrial animals has been essential to the human success story, the breeding of aquatic organisms has only recently received serious attention. Aquaculture research urgently needs both specific genetic resources for existing aquatic species, and generalised workflows and pipelines for the generation of resources for newly cultivated species. This study presents a stochastic simulation of a selective program for the gilthead seabream (Sparus aurata L.). The simulation models the change of a non-selective breeding program to a scheme improving growth rate by mass selection. The effect of selection on growth rate, inbreeding and projected profits are modelled explicitly. The simulation predicts a profitable and sound breeding scheme for gilthead seabream and can also be easily adapted for new traits and species. A workflow for the filtration of an optimal number genetic variants for molecular parentage assignment was also developed and validated in Atlantic salmon (Salmo salar L.). A discovery dataset of 102 Atlantic salmon from three distinct aquaculture strains were subject to restriction site associated DNA marker sequencing. The resultant single nucleotide polymorphisms were filtered according to quality, property and suitability for probe-based high-throughput genotyping technology. The final SNP panel consisted of 94 mass genotyping assays that gave 100% accurate parentage in independent samples of known pedigree. Finally, a set of standardised trait descriptors were designed for bivalve molluscs to accompany next generation sequencing submissions. These standards are needed to provide consistent trait measurements between investigators for quality control and to enable interoperability of phenotypic and genotypic data in future meta analyses.The evolution and regulation of the chordate ParaHox clusterGarstang, Myles Granthttps://hdl.handle.net/10023/117882019-07-01T10:16:46Z2016-06-22T00:00:00ZThe ParaHox cluster is the evolutionary sister of the Hox cluster. Like the Hox cluster, the ParaHox cluster is subject to complex regulatory phenomena such as collinearity. Despite the breakup of the ParaHox cluster within many animals, intact and collinear clusters have now been discovered within the chordate phyla in amphioxus and the vertebrates, and more recently within the hemichordates and echinoderms. The archetypal ParaHox cluster of amphioxus places it in a unique position in which to examine the regulatory mechanisms controlling ParaHox gene expression within the last common ancestor of chordates, and perhaps even the wider Deuterostomia. In this thesis, the genomic and regulatory landscape of the amphioxus ParaHox cluster is characterised in detail. New genomic and transcriptomic resources are used to better characterise the B.floridae ParaHox cluster and surrounding genomic region, and conserved non-coding regions and regulatory motifs are identified across the ParaHox cluster of three species of amphioxus. In conjunction with this, the impact of retrotransposition upon the ParaHox cluster is examined and analyses of transposable elements and the AmphiSCP1 retrogene reveal that the ParaHox cluster may be more insulated from outside influence than previously thought. Finally, the detailed analyses of a regulatory element upstream of AmphiGsx reveals conserved mechanisms regulating Gsx CNS expression within the chordates, and TCF/Lef is likely a direct regulator of AmphiGsx within the CNS. The work in this thesis makes use of new genomic and transcriptomic resources available for amphioxus to better characterise the genomic and regulatory landscape of the amphioxus ParaHox cluster, serving as a basis for the improved identification and characterisation of functional regulatory elements and conserved regulatory mechanisms. This work also highlights the potential of Ciona intestinalis as a ‘living test tube’ to allow the detailed characterisation of amphioxus ParaHox regulatory elements.
2016-06-22T00:00:00ZGarstang, Myles GrantThe ParaHox cluster is the evolutionary sister of the Hox cluster. Like the Hox cluster, the ParaHox cluster is subject to complex regulatory phenomena such as collinearity. Despite the breakup of the ParaHox cluster within many animals, intact and collinear clusters have now been discovered within the chordate phyla in amphioxus and the vertebrates, and more recently within the hemichordates and echinoderms. The archetypal ParaHox cluster of amphioxus places it in a unique position in which to examine the regulatory mechanisms controlling ParaHox gene expression within the last common ancestor of chordates, and perhaps even the wider Deuterostomia. In this thesis, the genomic and regulatory landscape of the amphioxus ParaHox cluster is characterised in detail. New genomic and transcriptomic resources are used to better characterise the B.floridae ParaHox cluster and surrounding genomic region, and conserved non-coding regions and regulatory motifs are identified across the ParaHox cluster of three species of amphioxus. In conjunction with this, the impact of retrotransposition upon the ParaHox cluster is examined and analyses of transposable elements and the AmphiSCP1 retrogene reveal that the ParaHox cluster may be more insulated from outside influence than previously thought. Finally, the detailed analyses of a regulatory element upstream of AmphiGsx reveals conserved mechanisms regulating Gsx CNS expression within the chordates, and TCF/Lef is likely a direct regulator of AmphiGsx within the CNS. The work in this thesis makes use of new genomic and transcriptomic resources available for amphioxus to better characterise the genomic and regulatory landscape of the amphioxus ParaHox cluster, serving as a basis for the improved identification and characterisation of functional regulatory elements and conserved regulatory mechanisms. This work also highlights the potential of Ciona intestinalis as a ‘living test tube’ to allow the detailed characterisation of amphioxus ParaHox regulatory elements.A plant-level analysis of the spill-over effects of the German EnergiewendeMulder, MachielScholtens, Berthttps://hdl.handle.net/10023/117702023-04-25T23:46:46Z2016-12-01T00:00:00ZIn order to analyse international effects of national energy policies, we investigate the spill-over effects of the German Energiewende on the Dutch power market, which is closely connected to the German market. We estimate the impact of the German supply of wind and solar electricity on the Dutch day-ahead price of electricity and the utilisation of the conventional power plants. We take cross-border capacity constraints into account and use hourly plant-level data over 2006–2014. We find that the price elasticity of German wind on Dutch day-ahead prices is −0.03. However, this effect vanishes when the cross-border capacity is fully utilised. We find a modest negative impact on the utilisation of the Dutch power plants. As such, we conclude that the German Energiewende has had modest spill-over effects to the Dutch market. The recent dramatic performance of the Dutch gas-fired plants can be attributed to the changes in the relative prices of coal versus natural gas. We conclude that national energy policies in one country do not necessarily strongly affect neighbouring markets in case of constrained cross-border capacities.
2016-12-01T00:00:00ZMulder, MachielScholtens, BertIn order to analyse international effects of national energy policies, we investigate the spill-over effects of the German Energiewende on the Dutch power market, which is closely connected to the German market. We estimate the impact of the German supply of wind and solar electricity on the Dutch day-ahead price of electricity and the utilisation of the conventional power plants. We take cross-border capacity constraints into account and use hourly plant-level data over 2006–2014. We find that the price elasticity of German wind on Dutch day-ahead prices is −0.03. However, this effect vanishes when the cross-border capacity is fully utilised. We find a modest negative impact on the utilisation of the Dutch power plants. As such, we conclude that the German Energiewende has had modest spill-over effects to the Dutch market. The recent dramatic performance of the Dutch gas-fired plants can be attributed to the changes in the relative prices of coal versus natural gas. We conclude that national energy policies in one country do not necessarily strongly affect neighbouring markets in case of constrained cross-border capacities.Physiological constraints and energetic costs of diving behaviour in marine mammals : a review of studies using trained Steller sea lions diving in the open oceanRosen, DavidHindle, AllysonFahlman, AndreasGerlinsky, CarlingGoundie, ElizabethHastie, Gordon DrummondVolpov, BethTrites, Andrewhttps://hdl.handle.net/10023/117652023-04-25T23:46:33Z2017-01-01T00:00:00ZMarine mammals are characterized as having physiological specializations that maximize the use of oxygen stores to prolong time spent under water. However, it has been difficult to undertake the requisite controlled studies to determine the physiological limitations and trade-offs that marine mammals face while diving in the wild under varying environmental and nutritional conditions. For the past decade, Steller sea lions (Eumetopias jubatus) trained to swim and dive in the open ocean away from the physical confines of pools participated in studies that investigated the interactions between diving behaviour, energetic costs, physiological constraints, and prey availability. Many of these studies measured the cost of diving to understand how it varies with behaviour and environmental and physiological conditions. Collectively, these studies show that the type of diving (dive bouts or single dives), the level of underwater activity, the depth and duration of dives, and the nutritional status and physical condition of the animal affect the cost of diving and foraging. They show that dive depth, dive and surface duration, and the type of dive result in physiological adjustments (heart rate, gas exchange) that may be independent of energy expenditure. They also demonstrate that changes in prey abundance and nutritional status cause sea lions to alter the balance between time spent at the surface acquiring oxygen (and offloading CO2 and other metabolic by-products) and time spent at depth acquiring prey. These new insights into the physiological basis of diving behaviour further our understanding of the potential scope for behavioural responses of marine mammals to environmental changes, the energetic significance of these adjustments, and the consequences of approaching physiological limits.
The research was funded through a number of sources, including grants provided by the Natural Sciences and Engineering Research Council (Canada) and from the US National Oceanic and Atmospheric Administration to the North Pacific Universities Marine Mammal Research Consortium through the North Pacific Marine Science Foundation.
2017-01-01T00:00:00ZRosen, DavidHindle, AllysonFahlman, AndreasGerlinsky, CarlingGoundie, ElizabethHastie, Gordon DrummondVolpov, BethTrites, AndrewMarine mammals are characterized as having physiological specializations that maximize the use of oxygen stores to prolong time spent under water. However, it has been difficult to undertake the requisite controlled studies to determine the physiological limitations and trade-offs that marine mammals face while diving in the wild under varying environmental and nutritional conditions. For the past decade, Steller sea lions (Eumetopias jubatus) trained to swim and dive in the open ocean away from the physical confines of pools participated in studies that investigated the interactions between diving behaviour, energetic costs, physiological constraints, and prey availability. Many of these studies measured the cost of diving to understand how it varies with behaviour and environmental and physiological conditions. Collectively, these studies show that the type of diving (dive bouts or single dives), the level of underwater activity, the depth and duration of dives, and the nutritional status and physical condition of the animal affect the cost of diving and foraging. They show that dive depth, dive and surface duration, and the type of dive result in physiological adjustments (heart rate, gas exchange) that may be independent of energy expenditure. They also demonstrate that changes in prey abundance and nutritional status cause sea lions to alter the balance between time spent at the surface acquiring oxygen (and offloading CO2 and other metabolic by-products) and time spent at depth acquiring prey. These new insights into the physiological basis of diving behaviour further our understanding of the potential scope for behavioural responses of marine mammals to environmental changes, the energetic significance of these adjustments, and the consequences of approaching physiological limits.Erwin Schrödinger and quantum wave mechanicsO'Connor, John J.Robertson, Edmund F.https://hdl.handle.net/10023/115432024-02-26T00:43:09Z2017-08-22T00:00:00ZThe fathers of matrix quantum mechanics believed that the quantum particles are unanschaulich (unvisualizable) and that quantum particles pop into existence only when we measure them. Challenging the orthodoxy, in 1926 Erwin Schrödinger developed his wave equation that describes the quantum particles as a packet of quantum probability amplitudes evolving in space and time. Thus, Schrödinger visualized the unvisualizable and lifted the veil that has been obscuring the wonders of the quantum world.
2017-08-22T00:00:00ZO'Connor, John J.Robertson, Edmund F.The fathers of matrix quantum mechanics believed that the quantum particles are unanschaulich (unvisualizable) and that quantum particles pop into existence only when we measure them. Challenging the orthodoxy, in 1926 Erwin Schrödinger developed his wave equation that describes the quantum particles as a packet of quantum probability amplitudes evolving in space and time. Thus, Schrödinger visualized the unvisualizable and lifted the veil that has been obscuring the wonders of the quantum world.Beyond metaphor : archaeology as a social and artistic practiceSmith, Christopher Johnhttps://hdl.handle.net/10023/113022023-04-18T10:16:15Z2017-01-26T00:00:00ZThis article summarises recent work on the engagement between art and archaeology, but seeks to embed this in a longer history of archaeology as a metaphor for other cultural and social practices, and at the same time to compare the ways in which archaeologists and other practitioners operate within the field of cultural production.
2017-01-26T00:00:00ZSmith, Christopher JohnThis article summarises recent work on the engagement between art and archaeology, but seeks to embed this in a longer history of archaeology as a metaphor for other cultural and social practices, and at the same time to compare the ways in which archaeologists and other practitioners operate within the field of cultural production.In search of the gentilshommes campagnards: noble diversity and social structure in Burgundy, 1682-1789Carr, Susanhttps://hdl.handle.net/10023/112712019-04-01T11:10:10Z2017-08-01T00:00:00ZThis study of the gentilshommes campagnards of Burgundy reconsiders the supposed decline of the population of old rural noble families during the last century of the ancien régime. Historical debate has focused on various contributing factors in this ‘decline’, such as government centralisation of the seigneurial system, venal ennoblement, noble poverty, and the social and cultural divide between aristocratic elites and minor nobility, old rural military landowning families and newer professional robe nobility. Re-visiting these themes, integrating them with an analysis of official records and surveys of the Burgundian noble population of the period, and looking afresh at notions of noble identity allows this volume to challenge the established view of a noble population and culture in decline. Contemporary sources not only reveal the existence of a sizeable community of gentilshommes, diverse in origins, identities and cultures, but also show that far from fading into provincial obscurity, this community had adapted and evolved, and continued to thrive right up to the eve of the Revolution.
Third party material in this work are included in the work's Creative Commons license, unless indicated otherwise in the credit line. The front cover image is (c) Bibliothèque Nationale de France.
2017-08-01T00:00:00ZCarr, SusanThis study of the gentilshommes campagnards of Burgundy reconsiders the supposed decline of the population of old rural noble families during the last century of the ancien régime. Historical debate has focused on various contributing factors in this ‘decline’, such as government centralisation of the seigneurial system, venal ennoblement, noble poverty, and the social and cultural divide between aristocratic elites and minor nobility, old rural military landowning families and newer professional robe nobility. Re-visiting these themes, integrating them with an analysis of official records and surveys of the Burgundian noble population of the period, and looking afresh at notions of noble identity allows this volume to challenge the established view of a noble population and culture in decline. Contemporary sources not only reveal the existence of a sizeable community of gentilshommes, diverse in origins, identities and cultures, but also show that far from fading into provincial obscurity, this community had adapted and evolved, and continued to thrive right up to the eve of the Revolution.Foundational and translational research opportunities to improve plant healthMichelmore, RichardCoaker, GittaBart, RebeccaBeattie, GwynBent, AndrewBruce, TobyCameron, DuncanDangl, JeffDinesh-Kumar, SavithrammaEdwards, RobEves-van den Akker, SebastianGassmann, WalterGreenberg, JeanHanley-Bowdoin, LindaHarrison, RichardHe, PingHarvey, JaggerHuffaker, AlisaHulbert, ScotInnes, RogerJones, JonathanKaloshian, IsghouhiKamoun, SophienKatagiri, FumiakiLeach, JanMa, WenboMcDowell, JohnMedford, JuneMeyers, BlakeNelson, RebeccaOliver, RichardQi, YipingSaunders, DianeShaw, MichaelSmart, ChristineSubudhi, PrasantaTorrance, LesleyTyler, BrettValent, BarbaraWalsh, Johnhttps://hdl.handle.net/10023/111422023-04-25T23:49:10Z2017-07-01T00:00:00ZThis whitepaper reports the deliberations of a workshop focused on biotic challenges to plant health held in Washington, D.C. in September 2016. Ensuring health of food plants is critical to maintaining the quality and productivity of crops and for sustenance of the rapidly growing human population. There is a close linkage between food security and societal stability; however, global food security is threatened by the vulnerability of our agricultural systems to numerous pests, pathogens, weeds, and environmental stresses. These threats are aggravated by climate change, the globalization of agriculture, and an over-reliance on non-sustainable inputs. New analytical and computational technologies are providing unprecedented resolution at a variety of molecular, cellular, organismal, and population scales for crop plants as well as pathogens, pests, beneficial microbes, and weeds. It is now possible to both characterize useful or deleterious variation as well as precisely manipulate it. Data-driven, informed decisions based on knowledge of the variation of biotic challenges and of natural and synthetic variation in crop plants will enable deployment of durable interventions throughout the world. These should be integral, dynamic components of agricultural strategies for sustainable agriculture.
2017-07-01T00:00:00ZMichelmore, RichardCoaker, GittaBart, RebeccaBeattie, GwynBent, AndrewBruce, TobyCameron, DuncanDangl, JeffDinesh-Kumar, SavithrammaEdwards, RobEves-van den Akker, SebastianGassmann, WalterGreenberg, JeanHanley-Bowdoin, LindaHarrison, RichardHe, PingHarvey, JaggerHuffaker, AlisaHulbert, ScotInnes, RogerJones, JonathanKaloshian, IsghouhiKamoun, SophienKatagiri, FumiakiLeach, JanMa, WenboMcDowell, JohnMedford, JuneMeyers, BlakeNelson, RebeccaOliver, RichardQi, YipingSaunders, DianeShaw, MichaelSmart, ChristineSubudhi, PrasantaTorrance, LesleyTyler, BrettValent, BarbaraWalsh, JohnThis whitepaper reports the deliberations of a workshop focused on biotic challenges to plant health held in Washington, D.C. in September 2016. Ensuring health of food plants is critical to maintaining the quality and productivity of crops and for sustenance of the rapidly growing human population. There is a close linkage between food security and societal stability; however, global food security is threatened by the vulnerability of our agricultural systems to numerous pests, pathogens, weeds, and environmental stresses. These threats are aggravated by climate change, the globalization of agriculture, and an over-reliance on non-sustainable inputs. New analytical and computational technologies are providing unprecedented resolution at a variety of molecular, cellular, organismal, and population scales for crop plants as well as pathogens, pests, beneficial microbes, and weeds. It is now possible to both characterize useful or deleterious variation as well as precisely manipulate it. Data-driven, informed decisions based on knowledge of the variation of biotic challenges and of natural and synthetic variation in crop plants will enable deployment of durable interventions throughout the world. These should be integral, dynamic components of agricultural strategies for sustainable agriculture.Thomas Hobbes: theorist of the lawLang, Anthony F.Slomp, Gabriellahttps://hdl.handle.net/10023/111082024-02-17T00:41:23Z2015-12-28T00:00:00ZThis short article introduces the papers that follow on the topic of Hobbes as a theorist of the law. It provides an overview of Hobbes reputation as a theorist of law in both domestic and international theory. The paper summarizes the papers that follow and suggest how they fit into the wider literature on Hobbes, legal theory, and constitutional theory.
2015-12-28T00:00:00ZLang, Anthony F.Slomp, GabriellaThis short article introduces the papers that follow on the topic of Hobbes as a theorist of the law. It provides an overview of Hobbes reputation as a theorist of law in both domestic and international theory. The paper summarizes the papers that follow and suggest how they fit into the wider literature on Hobbes, legal theory, and constitutional theory.Memorials of endurance and adventure : exhibiting British polar exploration, 1819 – c.1939Murray, Katiehttps://hdl.handle.net/10023/110872020-06-16T02:03:51Z2017-06-22T00:00:00ZOver eighty polar-themed exhibitions were held in Britain between 1819 and the 1930s, a time of intense exploration of both the Arctic and Antarctic. These varied from panoramas and human exhibits to displays of ‘relics’, equipment, photographs and artwork, waxworks and displays shown as part of a Great Exhibition. This period also saw the creation of the first dedicated polar museums. These displays were visited by thousands of people throughout the country, helping to mediate the subject of exploration for a public audience.
Despite this, the role exhibitions played in forming popular views of the polar regions has not been fully assessed. This thesis addresses this gap. It is the first to consider all the polar exhibitions held during this period as a collective body, making it possible to study how they developed over time and in response to changing circumstances.
The thesis uses a variety of archival sources to both reconstruct the displays and place them in their historical and museological contexts. The study shows that exhibitions evolved in response to changes both in the museum sector and in exploration culture. It demonstrates that, while they were originally identified with the shows of the entertainment industry, polar exhibitions began to take on more of the characteristics of museum displays. At the same time their dominant themes changed; the natural world was relegated in favour of ideas relating to the human experience of the regions such as heroism, adventure and everyday life in an exotic environment. While other media may have been more effective in disseminating ideas about exploration, visitors could find the experience of visiting an exhibition more compelling. This thesis contributes to our understanding of this distinct role that exhibitions played in presenting the polar regions to the British public.
Electronic version excludes material for which permission has not been granted by the rights holder
2017-06-22T00:00:00ZMurray, KatieOver eighty polar-themed exhibitions were held in Britain between 1819 and the 1930s, a time of intense exploration of both the Arctic and Antarctic. These varied from panoramas and human exhibits to displays of ‘relics’, equipment, photographs and artwork, waxworks and displays shown as part of a Great Exhibition. This period also saw the creation of the first dedicated polar museums. These displays were visited by thousands of people throughout the country, helping to mediate the subject of exploration for a public audience.
Despite this, the role exhibitions played in forming popular views of the polar regions has not been fully assessed. This thesis addresses this gap. It is the first to consider all the polar exhibitions held during this period as a collective body, making it possible to study how they developed over time and in response to changing circumstances.
The thesis uses a variety of archival sources to both reconstruct the displays and place them in their historical and museological contexts. The study shows that exhibitions evolved in response to changes both in the museum sector and in exploration culture. It demonstrates that, while they were originally identified with the shows of the entertainment industry, polar exhibitions began to take on more of the characteristics of museum displays. At the same time their dominant themes changed; the natural world was relegated in favour of ideas relating to the human experience of the regions such as heroism, adventure and everyday life in an exotic environment. While other media may have been more effective in disseminating ideas about exploration, visitors could find the experience of visiting an exhibition more compelling. This thesis contributes to our understanding of this distinct role that exhibitions played in presenting the polar regions to the British public.A liberative imagination : reconsidering the fiction of Charlotte Brontë in light of feminist theologySwanson, Kjhttps://hdl.handle.net/10023/110512019-03-29T13:41:47Z2017-06-20T00:00:00ZThis thesis seeks to show the ways in which Charlotte Brontë’s fiction anticipates the concerns of contemporary feminist theology. Whilst Charlotte Brontë’s novels have held a place of honor in feminist literary criticism for decades, there has been a critical tendency to associate the proto-feminism of Brontë’s narratives with a rejection of Christianity—namely, that Brontë’s heroines achieve their personal, social and spiritual emancipation by throwing off the shackles of a patriarchal Church Establishment. And although recent scholarly interest in Victorian Christianity has led to frequent interpretations that regard Brontë’s texts as upholding a Christian worldview, in many such cases, the theology asserted in those interpretations arguably undermines the liberative impulse of the narratives. In both cases, the religious and romantic plots of Brontë’s novels are viewed as incompatible. This thesis suggests that by reading Brontë’s fiction in light of an interdisciplinary perspective that interweaves feminist and theological concerns, the narrative journeys of Brontë’s heroines might be read as affirming both Christian faith and female empowerment. Specifically, this thesis will examine the ways in which feminist theologians have identified the need for Christian doctrines of sin and grace to be articulated in a manner that better reflects women’s experiences. By exploring the interrelationship between women’s writing and women’s faith, particularly as it relates to the literary origins of feminist theology and Brontë’s position within the nineteenth-century female publishing boom, Brontë’s liberative imagination for female flourishing can be re-examined. As will be argued, when considered from the vantage point of feminist theology, 'Jane Eyre', 'Shirley', and 'Villette' portray women’s need to experience grace as self-construction and interdependence rather than self-denial and subjugation.
2017-06-20T00:00:00ZSwanson, KjThis thesis seeks to show the ways in which Charlotte Brontë’s fiction anticipates the concerns of contemporary feminist theology. Whilst Charlotte Brontë’s novels have held a place of honor in feminist literary criticism for decades, there has been a critical tendency to associate the proto-feminism of Brontë’s narratives with a rejection of Christianity—namely, that Brontë’s heroines achieve their personal, social and spiritual emancipation by throwing off the shackles of a patriarchal Church Establishment. And although recent scholarly interest in Victorian Christianity has led to frequent interpretations that regard Brontë’s texts as upholding a Christian worldview, in many such cases, the theology asserted in those interpretations arguably undermines the liberative impulse of the narratives. In both cases, the religious and romantic plots of Brontë’s novels are viewed as incompatible. This thesis suggests that by reading Brontë’s fiction in light of an interdisciplinary perspective that interweaves feminist and theological concerns, the narrative journeys of Brontë’s heroines might be read as affirming both Christian faith and female empowerment. Specifically, this thesis will examine the ways in which feminist theologians have identified the need for Christian doctrines of sin and grace to be articulated in a manner that better reflects women’s experiences. By exploring the interrelationship between women’s writing and women’s faith, particularly as it relates to the literary origins of feminist theology and Brontë’s position within the nineteenth-century female publishing boom, Brontë’s liberative imagination for female flourishing can be re-examined. As will be argued, when considered from the vantage point of feminist theology, 'Jane Eyre', 'Shirley', and 'Villette' portray women’s need to experience grace as self-construction and interdependence rather than self-denial and subjugation.Inter- and intra-year variation in foraging areas of breeding kittiwakes (Rissa tridactyla)Robertson, G. S.Bolton, M.Grecian, W. J.Monaghan, P.https://hdl.handle.net/10023/107752023-04-25T23:48:54Z2014-09-01T00:00:00ZWhile seabird conservation efforts have largely focused on protection from threats at the colony (e.g. reducing disturbance and predation), attention is increasingly being given to implementing protection measures for foraging areas at sea. For this to be effective, important foraging areas must be identified. Although numerous studies have examined seabird foraging behaviour, information is still lacking on the variability in area utilisation within and among breeding seasons. GPS devices were attached to adult black-legged kittiwakes breeding at an expanding North Sea colony (55°20′N, 1°32′W) during both incubation and chick-rearing in 2012 and during chick-rearing in 2011, to determine whether foraging areas remained consistent and to identify the oceanographic characteristics of areas used for foraging. The type and size of prey items consumed at different stages of the breeding cycle was also examined. During incubation (April-May 2012), kittiwakes foraged substantially further from the colony and fed on larger sandeels than when feeding chicks, and there was significant inter-annual variation in foraging areas used during the chick-rearing period (June-July 2011 and 2012). Foraging areas were characterised by cooler sea surface temperatures and areas of high chlorophyll a concentration, although association with specific oceanographic features changed within the breeding season and between years. These results emphasise the importance of considering how foraging areas and reliance on specific oceanographic conditions change over time when seeking to identify important marine areas for seabirds.
This work was supported by the National Environment Research Council (award number NE/I528369/1) and the Royal Society for the Protection of Birds through a CASE studentship to the University of Glasgow.
2014-09-01T00:00:00ZRobertson, G. S.Bolton, M.Grecian, W. J.Monaghan, P.While seabird conservation efforts have largely focused on protection from threats at the colony (e.g. reducing disturbance and predation), attention is increasingly being given to implementing protection measures for foraging areas at sea. For this to be effective, important foraging areas must be identified. Although numerous studies have examined seabird foraging behaviour, information is still lacking on the variability in area utilisation within and among breeding seasons. GPS devices were attached to adult black-legged kittiwakes breeding at an expanding North Sea colony (55°20′N, 1°32′W) during both incubation and chick-rearing in 2012 and during chick-rearing in 2011, to determine whether foraging areas remained consistent and to identify the oceanographic characteristics of areas used for foraging. The type and size of prey items consumed at different stages of the breeding cycle was also examined. During incubation (April-May 2012), kittiwakes foraged substantially further from the colony and fed on larger sandeels than when feeding chicks, and there was significant inter-annual variation in foraging areas used during the chick-rearing period (June-July 2011 and 2012). Foraging areas were characterised by cooler sea surface temperatures and areas of high chlorophyll a concentration, although association with specific oceanographic features changed within the breeding season and between years. These results emphasise the importance of considering how foraging areas and reliance on specific oceanographic conditions change over time when seeking to identify important marine areas for seabirds.Contrasting migratory responses of two closely-related seabirds to long-term climate changeGrecian, W. JamesTaylor, Graeme A.Loh, GraemeMcGill, Rona A. R.Miskelly, Colin M.Phillips, Richard A.Thompson, David R.Furness, Robert W.https://hdl.handle.net/10023/107262023-04-25T23:48:52Z2016-11-09T00:00:00ZMany marine predators migrate between breeding and non-breeding areas to target resources that are seasonal but spatio-temporally predictable, and so are vulnerable to climate-induced changes in prey phenology and abundance. In the Southern Ocean, small petrels are major consumers, but perturbations in the ecosystem through ocean warming are altering food-web structure and have been linked to poleward shifts in the distribution of their cold-water zooplankton prey. In this study, we focused on 2 small congeneric petrels: the broad-billed prion Pachyptila vittata and the Antarctic prion P. desolata. Both are planktivorous, but the broad-billed prion specialises in feeding on large copepods. We investigated historical trends in non-breeding distribution by analysing feather stable isotope ratios from a time-series dating back to 1926, and examined contemporary non-breeding distributions of broad-billed prions tracked using miniaturised geolocation-immersion loggers. After controlling temporally for the Suess effect, we found that the δ13C signatures of Antarctic prions, but not broad-billed prions, declined during the study period. This suggests a southward shift in Antarctic prion non-breeding distribution over the last century. Both species exhibited significant declines in δ15N during the same period, indicative of long-term decreases in marine productivity in their moulting areas, or changes in the trophic structure of prey communities. Tracked broad-billed prions migrated ca. 1000 km to an area east of the breeding colony where the Louisville seamount chain bisects the subtropical front. Topographically driven upwellings are stable and predictable features and may be crucial in aggregating plankton. Targeting seamounts could therefore mitigate the impact of climate-induced prey shifts by providing refugia for the broad-billed prion.
2016-11-09T00:00:00ZGrecian, W. JamesTaylor, Graeme A.Loh, GraemeMcGill, Rona A. R.Miskelly, Colin M.Phillips, Richard A.Thompson, David R.Furness, Robert W.Many marine predators migrate between breeding and non-breeding areas to target resources that are seasonal but spatio-temporally predictable, and so are vulnerable to climate-induced changes in prey phenology and abundance. In the Southern Ocean, small petrels are major consumers, but perturbations in the ecosystem through ocean warming are altering food-web structure and have been linked to poleward shifts in the distribution of their cold-water zooplankton prey. In this study, we focused on 2 small congeneric petrels: the broad-billed prion Pachyptila vittata and the Antarctic prion P. desolata. Both are planktivorous, but the broad-billed prion specialises in feeding on large copepods. We investigated historical trends in non-breeding distribution by analysing feather stable isotope ratios from a time-series dating back to 1926, and examined contemporary non-breeding distributions of broad-billed prions tracked using miniaturised geolocation-immersion loggers. After controlling temporally for the Suess effect, we found that the δ13C signatures of Antarctic prions, but not broad-billed prions, declined during the study period. This suggests a southward shift in Antarctic prion non-breeding distribution over the last century. Both species exhibited significant declines in δ15N during the same period, indicative of long-term decreases in marine productivity in their moulting areas, or changes in the trophic structure of prey communities. Tracked broad-billed prions migrated ca. 1000 km to an area east of the breeding colony where the Louisville seamount chain bisects the subtropical front. Topographically driven upwellings are stable and predictable features and may be crucial in aggregating plankton. Targeting seamounts could therefore mitigate the impact of climate-induced prey shifts by providing refugia for the broad-billed prion.Structure and function of heparan sulfate degrading sulfatasesGriffin, Laura Susanhttps://hdl.handle.net/10023/103592017-02-24T10:28:06Z2017-06-21T00:00:00Z2017-06-21T00:00:00ZGriffin, Laura SusanA behavioural and genomic approach to studying the evolution of reproductive isolation : a contact zone between closely related field crickets in the genus TeleogryllusMoran, Peterhttps://hdl.handle.net/10023/102602019-03-29T10:42:57Z2017-06-21T00:00:00ZWhat processes contribute to the evolution of reproductive isolation and the coexistence of interfertile species in the same habitat? This thesis investigates the relative roles of species interactions and intraspecific processes in contributing to reproductive isolation. I combine behavioural and genomic approaches to test hypotheses about what mechanisms maintain the general species boundary between two closely related field cricket species: Teleogryllus oceanicus and T. commodus. These species are a classic study system for sexual communication and readily hybridize in the laboratory, however little is known about species interactions in sympatric populations. I examine patterns of geographic variation in two key sexual traits: calling song and cuticular hydrocarbons (CHCs), and the geographic distribution of genetic variation across a broad sample of allopatric and sympatric populations. I test whether X chromosomes play a pronounced role in population divergence and reproductive isolation. Using close range mating trials and hybridization experiments I identify numerous pre-mating and post-mating barriers between the species. The results indicate that the species are currently reproductively isolated and the pattern of population differentiation does not strongly support contemporary species interactions contributing to phenotypic diversity. Numerous barriers exist between the species, in particular hybrid females are sterile in both cross directions, while hybrid males are relatively fertile. This provides a rare exception to Haldane’s rule which is central to many genetic theories of speciation. Established theory predicts that X chromosomes should play a pronounced role in the evolution of both pre- and postzygotic barriers. Contrary to this, I found no evidence that X chromosomes contribute to hybrid female sterility. Moreover, X-linked loci exhibited an unexpected pattern of reduced population differentiation within species, but increased species divergence compared to autosomal loci, which may indicate selective sweeps or sex-biased processes. Taken together, the results suggest that the causes and consequences of X chromosome evolution, in particular among XO taxa, may contradict some of the established theories.
2017-06-21T00:00:00ZMoran, PeterWhat processes contribute to the evolution of reproductive isolation and the coexistence of interfertile species in the same habitat? This thesis investigates the relative roles of species interactions and intraspecific processes in contributing to reproductive isolation. I combine behavioural and genomic approaches to test hypotheses about what mechanisms maintain the general species boundary between two closely related field cricket species: Teleogryllus oceanicus and T. commodus. These species are a classic study system for sexual communication and readily hybridize in the laboratory, however little is known about species interactions in sympatric populations. I examine patterns of geographic variation in two key sexual traits: calling song and cuticular hydrocarbons (CHCs), and the geographic distribution of genetic variation across a broad sample of allopatric and sympatric populations. I test whether X chromosomes play a pronounced role in population divergence and reproductive isolation. Using close range mating trials and hybridization experiments I identify numerous pre-mating and post-mating barriers between the species. The results indicate that the species are currently reproductively isolated and the pattern of population differentiation does not strongly support contemporary species interactions contributing to phenotypic diversity. Numerous barriers exist between the species, in particular hybrid females are sterile in both cross directions, while hybrid males are relatively fertile. This provides a rare exception to Haldane’s rule which is central to many genetic theories of speciation. Established theory predicts that X chromosomes should play a pronounced role in the evolution of both pre- and postzygotic barriers. Contrary to this, I found no evidence that X chromosomes contribute to hybrid female sterility. Moreover, X-linked loci exhibited an unexpected pattern of reduced population differentiation within species, but increased species divergence compared to autosomal loci, which may indicate selective sweeps or sex-biased processes. Taken together, the results suggest that the causes and consequences of X chromosome evolution, in particular among XO taxa, may contradict some of the established theories.Structural and mechanistic studies of specific carbohydrate processing enzymesPengelly, Robert Josephhttps://hdl.handle.net/10023/102542017-02-09T10:24:15Z2017-06-21T00:00:00Z2017-06-21T00:00:00ZPengelly, Robert JosephThe impact of World Bank and International Monetary Fund programme lending on health care delivery, health conditions and health status in sub-Saharan Africa, 1980 to 1992Evans, Christopher J.https://hdl.handle.net/10023/100132019-03-29T15:53:15Z1996-07-01T00:00:00ZThe World Bank and the International Monetary Fund have been active in Africa for
several decades. In the early 1980s both institutions expanded the role that they play
in the restructuring of African economies through the introduction of structural
adjustment loans. These programme loans sought to provide the basis for sustainable
economic expansion following a period of near economic collapse in the region. In
the case of the Fund, public expenditure reducing and expenditure switching policies
were encouraged. The Bank, also, was active in these areas and focused on long-term
measures to restore efficiency to the ailing economies. These policies, although not
novel, were implemented on a large scale were perceived to have a pervasive
influence on the economic and social performance of African countries.
It was theorised by some that such programme lending would have a long-run
beneficial impact on social development. However, other authors, observers and
researchers have criticised the activities of the Bretton Woods institutions. First, the
loans have been heavily criticised in the past for the supposedly heavy handed nature
that Bank and Fund staff use in implementing their programmes. The main idea is
that the institutions have too much leverage when bargaining with African
governments to undertake reforms. Second, it has been said that the use of
programme loans will have adverse consequences for national welfare. UNICEF, the
main critic, has pointed out, and provided evidence, to indicate that vulnerable groups
in society may suffer under adjustment schemes.
This thesis looks at the areas of macroeconomic reforms and the impact that
they may have on one part of the social area: the health sector. The thesis examines
the pre-adjustment situation in Sub Saharan Africa and reviews the role and the tools
that the Bank and the Fund have at their disposal to tackle economic problems. The
thesis then moves on to explore the linkages between these policy weapons and
changes in health care development. In order to fully understand the implications for
Africa considerable attention is devoted to exploring the health problems that the
region faces and the health care delivery systems and health conditions that are
prevalent in many of the countries. The last part of the thesis provides an aggregate
study and a case study analysis of the impact of adjustment in Africa. Although, it is
determined that the impact, overall, has not been unfavourable, recommendations for
the future design of adjustment programmes is offered in the conclusion.
1996-07-01T00:00:00ZEvans, Christopher J.The World Bank and the International Monetary Fund have been active in Africa for
several decades. In the early 1980s both institutions expanded the role that they play
in the restructuring of African economies through the introduction of structural
adjustment loans. These programme loans sought to provide the basis for sustainable
economic expansion following a period of near economic collapse in the region. In
the case of the Fund, public expenditure reducing and expenditure switching policies
were encouraged. The Bank, also, was active in these areas and focused on long-term
measures to restore efficiency to the ailing economies. These policies, although not
novel, were implemented on a large scale were perceived to have a pervasive
influence on the economic and social performance of African countries.
It was theorised by some that such programme lending would have a long-run
beneficial impact on social development. However, other authors, observers and
researchers have criticised the activities of the Bretton Woods institutions. First, the
loans have been heavily criticised in the past for the supposedly heavy handed nature
that Bank and Fund staff use in implementing their programmes. The main idea is
that the institutions have too much leverage when bargaining with African
governments to undertake reforms. Second, it has been said that the use of
programme loans will have adverse consequences for national welfare. UNICEF, the
main critic, has pointed out, and provided evidence, to indicate that vulnerable groups
in society may suffer under adjustment schemes.
This thesis looks at the areas of macroeconomic reforms and the impact that
they may have on one part of the social area: the health sector. The thesis examines
the pre-adjustment situation in Sub Saharan Africa and reviews the role and the tools
that the Bank and the Fund have at their disposal to tackle economic problems. The
thesis then moves on to explore the linkages between these policy weapons and
changes in health care development. In order to fully understand the implications for
Africa considerable attention is devoted to exploring the health problems that the
region faces and the health care delivery systems and health conditions that are
prevalent in many of the countries. The last part of the thesis provides an aggregate
study and a case study analysis of the impact of adjustment in Africa. Although, it is
determined that the impact, overall, has not been unfavourable, recommendations for
the future design of adjustment programmes is offered in the conclusion.Timing properties and correctness for structured parallel programs on x86-64 multicoresHammond, KevinBrown, Christopher MarkSarkar, Susmithttps://hdl.handle.net/10023/99352023-01-03T11:30:13Z2016-01-01T00:00:00ZThis paper determines correctness and timing properties for structured parallel programs on x86-64 multicores. Multicore architectures are increasingly common, but real architectures have unpredictable timing properties, and even correctness is not obvious above the relaxed-memory concurrency models that are enforced by commonly-used hardware. This paper takes a rigorous approach to correctness and timing properties, examining common locking protocols from first principles, and extending this through queues to structured parallel constructs. We prove functional correctness and derive simple timing models, and both extend for the first time from low-level primitives to high-level parallel patterns. Our derived high-level timing models for structured parallel programs allow us to accurately predict upper bounds on program execution times on x86-64 multicores.
2016-01-01T00:00:00ZHammond, KevinBrown, Christopher MarkSarkar, SusmitThis paper determines correctness and timing properties for structured parallel programs on x86-64 multicores. Multicore architectures are increasingly common, but real architectures have unpredictable timing properties, and even correctness is not obvious above the relaxed-memory concurrency models that are enforced by commonly-used hardware. This paper takes a rigorous approach to correctness and timing properties, examining common locking protocols from first principles, and extending this through queues to structured parallel constructs. We prove functional correctness and derive simple timing models, and both extend for the first time from low-level primitives to high-level parallel patterns. Our derived high-level timing models for structured parallel programs allow us to accurately predict upper bounds on program execution times on x86-64 multicores.Orientation of OLED emitter molecules revealed by XRDMurawski, CarolineElschner, ChrisLenk, SimoneReineke, SebastianGather, Malte Christianhttps://hdl.handle.net/10023/98622023-04-19T00:41:20Z2016-11-14T00:00:00ZThin films of the phosphorescent emitters Ir(ppy)3 and Ir(ppy)2(acac) are investigated by GIXRD and GIWAXS. Both molecules form crystalline grains and exhibit a preferred orientation that is pertained even when doped into a host.
We thank Dr. Lutz Wilde at Fraunhofer IPMS, Center Nanoelectronic Technologies, Dresden for carrying out the GIXRD measurements. CM acknowledges funding by the Graduate Academy of the TU Dresden and by the European Commission through a Marie Skłodowska Curie individual fellowship (703387).
2016-11-14T00:00:00ZMurawski, CarolineElschner, ChrisLenk, SimoneReineke, SebastianGather, Malte ChristianThin films of the phosphorescent emitters Ir(ppy)3 and Ir(ppy)2(acac) are investigated by GIXRD and GIWAXS. Both molecules form crystalline grains and exhibit a preferred orientation that is pertained even when doped into a host.Organic light-emitting diodes for optogenetic stimulation of Drosophila larvaeMurawski, CarolineMorton, AndrewSamuel, Ifor David WilliamPulver, StefanGather, Malte Christianhttps://hdl.handle.net/10023/98612024-03-02T00:39:41Z2016-11-14T00:00:00ZOptogenetics is an emerging method in biology that enables controlling neurons with light. We use organic light-emitting diodes to stimulate neurons in Drosophila larvae and investigate subsequent behavioral changes at different light intensities.
We are grateful for financial support from the Scottish Funding Council (through SUPA), Human Frontier Science Program (RGY0074/2013), Wellcome Trust Institutional Strategic Support Fund St Andrews, the RS Macdonald Charitable Trust, and EPSRC via grant EP/J01771X/1. CM acknowledges funding by the European Commission through a Marie Skłodowska Curie individual fellowship (703387).
2016-11-14T00:00:00ZMurawski, CarolineMorton, AndrewSamuel, Ifor David WilliamPulver, StefanGather, Malte ChristianOptogenetics is an emerging method in biology that enables controlling neurons with light. We use organic light-emitting diodes to stimulate neurons in Drosophila larvae and investigate subsequent behavioral changes at different light intensities.A critical analysis of the role of the internet in the preparation and planning of acts of terrorismHolbrook, Donaldhttps://hdl.handle.net/10023/94862023-04-25T23:41:59Z2015-09-01T00:00:00ZThe purpose of this paper is to offer a critical assessment of the way in which the internet and online material features as part of the process individuals embark on to plan acts of terrorism. The paper begins by evaluating concepts used to describe the role of the internet in the context of terrorism and political violence before analysing a single case study in detail in order to explore particular nuances that emerge which shed light on the relationship between perpetrator on the one hand and online content and behaviour on the other. The case study, in turn, is developed into a conceptual appraisal of terrorist use of the internet. The paper concludes by exploring the important distinction between the “theoretical” application of online learning as set out in terrorist propaganda and the hurdles that individuals face in practice.
2015-09-01T00:00:00ZHolbrook, DonaldThe purpose of this paper is to offer a critical assessment of the way in which the internet and online material features as part of the process individuals embark on to plan acts of terrorism. The paper begins by evaluating concepts used to describe the role of the internet in the context of terrorism and political violence before analysing a single case study in detail in order to explore particular nuances that emerge which shed light on the relationship between perpetrator on the one hand and online content and behaviour on the other. The case study, in turn, is developed into a conceptual appraisal of terrorist use of the internet. The paper concludes by exploring the important distinction between the “theoretical” application of online learning as set out in terrorist propaganda and the hurdles that individuals face in practice.Magna CartaHolt, Jameshttps://hdl.handle.net/10023/94442024-03-24T00:46:42Z2015-05-01T00:00:00Z3rd edition of classic work, with new introduction and additional material
2015-05-01T00:00:00ZHolt, James3rd edition of classic work, with new introduction and additional materialA novel archaeal DNA repair factor that acts with the UvrABC system to repair mitomycin C-induced DNA damage in a PCNA-dependent mannerGiroux, XavierMacNeill, Stuarthttps://hdl.handle.net/10023/94242023-04-18T10:02:29Z2015-12-22T00:00:00ZThe sliding clamp PCNA plays a vital role in a number of DNA repair pathways in eukaryotes and archaea by acting as a stable platform onto which other essential protein factors assemble. Many of these proteins interact with PCNA via a short peptide sequence known as a PIP (PCNA interacting protein) motif. Here we describe the identification and functional analysis of a novel PCNA interacting protein NreA that is conserved in the archaea and which has a PIP motif at its C-terminus. Using the genetically tractable euryarchaeon Haloferax volcanii as a model system, we show that the NreA protein is not required for cell viability but that loss of NreA (or replacement of the wild-type protein with a truncated version lacking the C-terminal PIP motif) results in an increased sensitivity to the DNA damaging agent mitomycin C (MMC) that correlates with delayed repair of MMC-induced chromosomal DNA damage monitored by pulsed-field gel electrophoresis (PFGE). Genetic epistasis analysis in Hfx. volcanii suggests that NreA works together with the UvrABC proteins in repairing DNA damage resulting from exposure to MMC. The wide distribution of NreA family members implies an important role for the protein in DNA damage repair in all archaeal lineages.
This work was supported by the USAF Office of Scientific Research under award number FA9550-10-1-0421.
2015-12-22T00:00:00ZGiroux, XavierMacNeill, StuartThe sliding clamp PCNA plays a vital role in a number of DNA repair pathways in eukaryotes and archaea by acting as a stable platform onto which other essential protein factors assemble. Many of these proteins interact with PCNA via a short peptide sequence known as a PIP (PCNA interacting protein) motif. Here we describe the identification and functional analysis of a novel PCNA interacting protein NreA that is conserved in the archaea and which has a PIP motif at its C-terminus. Using the genetically tractable euryarchaeon Haloferax volcanii as a model system, we show that the NreA protein is not required for cell viability but that loss of NreA (or replacement of the wild-type protein with a truncated version lacking the C-terminal PIP motif) results in an increased sensitivity to the DNA damaging agent mitomycin C (MMC) that correlates with delayed repair of MMC-induced chromosomal DNA damage monitored by pulsed-field gel electrophoresis (PFGE). Genetic epistasis analysis in Hfx. volcanii suggests that NreA works together with the UvrABC proteins in repairing DNA damage resulting from exposure to MMC. The wide distribution of NreA family members implies an important role for the protein in DNA damage repair in all archaeal lineages.Hope unexpected : an account of the Lebanese Christians' encounter with Syrian refugeesGourlay, Marjorie G.https://hdl.handle.net/10023/93302019-03-29T13:43:26Z2016-06-01T00:00:00ZThis research explores the place of the Church in Lebanon and its response to
the present Syrian refugee crisis. By means of interviews with a small number of
Christian leaders in Beirut, this study narrates a current reality from a positive
perspective and offers preliminary steps towards articulating a Christian response to
the present political turmoil. Although historically and physically divided, the
Lebanese churches are united in their readiness to respond with hospitality. In
attending to basic human needs, offering water, food and shelter to those who until
recently were considered enemies, Lebanese Christians have a powerful message of
forgiveness and healing. Prompted by both Arab and Christian traditions, the
Lebanese Christians are choosing hospitality and, in doing so, are finding unexpected
hope. This study argues that the Lebanese Church as a whole can be seen as a
positive contributor to the common good in both Lebanon and the Middle East, and as
an example to western churches as they engage with the current migration crisis in
Europe.
2016-06-01T00:00:00ZGourlay, Marjorie G.This research explores the place of the Church in Lebanon and its response to
the present Syrian refugee crisis. By means of interviews with a small number of
Christian leaders in Beirut, this study narrates a current reality from a positive
perspective and offers preliminary steps towards articulating a Christian response to
the present political turmoil. Although historically and physically divided, the
Lebanese churches are united in their readiness to respond with hospitality. In
attending to basic human needs, offering water, food and shelter to those who until
recently were considered enemies, Lebanese Christians have a powerful message of
forgiveness and healing. Prompted by both Arab and Christian traditions, the
Lebanese Christians are choosing hospitality and, in doing so, are finding unexpected
hope. This study argues that the Lebanese Church as a whole can be seen as a
positive contributor to the common good in both Lebanon and the Middle East, and as
an example to western churches as they engage with the current migration crisis in
Europe.Lipidomic analysis of fats and oils – a lot more than just omega-3Smith, Terry Khttps://hdl.handle.net/10023/92432023-04-18T10:00:30Z2015-01-01T00:00:00ZEdible oils and fats are among the most abundant cooking ingredients in the world, and are an important part of a healthy balanced diet, especially if they are high in omega-6 and omega-3 polyunsaturated fatty acids. Rather than just the total fatty acid compositions, the analysis of individual lipid species within these oils and fats has become increasingly important. Within the past decade several mass spectrometric lipidomics methods have been adapted and applied to the analysis of edible oils and fats. These methodologies are vital for the analysis of a plethora of lipid species that will be important for numerous health and sustainability issues in the future.
TKS research is supported in part by the Wellcome Trust, SUSLA, BBSRC and the European Community’s Seventh Framework Programme under grant agreement No. 602773 (Project KINDReD)
2015-01-01T00:00:00ZSmith, Terry KEdible oils and fats are among the most abundant cooking ingredients in the world, and are an important part of a healthy balanced diet, especially if they are high in omega-6 and omega-3 polyunsaturated fatty acids. Rather than just the total fatty acid compositions, the analysis of individual lipid species within these oils and fats has become increasingly important. Within the past decade several mass spectrometric lipidomics methods have been adapted and applied to the analysis of edible oils and fats. These methodologies are vital for the analysis of a plethora of lipid species that will be important for numerous health and sustainability issues in the future.The Group of 7 and international terrorism : the snowball effect that never materializedBlumenau, Bernhardhttps://hdl.handle.net/10023/91832023-04-25T23:43:19Z2016-04-01T00:00:00ZThe article looks at the Group of 7 (G7) efforts to fight international terrorism in the 1970s and early 1980s. It examines the G7 statement against hijacking, the Bonn Declaration of 1978, and assesses how the G7 dealt with it after the adoption of the Declaration. The article illustrates that after a short phase of enthusiasm just after the Declaration’s adoption, the G7 members’ united front against terrorism quickly eroded. The G7 failed to secure support from other countries and realized the economic and political costs that the implementation of the Declaration could produce. Therefore, it was pushed to the backburner. The Declaration was largely of symbolic and only of very little practical importance. Yet, it still pointed to the new approach of the G7 – present until today – that moved away from a purely economic agenda towards a progressively more political one.
2016-04-01T00:00:00ZBlumenau, BernhardThe article looks at the Group of 7 (G7) efforts to fight international terrorism in the 1970s and early 1980s. It examines the G7 statement against hijacking, the Bonn Declaration of 1978, and assesses how the G7 dealt with it after the adoption of the Declaration. The article illustrates that after a short phase of enthusiasm just after the Declaration’s adoption, the G7 members’ united front against terrorism quickly eroded. The G7 failed to secure support from other countries and realized the economic and political costs that the implementation of the Declaration could produce. Therefore, it was pushed to the backburner. The Declaration was largely of symbolic and only of very little practical importance. Yet, it still pointed to the new approach of the G7 – present until today – that moved away from a purely economic agenda towards a progressively more political one.What is a schema? : Invited contribution to symposium on Philippe DescolaToren, Christinahttps://hdl.handle.net/10023/91652023-04-18T10:07:31Z2014-01-01T00:00:00ZComment on Descola, Philippe. 2013. Beyond nature and culture. Translated by Janet Lloyd with a foreword by Marshall Sahlins. Chicago: University of Chicago Press.
2014-01-01T00:00:00ZToren, ChristinaComment on Descola, Philippe. 2013. Beyond nature and culture. Translated by Janet Lloyd with a foreword by Marshall Sahlins. Chicago: University of Chicago Press.The Grail of original meaning : uses of the past in American constitutional theoryKidd, Colin Craighttps://hdl.handle.net/10023/90812023-04-18T10:11:07Z2016-12-01T00:00:00ZOriginalist jurisprudence, which enjoins a faithful adherence to the values enshrined in the late eighteenth-century Constitution, has become a prominent feature of contemporary American conservatism. Recovering the original meaning of the Constitution is far from straightforward, and raises major issues of historical interpretation. How far do the assumed historical underpinnings of originalist interpretation mesh with the findings of academic historians? To what extent has the conservative invocation of the Founding Fathers obscured a lost American Enlightenment? Nor is ‘tradition’ in American Constitutional law an unproblematic matter. How far does a desire to restore the original meaning of the Constitution ignore the role of ‘stare decisis’ (precedent) in America's common law heritage? It transpires, moreover, that the various schemes of historical interpretation in American Constitutional jurisprudence do not map easily onto a simple liberal–conservative divide.
2016-12-01T00:00:00ZKidd, Colin CraigOriginalist jurisprudence, which enjoins a faithful adherence to the values enshrined in the late eighteenth-century Constitution, has become a prominent feature of contemporary American conservatism. Recovering the original meaning of the Constitution is far from straightforward, and raises major issues of historical interpretation. How far do the assumed historical underpinnings of originalist interpretation mesh with the findings of academic historians? To what extent has the conservative invocation of the Founding Fathers obscured a lost American Enlightenment? Nor is ‘tradition’ in American Constitutional law an unproblematic matter. How far does a desire to restore the original meaning of the Constitution ignore the role of ‘stare decisis’ (precedent) in America's common law heritage? It transpires, moreover, that the various schemes of historical interpretation in American Constitutional jurisprudence do not map easily onto a simple liberal–conservative divide.Shared political responsibiiltyLang, Anthonyhttps://hdl.handle.net/10023/90772023-04-26T00:23:57Z2015-10-01T00:00:00ZThis chapter explores the nature of political responsibilty in relation to climate change. It argues that rather than identify specific agents responsible for climate change - an approach that dominates legal and moral theory - a political responsibility framework provides ways of thinking about global dilemmas in terms of political actions that we may undertake together. It draws on the theoretical notion of 'shared responsibility' to develop this concept.
2015-10-01T00:00:00ZLang, AnthonyThis chapter explores the nature of political responsibilty in relation to climate change. It argues that rather than identify specific agents responsible for climate change - an approach that dominates legal and moral theory - a political responsibility framework provides ways of thinking about global dilemmas in terms of political actions that we may undertake together. It draws on the theoretical notion of 'shared responsibility' to develop this concept.¿Es eficaz el terrorismo? Consideraciones, problemas y marco de investigación futuraEnglish, Richardhttps://hdl.handle.net/10023/90092024-02-24T00:42:25Z2016-04-01T00:00:00ZFor both intellectual and practical reasons, the question "Does terrorism work?'' is vital. And yet it has largely been eclipsed by other debates within the scholarly literature on terrorism. This article considers some of the recent contributions to the emerging discussion of the question. It then outlines some of the problems inherent in the academic debate that has taken place thus far on the subject, and sketches a framework for making future scholarship in this area more inclusive, systematic and dialogically fruitful than it has been to date.
2016-04-01T00:00:00ZEnglish, RichardFor both intellectual and practical reasons, the question "Does terrorism work?'' is vital. And yet it has largely been eclipsed by other debates within the scholarly literature on terrorism. This article considers some of the recent contributions to the emerging discussion of the question. It then outlines some of the problems inherent in the academic debate that has taken place thus far on the subject, and sketches a framework for making future scholarship in this area more inclusive, systematic and dialogically fruitful than it has been to date.Taqizadeh and European civilisationAnsari, Ali Massoudhttps://hdl.handle.net/10023/89472023-04-18T10:08:05Z2017-07-13T00:00:00ZThe leading Iranian intellectual and nationalist Hasan Taqizadeh has been roundly condemned by posterity for his call to Iranians to embrace European civilisation in its entirety without qualification or compromise. Taqizadeh himself later conceded that the form of words he had used were injudicious, but he added that his intention had been to galvanise Iranians out of their self-destructive political stupor and it remains a reality that many of Taqizadeh's contemporaries were supportive of his call to arms. This paper reassesses Taqizadeh's position in the context of his historical and intellectual environment, which it is argued drew heavily from a “Whig” reading of the Enlightenment progress. It shows that Taqizadeh was not alone in drawing on this narrative while maintaining an important distinction between the positive aspects of British political thought and the shortcomings of British policy.
2017-07-13T00:00:00ZAnsari, Ali MassoudThe leading Iranian intellectual and nationalist Hasan Taqizadeh has been roundly condemned by posterity for his call to Iranians to embrace European civilisation in its entirety without qualification or compromise. Taqizadeh himself later conceded that the form of words he had used were injudicious, but he added that his intention had been to galvanise Iranians out of their self-destructive political stupor and it remains a reality that many of Taqizadeh's contemporaries were supportive of his call to arms. This paper reassesses Taqizadeh's position in the context of his historical and intellectual environment, which it is argued drew heavily from a “Whig” reading of the Enlightenment progress. It shows that Taqizadeh was not alone in drawing on this narrative while maintaining an important distinction between the positive aspects of British political thought and the shortcomings of British policy.Spines of the thistle : the popular constituency of the Jacobite Rising in 1745-6Layne, Darren S.https://hdl.handle.net/10023/88682019-04-01T11:11:08Z2016-04-19T00:00:00ZThis thesis examines the social record of popular Jacobitism during the 1745 Rising as expressed through its plebeian constituency. Such an assessment fills in the gaps largely ignored by scholars of the Jacobite period, who instead tend to concentrate upon the elites and the political and doctrinal ideologies espoused by influential gentry. Using a purpose-built database to compile and analyse a large number of resources including lists of prisoners, trial records, muster rolls, and government papers, a prosopographical survey of over 15,000 persona entries is presented. The study looks at four thematic aspects of popular Jacobitism, which describe motivation, constituency, recruitment, and consequences. These combine to provide a social profile of the ‘lesser sort’ of those persons involved in rebellion against the Hanoverian government, whether martial or civilian. The results suggest that practicality was a major influence in drawing the common people into civil war, and that the ideological tenets of Jacobitism, much diluted by 1745, took a backseat to issues of necessity. Widespread ambivalence to the political climate made harsh recruiting methods necessary, and rampant desertion reinforced that need until the army’s defeat at Culloden. Both the willing and unwilling supporters of Charles Edward Stuart’s landing in Scotland represented local, national, and international interests and stretched across class divides. Civilians contributed to the effort along with the soldiers, but limited martial support both domestic and foreign was insufficient to sustain the Stuart-sanctioned coup and the exiled dynasty’s hopes for a subsequent restoration. Understanding that weak punitive measures after 1715 enabled yet another rising thirty years later, the government’s response after Culloden was swift and brutal. Though its campaigns of containment and suppression strained the resources of the judicial system, effective punishment was seen as a necessity, dominating British policy even as the state was involved in a larger war on the Continent. This thesis demonstrates that plebeians used by the Jacobite elites were ill-equipped to support the strategies of the cause, yet they ultimately bore the brunt of the reparations for treasonous expressions, however questionable their commitment may have been.
2016-04-19T00:00:00ZLayne, Darren S.This thesis examines the social record of popular Jacobitism during the 1745 Rising as expressed through its plebeian constituency. Such an assessment fills in the gaps largely ignored by scholars of the Jacobite period, who instead tend to concentrate upon the elites and the political and doctrinal ideologies espoused by influential gentry. Using a purpose-built database to compile and analyse a large number of resources including lists of prisoners, trial records, muster rolls, and government papers, a prosopographical survey of over 15,000 persona entries is presented. The study looks at four thematic aspects of popular Jacobitism, which describe motivation, constituency, recruitment, and consequences. These combine to provide a social profile of the ‘lesser sort’ of those persons involved in rebellion against the Hanoverian government, whether martial or civilian. The results suggest that practicality was a major influence in drawing the common people into civil war, and that the ideological tenets of Jacobitism, much diluted by 1745, took a backseat to issues of necessity. Widespread ambivalence to the political climate made harsh recruiting methods necessary, and rampant desertion reinforced that need until the army’s defeat at Culloden. Both the willing and unwilling supporters of Charles Edward Stuart’s landing in Scotland represented local, national, and international interests and stretched across class divides. Civilians contributed to the effort along with the soldiers, but limited martial support both domestic and foreign was insufficient to sustain the Stuart-sanctioned coup and the exiled dynasty’s hopes for a subsequent restoration. Understanding that weak punitive measures after 1715 enabled yet another rising thirty years later, the government’s response after Culloden was swift and brutal. Though its campaigns of containment and suppression strained the resources of the judicial system, effective punishment was seen as a necessity, dominating British policy even as the state was involved in a larger war on the Continent. This thesis demonstrates that plebeians used by the Jacobite elites were ill-equipped to support the strategies of the cause, yet they ultimately bore the brunt of the reparations for treasonous expressions, however questionable their commitment may have been.Adult dental anxiety : recent assessment approaches and psychological management in a dental practice settingHumphris, Gerald MichaelSpyt, JamesHerbison, AliceKelsey, Tomhttps://hdl.handle.net/10023/88212024-03-06T00:42:38Z2016-05-01T00:00:00ZDental Anxiety of patients is a common feature of the everyday experience of dental practice. This article advocates the use of regular assessment of this psychological construct to assist in patient management. Various tools, such as the Modified Dental Anxiety Scale (MDAS), are available to monitor dental anxiety that are quick to complete and easy to interpret. Patient burden is low. A new mobile phone assessment system (DENTANX) is being developed for distribution. This application and other psychological interventions are being investigated to assist patients to receive dental care routinely.
2016-05-01T00:00:00ZHumphris, Gerald MichaelSpyt, JamesHerbison, AliceKelsey, TomDental Anxiety of patients is a common feature of the everyday experience of dental practice. This article advocates the use of regular assessment of this psychological construct to assist in patient management. Various tools, such as the Modified Dental Anxiety Scale (MDAS), are available to monitor dental anxiety that are quick to complete and easy to interpret. Patient burden is low. A new mobile phone assessment system (DENTANX) is being developed for distribution. This application and other psychological interventions are being investigated to assist patients to receive dental care routinely.A social movement theory typology of militant organisations : contextualising terrorismMarsden, Sarah Victoriahttps://hdl.handle.net/10023/85282023-04-25T23:40:30Z2015-01-01T00:00:00ZTypologies are ubiquitous in terrorism studies, illustrating their continued appeal as a tool to further our understanding of this form of political violence. Despite this, to date, the promise of an empirically derived typology has largely been neglected. In addressing this gap, this article sets out a typology developed from Social Movement Theory. Using a novel statistical technique to derive a three-dimensional framework for categorising militant groups, the typology incorporates both organisational characteristics and the wider political context. The result is a typology defined by three conceptual constructs: political capacity, war-making capacity, and network capacity. Alongside these organisational features, imposing measures of the wider political opportunity structure reveals eight types of militant organisation. To explore the utility of the framework, a preliminary analysis interprets the typology in light of the presence of wider conflict. That a robust relationship is found between the various types and whether groups were operating in peacetime, civil war, or low-intensity conflict, goes some way to demonstrating its utility as an analytical tool. Conclusions draw attention to the importance of contextualising militant groups in their socio-political setting, and the benefits of combining theory alongside empirical analysis to develop robust characterisations of violent organisations.
Date of acceptance 8/8/14
2015-01-01T00:00:00ZMarsden, Sarah VictoriaTypologies are ubiquitous in terrorism studies, illustrating their continued appeal as a tool to further our understanding of this form of political violence. Despite this, to date, the promise of an empirically derived typology has largely been neglected. In addressing this gap, this article sets out a typology developed from Social Movement Theory. Using a novel statistical technique to derive a three-dimensional framework for categorising militant groups, the typology incorporates both organisational characteristics and the wider political context. The result is a typology defined by three conceptual constructs: political capacity, war-making capacity, and network capacity. Alongside these organisational features, imposing measures of the wider political opportunity structure reveals eight types of militant organisation. To explore the utility of the framework, a preliminary analysis interprets the typology in light of the presence of wider conflict. That a robust relationship is found between the various types and whether groups were operating in peacetime, civil war, or low-intensity conflict, goes some way to demonstrating its utility as an analytical tool. Conclusions draw attention to the importance of contextualising militant groups in their socio-political setting, and the benefits of combining theory alongside empirical analysis to develop robust characterisations of violent organisations.The impact of the Security Council on the efficacy of the International Criminal Court and the responsibility to protectHehir, AidanLang, Anthonyhttps://hdl.handle.net/10023/83372024-03-17T00:41:45Z2015-03-01T00:00:00ZThis article argues that the manner in which the Security Council inhibits the consistent application of the Responsibility to Protect (R2P) and International Criminal Court (ICC) referrals reinforces their power in the international order without creating long term peace and stability. The Security Council’s discretionary powers allow it to subjectively determine which situations to address and which lawbreakers to prosecute; this consolidates, and indeed expands, the power of the Security Council in relation to other agents of international law. As a result, international cooperation to protect and promote human rights and punish human rights violators is currently impeded. This article argues that those concerned with the consistent enforcement of international human rights law, and the punishment of human rights violators, must accept the need for reforms to the current international order that would allow a better integration of R2P and the ICC into international law and practice. Our reforms – advanced in the form of general principles taken from legal theory – propose altering the Security Council’s powers and developing new judicial structures to enable the more consistent application of international law
2015-03-01T00:00:00ZHehir, AidanLang, AnthonyThis article argues that the manner in which the Security Council inhibits the consistent application of the Responsibility to Protect (R2P) and International Criminal Court (ICC) referrals reinforces their power in the international order without creating long term peace and stability. The Security Council’s discretionary powers allow it to subjectively determine which situations to address and which lawbreakers to prosecute; this consolidates, and indeed expands, the power of the Security Council in relation to other agents of international law. As a result, international cooperation to protect and promote human rights and punish human rights violators is currently impeded. This article argues that those concerned with the consistent enforcement of international human rights law, and the punishment of human rights violators, must accept the need for reforms to the current international order that would allow a better integration of R2P and the ICC into international law and practice. Our reforms – advanced in the form of general principles taken from legal theory – propose altering the Security Council’s powers and developing new judicial structures to enable the more consistent application of international lawComparative estuarine dynamics : trophic linkages and ecosystem functionKenworthy, Josephhttps://hdl.handle.net/10023/82402023-03-20T14:51:10Z2016-02-01T00:00:00ZEstuarine systems are of crucial importance to the provision of goods and services on a global scale. High human population densities in coastal systems have caused an increasing input of pollutants, of which nutrient pollution is of major concern. Increasingly, these areas are also impacted by physical disturbance, which can originate from anthropogenic sources (e.g. bait digging, shipping) or climate change causing increasingly frequent and intense storms. The individual impacts of such stressors on ecosystems have been investigated however their combined impacts have received less attention. Cumulative impacts of multiple stressors are unpredictable and will likely result in non-additive effects. Further, the effect of local environmental context on multiple stressors is a relatively understudied topic.
Work in this thesis compared the combined impact of nutrient enrichment and physical disturbance in Scotland and Australia, using a series of manipulative field experiments. Results demonstrate that response to stressors is highly context dependent, varying between and within geographic locations. While the background levels of stress may vary, by comparing these two locations it is possible to comment on the adaptations and response that communities within different parts of the world display when subjected to additional stress. This study demonstrates that environmental context must be considered when implementing future management practices.
Further work demonstrated that the impact of multiple stressors varies depending on how the stress is applied –whether stressors are applied simultaneously or whether there is a delay between two stressors. This study was among the first of its kind, assessing the implications of how multiple stressors react with each other given the order and intensity in which stressors were applied. Results demonstrated that systems can become sensitised to stress making them increasingly vulnerable to additional stress. Future research should be focussed on incorporating ecologically relevant scenarios of how stressors will impact estuaries while considering how environmental context will mediate impacts.
2016-02-01T00:00:00ZKenworthy, JosephEstuarine systems are of crucial importance to the provision of goods and services on a global scale. High human population densities in coastal systems have caused an increasing input of pollutants, of which nutrient pollution is of major concern. Increasingly, these areas are also impacted by physical disturbance, which can originate from anthropogenic sources (e.g. bait digging, shipping) or climate change causing increasingly frequent and intense storms. The individual impacts of such stressors on ecosystems have been investigated however their combined impacts have received less attention. Cumulative impacts of multiple stressors are unpredictable and will likely result in non-additive effects. Further, the effect of local environmental context on multiple stressors is a relatively understudied topic.
Work in this thesis compared the combined impact of nutrient enrichment and physical disturbance in Scotland and Australia, using a series of manipulative field experiments. Results demonstrate that response to stressors is highly context dependent, varying between and within geographic locations. While the background levels of stress may vary, by comparing these two locations it is possible to comment on the adaptations and response that communities within different parts of the world display when subjected to additional stress. This study demonstrates that environmental context must be considered when implementing future management practices.
Further work demonstrated that the impact of multiple stressors varies depending on how the stress is applied –whether stressors are applied simultaneously or whether there is a delay between two stressors. This study was among the first of its kind, assessing the implications of how multiple stressors react with each other given the order and intensity in which stressors were applied. Results demonstrated that systems can become sensitised to stress making them increasingly vulnerable to additional stress. Future research should be focussed on incorporating ecologically relevant scenarios of how stressors will impact estuaries while considering how environmental context will mediate impacts.Taking a molecular motor for a spin : helicase mechanism studied by spin labelling and PELDORConstantinescu Aruxandei, DianaPetrovic-Stojanovska, BiljanaSchiemann, OlavNaismith, JimWhite, Malcolm Fhttps://hdl.handle.net/10023/79262023-04-18T10:04:50Z2015-12-10T00:00:00ZThe complex molecular motions central to the functions of helicases have long attracted attention. Protein crystallography has provided transformative insights into these dynamic conformational changes, however important questions about the true nature of helicase configurations during the catalytic cycle remain. Using pulsed EPR (PELDOR or DEER) to measure interdomain distances in solution, we have examined two representative helicases: PcrA from superfamily 1 and XPD from superfamily 2. The data show that PcrA is a dynamic structure with domain movements that correlate with particular functional states, confirming and extending the information gleaned from crystal structures and other techniques. XPD in contrast is shown to be a rigid protein with almost no conformational changes resulting from nucleotide or DNA binding, which is well described by static crystal structures. Our results highlight the complimentary nature of PELDOR to crystallography and the power of its precision in understanding the conformational changes relevant to helicase function.
Welcome Trust programme grant [WT091825MA to M.F.W., J.H.N.]; Wellcome Trust multi-user equipment grant [099149/Z/12/Z]. Royal Society Wolfseon Merit Award (to M.F.W., J.H.N.). Funding for open access charge: Wellcome Trust [WT091825MA].
2015-12-10T00:00:00ZConstantinescu Aruxandei, DianaPetrovic-Stojanovska, BiljanaSchiemann, OlavNaismith, JimWhite, Malcolm FThe complex molecular motions central to the functions of helicases have long attracted attention. Protein crystallography has provided transformative insights into these dynamic conformational changes, however important questions about the true nature of helicase configurations during the catalytic cycle remain. Using pulsed EPR (PELDOR or DEER) to measure interdomain distances in solution, we have examined two representative helicases: PcrA from superfamily 1 and XPD from superfamily 2. The data show that PcrA is a dynamic structure with domain movements that correlate with particular functional states, confirming and extending the information gleaned from crystal structures and other techniques. XPD in contrast is shown to be a rigid protein with almost no conformational changes resulting from nucleotide or DNA binding, which is well described by static crystal structures. Our results highlight the complimentary nature of PELDOR to crystallography and the power of its precision in understanding the conformational changes relevant to helicase function.Truth incarnate : story as sacrament in the mythopoeic thought and fiction of C. S. Lewis and J. R. R. TolkienBuchanan, Travis Walkerhttps://hdl.handle.net/10023/78602021-02-17T10:22:46Z2015-11-30T00:00:00ZThe thesis is organized as two sections of two chapters each: the first section establishes a theoretical framework of a broad and reinvigorated Christian sacramentality within which to situate the second—an investigation of the theories and practice of the mythopoeic art of C. S. Lewis and J. R. R. Tolkien in this sacramental light.
The first chapter acknowledges the thoroughgoing disenchantment of modernity, an effect traced to the vanishing of a sacramental understanding of the world, and then explores the history of the sacramental concept that would seek to be reclaimed and reconceived as a possible means of the re-enchantment of Western culture such as in the recent work of David Brown.
An appreciative critique of Brown’s work is offered in chapter two before proposing an alternative understanding of a distinctly Christian and reinvigorated sacramentality anchored in the Incarnation and operating by Transposition. A notion of sacramental vision is developed from the perceptual basis in its classic definitions, and a sacramental understanding of story is considered from a theological perspective on the infinite generativity of meaning in texts, along with recent theories of affect and affordance.
The second half of the thesis expounds the views of mythopoeia held by Lewis and Tolkien in order to show how they are not only compatible with but lead to a sacramental understanding of story as developed in part one, with mythopoeia affording the recovery of a potentially transformative vision of reality, awakening it into focus in distinctly Christian ways (chapter three). The final chapter demonstrates how their mythopoeic theories are exemplified in their art, examining specific ways Till We Have Faces and The Lord of the Rings afford the recovery of a potentially transformative vision of various themes central to them. In closing it is suggested that such a sacramental understanding of story may contribute to the re-enchantment of Western culture, not to mention the re-mythologization and re-envisaging of Christianity, whose significance in these regards has been hitherto mostly unrecognized.
2015-11-30T00:00:00ZBuchanan, Travis WalkerThe thesis is organized as two sections of two chapters each: the first section establishes a theoretical framework of a broad and reinvigorated Christian sacramentality within which to situate the second—an investigation of the theories and practice of the mythopoeic art of C. S. Lewis and J. R. R. Tolkien in this sacramental light.
The first chapter acknowledges the thoroughgoing disenchantment of modernity, an effect traced to the vanishing of a sacramental understanding of the world, and then explores the history of the sacramental concept that would seek to be reclaimed and reconceived as a possible means of the re-enchantment of Western culture such as in the recent work of David Brown.
An appreciative critique of Brown’s work is offered in chapter two before proposing an alternative understanding of a distinctly Christian and reinvigorated sacramentality anchored in the Incarnation and operating by Transposition. A notion of sacramental vision is developed from the perceptual basis in its classic definitions, and a sacramental understanding of story is considered from a theological perspective on the infinite generativity of meaning in texts, along with recent theories of affect and affordance.
The second half of the thesis expounds the views of mythopoeia held by Lewis and Tolkien in order to show how they are not only compatible with but lead to a sacramental understanding of story as developed in part one, with mythopoeia affording the recovery of a potentially transformative vision of reality, awakening it into focus in distinctly Christian ways (chapter three). The final chapter demonstrates how their mythopoeic theories are exemplified in their art, examining specific ways Till We Have Faces and The Lord of the Rings afford the recovery of a potentially transformative vision of various themes central to them. In closing it is suggested that such a sacramental understanding of story may contribute to the re-enchantment of Western culture, not to mention the re-mythologization and re-envisaging of Christianity, whose significance in these regards has been hitherto mostly unrecognized.Occurrence, distribution and abundance of cetaceans in Onslow Bay, North Carolina, USARead, Andrew, J.Barco, S.Bell, J.Borchers, David LouisBurt, M LouiseCummings, E.W.Dunn, J.Fougeres, J.Hazen, L.Williams-Hodge, L.E.Laura, A-M.McAlarney, R.J.Nilsson, P.Pabst, D.A.Paxton, Charles G. M.Schneider, S.Z.Urian, KimWaples, D.M.McLellan, W.A.https://hdl.handle.net/10023/77722022-04-29T14:30:47Z2014-01-01T00:00:00ZIn this paper the occurrence, distribution and abundance of cetaceans in offshore waters of Onslow Bay, North Carolina, USA is described. Between June 2007 and June 2010 monthly aerial and shipboard line-transect surveys were conducted along ten 74km transects placed perpendicular to the shelf break. In total 42,676km of aerial trackline (218 sightings) and 5,209km of vessel trackline (100 sightings) were observed. Seven species of cetaceans were observed, but the fauna was dominated strongly by common bottlenose and Atlantic spotted dolphins. Both species were present year-round in the study area. Using photo-identification techniques, five bottlenose dolphins and one spotted dolphin were resighted during the three-year period. In general, the abundance of cetaceans in Onslow Bay was low and too few sightings were made to estimate monthly abundances for species other than bottlenose and spotted dolphins. Maximum monthly abundances of bottlenose and spotted dolphins were 4,100 (95% CI: 1,300–9,400) in May 2010 and 6,000 (95% CI: 2,500–17,400) in March 2009, respectively. Bottlenose dolphins were found throughout the study area, although they were encountered most frequently just off the shelf break. In contrast, spotted dolphins exhibited a strong preference for waters over the continental shelf and were not encountered beyond the shelf break.
2014-01-01T00:00:00ZRead, Andrew, J.Barco, S.Bell, J.Borchers, David LouisBurt, M LouiseCummings, E.W.Dunn, J.Fougeres, J.Hazen, L.Williams-Hodge, L.E.Laura, A-M.McAlarney, R.J.Nilsson, P.Pabst, D.A.Paxton, Charles G. M.Schneider, S.Z.Urian, KimWaples, D.M.McLellan, W.A.In this paper the occurrence, distribution and abundance of cetaceans in offshore waters of Onslow Bay, North Carolina, USA is described. Between June 2007 and June 2010 monthly aerial and shipboard line-transect surveys were conducted along ten 74km transects placed perpendicular to the shelf break. In total 42,676km of aerial trackline (218 sightings) and 5,209km of vessel trackline (100 sightings) were observed. Seven species of cetaceans were observed, but the fauna was dominated strongly by common bottlenose and Atlantic spotted dolphins. Both species were present year-round in the study area. Using photo-identification techniques, five bottlenose dolphins and one spotted dolphin were resighted during the three-year period. In general, the abundance of cetaceans in Onslow Bay was low and too few sightings were made to estimate monthly abundances for species other than bottlenose and spotted dolphins. Maximum monthly abundances of bottlenose and spotted dolphins were 4,100 (95% CI: 1,300–9,400) in May 2010 and 6,000 (95% CI: 2,500–17,400) in March 2009, respectively. Bottlenose dolphins were found throughout the study area, although they were encountered most frequently just off the shelf break. In contrast, spotted dolphins exhibited a strong preference for waters over the continental shelf and were not encountered beyond the shelf break.Status and future of research on the behavioural responses of marine mammals to U.S. Navy sonarHarris, Catriona MThomas, Lenhttps://hdl.handle.net/10023/77412023-04-26T00:22:24Z2015-01-01T00:00:00ZA review of the status and future of research into behavioral responses of marine mammals to naval sonar exposure was undertaken to evaluate the return on investment of current US Navy funded programs, identify the data needs and the contributions of current research programs to meeting data needs, and determine the ability to meet outstanding data needs given the current state of technology. As part of this review, a workshop was held from 21-22 April 2015 in Monterey, California. Workshop attendees were key representatives of Navy-funded behavioral response studies, as well as three external reviewers who were selected because of their expertise in animal behavior and behavioral responses to anthropogenic stimuli in the aquatic and terrestrial environments. Prior to the workshop, a questionnaire was circulated to canvass the opinions of members of the scientific community (primarily workshop attendees exclusive of external reviewers) on each of the research approaches taken to address this topic. The workshop was then structured around the questionnaire and responses received, via a series of discussion sessions. Afterwards, each research approach was evaluated independently by the external reviewers. This report presents a synthesis of the evaluations and recommendations of the external reviewers on current and future behavioral response research relevant to naval sonar. All reviewers agreed that excellent progress has been made on this topic and that each of the research approaches has contributed to our understanding of cetacean responses to naval sonar. The report includes specific comments and recommendations of the reviewers relevant to each approach, but also includes suggestions for priority species and a comprehensive list of recommendations for the future of BRS research in general (Tables 1 and 2). In summary it was recommended that BRS research be continued and extended to increase sample sizes and experimental replication, and temporal duration and spatial scale including more research in areas where the animals are presumably more naïve than on the naval ranges. It was noted that future investigations would benefit from combining experimentation and observation to enable linkage of short-term behavioral response to long-term fitness consequences of repeated exposure. Beaked whales were the species group ranked highest in terms of research priority. The importance of baseline studies and longer-term monitoring of animals before and after exposure is emphasized throughout.
2015-01-01T00:00:00ZHarris, Catriona MThomas, LenA review of the status and future of research into behavioral responses of marine mammals to naval sonar exposure was undertaken to evaluate the return on investment of current US Navy funded programs, identify the data needs and the contributions of current research programs to meeting data needs, and determine the ability to meet outstanding data needs given the current state of technology. As part of this review, a workshop was held from 21-22 April 2015 in Monterey, California. Workshop attendees were key representatives of Navy-funded behavioral response studies, as well as three external reviewers who were selected because of their expertise in animal behavior and behavioral responses to anthropogenic stimuli in the aquatic and terrestrial environments. Prior to the workshop, a questionnaire was circulated to canvass the opinions of members of the scientific community (primarily workshop attendees exclusive of external reviewers) on each of the research approaches taken to address this topic. The workshop was then structured around the questionnaire and responses received, via a series of discussion sessions. Afterwards, each research approach was evaluated independently by the external reviewers. This report presents a synthesis of the evaluations and recommendations of the external reviewers on current and future behavioral response research relevant to naval sonar. All reviewers agreed that excellent progress has been made on this topic and that each of the research approaches has contributed to our understanding of cetacean responses to naval sonar. The report includes specific comments and recommendations of the reviewers relevant to each approach, but also includes suggestions for priority species and a comprehensive list of recommendations for the future of BRS research in general (Tables 1 and 2). In summary it was recommended that BRS research be continued and extended to increase sample sizes and experimental replication, and temporal duration and spatial scale including more research in areas where the animals are presumably more naïve than on the naval ranges. It was noted that future investigations would benefit from combining experimentation and observation to enable linkage of short-term behavioral response to long-term fitness consequences of repeated exposure. Beaked whales were the species group ranked highest in terms of research priority. The importance of baseline studies and longer-term monitoring of animals before and after exposure is emphasized throughout.Predicting future European breeding distributions of British seabird species under climate change and unlimited/no dispersal scenariosRussell, Deborah Jill FraserWanless, SarahCollingham, Yvonne C.Huntley, BrianHamer, Keith C.https://hdl.handle.net/10023/77352023-04-25T23:42:21Z2015-11-02T00:00:00ZUnderstanding which traits make species vulnerable to climatic change and predicting future distributions permits conservation efforts to be focused on the most vulnerable species and the most appropriate sites. Here, we combine climate envelope models with predicted bioclimatic data from two emission scenarios leading up to 2100, to predict European breeding distributions of 23 seabird species that currently breed in the British Isles. Assuming unlimited dispersal, some species would be “winners” (increase the size of their range), but over 65% would lose range, some by up to 80%. These “losers” have a high vulnerability to low prey availability, and a northerly distribution meaning they would lack space to move into. Under the worst-case scenario of no dispersal, species are predicted to lose between 25% and 100% of their range, so dispersal ability is a key constraint on future range sizes. More globally, the results indicate, based on foraging ecology, which seabird species are likely to be most affected by climatic change. Neither of the emissions scenarios used in this study is extreme, yet they generate very different predictions for some species, illustrating that even small decreases in emissions could yield large benefits for conservation.
We thank the European Bird Census Council for their data on European seabird distributions. DJFR was supported by NERC UKPopNet.
2015-11-02T00:00:00ZRussell, Deborah Jill FraserWanless, SarahCollingham, Yvonne C.Huntley, BrianHamer, Keith C.Understanding which traits make species vulnerable to climatic change and predicting future distributions permits conservation efforts to be focused on the most vulnerable species and the most appropriate sites. Here, we combine climate envelope models with predicted bioclimatic data from two emission scenarios leading up to 2100, to predict European breeding distributions of 23 seabird species that currently breed in the British Isles. Assuming unlimited dispersal, some species would be “winners” (increase the size of their range), but over 65% would lose range, some by up to 80%. These “losers” have a high vulnerability to low prey availability, and a northerly distribution meaning they would lack space to move into. Under the worst-case scenario of no dispersal, species are predicted to lose between 25% and 100% of their range, so dispersal ability is a key constraint on future range sizes. More globally, the results indicate, based on foraging ecology, which seabird species are likely to be most affected by climatic change. Neither of the emissions scenarios used in this study is extreme, yet they generate very different predictions for some species, illustrating that even small decreases in emissions could yield large benefits for conservation.A description of LATTE outputsMarques, Tiago A.Thomas, Lenhttps://hdl.handle.net/10023/77202023-04-18T09:37:15Z2015-10-30T00:00:00Z2015-10-30T00:00:00ZMarques, Tiago A.Thomas, LenCalculating Time and the End of Time in the Carolingian World, c.740-820Palmer, James Trevorhttps://hdl.handle.net/10023/76002023-04-18T09:43:39Z2011-12-01T00:00:00ZThe hopes and fears associated with the imminence of apocalypse acted as catalysts for a number of significant changes in history. Relevant patterns of behaviour are not, however, always consistent. This paper examines the intellectual contexts for the (sometimes quite real) fear that the world might end or be revolutionised in c. AD800 with the advent of the ‘6000th year of the world’. It argues that, in the Carolingian world, apocalyptic belief was widespread but that it centred on an undefined sense of imminence and a concern for reform, rather than a prioritisation of specific dates. Indeed, building on recent developments in the study of computus (‘time-reckoning’), it is clear that chronological systems such as AD-dating were adapted and discussed – at length – for their relevance to paschal reckonings, not apocalypticism. Evidence here also points towards the relative independence of centres such as Auxerre, St Gall and Monte Cassino, where questions about time could be pursued without much or any central direction from figures such as Charlemagne. It is therefore dangerous to posit a relative ‘consensus of silence’ about apocalypticism to explain the thin evidence; and doubly dangerous to extrapolate from it that, for example, Charlemagne’s imperial coronation occurred on Christmas Day AD800 for undocumented apocalyptic reasons rather than for the pressing political concerns indicated in the sources. Apocalypticism was real in eighth-century Europe, but it was more varied than often thought.
2011-12-01T00:00:00ZPalmer, James TrevorThe hopes and fears associated with the imminence of apocalypse acted as catalysts for a number of significant changes in history. Relevant patterns of behaviour are not, however, always consistent. This paper examines the intellectual contexts for the (sometimes quite real) fear that the world might end or be revolutionised in c. AD800 with the advent of the ‘6000th year of the world’. It argues that, in the Carolingian world, apocalyptic belief was widespread but that it centred on an undefined sense of imminence and a concern for reform, rather than a prioritisation of specific dates. Indeed, building on recent developments in the study of computus (‘time-reckoning’), it is clear that chronological systems such as AD-dating were adapted and discussed – at length – for their relevance to paschal reckonings, not apocalypticism. Evidence here also points towards the relative independence of centres such as Auxerre, St Gall and Monte Cassino, where questions about time could be pursued without much or any central direction from figures such as Charlemagne. It is therefore dangerous to posit a relative ‘consensus of silence’ about apocalypticism to explain the thin evidence; and doubly dangerous to extrapolate from it that, for example, Charlemagne’s imperial coronation occurred on Christmas Day AD800 for undocumented apocalyptic reasons rather than for the pressing political concerns indicated in the sources. Apocalypticism was real in eighth-century Europe, but it was more varied than often thought.Images as proximity sensors : the incidence of conspecific foraging in Antarctic fur sealsHooker, Sascha KateBarychka, TatsianaJessopp, Mark JStaniland, Iain Jhttps://hdl.handle.net/10023/75812023-04-25T23:41:46Z2015-09-29T00:00:00ZBackground: Although there have been recent advances in the development of animal-attached ‘proximity’ tags to remotely record the interactions of multiple individuals, the efficacy of these devices depends on the instrumentation of sufficient animals that subsequently have spatial interactions. Among densely colonial mammals such as fur seals, this remains logistically difficult, and interactions between animals during foraging have not previously been recorded. Results: We collected data on conspecific interactions during diving at sea using still image and video cameras deployed on 23 Antarctic fur seals. Animals carried cameras for a total of 152 days, collecting 38,098 images and 369 movies (total time 7.35 h). Other fur seals were detected in 74% of deployments, with a maximum of five seals seen at one time (n = 122 images, 28 videos). No predators other than conspecifics were observed. Detection was primarily limited by light conditions, since conspecifics were usually further from each other than the 1-m range illuminated by camera flash under low light levels. Other seals were recorded at a range of depths (average 27 ± 14.3 m, max 66 m). In terms of bouts of dives, still images of other seals were recorded in 5 single dives (of 330) and 28 bouts of dives <2 min apart (of 187). Linear mixed models suggested a relationship between conspecific observations per dive and the number of krill images recorded per dive. Using light conditions as a proxy for detectability, other seals were more likely to be observed at the bottom of dives than during descent or ascent. Seals were also more likely to be closer to each other and oriented perpendicular to each other at the bottom of dives, and in the same direction as each other during ascent. Conclusions: These results are contrary to animal-attached camera observations of penguin foraging, suggesting differing group-foraging tactics for these marine predators. Group foraging could have consequences for models linking predator behaviour to prey field densities since this relationship may be affected by the presence of multiple predators at the same patch.
2015-09-29T00:00:00ZHooker, Sascha KateBarychka, TatsianaJessopp, Mark JStaniland, Iain JBackground: Although there have been recent advances in the development of animal-attached ‘proximity’ tags to remotely record the interactions of multiple individuals, the efficacy of these devices depends on the instrumentation of sufficient animals that subsequently have spatial interactions. Among densely colonial mammals such as fur seals, this remains logistically difficult, and interactions between animals during foraging have not previously been recorded. Results: We collected data on conspecific interactions during diving at sea using still image and video cameras deployed on 23 Antarctic fur seals. Animals carried cameras for a total of 152 days, collecting 38,098 images and 369 movies (total time 7.35 h). Other fur seals were detected in 74% of deployments, with a maximum of five seals seen at one time (n = 122 images, 28 videos). No predators other than conspecifics were observed. Detection was primarily limited by light conditions, since conspecifics were usually further from each other than the 1-m range illuminated by camera flash under low light levels. Other seals were recorded at a range of depths (average 27 ± 14.3 m, max 66 m). In terms of bouts of dives, still images of other seals were recorded in 5 single dives (of 330) and 28 bouts of dives <2 min apart (of 187). Linear mixed models suggested a relationship between conspecific observations per dive and the number of krill images recorded per dive. Using light conditions as a proxy for detectability, other seals were more likely to be observed at the bottom of dives than during descent or ascent. Seals were also more likely to be closer to each other and oriented perpendicular to each other at the bottom of dives, and in the same direction as each other during ascent. Conclusions: These results are contrary to animal-attached camera observations of penguin foraging, suggesting differing group-foraging tactics for these marine predators. Group foraging could have consequences for models linking predator behaviour to prey field densities since this relationship may be affected by the presence of multiple predators at the same patch.Procedure description : using AUTEC’s hydrophones surrounding a DTAGed whale to obtain localizationsMarques, Tiago A.Shaeffer, JessicaMoretti, DavidThomas, Lenhttps://hdl.handle.net/10023/75232022-04-11T11:30:08Z2015-01-01T00:00:00Z2015-01-01T00:00:00ZMarques, Tiago A.Shaeffer, JessicaMoretti, DavidThomas, LenDistribution ecology of Palearctic migrants in the humid Guinea savannah in West AfricaIvande, Samuel T.https://hdl.handle.net/10023/74462019-07-01T10:08:57Z2015-11-30T00:00:00ZDeclines in breeding populations of most migrants across much of the Palearctic have been linked to environmental conditions in their African non-breeding grounds. Studying winter distribution dynamics for these species is necessary to understand how factors in these areas may influence their overall population dynamics. This thesis explored in detail the distribution ecology of migrants in the Guinea savannah, the region from where wintering migrants currently show the greatest breeding population declines. In particular, I investigated some prevailing but hitherto little tested ecological hypothesis concerning impacts of geographical, vegetation and anthropogenic characteristics on the densities and winter distribution of migrants in Africa. Migrant distribution seemed to fit a pattern where decisions leading to winter habitat choice and association were hierarchical and jointly influenced by factors extrinsic and intrinsic to the habitats at large and finer scales respectively. Migrants were distributed in reasonable densities across a wide range of habitats. There was also evidence for an independent effect of latitude on densities and distribution, even after controlling for habitat characteristics. There was no evidence of large changes in latitudinal density patterns within a given winter season and site density patterns were generally consistent over the study duration. Migrants and taxonomically-related/ecologically similar Afrotropical residents showed similarities in habitat requirements and utilization, although migrants utilized habitats over a wider latitudinal range. Some migrants tended to show correspondence in site occurrence between consecutive winters but less so within a given winter season and there was an overall low transferability of habitat models for Palearctic migrants between sites in Nigeria. Collectively, the results describe distribution mechanisms typical for ecologically flexible species that can best be described as habitat generalists. As generalists, migrants are expected to show some resilience, especially in dealing with local and small scale changes on their wintering grounds such that these are unlikely to be the primary limiting factor in their population dynamics. However, the scale of ongoing habitat change across much of Africa is perhaps contributing to overcome the resilience engendered by their generalism. Conservation efforts for these mainly generalists species may therefore aim to preserve habitat on a large scale, perhaps through the promotion of sustainable land use practices.
2015-11-30T00:00:00ZIvande, Samuel T.Declines in breeding populations of most migrants across much of the Palearctic have been linked to environmental conditions in their African non-breeding grounds. Studying winter distribution dynamics for these species is necessary to understand how factors in these areas may influence their overall population dynamics. This thesis explored in detail the distribution ecology of migrants in the Guinea savannah, the region from where wintering migrants currently show the greatest breeding population declines. In particular, I investigated some prevailing but hitherto little tested ecological hypothesis concerning impacts of geographical, vegetation and anthropogenic characteristics on the densities and winter distribution of migrants in Africa. Migrant distribution seemed to fit a pattern where decisions leading to winter habitat choice and association were hierarchical and jointly influenced by factors extrinsic and intrinsic to the habitats at large and finer scales respectively. Migrants were distributed in reasonable densities across a wide range of habitats. There was also evidence for an independent effect of latitude on densities and distribution, even after controlling for habitat characteristics. There was no evidence of large changes in latitudinal density patterns within a given winter season and site density patterns were generally consistent over the study duration. Migrants and taxonomically-related/ecologically similar Afrotropical residents showed similarities in habitat requirements and utilization, although migrants utilized habitats over a wider latitudinal range. Some migrants tended to show correspondence in site occurrence between consecutive winters but less so within a given winter season and there was an overall low transferability of habitat models for Palearctic migrants between sites in Nigeria. Collectively, the results describe distribution mechanisms typical for ecologically flexible species that can best be described as habitat generalists. As generalists, migrants are expected to show some resilience, especially in dealing with local and small scale changes on their wintering grounds such that these are unlikely to be the primary limiting factor in their population dynamics. However, the scale of ongoing habitat change across much of Africa is perhaps contributing to overcome the resilience engendered by their generalism. Conservation efforts for these mainly generalists species may therefore aim to preserve habitat on a large scale, perhaps through the promotion of sustainable land use practices.Indexicality, transparency, and mental filesBall, Derek Nelsonhttps://hdl.handle.net/10023/72862023-04-18T09:54:28Z2014-01-01T00:00:00ZFrancois Recanati’s Mental Files (Oxford: Oxford University Press, 2012) presents a picture of the mind on which mental representations are indexical and transparent. I dispute this picture: there is no clear case for regarding mental representations as indexical, and there are counterexamples to transparency.
2014-01-01T00:00:00ZBall, Derek NelsonFrancois Recanati’s Mental Files (Oxford: Oxford University Press, 2012) presents a picture of the mind on which mental representations are indexical and transparent. I dispute this picture: there is no clear case for regarding mental representations as indexical, and there are counterexamples to transparency.Stimulation of glia reveals modulation of mammalian spinal motor networks by adenosineActon, DavidMiles, Gareth B.https://hdl.handle.net/10023/72342023-04-18T10:02:01Z2015-08-07T00:00:00ZDespite considerable evidence that glia can release modulators to influence the excitability of neighbouring neurons, the importance of gliotransmission for the operation of neural networks and in shaping behaviour remains controversial. Here we characterise the contribution of glia to the modulation of the mammalian spinal central pattern generator for locomotion, the output of which is directly relatable to a defined behaviour. Glia were stimulated by specific activation of protease-activated receptor-1 (PAR1), an endogenous G-protein coupled receptor preferentially expressed by spinal glia during ongoing activity of the spinal central pattern generator for locomotion. Selective activation of PAR1 by the agonist TFLLR resulted in a reversible reduction in the frequency of locomotor-related bursting recorded from ventral roots of spinal cord preparations isolated from neonatal mice. In the presence of the gliotoxins methionine sulfoximine or fluoroacetate, TFLLR had no effect, confirming the specificity of PAR1 activation to glia. The modulation of burst frequency upon PAR1 activation was blocked by the non-selective adenosine-receptor antagonist theophylline and by the A1-receptor antagonist 8-cyclopentyl-1,3-dipropylxanthine, but not by the A2A-receptor antagonist SCH5826, indicating production of extracellular adenosine upon glial stimulation, followed by A1-receptor mediated inhibition of neuronal activity. Modulation of network output following glial stimulation was also blocked by the ectonucleotidase inhibitor ARL67156, indicating glial release of ATP and its subsequent degradation to adenosine rather than direct release of adenosine. Glial stimulation had no effect on rhythmic activity recorded following blockade of inhibitory transmission, suggesting that glial cell-derived adenosine acts via inhibitory circuit components to modulate locomotor-related output. Finally, the modulation of network output by endogenous adenosine was found to scale with the frequency of network activity, implying activity-dependent release of adenosine. Together, these data indicate that glia play an active role in the modulation of mammalian locomotor networks, providing negative feedback control that may stabilise network activity.
This work was funded by the Wellcome Trust Institutional Strategic Support Fund for University of St. Andrews.
2015-08-07T00:00:00ZActon, DavidMiles, Gareth B.Despite considerable evidence that glia can release modulators to influence the excitability of neighbouring neurons, the importance of gliotransmission for the operation of neural networks and in shaping behaviour remains controversial. Here we characterise the contribution of glia to the modulation of the mammalian spinal central pattern generator for locomotion, the output of which is directly relatable to a defined behaviour. Glia were stimulated by specific activation of protease-activated receptor-1 (PAR1), an endogenous G-protein coupled receptor preferentially expressed by spinal glia during ongoing activity of the spinal central pattern generator for locomotion. Selective activation of PAR1 by the agonist TFLLR resulted in a reversible reduction in the frequency of locomotor-related bursting recorded from ventral roots of spinal cord preparations isolated from neonatal mice. In the presence of the gliotoxins methionine sulfoximine or fluoroacetate, TFLLR had no effect, confirming the specificity of PAR1 activation to glia. The modulation of burst frequency upon PAR1 activation was blocked by the non-selective adenosine-receptor antagonist theophylline and by the A1-receptor antagonist 8-cyclopentyl-1,3-dipropylxanthine, but not by the A2A-receptor antagonist SCH5826, indicating production of extracellular adenosine upon glial stimulation, followed by A1-receptor mediated inhibition of neuronal activity. Modulation of network output following glial stimulation was also blocked by the ectonucleotidase inhibitor ARL67156, indicating glial release of ATP and its subsequent degradation to adenosine rather than direct release of adenosine. Glial stimulation had no effect on rhythmic activity recorded following blockade of inhibitory transmission, suggesting that glial cell-derived adenosine acts via inhibitory circuit components to modulate locomotor-related output. Finally, the modulation of network output by endogenous adenosine was found to scale with the frequency of network activity, implying activity-dependent release of adenosine. Together, these data indicate that glia play an active role in the modulation of mammalian locomotor networks, providing negative feedback control that may stabilise network activity.The Ring Net : ring net herring fishing on the west coast of Scotland ; a documentary exhibition by Will MacleanAllerston, Patriciahttps://hdl.handle.net/10023/70712019-04-01T11:11:11Z1991-01-01T00:00:00ZThis dissertation focuses
on
The Ring Net,
a
documentary
exhibition by the
artist Will Maclean. The Ring Net is
a collection of drawings,
photographs and printed plans numbering more
than three hundred and forty
items,
which was originally shown at
the 'Third Eye Centre, Glasgow in
1978. It
subsequently
toured to
various venues, mostly
in Scotland, and
was later bought by The Scottish National Gallery of
Modern Art, Edinburgh
where
it is presently
held.
The
project
is based
on a particular method of sea
fishing which used
to
be
practised on
the West Coast
of
Scotland. The
subject of
fishing is a
consistent
feature in the
work of
Maclean,
although
this
particular
undertaking is
somewhat unusual as
the
artist
has
chosen a
documentary
approach.
The initial
period of research
for the
project was enabled
by
an
Edinburgh-based
charitable organisation,
the Scottish International
Education Trust. The
artist continued
to
work on
the
project
for
some
time
afterwards, and
the
eventual exhibition was not shown until
four
and
a half years
later.
The aim of
this dissertation is to look
at
The Ring Net in its
context.
The period of
its making
is
explored in some depth, as
is the showing of
the
project at the Third Eye Centre and the
various venues
included in its
tour. Though the methods and media used in The Ring Net
are
discussed,
they do
not constitute
the
main objective of
the
work.
More
space has
been devoted to the documentary
aspect of
the
project and
the
effect this
had on the finished result.
Unpublished sources such as a series of
letters from the artist
to
a collaborator
in Kintyre have been used to
some extent.
1991-01-01T00:00:00ZAllerston, PatriciaThis dissertation focuses
on
The Ring Net,
a
documentary
exhibition by the
artist Will Maclean. The Ring Net is
a collection of drawings,
photographs and printed plans numbering more
than three hundred and forty
items,
which was originally shown at
the 'Third Eye Centre, Glasgow in
1978. It
subsequently
toured to
various venues, mostly
in Scotland, and
was later bought by The Scottish National Gallery of
Modern Art, Edinburgh
where
it is presently
held.
The
project
is based
on a particular method of sea
fishing which used
to
be
practised on
the West Coast
of
Scotland. The
subject of
fishing is a
consistent
feature in the
work of
Maclean,
although
this
particular
undertaking is
somewhat unusual as
the
artist
has
chosen a
documentary
approach.
The initial
period of research
for the
project was enabled
by
an
Edinburgh-based
charitable organisation,
the Scottish International
Education Trust. The
artist continued
to
work on
the
project
for
some
time
afterwards, and
the
eventual exhibition was not shown until
four
and
a half years
later.
The aim of
this dissertation is to look
at
The Ring Net in its
context.
The period of
its making
is
explored in some depth, as
is the showing of
the
project at the Third Eye Centre and the
various venues
included in its
tour. Though the methods and media used in The Ring Net
are
discussed,
they do
not constitute
the
main objective of
the
work.
More
space has
been devoted to the documentary
aspect of
the
project and
the
effect this
had on the finished result.
Unpublished sources such as a series of
letters from the artist
to
a collaborator
in Kintyre have been used to
some extent.The alliances of a regional power : the case of Syria, 1970-1989Belcastro, Francescohttps://hdl.handle.net/10023/69482019-07-01T10:17:56Z2015-06-23T00:00:00ZThe topic of this dissertation is the alliances of a regional power. The framework used to explain this central aspect of International Relations is the realist one, and particularly the work of the Classical Realist Arnold Wolfers. The regional, state and domestic dimension are integrated in order to provide an “updated realist” interpretation of alliances, why states form them, maintain them or break them. This dissertation seeks to recover the concept of state’s goals that was central to Classical Realism and then “abandoned” when Neorealism became the dominant Realist paradigm. The case studies used in this research is Syria during the 1970-1989 phase and particularly five pivotal relations: the Egypt 1973 war alliance, the 1978 failed détente with Iraq, the 1979 Damascus-Tehran alliance, the regional client-superpower alliance with the USSR and finally the relation with the Kingdom of Saudi Arabia. By analysing Syria’s foreign policy and particularly these five relations this dissertation show how a framework based on realism provides a coherent and insightful interpretation of a regional power’s foreign policy.
2015-06-23T00:00:00ZBelcastro, FrancescoThe topic of this dissertation is the alliances of a regional power. The framework used to explain this central aspect of International Relations is the realist one, and particularly the work of the Classical Realist Arnold Wolfers. The regional, state and domestic dimension are integrated in order to provide an “updated realist” interpretation of alliances, why states form them, maintain them or break them. This dissertation seeks to recover the concept of state’s goals that was central to Classical Realism and then “abandoned” when Neorealism became the dominant Realist paradigm. The case studies used in this research is Syria during the 1970-1989 phase and particularly five pivotal relations: the Egypt 1973 war alliance, the 1978 failed détente with Iraq, the 1979 Damascus-Tehran alliance, the regional client-superpower alliance with the USSR and finally the relation with the Kingdom of Saudi Arabia. By analysing Syria’s foreign policy and particularly these five relations this dissertation show how a framework based on realism provides a coherent and insightful interpretation of a regional power’s foreign policy.Report and recommendations on multimedia materials for teaching and learning quantum physicsMason, BDębowska, EArpornthip, TGirwidz, RGreczyło, TKohnle, AMelder, TMichelini, MSanti, LSilva, Jhttps://hdl.handle.net/10023/69432023-04-19T00:39:16Z2015-06-30T00:00:00ZAn international collaboration of physicists, affiliated with Multimedia Physics for Teaching and Learning (MPTL) and MERLOT, performed a survey and review of multimedia-based learning materials for quantum physics and quantum mechanics. The review process was based on more than a decade of experience with similar topical learning material reviews. A total of approximately 250 items were considered for review and eight were recommended by the reviewers. These are described in this report. Observations about quantum learning resources and multimedia tools are included.
2015-06-30T00:00:00ZMason, BDębowska, EArpornthip, TGirwidz, RGreczyło, TKohnle, AMelder, TMichelini, MSanti, LSilva, JAn international collaboration of physicists, affiliated with Multimedia Physics for Teaching and Learning (MPTL) and MERLOT, performed a survey and review of multimedia-based learning materials for quantum physics and quantum mechanics. The review process was based on more than a decade of experience with similar topical learning material reviews. A total of approximately 250 items were considered for review and eight were recommended by the reviewers. These are described in this report. Observations about quantum learning resources and multimedia tools are included.The sacred–secular distinction in music during the eighteenth and nineteenth centuries in Austria and BavariaMayr, Christoph Davidhttps://hdl.handle.net/10023/69242019-03-29T13:43:19Z2015-06-23T00:00:00ZThis thesis explores the sacred–secular distinction in the musical life of Austria and Bavaria during the eighteenth and nineteenth century with particular focus on its legitimacy and feasibility. It examines the attempts made by Joseph II of Austria to separate sacred and secular sphere by banning secular music from the church and finds them to have failed. Joseph’s endeavours are compared to those of the Cecilian Movement, which, although similar in their aim, are found to be motivated very differently, yet equally unsuccessful. A study of the rise of the public concert and choral societies points towards new loci for secular music as well as the spiritual experience of music. Finally Anton Bruckner is discussed as an example for filling old and new loci with a successful synthesis of sacred and secular, both in his lived life and his musical composition. Bringing sacred and secular together conforms to the natural state of Christian life in the world and bears the potential for mutual benefit which outweighs the presumed advantages of distinct lines of separation.
2015-06-23T00:00:00ZMayr, Christoph DavidThis thesis explores the sacred–secular distinction in the musical life of Austria and Bavaria during the eighteenth and nineteenth century with particular focus on its legitimacy and feasibility. It examines the attempts made by Joseph II of Austria to separate sacred and secular sphere by banning secular music from the church and finds them to have failed. Joseph’s endeavours are compared to those of the Cecilian Movement, which, although similar in their aim, are found to be motivated very differently, yet equally unsuccessful. A study of the rise of the public concert and choral societies points towards new loci for secular music as well as the spiritual experience of music. Finally Anton Bruckner is discussed as an example for filling old and new loci with a successful synthesis of sacred and secular, both in his lived life and his musical composition. Bringing sacred and secular together conforms to the natural state of Christian life in the world and bears the potential for mutual benefit which outweighs the presumed advantages of distinct lines of separation.Abbatial elections : the case of the Loire Valley in the eleventh centuryHowie, Catriona Vhttps://hdl.handle.net/10023/68112020-02-29T03:02:59Z2015-06-25T00:00:00ZThis thesis examines a series of documents described as electoral charters, produced in monastic institutions of the Loire Valley from the late tenth to late eleventh centuries. By considering the variations in the formulas used for each charter, the study considers what the charters were saying about power or wanted to project about the powers at play in the events they described. Through this, the thesis demonstrates that the power of lordship projected by such documents was of a very traditional nature throughout the period in which they were being produced. The count’s role on each occasion showed him to be a dominant force with a power of lordship composed of possession and rights of property ownership, but also intangible elements, including a sacral interest.
By considering the context of events surrounding each charter of election, the thesis demonstrates that elements of this lordship could be more or less projected at different times in order that different statements might be made about the count. Thus, the symbolic expressions of power appear to have been bigger elements or more strongly emphasised in periods when the count’s political or military power was under pressure.
The differences in formulas used throughout the period of the charters’ production demonstrate that, despite the appearance of new elements that may appear to have been important novelties, these processes were likely to have been original to proceedings, and therefore the notions of a reform of investitures taking place in the mid-eleventh century must be nuanced. Instead of demonstrating a mutation in relationships between lord and Church, the documents demonstrate an alteration in style and content, becoming more narrative and verbose and in these ways revealing elements of the process of abbatial elevations that had previously been hidden from view.
2015-06-25T00:00:00ZHowie, Catriona VThis thesis examines a series of documents described as electoral charters, produced in monastic institutions of the Loire Valley from the late tenth to late eleventh centuries. By considering the variations in the formulas used for each charter, the study considers what the charters were saying about power or wanted to project about the powers at play in the events they described. Through this, the thesis demonstrates that the power of lordship projected by such documents was of a very traditional nature throughout the period in which they were being produced. The count’s role on each occasion showed him to be a dominant force with a power of lordship composed of possession and rights of property ownership, but also intangible elements, including a sacral interest.
By considering the context of events surrounding each charter of election, the thesis demonstrates that elements of this lordship could be more or less projected at different times in order that different statements might be made about the count. Thus, the symbolic expressions of power appear to have been bigger elements or more strongly emphasised in periods when the count’s political or military power was under pressure.
The differences in formulas used throughout the period of the charters’ production demonstrate that, despite the appearance of new elements that may appear to have been important novelties, these processes were likely to have been original to proceedings, and therefore the notions of a reform of investitures taking place in the mid-eleventh century must be nuanced. Instead of demonstrating a mutation in relationships between lord and Church, the documents demonstrate an alteration in style and content, becoming more narrative and verbose and in these ways revealing elements of the process of abbatial elevations that had previously been hidden from view.Abundance and distribution of delphinids in the Red Sea (Egypt)Costa, Marinahttps://hdl.handle.net/10023/68022019-07-01T10:17:53Z2015-06-24T00:00:00ZKnowledge about cetaceans in the Red Sea is limited with only a handful of sporadic or
spatially-limited studies carried out to date. Funded by the Italian Cooperation through
a Debt-for-Nature Swap programme and carried out in collaboration with the Egyptian
NGO HEPCA, this thesis presents the results from the first ever systematic vessel-based
surveys conducted in the southern Egyptian Red Sea from 2010 to 2013 using linetransect
methodology. The main aims of the thesis were (a) to estimate cetacean
abundance, (b) to determine distribution patterns and habitat use of the cetacean
species, (c) to investigate movement patterns for species for which individual
recognition techniques were suitable and (d) to identify areas of conservation concern
for cetaceans with a particular focus on existing protected areas. Eight species were
identified, of which five were commonly encountered (Stenella longirostris, S.
attenuata, Tursiops truncatus, T. aduncus, and Grampus griseus) and three were rare
(Pseudorca crassidens, Sousa plumbea, Balaenoptera edeni). Estimates of abundance
using design-based line transect sampling techniques were obtained for five species: S.
attenuata 10,268 (CV=0.26); S. longirostris 6,961 (CV=0.26); T. aduncus 659 (CV=0.69);
T. truncatus 509 (CV=0.33), and G. griseus 367 (CV=0.37). Habitat modelling revealed
that the two Stenella species were widely distributed across the study area. In
contrast, T. truncatus was concentrated in waters around Ras Banas peninsula (in
particular Satayah offshore reef), and T. aduncus was mainly found along the coast
with possibly separate sub-populations in the northern and southern study area. G.
griseus was only encountered in the southern part. The information provided in this
study will allow the development of a conservation strategy for the protected areas
and will serve as baseline information to carry out future survey work in the Red Sea.
2015-06-24T00:00:00ZCosta, MarinaKnowledge about cetaceans in the Red Sea is limited with only a handful of sporadic or
spatially-limited studies carried out to date. Funded by the Italian Cooperation through
a Debt-for-Nature Swap programme and carried out in collaboration with the Egyptian
NGO HEPCA, this thesis presents the results from the first ever systematic vessel-based
surveys conducted in the southern Egyptian Red Sea from 2010 to 2013 using linetransect
methodology. The main aims of the thesis were (a) to estimate cetacean
abundance, (b) to determine distribution patterns and habitat use of the cetacean
species, (c) to investigate movement patterns for species for which individual
recognition techniques were suitable and (d) to identify areas of conservation concern
for cetaceans with a particular focus on existing protected areas. Eight species were
identified, of which five were commonly encountered (Stenella longirostris, S.
attenuata, Tursiops truncatus, T. aduncus, and Grampus griseus) and three were rare
(Pseudorca crassidens, Sousa plumbea, Balaenoptera edeni). Estimates of abundance
using design-based line transect sampling techniques were obtained for five species: S.
attenuata 10,268 (CV=0.26); S. longirostris 6,961 (CV=0.26); T. aduncus 659 (CV=0.69);
T. truncatus 509 (CV=0.33), and G. griseus 367 (CV=0.37). Habitat modelling revealed
that the two Stenella species were widely distributed across the study area. In
contrast, T. truncatus was concentrated in waters around Ras Banas peninsula (in
particular Satayah offshore reef), and T. aduncus was mainly found along the coast
with possibly separate sub-populations in the northern and southern study area. G.
griseus was only encountered in the southern part. The information provided in this
study will allow the development of a conservation strategy for the protected areas
and will serve as baseline information to carry out future survey work in the Red Sea.Less cognitive conflict does not imply choice of the default option : Commentary on Kieslich and Hilbig (2014)Myrseth, Kristian OveWollbrant, Connyhttps://hdl.handle.net/10023/67882022-09-25T11:30:13Z2015-05-01T00:00:00ZKieslich and Hilbig (2014) employ a mouse-tracking technique to measure decision conflict in social dilemmas. They report that defectors exhibit more conflict than do cooperators. They infer that cooperation thus is the reflexive, default behavior. We argue, however, that their analysis fails to discriminate between reflexive versus cognitively controlled behavioral responses. This is because cognitive conflict can emanate from resisting impulse successfully—or unsuccessfully.
2015-05-01T00:00:00ZMyrseth, Kristian OveWollbrant, ConnyKieslich and Hilbig (2014) employ a mouse-tracking technique to measure decision conflict in social dilemmas. They report that defectors exhibit more conflict than do cooperators. They infer that cooperation thus is the reflexive, default behavior. We argue, however, that their analysis fails to discriminate between reflexive versus cognitively controlled behavioral responses. This is because cognitive conflict can emanate from resisting impulse successfully—or unsuccessfully.Examining fish quality : the evaluation of the use of lipids as a measure of condition in wild Atlantic salmonHowe, Alexandra Janehttps://hdl.handle.net/10023/67282019-07-01T10:20:09Z2015-06-24T00:00:00ZConsidering the response of organisms to their environment is difficult; it is made more so if population numbers cannot be closely monitored. In such cases different methods of population assessment are required. This thesis uses lipids as a measure of Atlantic salmon (Salmo salar L.) quality and investigates its usefulness in indicating fish condition.
The first study examines the relationship between fish total lipid content and W[sub]R condition factor; this study clearly demonstrates that there is a significant positive relationship between the condition factor of a fish and its total lipid content. In the following study the lipid storage between the different tissues of the Atlantic salmon is considered. This indicates that the red muscle and the adipose tissues hold higher concentrations of lipid than the white muscle. However, the white muscle makes up the majority of lipid tissue mass in the Atlantic salmon so contains the bulk of stored lipid in a fish, at low concentration.
The next study investigates the effect of spawning on Atlantic salmon condition. Salmon can be seen preferentially conserving lipid in their musculature and drawing down the lipid stored in their adipose tissues. The following study looked at one key lipid group, triacylglycerides, in salmon. Triacylglycerides are energetically important in fish and this study found that the spawning process depleted triacylglyceride reserves, but that the red muscle conserves triacylglycerides even after spawning.
The final study considers the relationship between maternal quality and egg quality, identifying that longer Atlantic salmon produce eggs with more lipid after spawning migration. Egg lipid concentrations were comparably maintained between fish. Monitoring quality in this way is a useful tool to determine population wellbeing and help indicate where populations are compromised.
2015-06-24T00:00:00ZHowe, Alexandra JaneConsidering the response of organisms to their environment is difficult; it is made more so if population numbers cannot be closely monitored. In such cases different methods of population assessment are required. This thesis uses lipids as a measure of Atlantic salmon (Salmo salar L.) quality and investigates its usefulness in indicating fish condition.
The first study examines the relationship between fish total lipid content and W[sub]R condition factor; this study clearly demonstrates that there is a significant positive relationship between the condition factor of a fish and its total lipid content. In the following study the lipid storage between the different tissues of the Atlantic salmon is considered. This indicates that the red muscle and the adipose tissues hold higher concentrations of lipid than the white muscle. However, the white muscle makes up the majority of lipid tissue mass in the Atlantic salmon so contains the bulk of stored lipid in a fish, at low concentration.
The next study investigates the effect of spawning on Atlantic salmon condition. Salmon can be seen preferentially conserving lipid in their musculature and drawing down the lipid stored in their adipose tissues. The following study looked at one key lipid group, triacylglycerides, in salmon. Triacylglycerides are energetically important in fish and this study found that the spawning process depleted triacylglyceride reserves, but that the red muscle conserves triacylglycerides even after spawning.
The final study considers the relationship between maternal quality and egg quality, identifying that longer Atlantic salmon produce eggs with more lipid after spawning migration. Egg lipid concentrations were comparably maintained between fish. Monitoring quality in this way is a useful tool to determine population wellbeing and help indicate where populations are compromised.Romanization 2.0 and its alternativesWoolf, Greghttps://hdl.handle.net/10023/67162023-04-18T09:51:51Z2014-06-01T00:00:00ZThis essay argues that Romanization revolves around understanding objects in motion and that Roman archaeologists should therefore focus on (1) globalization theory and (2) material-culture studies as important theoretical directions for the (near) future. The present state and scope of the Romanization debate, however, seem to prevent a fruitful development in that direction. The first part of this paper therefore briefly analyses the Romanization debate and argues that large parts of ‘Anglo-Saxon Roman archaeology’ have never been really post-colonial, but in fact from the mid1990s onwards developed a theoretical position that should be characterized as anticolonial. This ideologically motivated development has resulted in several unhealthy divides within the field, as well as in an uncomfortable ending of the Romanization debate. The present consensus within English-speaking Roman archaeology ‘to do away with Romanization’ does not seem to get us at all ‘beyond Romans and Natives’, and, moreover, has effectively halted most of the discussion about how to understand and conceptualize ‘Rome’. The second part of the article presents two propositions outlining how to move forward: globalization theory and material-culture studies. Through this focus we will be able to better understand ‘Rome’ as (indicating) objects in motion and the human–thing entanglements resulting from a remarkable punctuation of connectivity. This focus is important as an alternative perspective to all existing narratives about Romanization because these remain fundamentally historical, in the sense that they reduce objects to expressions (of identity) alone. It is time for our discussions about ‘Rome’ to move ‘beyond representation’ and to become genuinely archaeological at last, by making material culture, with its agency and materiality, central to the analyses.
2014-06-01T00:00:00ZWoolf, GregThis essay argues that Romanization revolves around understanding objects in motion and that Roman archaeologists should therefore focus on (1) globalization theory and (2) material-culture studies as important theoretical directions for the (near) future. The present state and scope of the Romanization debate, however, seem to prevent a fruitful development in that direction. The first part of this paper therefore briefly analyses the Romanization debate and argues that large parts of ‘Anglo-Saxon Roman archaeology’ have never been really post-colonial, but in fact from the mid1990s onwards developed a theoretical position that should be characterized as anticolonial. This ideologically motivated development has resulted in several unhealthy divides within the field, as well as in an uncomfortable ending of the Romanization debate. The present consensus within English-speaking Roman archaeology ‘to do away with Romanization’ does not seem to get us at all ‘beyond Romans and Natives’, and, moreover, has effectively halted most of the discussion about how to understand and conceptualize ‘Rome’. The second part of the article presents two propositions outlining how to move forward: globalization theory and material-culture studies. Through this focus we will be able to better understand ‘Rome’ as (indicating) objects in motion and the human–thing entanglements resulting from a remarkable punctuation of connectivity. This focus is important as an alternative perspective to all existing narratives about Romanization because these remain fundamentally historical, in the sense that they reduce objects to expressions (of identity) alone. It is time for our discussions about ‘Rome’ to move ‘beyond representation’ and to become genuinely archaeological at last, by making material culture, with its agency and materiality, central to the analyses.Identification of a candidate Rad1 subunit for the kinetoplastid 9-1-1 (Rad9-Hus1-Rad1) complexMacNeill, Stuarthttps://hdl.handle.net/10023/67042023-04-18T09:56:36Z2014-12-19T00:00:00ZThe trimeric 9-1-1 (Rad9-Hus1-Rad1) complex plays an important role in the eukaryotic DNA damage response by recruiting DNA repair factors and checkpoint mediators to damaged sites. Extensively characterised in mammals and yeast, evidence is now emerging that 9-1-1 function is conserved beyond the relatively narrow evolutionary range of the Opisthokonts. Kinetoplastid Rad9 and Hus1 proteins have been identified and shown to be involved in the DNA damage response but Rad1 has remained elusive. In this study, PSI-BLAST iterative database searching, phylogenetic and structural modeling techniques are used to identify and characterise candidate Rad1 proteins in kinetoplastid organisms.
Date of Acceptance: 12/12/2014
2014-12-19T00:00:00ZMacNeill, StuartThe trimeric 9-1-1 (Rad9-Hus1-Rad1) complex plays an important role in the eukaryotic DNA damage response by recruiting DNA repair factors and checkpoint mediators to damaged sites. Extensively characterised in mammals and yeast, evidence is now emerging that 9-1-1 function is conserved beyond the relatively narrow evolutionary range of the Opisthokonts. Kinetoplastid Rad9 and Hus1 proteins have been identified and shown to be involved in the DNA damage response but Rad1 has remained elusive. In this study, PSI-BLAST iterative database searching, phylogenetic and structural modeling techniques are used to identify and characterise candidate Rad1 proteins in kinetoplastid organisms.The political economy of resistance in post-conflict South SudanYoung, Graemehttps://hdl.handle.net/10023/66082019-04-01T08:19:10Z2014-03-01T00:00:00ZDespite recent scholarly attention, the phenomenon of resistance in post-conflict
environments remains largely under-conceptualized. This represents a major shortcoming in the theory and praxis of post-conflict peacebuilding and development. Seeking to address this problem, this study explores how, why and by whom the economic dimensions of contemporary peacebuilding and development projects are contested in their local applications, using South Sudan as a case study. A theoretical framework for analysing resistance is proposed and subsequently employed to provide insights into activities that are cast as informal, illicit or illegitimate by dominant neoliberal orthodoxy. This is done in
three distinct yet overlapping ways. First, the role that informal economic activity plays in the political economy of post-conflict South Sudan is examined. Informal economic activity is conceptualized as a form of resistance to the failings of the formal sphere, but also as a form of power where agency is absent and that is encouraged as a type of local neoliberalism. Second, the legitimate/illegitimate and licit/illicit dichotomies that define
economic activity in post-conflict South Sudan are problematized through an exploration of current debates surrounding corruption and land tenure. These debates demonstrate how neoliberal economic orthodoxy breaks down and becomes redefined in its local contacts. Finally, the centre/periphery dynamics that define the political economy of South Sudan’s
borderlands are conceptualized in terms of power and resistance, and resistance is shown to be fundamentally tied to power in ways that are characterized by subjectivity and hybridity. Resistance plays an important role in post-conflict environments. Addressing its economic dimensions must be a central task of contemporary peacebuilding and development projects.
2014-03-01T00:00:00ZYoung, GraemeDespite recent scholarly attention, the phenomenon of resistance in post-conflict
environments remains largely under-conceptualized. This represents a major shortcoming in the theory and praxis of post-conflict peacebuilding and development. Seeking to address this problem, this study explores how, why and by whom the economic dimensions of contemporary peacebuilding and development projects are contested in their local applications, using South Sudan as a case study. A theoretical framework for analysing resistance is proposed and subsequently employed to provide insights into activities that are cast as informal, illicit or illegitimate by dominant neoliberal orthodoxy. This is done in
three distinct yet overlapping ways. First, the role that informal economic activity plays in the political economy of post-conflict South Sudan is examined. Informal economic activity is conceptualized as a form of resistance to the failings of the formal sphere, but also as a form of power where agency is absent and that is encouraged as a type of local neoliberalism. Second, the legitimate/illegitimate and licit/illicit dichotomies that define
economic activity in post-conflict South Sudan are problematized through an exploration of current debates surrounding corruption and land tenure. These debates demonstrate how neoliberal economic orthodoxy breaks down and becomes redefined in its local contacts. Finally, the centre/periphery dynamics that define the political economy of South Sudan’s
borderlands are conceptualized in terms of power and resistance, and resistance is shown to be fundamentally tied to power in ways that are characterized by subjectivity and hybridity. Resistance plays an important role in post-conflict environments. Addressing its economic dimensions must be a central task of contemporary peacebuilding and development projects.Syria : why is the Arab Spring turning into a long winterAlzamalkani, Munzer Eidhttps://hdl.handle.net/10023/66002017-04-04T10:05:03Z2015-06-23T00:00:00ZThis thesis analyses the problematic trajectory of the Syrian Revolution 2011, which
was inspired by the Arab Spring. It first evaluates the causes of the revolution during
Bashar al-Asad’s era. An era was aimed to be a transition from authoritarianism to
democracy and from suppression to fair openness. It second investigates the factors
behind turning the Arab Spring into a Syrian winter, plunging the country into internal
war and uncontrolled violence. The research is based on a qualitative approach that
includes interviews as a source of information and analysis. Factors covered are the
disintegration of Syrian society as the greatest challenge for the civil uprising and
mass mobilization as well as the regime’s coherent inner core accounting for the
regime’s violence and persistence. As violence breeds violence, the revolutionaries
decided to react violently towards the regime brutality descending the country into an
internal war. The formulation of the Free Syrian Army was formalized, but could not
transform into a proper military formation, and so could not control the spread of
violence in the country. The inclination towards Jihad was evident and common, and
associated with resorting to violence because the revolutionaries are Muslims, and
believed in Jihad as a way to defend themselves and their families. However, Jihad
became more formalized with the arrival of global Jihadists to Syria, forming Jihadist
groups and controlling parts of Syria. The stance of the international community was
another big obstacle helped escalating, but not terminating the conflict. A conflict
could develop into a devastating regional crisis changing the structure of the Middle
East and changing the international politics of this vital region.
2015-06-23T00:00:00ZAlzamalkani, Munzer EidThis thesis analyses the problematic trajectory of the Syrian Revolution 2011, which
was inspired by the Arab Spring. It first evaluates the causes of the revolution during
Bashar al-Asad’s era. An era was aimed to be a transition from authoritarianism to
democracy and from suppression to fair openness. It second investigates the factors
behind turning the Arab Spring into a Syrian winter, plunging the country into internal
war and uncontrolled violence. The research is based on a qualitative approach that
includes interviews as a source of information and analysis. Factors covered are the
disintegration of Syrian society as the greatest challenge for the civil uprising and
mass mobilization as well as the regime’s coherent inner core accounting for the
regime’s violence and persistence. As violence breeds violence, the revolutionaries
decided to react violently towards the regime brutality descending the country into an
internal war. The formulation of the Free Syrian Army was formalized, but could not
transform into a proper military formation, and so could not control the spread of
violence in the country. The inclination towards Jihad was evident and common, and
associated with resorting to violence because the revolutionaries are Muslims, and
believed in Jihad as a way to defend themselves and their families. However, Jihad
became more formalized with the arrival of global Jihadists to Syria, forming Jihadist
groups and controlling parts of Syria. The stance of the international community was
another big obstacle helped escalating, but not terminating the conflict. A conflict
could develop into a devastating regional crisis changing the structure of the Middle
East and changing the international politics of this vital region.Terrorism and the state : intra-state dynamics and the response to non-state terrorismMcConaghy, Kieranhttps://hdl.handle.net/10023/65352019-04-01T08:18:14Z2015-06-23T00:00:00ZAlthough there has been a wealth of academic literature which has examined counter-terrorism, both in the general sense and in case study focused approaches, there has seldom been an engagement in terrorism studies literature on the nature of the state itself and how this impacts upon the particular response to terrorism. Existing literature has a tendency to either examine one branch of the state or to treat (explicitly or implicitly) the state as a unitary actor.
This thesis challenges the view of the state as a unitary actor, looking beneath the surface of the state, investigating intra-state dynamics and the consequences for counter-terrorism. I highlight that the state by its nature is ‘peopled’, demonstrating through comparative analysis of case studies from Spain, France, and the United Kingdom, how the individual identities and dispositions of state personnel at all levels from elites to entry level positions determine the nature and characteristics of particular states.
I show that if we accept that the state is peopled, we must pay attention to a series of traits that I argue all states exhibit to understand why campaigns of counter-terrorism take the shape and form that they do. I posit that we must understand the role that emotional and visceral action by state personnel in response to terrorism plays, how the character of particular state organisations can impact upon the trajectory of conflicts, and how issues of intra-state competition and coordination can frustrate even the best laid counter-terrorism strategies. Furthermore, I show how the propensity for sub- state political violence to ‘terrorise’ populations makes the response to terrorism a powerful political tool, and how it has been deployed in the past for political gain rather than purely as an instrument to improve security.
I conclude that future academic analyses of counter-terrorism must take this into consideration, and likewise, state personnel must be mindful of the nature and character of their state should they wish to effectively prevent terrorism and protect human rights and the rule of law.
2015-06-23T00:00:00ZMcConaghy, KieranAlthough there has been a wealth of academic literature which has examined counter-terrorism, both in the general sense and in case study focused approaches, there has seldom been an engagement in terrorism studies literature on the nature of the state itself and how this impacts upon the particular response to terrorism. Existing literature has a tendency to either examine one branch of the state or to treat (explicitly or implicitly) the state as a unitary actor.
This thesis challenges the view of the state as a unitary actor, looking beneath the surface of the state, investigating intra-state dynamics and the consequences for counter-terrorism. I highlight that the state by its nature is ‘peopled’, demonstrating through comparative analysis of case studies from Spain, France, and the United Kingdom, how the individual identities and dispositions of state personnel at all levels from elites to entry level positions determine the nature and characteristics of particular states.
I show that if we accept that the state is peopled, we must pay attention to a series of traits that I argue all states exhibit to understand why campaigns of counter-terrorism take the shape and form that they do. I posit that we must understand the role that emotional and visceral action by state personnel in response to terrorism plays, how the character of particular state organisations can impact upon the trajectory of conflicts, and how issues of intra-state competition and coordination can frustrate even the best laid counter-terrorism strategies. Furthermore, I show how the propensity for sub- state political violence to ‘terrorise’ populations makes the response to terrorism a powerful political tool, and how it has been deployed in the past for political gain rather than purely as an instrument to improve security.
I conclude that future academic analyses of counter-terrorism must take this into consideration, and likewise, state personnel must be mindful of the nature and character of their state should they wish to effectively prevent terrorism and protect human rights and the rule of law.Mechanical properties of fish myotomal muscleDavies, Melissa Lynne F.https://hdl.handle.net/10023/65012019-07-01T10:10:55Z1995-01-01T00:00:00Z1995-01-01T00:00:00ZDavies, Melissa Lynne F.Overhearing : Hindu & Christian perspectives on artistryHearn, Emily K.https://hdl.handle.net/10023/65002019-07-01T10:04:11Z2014-12-01T00:00:00ZThis thesis is concerned with the hypothesis that an intellectual conversation between Christian and Hindu traditions on questions of aesthetic concern may not only prove mutually illuminating as such but also touch obliquely upon matters of religious and theological concern without exciting the defensive response often posed by more familiar strategies of inter-faith ‘dialogue’. It seeks to establish the existence of sufficient conditions for such a conversation within the respective traditions.
The Introduction considers the relevant model of ‘conversation’ distinguishing it from other forms of encounter between religious traditions. It proceeds by identifying three shared concerns: freedom and constraint, aesthetic experience and religious encounters, and the relationship between the material artwork and its significance.
The first three chapters address them by examining various elements in Hindu traditions, including a detailed treatment of the Śilpaśāstras, a comprehensive consideration of the concept of rasa and its relation to religious experience, and an exploration of the role of the senses in scriptural traditions, the importance of Form and the value of the art object as a devotional aid. Finally it outlines the notion darśan, of seeing and being seen by a deity through a material image.
The last three chapters address them by examining the work of Christian theologians including Dorothy Sayers on Art as Idea, exploring bequeathed traditions in iconography and the music of John Tavener, and expounding Tolkien’s category of ‘sub-creation’. It considers the work of David Brown, Richard Viladesau, John Ruskin, Frank Burch Brown and Abraham Kuyper who span a putative spectrum of equating aesthetic and religious experience at one end and strictly demarcating between them at the other end. It explores the relationship of the physical art object with its spiritual significance in the work of Dorothy Sayers, John Carey, Rowan Williams, David Brown and Trevor Hart.
2014-12-01T00:00:00ZHearn, Emily K.This thesis is concerned with the hypothesis that an intellectual conversation between Christian and Hindu traditions on questions of aesthetic concern may not only prove mutually illuminating as such but also touch obliquely upon matters of religious and theological concern without exciting the defensive response often posed by more familiar strategies of inter-faith ‘dialogue’. It seeks to establish the existence of sufficient conditions for such a conversation within the respective traditions.
The Introduction considers the relevant model of ‘conversation’ distinguishing it from other forms of encounter between religious traditions. It proceeds by identifying three shared concerns: freedom and constraint, aesthetic experience and religious encounters, and the relationship between the material artwork and its significance.
The first three chapters address them by examining various elements in Hindu traditions, including a detailed treatment of the Śilpaśāstras, a comprehensive consideration of the concept of rasa and its relation to religious experience, and an exploration of the role of the senses in scriptural traditions, the importance of Form and the value of the art object as a devotional aid. Finally it outlines the notion darśan, of seeing and being seen by a deity through a material image.
The last three chapters address them by examining the work of Christian theologians including Dorothy Sayers on Art as Idea, exploring bequeathed traditions in iconography and the music of John Tavener, and expounding Tolkien’s category of ‘sub-creation’. It considers the work of David Brown, Richard Viladesau, John Ruskin, Frank Burch Brown and Abraham Kuyper who span a putative spectrum of equating aesthetic and religious experience at one end and strictly demarcating between them at the other end. It explores the relationship of the physical art object with its spiritual significance in the work of Dorothy Sayers, John Carey, Rowan Williams, David Brown and Trevor Hart.MOOCs with attitudes : Insights from a practitioner based investigationChadaj, MonikaBaxter, GordonAllison, Colinhttps://hdl.handle.net/10023/64942023-04-19T00:39:23Z2014-10-01T00:00:00ZIn the current educational landscape of shrinking public budgets and increasing costs, MOOCs have become one of the most dominant discourses in higher education (HE). However, due to their short history, they are only just beginning to be systematically investigated. In an attempt to shed more light on the MOOC phenomenon, this study complements other approaches by eliciting institutional attitudes to MOOC provision using qualitative content analysis on responses captured in a series of semi-structured interviews with participants who hold senior positions in universities and who are involved in creating institutional policy and/or the design and delivery of MOOCs. A context for these interviews was created by looking at MOOCs from historical, pedagogical, monetary and technological perspectives. Five topics emerged that were subsequently used as common points of reference for comparisons across the interviews: motivation, monetization, pedagogy, traditional universities and public access to higher education. The analysis of attitudes to, and the importance of, these topics are summarized, and also illustrated through quotes from the participants. Interestingly, it does not appear that MOOCs are regarded by insiders as disruptive as the media presents them, but rather are seen primarily as marketing vehicles for global education brands.
2014-10-01T00:00:00ZChadaj, MonikaBaxter, GordonAllison, ColinIn the current educational landscape of shrinking public budgets and increasing costs, MOOCs have become one of the most dominant discourses in higher education (HE). However, due to their short history, they are only just beginning to be systematically investigated. In an attempt to shed more light on the MOOC phenomenon, this study complements other approaches by eliciting institutional attitudes to MOOC provision using qualitative content analysis on responses captured in a series of semi-structured interviews with participants who hold senior positions in universities and who are involved in creating institutional policy and/or the design and delivery of MOOCs. A context for these interviews was created by looking at MOOCs from historical, pedagogical, monetary and technological perspectives. Five topics emerged that were subsequently used as common points of reference for comparisons across the interviews: motivation, monetization, pedagogy, traditional universities and public access to higher education. The analysis of attitudes to, and the importance of, these topics are summarized, and also illustrated through quotes from the participants. Interestingly, it does not appear that MOOCs are regarded by insiders as disruptive as the media presents them, but rather are seen primarily as marketing vehicles for global education brands.Bilingualism in Calca, Department of Cuzco, PeruHoggarth, Paulinehttps://hdl.handle.net/10023/64562019-07-01T10:12:19Z1973-06-01T00:00:00Z1973-06-01T00:00:00ZHoggarth, PaulineA "proper job" : acting as vocation and work in theological perspective with particular reference to Dorothy L SayersStarks, Gwendolyn Aileen Paceyhttps://hdl.handle.net/10023/63902023-09-26T02:06:03Z2014-06-24T00:00:00ZIn this dissertation, I will be looking at the actor as a craftsperson and artist from
both a secular and a theological standpoint in order to determine if the labour of acting
can be considered both as work, a “proper job”; and as a calling from God, a vocation.
The main questions prompting and shaping this dissertation have arisen out of my own
personal experience as an actor struggling both in the performing arts business and with
my Christian faith. So, the opening chapter will introduce a personal background
approach to the dissertation. It will summarize the experiences that brought me to the
place of asking these two questions. It will also serve as an introduction to the life of
Dorothy L. Sayers, outlining her own life and demonstrating why she is important to our
work as actors. Chapter Two will then cover historical data on Anti-Theatrical
Prejudice, laying the foundation for the ongoing discomfort with and misunderstanding
regarding the actor’s craft. Chapters Three and Four will examine separately our
notions of work (Three) and then of vocation (Four) in order to gain a broader view of
these two terms. At this point, we will have laid the path to reintroduce Dorothy L.
Sayers in Chapters Five, Six and Seven, both as a partner in conversation and as one
who held this broader understanding of the terms work and vocation and applied them
to creative activities, in particular acting. The final chapter will look at acting as
connected to the basic features of life. It, among other things, will revisit some of the
anti-theatre argument; pick up on ideas such as the imagination’s ability to rehearse life;
and will examine some uses of acting as a means of human exploration and social
change. Finally, we will explore the artistry, technique, and craft of the actor, to firmly
establish the place of acting in society as an important task, a “proper job,” and a
Christian vocation.
2014-06-24T00:00:00ZStarks, Gwendolyn Aileen PaceyIn this dissertation, I will be looking at the actor as a craftsperson and artist from
both a secular and a theological standpoint in order to determine if the labour of acting
can be considered both as work, a “proper job”; and as a calling from God, a vocation.
The main questions prompting and shaping this dissertation have arisen out of my own
personal experience as an actor struggling both in the performing arts business and with
my Christian faith. So, the opening chapter will introduce a personal background
approach to the dissertation. It will summarize the experiences that brought me to the
place of asking these two questions. It will also serve as an introduction to the life of
Dorothy L. Sayers, outlining her own life and demonstrating why she is important to our
work as actors. Chapter Two will then cover historical data on Anti-Theatrical
Prejudice, laying the foundation for the ongoing discomfort with and misunderstanding
regarding the actor’s craft. Chapters Three and Four will examine separately our
notions of work (Three) and then of vocation (Four) in order to gain a broader view of
these two terms. At this point, we will have laid the path to reintroduce Dorothy L.
Sayers in Chapters Five, Six and Seven, both as a partner in conversation and as one
who held this broader understanding of the terms work and vocation and applied them
to creative activities, in particular acting. The final chapter will look at acting as
connected to the basic features of life. It, among other things, will revisit some of the
anti-theatre argument; pick up on ideas such as the imagination’s ability to rehearse life;
and will examine some uses of acting as a means of human exploration and social
change. Finally, we will explore the artistry, technique, and craft of the actor, to firmly
establish the place of acting in society as an important task, a “proper job,” and a
Christian vocation.Practicing peacebuilding differently : a legal empowerment project, a randomised control trial and practical hybridity in LiberiaGraef, J. Julianhttps://hdl.handle.net/10023/63842023-03-20T13:45:59Z2014-05-30T00:00:00ZHybridity, as it is currently understood in the Peace and Conflict Studies (PCS) and International Relations (IR) literature, is defined by the complex interactions between ‘the liberal peace’ and ‘the local’. However, under this theoretical liberal-local rubric, the ways in which power is practiced has already been determined; how resistance is expressed and the forms it assumes have already been established. While it has yielded numerous important insights into how power circulates and resistance manifests in peacebuilding operations, the theoretical approach conceals other significant dynamics which escape detection by ‘the liberal peace’ and ‘the local’. However, these undetected dimensions of hybridity comprise the very processes that emerge in ways which destabilise the boundaries between ‘the liberal peace’ and ‘the local’ and reshape the contours of the emerging post-liberal peace.
Instead of accepting the liberal-local distinction which defines this theoretical hybridity, this thesis advances an alternative methodological approach to exploring the tensions at play in peacebuilding projects. Rather than deploying theoretical distinctions in order to explain or understand complex hybrid processes, this thesis develops a methodological strategy for exploring the tensions between how actors design a peacebuilding project and how that project changes as actors work to translate that project into complex, everyday living sites (Callon, 1986; Law, 1997; Akrich, 1992). This tension is expressed as practical hybridity. The process of practical hybridity unfolds as the concrete material changes, modifications, and adaptations that emerge as actors appropriate and contingently translate organised practices in new ways and for different purposes. Through an ongoing process of practical hybridity, the boundaries and distinction which define the distinction between ‘the liberal peace’ and ‘the local’ become increasingly unstable. Amidst this instability, the practices which characterised ‘the liberal peace’ are becoming stretched into a post-liberal peace.
Drawing on the work of Richmond (2011a; Richmond & Mitchell, 2012), Latour (1987b; 1988; 2004), and Schatzki (2002), and based on over five months of field research, this this thesis traces the process of practical hybridity at play during the implementation and evaluation of a peacebuilding project in Liberia. I participated as a research assistant on a Randomised Control Trial (RCT), implemented by a small research team under the auspices of the Oxford University’s Centre for the Study of African Economies (CSAE). The team was assessing the impact of a legal empowerment programme managed by The Carter Center: the Community Justice Advisor (CJA) programme. As the CSAE’s evaluation of the CJA programme unfolded, many dynamics associated with theoretical liberal-local hybridity surfaced; however, it also became apparent that this theoretical formulation obscured important dimensions which were reshaping what peacebuilding practice is in the process of becoming in the emerging post-liberal world.
2014-05-30T00:00:00ZGraef, J. JulianHybridity, as it is currently understood in the Peace and Conflict Studies (PCS) and International Relations (IR) literature, is defined by the complex interactions between ‘the liberal peace’ and ‘the local’. However, under this theoretical liberal-local rubric, the ways in which power is practiced has already been determined; how resistance is expressed and the forms it assumes have already been established. While it has yielded numerous important insights into how power circulates and resistance manifests in peacebuilding operations, the theoretical approach conceals other significant dynamics which escape detection by ‘the liberal peace’ and ‘the local’. However, these undetected dimensions of hybridity comprise the very processes that emerge in ways which destabilise the boundaries between ‘the liberal peace’ and ‘the local’ and reshape the contours of the emerging post-liberal peace.
Instead of accepting the liberal-local distinction which defines this theoretical hybridity, this thesis advances an alternative methodological approach to exploring the tensions at play in peacebuilding projects. Rather than deploying theoretical distinctions in order to explain or understand complex hybrid processes, this thesis develops a methodological strategy for exploring the tensions between how actors design a peacebuilding project and how that project changes as actors work to translate that project into complex, everyday living sites (Callon, 1986; Law, 1997; Akrich, 1992). This tension is expressed as practical hybridity. The process of practical hybridity unfolds as the concrete material changes, modifications, and adaptations that emerge as actors appropriate and contingently translate organised practices in new ways and for different purposes. Through an ongoing process of practical hybridity, the boundaries and distinction which define the distinction between ‘the liberal peace’ and ‘the local’ become increasingly unstable. Amidst this instability, the practices which characterised ‘the liberal peace’ are becoming stretched into a post-liberal peace.
Drawing on the work of Richmond (2011a; Richmond & Mitchell, 2012), Latour (1987b; 1988; 2004), and Schatzki (2002), and based on over five months of field research, this this thesis traces the process of practical hybridity at play during the implementation and evaluation of a peacebuilding project in Liberia. I participated as a research assistant on a Randomised Control Trial (RCT), implemented by a small research team under the auspices of the Oxford University’s Centre for the Study of African Economies (CSAE). The team was assessing the impact of a legal empowerment programme managed by The Carter Center: the Community Justice Advisor (CJA) programme. As the CSAE’s evaluation of the CJA programme unfolded, many dynamics associated with theoretical liberal-local hybridity surfaced; however, it also became apparent that this theoretical formulation obscured important dimensions which were reshaping what peacebuilding practice is in the process of becoming in the emerging post-liberal world.The war of identities amidst the Syrian uprising : the continual reproduction of sub-state identities and the quest to reconstruct Syrian national identityRifai, Olahttps://hdl.handle.net/10023/63532021-10-30T02:00:36Z2014-06-01T00:00:00ZThis thesis is about identity clashes during the first two years of the Syrian uprising (from 15th of March 2011 to 15th of March 2013). Chiefly, it attempts to answer the following questions: what roles do identities play in the construction of power among the various identity groups? What were the reasons for the identity clashes that occurred during the Syrian uprising?. How can we evaluate the reproduction of identity during the uprising?. The Alawite, Sunni, Kurdish and Syrian national identities are used to illustrate how in the course of the uprising, these identities were consistently being reproduced as each group vied for power. This thesis argues that during the Syrian uprising these identities were subject to an enduring process of reproduction and reinforcement by discourse directed from above and from below, in which symbolic and materialistic elements played a vital role. The mode of analysis for this thesis is framed by the modernist and symbolist approaches to theories of nationalism and is underpinned by the theory of communal violence.
2014-06-01T00:00:00ZRifai, OlaThis thesis is about identity clashes during the first two years of the Syrian uprising (from 15th of March 2011 to 15th of March 2013). Chiefly, it attempts to answer the following questions: what roles do identities play in the construction of power among the various identity groups? What were the reasons for the identity clashes that occurred during the Syrian uprising?. How can we evaluate the reproduction of identity during the uprising?. The Alawite, Sunni, Kurdish and Syrian national identities are used to illustrate how in the course of the uprising, these identities were consistently being reproduced as each group vied for power. This thesis argues that during the Syrian uprising these identities were subject to an enduring process of reproduction and reinforcement by discourse directed from above and from below, in which symbolic and materialistic elements played a vital role. The mode of analysis for this thesis is framed by the modernist and symbolist approaches to theories of nationalism and is underpinned by the theory of communal violence.Latin books published in Paris, 1501-1540Mullins, Sophiehttps://hdl.handle.net/10023/63332020-07-01T02:02:46Z2014-06-01T00:00:00ZThis is a study of the Parisian Latin book industry in the first four decades of the sixteenth century. It challenges the assumption that the Reformation brought about a profound change in the European print world. Luther’s engagement with a mass audience is believed to have led to an increase in the number of vernacular publications produced by printers throughout Europe. This was not the case in Paris. Parisian booksellers traded on their established expertise with certain genres, such as theological texts, educational books, and works by classical authors, to maximise their readership both in Paris and farther afield.
Working in close proximity inspired the Parisian bookmen to unity and collaboration rather than enmity and direct competition. When printers, booksellers and publishers collaborated they were able to undertake bigger and riskier projects. Such projects might have involved testing new markets or technologies (such as Greek or music printing), or simply producing a book which required a high capital investment. The familial unity extended to the widows of printers, some of whom were able to capitalise on this and build substantial businesses of their own. This high level of collaboration and the continued focus on the established Latin market give the Parisian book world its very specific character. It also helped Paris build an international reputation for high-quality books.
2014-06-01T00:00:00ZMullins, SophieThis is a study of the Parisian Latin book industry in the first four decades of the sixteenth century. It challenges the assumption that the Reformation brought about a profound change in the European print world. Luther’s engagement with a mass audience is believed to have led to an increase in the number of vernacular publications produced by printers throughout Europe. This was not the case in Paris. Parisian booksellers traded on their established expertise with certain genres, such as theological texts, educational books, and works by classical authors, to maximise their readership both in Paris and farther afield.
Working in close proximity inspired the Parisian bookmen to unity and collaboration rather than enmity and direct competition. When printers, booksellers and publishers collaborated they were able to undertake bigger and riskier projects. Such projects might have involved testing new markets or technologies (such as Greek or music printing), or simply producing a book which required a high capital investment. The familial unity extended to the widows of printers, some of whom were able to capitalise on this and build substantial businesses of their own. This high level of collaboration and the continued focus on the established Latin market give the Parisian book world its very specific character. It also helped Paris build an international reputation for high-quality books.The cult of Corpus Christi in early modern Bavaria : pilgrimages, processions, and confraternities between 1550 and 1750Pentzlin, Nadja Irmgardhttps://hdl.handle.net/10023/63252020-04-02T02:03:17Z2015-06-25T00:00:00ZTransubstantiation and the cult of Corpus Christi became crucial Counter-Reformation symbols which were assigned an even more significant role during the process of Catholic renewal from the mid-sixteenth to the mid-eighteenth century. Practices outside Mass, such as pilgrimages, processions, and prayers in front of the consecrated host flourished, in particular, in early modern Bavaria. The former Duchy of Bavaria has generally been regarded as the archetypal ‘confessional’ state, as the Bavarian dukes from the House of Wittelsbach took the lead in propagating the cult of the Eucharist. They acted as patrons of Baroque Catholicism which was presented to the public as an obvious visual marker of Catholic identity. This study therefore investigates how the Eucharist was popularised in the Catholic duchy between 1550 and 1750, focusing on three major themes: pilgrimages, confraternities, and the Corpus Christi procession.
This study does not, however, approach the renewal of Catholicism in terms of a top-down process implemented by the Wittelsbach dukes as a method of stately power and control. Rather than arguing in favour of a state-sponsored piety imposed from above, this work explores the formation of Catholic confessional identity as a two-way-process of binding together elite and popular piety, and emphasizes the active role of the populace in constituting this identity. This is why this investigation draws primarily on research from local archives, using a rich body of both textual and visual evidence. Focusing especially on the visual aspects of Catholic piety, this project works towards an interdisciplinary approach in order to understand the ways in which Eucharistic devotion outside Mass was presented to and received by local communities within particular visual environments.
2015-06-25T00:00:00ZPentzlin, Nadja IrmgardTransubstantiation and the cult of Corpus Christi became crucial Counter-Reformation symbols which were assigned an even more significant role during the process of Catholic renewal from the mid-sixteenth to the mid-eighteenth century. Practices outside Mass, such as pilgrimages, processions, and prayers in front of the consecrated host flourished, in particular, in early modern Bavaria. The former Duchy of Bavaria has generally been regarded as the archetypal ‘confessional’ state, as the Bavarian dukes from the House of Wittelsbach took the lead in propagating the cult of the Eucharist. They acted as patrons of Baroque Catholicism which was presented to the public as an obvious visual marker of Catholic identity. This study therefore investigates how the Eucharist was popularised in the Catholic duchy between 1550 and 1750, focusing on three major themes: pilgrimages, confraternities, and the Corpus Christi procession.
This study does not, however, approach the renewal of Catholicism in terms of a top-down process implemented by the Wittelsbach dukes as a method of stately power and control. Rather than arguing in favour of a state-sponsored piety imposed from above, this work explores the formation of Catholic confessional identity as a two-way-process of binding together elite and popular piety, and emphasizes the active role of the populace in constituting this identity. This is why this investigation draws primarily on research from local archives, using a rich body of both textual and visual evidence. Focusing especially on the visual aspects of Catholic piety, this project works towards an interdisciplinary approach in order to understand the ways in which Eucharistic devotion outside Mass was presented to and received by local communities within particular visual environments.'Placing value' : reframing conceptions of the importance of the community parkOldfield, Alice E.https://hdl.handle.net/10023/63202019-11-07T03:04:40Z2014-12-01T00:00:00ZIn the UK, urban parks face a precarious future and, with projected cuts of over 65% to local authority discretionary funding (Local Government Association, 2012:2), it is ever more important to understand their value. This study interrogates the value of these resources from the perspective of the individual and, through a mixed method comparative case study of two community parks in Leeds, West Yorkshire, identifies four key challenges to existing framings of their significance.
Drawing on primary observational, social survey and interview data, boundaries constructed between forms of value are, firstly, problematized with fluidity recognised between use and non-use aspects. Secondly, a range of previously-omitted past-related values are identified. Negative elements of significance are, then, thirdly, highlighted as heavily interwoven with positive accounts of importance and emphasised as key omissions in prior representations of value. Before, finally, value is stressed as spatially relative, with comparison with other leisure resources noted as an inherent facet of accounts. Taken together, these challenges demarcate an individual perspective of value as notably distinct from those levelled at other scales, such as the firm or community, as it emphasised that, from this perspective, the value of a resource must be rethought as a relational property created in the interaction between people and their environment, rather than an absolute property assigned to a space.
Organisations, such as Nesta (Neal, 2013:21) have emphasised a need to ‘rethink’ the funding and management of urban parks, moving towards “mixed funding models”, incorporating some level of community voluntarism. This assumed involvement is, however, premised on community engagement which is far from certain. As such, there is a pressing need to understand the value attached to urban parks to understand the scope for expectations of voluntarism to be truly fulfilled.
2014-12-01T00:00:00ZOldfield, Alice E.In the UK, urban parks face a precarious future and, with projected cuts of over 65% to local authority discretionary funding (Local Government Association, 2012:2), it is ever more important to understand their value. This study interrogates the value of these resources from the perspective of the individual and, through a mixed method comparative case study of two community parks in Leeds, West Yorkshire, identifies four key challenges to existing framings of their significance.
Drawing on primary observational, social survey and interview data, boundaries constructed between forms of value are, firstly, problematized with fluidity recognised between use and non-use aspects. Secondly, a range of previously-omitted past-related values are identified. Negative elements of significance are, then, thirdly, highlighted as heavily interwoven with positive accounts of importance and emphasised as key omissions in prior representations of value. Before, finally, value is stressed as spatially relative, with comparison with other leisure resources noted as an inherent facet of accounts. Taken together, these challenges demarcate an individual perspective of value as notably distinct from those levelled at other scales, such as the firm or community, as it emphasised that, from this perspective, the value of a resource must be rethought as a relational property created in the interaction between people and their environment, rather than an absolute property assigned to a space.
Organisations, such as Nesta (Neal, 2013:21) have emphasised a need to ‘rethink’ the funding and management of urban parks, moving towards “mixed funding models”, incorporating some level of community voluntarism. This assumed involvement is, however, premised on community engagement which is far from certain. As such, there is a pressing need to understand the value attached to urban parks to understand the scope for expectations of voluntarism to be truly fulfilled.Molecular studies of the Tacaribe virus nucleoprotein (NP): identification and characterisation of virus-host interactions as novel anti-arenavirus drug targetsMeyer, Bjoernhttps://hdl.handle.net/10023/63192019-03-29T10:30:05Z2014-01-01T00:00:00ZArenaviruses cause an estimated 300,000 – 500,000 infections annually. Currently there is no arenavirus-specific antiviral drug available to treat these infections. This study sought to use the non-pathogenic New World arenavirus Tacaribe virus (TCRV) as a model for the pathogenic Junin virus (JUNV) and Machupo virus (MACV) that cause haemorrhagic fevers in South America. TCRV was used to explore three different approaches in the search for an antiviral drug against arenavirus infection targeted specifically against the viral nucleoprotein (NP). Of the four expressed arenaviral proteins, NP is the most abundant and is thought to be of multifunctional nature involved in viral replication, suppression of the innate immune system and viral egress. The approaches to find targets for broad-spectrum anti-arenaviral drugs were high throughput screens (HTS) with purified NP using thermal shift assays, exploring the virus interactions with the innate immune system and identifying virus-host protein-protein interactions. HTS resulted in the identification of two small-molecule compounds, [5-(2-Furyl)thien-2-yl]methanol and cyclosporine A (CsA), showing broad-spectrum activity against arenaviruses. Interferon-stimulated genes (ISGs), such as IFIT3, were identified to reduce viral titres and potential 202 protein-interactions between NP and host cell proteins were identified, of which the interaction with apoptosis-inducing factor 1 (AIF1) was described further. To characterise the importance of these interactions as potential drug targets further, a TCRV reverse genetics system was constructed.
2014-01-01T00:00:00ZMeyer, BjoernArenaviruses cause an estimated 300,000 – 500,000 infections annually. Currently there is no arenavirus-specific antiviral drug available to treat these infections. This study sought to use the non-pathogenic New World arenavirus Tacaribe virus (TCRV) as a model for the pathogenic Junin virus (JUNV) and Machupo virus (MACV) that cause haemorrhagic fevers in South America. TCRV was used to explore three different approaches in the search for an antiviral drug against arenavirus infection targeted specifically against the viral nucleoprotein (NP). Of the four expressed arenaviral proteins, NP is the most abundant and is thought to be of multifunctional nature involved in viral replication, suppression of the innate immune system and viral egress. The approaches to find targets for broad-spectrum anti-arenaviral drugs were high throughput screens (HTS) with purified NP using thermal shift assays, exploring the virus interactions with the innate immune system and identifying virus-host protein-protein interactions. HTS resulted in the identification of two small-molecule compounds, [5-(2-Furyl)thien-2-yl]methanol and cyclosporine A (CsA), showing broad-spectrum activity against arenaviruses. Interferon-stimulated genes (ISGs), such as IFIT3, were identified to reduce viral titres and potential 202 protein-interactions between NP and host cell proteins were identified, of which the interaction with apoptosis-inducing factor 1 (AIF1) was described further. To characterise the importance of these interactions as potential drug targets further, a TCRV reverse genetics system was constructed.Surface plasmon polariton modification in top-emitting organic light-emitting diodes for enhanced light outcouplingFuchs, C.Schwab, T.Wieczorek, M.Gather, M.C.Hofmann, S.Leo, K.Scholz, R.https://hdl.handle.net/10023/61582022-04-14T11:30:29Z2014-01-01T00:00:00ZWe report on the enhanced light outcoupling efficiency of monochrome top-emitting organic light-emitting diodes (OLEDs). These OLEDs incorporate a hole transport layer (HTL) material with a substantially lower refractive index (∼ 1:5) than the emitter material or the standard HTL material (∼ 1:8) of a reference device. This low-index HTL is situated between the opaque bottom metal contact (anode) and the active emission layer. Compared to an HTL with common refractive index, the dispersion relation of the surface plasmon polariton (SPP) mode from the opaque metal contact is shifted to smaller in-plane wavenumbers. This shift enhances the outcoupling efficiency as it reduces the total dissipated power of the emitter. Furthermore, the excitation of the coupled SPPs at the thin transparent metal top contact (cathode) is avoided by using an ultrathin top electrode. Hence, the coupling of the electroluminescence from the emitter molecules to all non-radiative evanescent modes, with respect to the emitter material, is reduced by at least a factor of two, additionally increasing the outcoupling efficiency. Furthermore, for sufficiently high refractive index contrast the shift of the SPP at the anode/organic interface can lead to in-plane wavenumbers smaller than the wavenumber within the organic emitter layer and outcoupling of all excited modes by high index light extraction structures, e.g. microlens, seems feasible. In accordance to optical simulations, the external quantum efficiency is enhanced by about 20% for monochrome green emitting OLEDs with low refractive index HTL compared to a reference sample.
2014-01-01T00:00:00ZFuchs, C.Schwab, T.Wieczorek, M.Gather, M.C.Hofmann, S.Leo, K.Scholz, R.We report on the enhanced light outcoupling efficiency of monochrome top-emitting organic light-emitting diodes (OLEDs). These OLEDs incorporate a hole transport layer (HTL) material with a substantially lower refractive index (∼ 1:5) than the emitter material or the standard HTL material (∼ 1:8) of a reference device. This low-index HTL is situated between the opaque bottom metal contact (anode) and the active emission layer. Compared to an HTL with common refractive index, the dispersion relation of the surface plasmon polariton (SPP) mode from the opaque metal contact is shifted to smaller in-plane wavenumbers. This shift enhances the outcoupling efficiency as it reduces the total dissipated power of the emitter. Furthermore, the excitation of the coupled SPPs at the thin transparent metal top contact (cathode) is avoided by using an ultrathin top electrode. Hence, the coupling of the electroluminescence from the emitter molecules to all non-radiative evanescent modes, with respect to the emitter material, is reduced by at least a factor of two, additionally increasing the outcoupling efficiency. Furthermore, for sufficiently high refractive index contrast the shift of the SPP at the anode/organic interface can lead to in-plane wavenumbers smaller than the wavenumber within the organic emitter layer and outcoupling of all excited modes by high index light extraction structures, e.g. microlens, seems feasible. In accordance to optical simulations, the external quantum efficiency is enhanced by about 20% for monochrome green emitting OLEDs with low refractive index HTL compared to a reference sample.Mapping parallel programs to heterogeneous CPU/GPU architectures using a Monte Carlo Tree SearchGoli, MehdiMcCall, JohnBrown, Christopher MarkJanjic, VladimirHammond, Kevinhttps://hdl.handle.net/10023/61572022-04-13T14:30:10Z2013-06-20T00:00:00ZThe single core processor, which has dominated for over 30 years, is now obsolete with recent trends increasing towards parallel systems, demanding a huge shift in programming techniques and practices. Moreover, we are rapidly moving towards an age where almost all programming will be targeting parallel systems. Parallel hardware is rapidly evolving, with large heterogeneous systems, typically comprising a mixture of CPUs and GPUs, becoming the mainstream. Additionally, with this increasing heterogeneity comes increasing complexity: not only does the programmer have to worry about where and how to express the parallelism, they must also express an efficient mapping of resources to the available system. This generally requires in-depth expert knowledge that most application programmers do not have. In this paper we describe a new technique that derives, automatically, optimal mappings for an application onto a heterogeneous architecture, using a Monte Carlo Tree Search algorithm. Our technique exploits high-level design patterns, targeting a set of well-specified parallel skeletons. We demonstrate that our MCTS on a convolution example obtained speedups that are within 5% of the speedups achieved by a hand-tuned version of the same application.
2013-06-20T00:00:00ZGoli, MehdiMcCall, JohnBrown, Christopher MarkJanjic, VladimirHammond, KevinThe single core processor, which has dominated for over 30 years, is now obsolete with recent trends increasing towards parallel systems, demanding a huge shift in programming techniques and practices. Moreover, we are rapidly moving towards an age where almost all programming will be targeting parallel systems. Parallel hardware is rapidly evolving, with large heterogeneous systems, typically comprising a mixture of CPUs and GPUs, becoming the mainstream. Additionally, with this increasing heterogeneity comes increasing complexity: not only does the programmer have to worry about where and how to express the parallelism, they must also express an efficient mapping of resources to the available system. This generally requires in-depth expert knowledge that most application programmers do not have. In this paper we describe a new technique that derives, automatically, optimal mappings for an application onto a heterogeneous architecture, using a Monte Carlo Tree Search algorithm. Our technique exploits high-level design patterns, targeting a set of well-specified parallel skeletons. We demonstrate that our MCTS on a convolution example obtained speedups that are within 5% of the speedups achieved by a hand-tuned version of the same application.Gammaherpesvirus infection modulates the temporal and spatial expression of SCGB1A1 (CCSP) and BPIFA1 (SPLUNC1) in the respiratory tractLeeming, Gail HKipar, AnjaHughes, David JBingle, LynneBennett, ElaineMoyo, Nathifa ATripp, Ralph ABigley, Alison LBingle, Colin DSample, Jeffery TStewart, James Phttps://hdl.handle.net/10023/60042024-03-26T00:41:48Z2015-06-01T00:00:00ZMurine γ-herpesvirus 68 (MHV-68) infection of Mus musculus-derived strains of mice is an established model of γ-herpesvirus infection. We have previously developed an alternative system using a natural host, the wood mouse (Apodemus sylvaticus), and shown that the MHV-68 M3 chemokine-binding protein contributes significantly to MHV-68 pathogenesis. Here we demonstrate in A. sylvaticus using high-density micro-arrays that M3 influences the expression of genes involved in the host response including Scgb1a1 and Bpifa1 that encode potential innate defense proteins secreted into the respiratory tract. Further analysis of MHV-68-infected animals showed that the levels of both protein and RNA for SCGB1A1 and BPIFA1 were decreased at day 7 post infection (p.i.) but increased at day 14 p.i. as compared with M3-deficient and mock-infected animals. The modulation of expression was most pronounced in bronchioles but was also present in the bronchi and trachea. Double staining using RNA in situ hybridization and immunohistology demonstrated that much of the BPIFA1 expression occurs in club cells along with SCGB1A1 and that BPIFA1 is stored within granules in these cells. The increase in SCGB1A1 and BPIFA1 expression at day 14 p.i. was associated with the differentiation of club cells into mucus-secreting cells. Our data highlight the role of club cells and the potential of SCGB1A1 and BPIFA1 as innate defense mediators during respiratory virus infection.
This work was supported by a Royal Society (London) University Research Fellowship (to JPS), by Biotechnology and Biological Sciences Research Council (UK) grants BB/K009664/1 (to JPS, AK, and GHL) and BB/K009737/1 (CDB and LB), US Public Health Service grant CA090208, the Penn State Hershey Cancer Institute, and a Biotechnology and Biological Sciences Research Council studentship (to GHL).
2015-06-01T00:00:00ZLeeming, Gail HKipar, AnjaHughes, David JBingle, LynneBennett, ElaineMoyo, Nathifa ATripp, Ralph ABigley, Alison LBingle, Colin DSample, Jeffery TStewart, James PMurine γ-herpesvirus 68 (MHV-68) infection of Mus musculus-derived strains of mice is an established model of γ-herpesvirus infection. We have previously developed an alternative system using a natural host, the wood mouse (Apodemus sylvaticus), and shown that the MHV-68 M3 chemokine-binding protein contributes significantly to MHV-68 pathogenesis. Here we demonstrate in A. sylvaticus using high-density micro-arrays that M3 influences the expression of genes involved in the host response including Scgb1a1 and Bpifa1 that encode potential innate defense proteins secreted into the respiratory tract. Further analysis of MHV-68-infected animals showed that the levels of both protein and RNA for SCGB1A1 and BPIFA1 were decreased at day 7 post infection (p.i.) but increased at day 14 p.i. as compared with M3-deficient and mock-infected animals. The modulation of expression was most pronounced in bronchioles but was also present in the bronchi and trachea. Double staining using RNA in situ hybridization and immunohistology demonstrated that much of the BPIFA1 expression occurs in club cells along with SCGB1A1 and that BPIFA1 is stored within granules in these cells. The increase in SCGB1A1 and BPIFA1 expression at day 14 p.i. was associated with the differentiation of club cells into mucus-secreting cells. Our data highlight the role of club cells and the potential of SCGB1A1 and BPIFA1 as innate defense mediators during respiratory virus infection.Repeating history : execution replay for Parallel Haskell programsFerrerio, HenriqueJanjic, VladimirCastro, LauraHammond, Kevinhttps://hdl.handle.net/10023/58952023-04-19T00:38:26Z2013-01-01T00:00:00ZParallel profiling tools, such as ThreadScope for Parallel Haskell, allow programmers to obtain information about the performance of their parallel programs. However, the information they provide is not always sufficiently detailed to precisely pinpoint the cause of some per- formance problems. Often, this is because the cost of obtaining that information would be prohibitive for a complete program execution. In this paper, we adapt the well-known technique of execution replay to make it possible to simulate a previous run of a program. We ensure that the non-deterministic parallel behaviour of the application is prop- erly emulated while the deterministic functional code is run unmodified. In this way, we can gather additional data about the behaviour of a par- allel program by replaying some parts of it with more detailed profiling information. We exploit this ability to identify performance bottlenecks in a quicksort implementation, and to derive a version that gives better speedups on multicore machines.
2013-01-01T00:00:00ZFerrerio, HenriqueJanjic, VladimirCastro, LauraHammond, KevinParallel profiling tools, such as ThreadScope for Parallel Haskell, allow programmers to obtain information about the performance of their parallel programs. However, the information they provide is not always sufficiently detailed to precisely pinpoint the cause of some per- formance problems. Often, this is because the cost of obtaining that information would be prohibitive for a complete program execution. In this paper, we adapt the well-known technique of execution replay to make it possible to simulate a previous run of a program. We ensure that the non-deterministic parallel behaviour of the application is prop- erly emulated while the deterministic functional code is run unmodified. In this way, we can gather additional data about the behaviour of a par- allel program by replaying some parts of it with more detailed profiling information. We exploit this ability to identify performance bottlenecks in a quicksort implementation, and to derive a version that gives better speedups on multicore machines.Maximal subsemigroups of the semigroup of all mappings on an infinite setEast, J.Mitchell, James DavidPéresse, Y.https://hdl.handle.net/10023/57932023-04-18T09:45:45Z2015-03-01T00:00:00ZIn this paper we classify the maximal subsemigroups of the full transformation semigroup ΩΩ, which consists of all mappings on the infinite set Ω, containing certain subgroups of the symmetric group Sym (Ω) on Ω. In 1965 Gavrilov showed that there are five maximal subsemigroups of ΩΩ containing Sym (Ω) when Ω is countable, and in 2005 Pinsker extended Gavrilov's result to sets of arbitrary cardinality. We classify the maximal subsemigroups of ΩΩ on a set Ω of arbitrary infinite cardinality containing one of the following subgroups of Sym (Ω): the pointwise stabiliser of a non-empty finite subset of Ω, the stabiliser of an ultrafilter on Ω, or the stabiliser of a partition of Ω into finitely many subsets of equal cardinality. If G is any of these subgroups, then we deduce a characterisation of the mappings f, g ∈ ΩΩ such that the semigroup generated by G ∪ {f, g} equals ΩΩ.
2015-03-01T00:00:00ZEast, J.Mitchell, James DavidPéresse, Y.In this paper we classify the maximal subsemigroups of the full transformation semigroup ΩΩ, which consists of all mappings on the infinite set Ω, containing certain subgroups of the symmetric group Sym (Ω) on Ω. In 1965 Gavrilov showed that there are five maximal subsemigroups of ΩΩ containing Sym (Ω) when Ω is countable, and in 2005 Pinsker extended Gavrilov's result to sets of arbitrary cardinality. We classify the maximal subsemigroups of ΩΩ on a set Ω of arbitrary infinite cardinality containing one of the following subgroups of Sym (Ω): the pointwise stabiliser of a non-empty finite subset of Ω, the stabiliser of an ultrafilter on Ω, or the stabiliser of a partition of Ω into finitely many subsets of equal cardinality. If G is any of these subgroups, then we deduce a characterisation of the mappings f, g ∈ ΩΩ such that the semigroup generated by G ∪ {f, g} equals ΩΩ.To walk upon the grass : the impact of the University of St Andrews' Lady Literate in Arts, 1877-1892Smith, Elisabeth Margarethttps://hdl.handle.net/10023/55702019-10-15T02:04:38Z2014-01-01T00:00:00ZIn 1877 the University of St Andrews initiated a unique qualification, the Lady Literate in Arts, which
came into existence initially as the LA, the Literate in Arts, a higher certificate available to women
only. Awarded by examination but as a result of a programme of distance learning, it was conceived
and explicitly promoted as a degree-level qualification at a time when women had no access to
matriculation at Scottish universities and little anywhere in the United Kingdom. From small
beginnings it expanded both in numbers of candidates and in spread of subjects and it lasted until
the early 1930s by which time over 36,000 examinations had been taken and more than 5,000
women had completed the course. The scheme had emerged in response to various needs and
external pressures which shaped its character. The purpose of this thesis is to assess the nature and
achievements of the LLA in its first fifteen years and to establish its place within the wider
movement for female equality of status and opportunity which developed in the later decades of the
nineteenth century.
The conditions under which the university introduced the LLA, its reasons for doing so, the nature of
the qualification, its progress and development in the years before 1892 when women were
admitted to Scottish universities as undergraduates and the consequences for the university itself
are all examined in detail. The geographical and social origins and the educational backgrounds of
the candidates themselves are analysed along with their age structure, their uptake of LLA subjects
and the completion rates for the award. All of these are considered against the background of the
students' later careers and life experiences.
This thesis aims to discover the extent to which the LLA was influential in shaping the lives of its
participants and in advancing the broader case for female higher education. It seeks to establish for
the first time the contribution that St Andrews LLA women made to society at large and to the wider
movement for female emancipation.
2014-01-01T00:00:00ZSmith, Elisabeth MargaretIn 1877 the University of St Andrews initiated a unique qualification, the Lady Literate in Arts, which
came into existence initially as the LA, the Literate in Arts, a higher certificate available to women
only. Awarded by examination but as a result of a programme of distance learning, it was conceived
and explicitly promoted as a degree-level qualification at a time when women had no access to
matriculation at Scottish universities and little anywhere in the United Kingdom. From small
beginnings it expanded both in numbers of candidates and in spread of subjects and it lasted until
the early 1930s by which time over 36,000 examinations had been taken and more than 5,000
women had completed the course. The scheme had emerged in response to various needs and
external pressures which shaped its character. The purpose of this thesis is to assess the nature and
achievements of the LLA in its first fifteen years and to establish its place within the wider
movement for female equality of status and opportunity which developed in the later decades of the
nineteenth century.
The conditions under which the university introduced the LLA, its reasons for doing so, the nature of
the qualification, its progress and development in the years before 1892 when women were
admitted to Scottish universities as undergraduates and the consequences for the university itself
are all examined in detail. The geographical and social origins and the educational backgrounds of
the candidates themselves are analysed along with their age structure, their uptake of LLA subjects
and the completion rates for the award. All of these are considered against the background of the
students' later careers and life experiences.
This thesis aims to discover the extent to which the LLA was influential in shaping the lives of its
participants and in advancing the broader case for female higher education. It seeks to establish for
the first time the contribution that St Andrews LLA women made to society at large and to the wider
movement for female emancipation.The protein coexpression problem in biotechnology and biomedicine : virus 2A and 2A-like sequences provide a solutionLuke, Garry AlecRyan, Martin Denishttps://hdl.handle.net/10023/55182024-03-28T00:41:20Z2013-10-01T00:00:00ZSynthetic biology enables us to create genes virtually at will. Ensuring that multiple genes are efficiently co-expressed within the same cell – to assemble multimeric complexes, to transfer biochemical pathways, to transfer ‘traits’, is more problematic. Viruses such as picornaviruses accomplish exactly this task: they generate multiple, different, proteins from a single open reading frame. The study of how foot-and-mouth disease virus (FMDV) controls it’s protein biogenesis lead to the discovery of a short oligopeptide sequence, ‘2A’, that is able to mediate a co-translational ‘cleavage’ between proteins. 2A and ‘2A-like’ sequences (from other viruses and cellular sequences) can be used to concatenate multiple gene sequences into a single gene, ensuring their co-expression within the same cell. These sequences are now being used in the treatment of cancer, in the production of pluripotent stem cells, to create transgenic plants and animals amongst a host of other biotechnological and biomedical applications.
The authors acknowledge the support of the UK Biotechnology and Biological Sciences Research Council (BBSRC), the Wellcome Trust and the UK Medical Research Council (MRC).
2013-10-01T00:00:00ZLuke, Garry AlecRyan, Martin DenisSynthetic biology enables us to create genes virtually at will. Ensuring that multiple genes are efficiently co-expressed within the same cell – to assemble multimeric complexes, to transfer biochemical pathways, to transfer ‘traits’, is more problematic. Viruses such as picornaviruses accomplish exactly this task: they generate multiple, different, proteins from a single open reading frame. The study of how foot-and-mouth disease virus (FMDV) controls it’s protein biogenesis lead to the discovery of a short oligopeptide sequence, ‘2A’, that is able to mediate a co-translational ‘cleavage’ between proteins. 2A and ‘2A-like’ sequences (from other viruses and cellular sequences) can be used to concatenate multiple gene sequences into a single gene, ensuring their co-expression within the same cell. These sequences are now being used in the treatment of cancer, in the production of pluripotent stem cells, to create transgenic plants and animals amongst a host of other biotechnological and biomedical applications.A genetic algorithm for face fittingHunter, David WilliamTiddeman, Bernard PaulPerrett, David Ianhttps://hdl.handle.net/10023/54432022-04-14T20:39:20Z2012-02-01T00:00:00ZAccurate estimation of the shape of human faces has many applications from computer-imaging to psychological research. One well known method is to fit a Three Dimensional Morphable Model to a target image. This method is attractive as the faces it constructs are already projected onto an orthogonal basis making further manipulation and analysis easier. So far its use in these fields has been limited the inaccuracy and inconvenience of current face-fitting methods. We present a method based on Genetic Algorithms that avoid the local minima and gradient image errors that current methods suffer from. It has the added advantage of requiring no manual interaction to initialise or guide the fitting process.
2012-02-01T00:00:00ZHunter, David WilliamTiddeman, Bernard PaulPerrett, David IanAccurate estimation of the shape of human faces has many applications from computer-imaging to psychological research. One well known method is to fit a Three Dimensional Morphable Model to a target image. This method is attractive as the faces it constructs are already projected onto an orthogonal basis making further manipulation and analysis easier. So far its use in these fields has been limited the inaccuracy and inconvenience of current face-fitting methods. We present a method based on Genetic Algorithms that avoid the local minima and gradient image errors that current methods suffer from. It has the added advantage of requiring no manual interaction to initialise or guide the fitting process.A Bayesian space-time model for discrete spread processes on a latticeLong, J.A.Nelson, T.A.Robertson, ColinNathoo, F.S.https://hdl.handle.net/10023/54182023-04-25T23:37:31Z2012-06-01T00:00:00ZIn this article we present a Bayesian Markov model for investigating environmental spread processes. We formulate a model where the spread of a disease over a heterogeneous landscape through time is represented as a probabilistic function of two processes: local diffusion and random-jump dispersal. This formulation represents two mechanisms of spread which result in highly peaked and long-tailed distributions of dispersal distances (i.e., local and long-distance spread), commonly observed in the spread of infectious diseases and biological invasions. We demonstrate the properties of this model using a simulation experiment and an empirical case study - the spread of mountain pine beetle in western Canada. Posterior predictive checking was used to validate the number of newly inhabited regions in each time period. The model performed well in the simulation study in which a goodness-of-fit statistic measuring the number of newly inhabited regions in each time interval fell within the 95% posterior predictive credible interval in over 97% of simulations. The case study of a mountain pine beetle infestation in western Canada (1999-2009) extended the base model in two ways. First, spatial covariates thought to impact the local diffusion parameters, elevation and forest cover, were included in the model. Second, a refined definition for translocation or jump-dispersal based on mountain pine beetle ecology was incorporated improving the fit of the model. Posterior predictive checks on the mountain pine beetle model found that the observed goodness-of-fit test statistic fell within the 95% posterior predictive credible interval for 8 out of 10. years. The simulation study and case study provide evidence that the model presented here is both robust and flexible; and is therefore appropriate for a wide range of spread processes in epidemiology and ecology.
Funding for this work was provided by GEOIDE through the Government of Canada’s Networks for Centres of Excellence program.
2012-06-01T00:00:00ZLong, J.A.Nelson, T.A.Robertson, ColinNathoo, F.S.In this article we present a Bayesian Markov model for investigating environmental spread processes. We formulate a model where the spread of a disease over a heterogeneous landscape through time is represented as a probabilistic function of two processes: local diffusion and random-jump dispersal. This formulation represents two mechanisms of spread which result in highly peaked and long-tailed distributions of dispersal distances (i.e., local and long-distance spread), commonly observed in the spread of infectious diseases and biological invasions. We demonstrate the properties of this model using a simulation experiment and an empirical case study - the spread of mountain pine beetle in western Canada. Posterior predictive checking was used to validate the number of newly inhabited regions in each time period. The model performed well in the simulation study in which a goodness-of-fit statistic measuring the number of newly inhabited regions in each time interval fell within the 95% posterior predictive credible interval in over 97% of simulations. The case study of a mountain pine beetle infestation in western Canada (1999-2009) extended the base model in two ways. First, spatial covariates thought to impact the local diffusion parameters, elevation and forest cover, were included in the model. Second, a refined definition for translocation or jump-dispersal based on mountain pine beetle ecology was incorporated improving the fit of the model. Posterior predictive checks on the mountain pine beetle model found that the observed goodness-of-fit test statistic fell within the 95% posterior predictive credible interval for 8 out of 10. years. The simulation study and case study provide evidence that the model presented here is both robust and flexible; and is therefore appropriate for a wide range of spread processes in epidemiology and ecology.Italian queens in the ninth and tenth centuriesCimino, Robertahttps://hdl.handle.net/10023/53592019-04-01T10:57:04Z2014-06-26T00:00:00ZThis thesis investigates the role of queens in ninth and tenth century Italy. During the Carolingian period the Italian kingdom saw significant involvement of royal women in political affairs. This trend continued after the Carolingian empire collapsed in 888, as Italy became the theatre of struggles for the royal and imperial title, which resulted in a quick succession of local rulers. By investigating Italian queens, my work aims at reassessing some aspects of Italian royal politics. Furthermore, it contributes to the study of medieval queenship, exploring a context which has been overlooked with regard to female authority. The work which has been done on queens over the last decades has attempted to build a coherent model of early medieval queenship; scholars have often privileged the analysis of continuities and similarities in the study of queens’ prerogatives and resources. This thesis challenges this model and underlines the peculiarities of individual queens. My analysis demonstrates that, by deconstructing the coherent model established by historiography, it is possible to underline the individual experiences, resources and strengths of each royal woman, and therefore create a new way to look at the history of queens and queenship.
The thesis is divided into four main thematic sections. After having introduced the subject and the relevant historiography on the topic in the introduction, in Chapter 2 I consider ideas about queenship as expressed by narrative and normative sources. Chapter 3 deals with royal diplomas, which are a valuable resource for the understanding of queens’ reigns. Chapter 4 analyses queens’ dowers and monastic patronage. Chapter 5 examines the experience of Italian royal widows. Finally, the conclusive chapter outlines the significance of this thesis for the broader understanding of medieval queenship.
2014-06-26T00:00:00ZCimino, RobertaThis thesis investigates the role of queens in ninth and tenth century Italy. During the Carolingian period the Italian kingdom saw significant involvement of royal women in political affairs. This trend continued after the Carolingian empire collapsed in 888, as Italy became the theatre of struggles for the royal and imperial title, which resulted in a quick succession of local rulers. By investigating Italian queens, my work aims at reassessing some aspects of Italian royal politics. Furthermore, it contributes to the study of medieval queenship, exploring a context which has been overlooked with regard to female authority. The work which has been done on queens over the last decades has attempted to build a coherent model of early medieval queenship; scholars have often privileged the analysis of continuities and similarities in the study of queens’ prerogatives and resources. This thesis challenges this model and underlines the peculiarities of individual queens. My analysis demonstrates that, by deconstructing the coherent model established by historiography, it is possible to underline the individual experiences, resources and strengths of each royal woman, and therefore create a new way to look at the history of queens and queenship.
The thesis is divided into four main thematic sections. After having introduced the subject and the relevant historiography on the topic in the introduction, in Chapter 2 I consider ideas about queenship as expressed by narrative and normative sources. Chapter 3 deals with royal diplomas, which are a valuable resource for the understanding of queens’ reigns. Chapter 4 analyses queens’ dowers and monastic patronage. Chapter 5 examines the experience of Italian royal widows. Finally, the conclusive chapter outlines the significance of this thesis for the broader understanding of medieval queenship.Perceptual integration across natural monocular regionsZeiner, Katharina MariaSpitschan, ManuelHarris, Juliehttps://hdl.handle.net/10023/53492022-04-12T11:30:28Z2014-03-05T00:00:00ZNatural scenes contain hidden regions, or occlusions, that differ in the two eyes, resulting in monocular regions that can only be seen by one eye. Such monocular regions appear to not be suppressed but seem to be integrated into the scene percept. Here we explore how the two eyes' views are combined to represent a scene that contains monocular regions, partially hidden behind a foreground occluding “fence.” We measured performance in a density/numerosity discrimination task for scenes containing differing amounts of binocular and monocular information. We find that information from a number of separate monocular regions can be integrated into our overall percept of dot density/numerosity, although different observers use different strategies. If, however, both monocular and binocular information is present, observers appear to ignore the purely monocular regions, relying solely on the binocular information when making density/numerosity judgments. Our work suggests that binocular regions are favored over monocular regions, such that information from monocular regions is effectively ignored when binocular regions are present in a scene.
2014-03-05T00:00:00ZZeiner, Katharina MariaSpitschan, ManuelHarris, JulieNatural scenes contain hidden regions, or occlusions, that differ in the two eyes, resulting in monocular regions that can only be seen by one eye. Such monocular regions appear to not be suppressed but seem to be integrated into the scene percept. Here we explore how the two eyes' views are combined to represent a scene that contains monocular regions, partially hidden behind a foreground occluding “fence.” We measured performance in a density/numerosity discrimination task for scenes containing differing amounts of binocular and monocular information. We find that information from a number of separate monocular regions can be integrated into our overall percept of dot density/numerosity, although different observers use different strategies. If, however, both monocular and binocular information is present, observers appear to ignore the purely monocular regions, relying solely on the binocular information when making density/numerosity judgments. Our work suggests that binocular regions are favored over monocular regions, such that information from monocular regions is effectively ignored when binocular regions are present in a scene.Optimisation of engineered Escherichia coli biofilms for enzymatic biosynthesis of L-halotryptophansPerni, S.Hackett, L.Goss, R.J.M.Simmons, M.J.Overton, T.W.https://hdl.handle.net/10023/52412022-04-12T14:30:25Z2013-11-04T00:00:00ZEngineered biofilms comprising a single recombinant species have demonstrated remarkable activity as novel biocatalysts for a range of applications. In this work, we focused on the biotransformation of 5-haloindole into 5-halotryptophan, a pharmaceutical intermediate, using Escherichia coli expressing a recombinant tryptophan synthase enzyme encoded by plasmid pSTB7. To optimise the reaction we compared two E. coli K-12 strains (MC4100 and MG1655) and their ompR234 mutants, which overproduce the adhesin curli (PHL644 and PHL628). The ompR234 mutation increased the quantity of biofilm in both MG1655 and MC4100 backgrounds. In all cases, no conversion of 5-haloindoles was observed using cells without the pSTB7 plasmid. Engineered biofilms of strains PHL628 pSTB7 and PHL644 pSTB7 generated more 5-halotryptophan than their corresponding planktonic cells. Flow cytometry revealed that the vast majority of cells were alive after 24 hour biotransformation reactions, both in planktonic and biofilm forms, suggesting that cell viability was not a major factor in the greater performance of biofilm reactions. Monitoring 5-haloindole depletion, 5-halotryptophan synthesis and the percentage conversion of the biotransformation reaction suggested that there were inherent differences between strains MG1655 and MC4100, and between planktonic and biofilm cells, in terms of tryptophan and indole metabolism and transport. The study has reinforced the need to thoroughly investigate bacterial physiology and make informed strain selections when developing biotransformation reactions.
This study was funded by a UK Biotechnology & Biological Sciences Research Council grant (BB/I006834/1) to MJS, RJMG and TWO and a quota PhD studentship to LH. The Accuri C6 instrument was awarded to TWO as a BD Accuri Creativity Award.
2013-11-04T00:00:00ZPerni, S.Hackett, L.Goss, R.J.M.Simmons, M.J.Overton, T.W.Engineered biofilms comprising a single recombinant species have demonstrated remarkable activity as novel biocatalysts for a range of applications. In this work, we focused on the biotransformation of 5-haloindole into 5-halotryptophan, a pharmaceutical intermediate, using Escherichia coli expressing a recombinant tryptophan synthase enzyme encoded by plasmid pSTB7. To optimise the reaction we compared two E. coli K-12 strains (MC4100 and MG1655) and their ompR234 mutants, which overproduce the adhesin curli (PHL644 and PHL628). The ompR234 mutation increased the quantity of biofilm in both MG1655 and MC4100 backgrounds. In all cases, no conversion of 5-haloindoles was observed using cells without the pSTB7 plasmid. Engineered biofilms of strains PHL628 pSTB7 and PHL644 pSTB7 generated more 5-halotryptophan than their corresponding planktonic cells. Flow cytometry revealed that the vast majority of cells were alive after 24 hour biotransformation reactions, both in planktonic and biofilm forms, suggesting that cell viability was not a major factor in the greater performance of biofilm reactions. Monitoring 5-haloindole depletion, 5-halotryptophan synthesis and the percentage conversion of the biotransformation reaction suggested that there were inherent differences between strains MG1655 and MC4100, and between planktonic and biofilm cells, in terms of tryptophan and indole metabolism and transport. The study has reinforced the need to thoroughly investigate bacterial physiology and make informed strain selections when developing biotransformation reactions.Vortical control of forced two-dimensional turbulenceFontane, Jerome Jacob LouisDritschel, David GerardScott, Richard Kirknesshttps://hdl.handle.net/10023/52362023-04-18T09:50:15Z2013-01-14T00:00:00ZA new numerical technique for the simulation of forced two-dimensional turbulence[D. Dritschel and J. Fontane, “The combined Lagrangian advection method,” J. Comput. Phys.229, 5408–5417 (Year: 2010)10.1016/j.jcp.2010.03.048] is used to examine the validity of Kraichnan-Batchelor scaling laws at higher Reynolds number than previously accessible with classical pseudo-spectral methods, making use of large simulation ensembles to allow a detailed consideration of the inverse cascade in a quasi-steady state. Our results support the recent finding of Scott [R. Scott, “Nonrobustness of the two-dimensional turbulent inverse cascade,” Phys. Rev. E75, 046301 (Year: 2007)10.1103/PhysRevE.75.046301], namely that when a direct enstrophy cascading range is well-represented numerically, a steeper energy spectrum proportional to k−2 is obtained in place of the classical k −5/3 prediction. It is further shown that this steep spectrum is associated with a faster growth of energy at large scales, scaling like t −1 rather than Kraichnan's prediction of t −3/2. The deviation from Kraichnan's theory is related to the emergence of a population of vortices that dominate the distribution of energy across scales, and whose number density and vorticity distribution with respect to vortex area are related to the shape of the enstrophy spectrum. An analytical model is proposed which closely matches the numerical spectra between the large scales and the forcing scale.
Jérôme Fontane is supported by the European Community in the framework of the CONVECT project under Grant No. PIEF-GA-2008-221003.
2013-01-14T00:00:00ZFontane, Jerome Jacob LouisDritschel, David GerardScott, Richard KirknessA new numerical technique for the simulation of forced two-dimensional turbulence[D. Dritschel and J. Fontane, “The combined Lagrangian advection method,” J. Comput. Phys.229, 5408–5417 (Year: 2010)10.1016/j.jcp.2010.03.048] is used to examine the validity of Kraichnan-Batchelor scaling laws at higher Reynolds number than previously accessible with classical pseudo-spectral methods, making use of large simulation ensembles to allow a detailed consideration of the inverse cascade in a quasi-steady state. Our results support the recent finding of Scott [R. Scott, “Nonrobustness of the two-dimensional turbulent inverse cascade,” Phys. Rev. E75, 046301 (Year: 2007)10.1103/PhysRevE.75.046301], namely that when a direct enstrophy cascading range is well-represented numerically, a steeper energy spectrum proportional to k−2 is obtained in place of the classical k −5/3 prediction. It is further shown that this steep spectrum is associated with a faster growth of energy at large scales, scaling like t −1 rather than Kraichnan's prediction of t −3/2. The deviation from Kraichnan's theory is related to the emergence of a population of vortices that dominate the distribution of energy across scales, and whose number density and vorticity distribution with respect to vortex area are related to the shape of the enstrophy spectrum. An analytical model is proposed which closely matches the numerical spectra between the large scales and the forcing scale.The effect of slip length on vortex rebound from a rigid boundarySutherland, D.Macaskill, C.Dritschel, D.G.https://hdl.handle.net/10023/52322023-04-18T09:53:11Z2013-09-23T00:00:00ZThe problem of a dipole incident normally on a rigid boundary, for moderate to large Reynolds numbers, has recently been treated numerically using a volume penalisation method by Nguyen van yen, Farge, and Schneider [Phys. Rev. Lett.106, 184502 (2011)]. Their results indicate that energy dissipating structures persist in the inviscid limit. They found that the use of penalisation methods intrinsically introduces some slip at the boundary wall, where the slip approaches zero as the Reynolds number goes to infinity, so reducing to the no-slip case in this limit. We study the same problem, for both no-slip and partial slip cases, using compact differences on a Chebyshev grid in the direction normal to the wall and Fourier methods in the direction along the wall. We find that for the no-slip case there is no indication of the persistence of energy dissipating structures in the limit as viscosity approaches zero and that this also holds for any fixed slip length. However, when the slip length is taken to vary inversely with Reynolds number then the results of Nguyen van yen et al. are regained. It therefore appears that the prediction that energy dissipating structures persist in the inviscid limit follows from the two limits of wall slip length going to zero, and viscosity going to zero, not being treated independently in their use of the volume penalisation method.
2013-09-23T00:00:00ZSutherland, D.Macaskill, C.Dritschel, D.G.The problem of a dipole incident normally on a rigid boundary, for moderate to large Reynolds numbers, has recently been treated numerically using a volume penalisation method by Nguyen van yen, Farge, and Schneider [Phys. Rev. Lett.106, 184502 (2011)]. Their results indicate that energy dissipating structures persist in the inviscid limit. They found that the use of penalisation methods intrinsically introduces some slip at the boundary wall, where the slip approaches zero as the Reynolds number goes to infinity, so reducing to the no-slip case in this limit. We study the same problem, for both no-slip and partial slip cases, using compact differences on a Chebyshev grid in the direction normal to the wall and Fourier methods in the direction along the wall. We find that for the no-slip case there is no indication of the persistence of energy dissipating structures in the limit as viscosity approaches zero and that this also holds for any fixed slip length. However, when the slip length is taken to vary inversely with Reynolds number then the results of Nguyen van yen et al. are regained. It therefore appears that the prediction that energy dissipating structures persist in the inviscid limit follows from the two limits of wall slip length going to zero, and viscosity going to zero, not being treated independently in their use of the volume penalisation method.Out of the wilderness : a fourteenth-century English drawing of John the BaptistLuxford, Julian Marcushttps://hdl.handle.net/10023/52152023-04-18T09:40:39Z2010-01-01T00:00:00ZLondon, British Library, MS Royal 10 B XIV contains a large drawing of St. John the Baptist that is both exceptional for its quality and iconographically unique. Not previously noticed by art historians, it constitutes an important addition to English art of the early to mid-fourteenth century. This paper explores the physical nature of the drawing, its bibliographical context (in a book of natural philosophy), the nature and meaning of its imagery, and its artistic context and associations, within the broader framework of its ownership and use by Benedictine monks of Saint Augustine's Abbey, Canterbury. The drawing is considered a symptom of a wider interest in the acquisition of manuscript illumination at the abbey during the first half of the fourteenth century. It can be dated to about 1335-40 and is thought to have been executed in southeast England or East Anglia, where the works of art to which it is closest in stylistic and iconographic terms were produced. The iconography includes a number of motifs rare or unparalleled in images of John the Baptist, including a figure of Salome beneath the saint's feet and, most remarkably, a monumental Gothic arch composed of living oak trees, which frames the saint. The detail and semantic richness of this imagery make it practically certain that the drawing was made as a focus of devotion, probably for the manuscript's first recorded owner, the Oxford scholar-monk John of Lingfield.
2010-01-01T00:00:00ZLuxford, Julian MarcusLondon, British Library, MS Royal 10 B XIV contains a large drawing of St. John the Baptist that is both exceptional for its quality and iconographically unique. Not previously noticed by art historians, it constitutes an important addition to English art of the early to mid-fourteenth century. This paper explores the physical nature of the drawing, its bibliographical context (in a book of natural philosophy), the nature and meaning of its imagery, and its artistic context and associations, within the broader framework of its ownership and use by Benedictine monks of Saint Augustine's Abbey, Canterbury. The drawing is considered a symptom of a wider interest in the acquisition of manuscript illumination at the abbey during the first half of the fourteenth century. It can be dated to about 1335-40 and is thought to have been executed in southeast England or East Anglia, where the works of art to which it is closest in stylistic and iconographic terms were produced. The iconography includes a number of motifs rare or unparalleled in images of John the Baptist, including a figure of Salome beneath the saint's feet and, most remarkably, a monumental Gothic arch composed of living oak trees, which frames the saint. The detail and semantic richness of this imagery make it practically certain that the drawing was made as a focus of devotion, probably for the manuscript's first recorded owner, the Oxford scholar-monk John of Lingfield.Characterizing Visual Attention during Driving and Non-driving Hazard Perception TasksMacKenzie, Andrew KerrHarris, Juliehttps://hdl.handle.net/10023/50662023-04-19T00:38:43Z2014-03-26T00:00:00ZResearch into driving skill, particularly of hazard perception, often involves studies where participants either view pictures of driving scenarios or use movie viewing paradigms. However oculomotor strategies tend to change between active and passive tasks and attentional limitations are introduced during real driving. Here we present a study using eye tracking methods, to contrast oculomotor behaviour differences across a passive video based hazard perception task and an active hazard perception simulated driving task. The differences presented highlight a requirement to study driving skill under more active conditions, where the participant is engaged with a driving task. Our results suggest that more standard, passive tests, may have limited utility when developing visual models of driving behaviour. The results presented here have implications for driver safety measures and provide further insights into how vision and action interact during natural activity.
Funding: EPSRC DTG
2014-03-26T00:00:00ZMacKenzie, Andrew KerrHarris, JulieResearch into driving skill, particularly of hazard perception, often involves studies where participants either view pictures of driving scenarios or use movie viewing paradigms. However oculomotor strategies tend to change between active and passive tasks and attentional limitations are introduced during real driving. Here we present a study using eye tracking methods, to contrast oculomotor behaviour differences across a passive video based hazard perception task and an active hazard perception simulated driving task. The differences presented highlight a requirement to study driving skill under more active conditions, where the participant is engaged with a driving task. Our results suggest that more standard, passive tests, may have limited utility when developing visual models of driving behaviour. The results presented here have implications for driver safety measures and provide further insights into how vision and action interact during natural activity.The conserved transmembrane proteoglycan Perdido/Kon-tiki is essential for myofibrillogenesis and sarcomeric structure in DrosophilaPérez-Moreno, J JBischoff, MMartín-Bermudo, M DEstrada, Bhttps://hdl.handle.net/10023/50402024-03-22T00:41:02Z2014-07-01T00:00:00ZMuscle differentiation requires the assembly of high-order structures called myofibrils, composed of sarcomeres. Even though the molecular organization of sarcomeres is well known, the mechanisms underlying myofibrillogenesis are poorly understood. It has been proposed that integrin-dependent adhesion nucleates myofibril at the periphery of the muscle cell to sustain sarcomere assembly. Here, we report a role for the gene perdido (perd, also known as kon-tiki, a transmembrane chondroitin proteoglycan) in myofibrillogenesis. Expression of perd RNAi in muscles, prior to adult myogenesis, can induce misorientation and detachment of Drosophila adult abdominal muscles. In comparison to controls, perd-depleted muscles contain fewer myofibrils, localized at the cell periphery. These myofibrils are detached from each other and display a defective sarcomeric structure. Our results demonstrate that the extracellular matrix receptor Perd has a specific role in the assembly of myofibrils and in sarcomeric organization. We suggest that Perd acts downstream or in parallel to integrins to enable the connection of nascent myofibrils to the Z-bands. Our work identifies the Drosophila adult abdominal muscles as a model to investigate in vivo the mechanisms behind myofibrillogenesis.
M.B. was funded by a Wellcome Trust Senior Investigator Award to P. Lawrence (WT096645MA).
2014-07-01T00:00:00ZPérez-Moreno, J JBischoff, MMartín-Bermudo, M DEstrada, BMuscle differentiation requires the assembly of high-order structures called myofibrils, composed of sarcomeres. Even though the molecular organization of sarcomeres is well known, the mechanisms underlying myofibrillogenesis are poorly understood. It has been proposed that integrin-dependent adhesion nucleates myofibril at the periphery of the muscle cell to sustain sarcomere assembly. Here, we report a role for the gene perdido (perd, also known as kon-tiki, a transmembrane chondroitin proteoglycan) in myofibrillogenesis. Expression of perd RNAi in muscles, prior to adult myogenesis, can induce misorientation and detachment of Drosophila adult abdominal muscles. In comparison to controls, perd-depleted muscles contain fewer myofibrils, localized at the cell periphery. These myofibrils are detached from each other and display a defective sarcomeric structure. Our results demonstrate that the extracellular matrix receptor Perd has a specific role in the assembly of myofibrils and in sarcomeric organization. We suggest that Perd acts downstream or in parallel to integrins to enable the connection of nascent myofibrils to the Z-bands. Our work identifies the Drosophila adult abdominal muscles as a model to investigate in vivo the mechanisms behind myofibrillogenesis.Behavioral observation of xenopus tadpole swimming for neuroscience labsLi, WenchangWagner, Monica AnnePorter, Nicola Jeanhttps://hdl.handle.net/10023/50382023-04-18T09:51:38Z2014-01-01T00:00:00ZNeuroscience labs benefit from reliable, easily - monitored neural responses mediated by well - studied neural pathways . Xenopus laevis tadpoles have been used as a simple vertebrate model preparation in motor control studies. Most of the neuronal pathways underlying different aspects of tadpole swimming behavior have been revealed. These include the skin mechanosensory touch and pineal eye light - sensing pathways whose activation can initiate swimming , and the cement gland pressure - sensing pathway responsible for stopping swimming. A simple transection in the hindbrain can cut off the pineal eye and cement gland pathways from the swimming circuit in the spinal cord, resulting in losses of corresponding functions. Additionally, some pharmacological experiments targeting neurotransmission can be designed to affect swimming and, fluorescence - conjugated α -bungarotoxin can be used to label nicotinic receptors at neuromuscular junctions. These experiments can be readily adapted for undergraduate neuroscience teaching labs. Possible expansions of some experiments for more sophisticated pharmacological or neurophysiological labs are also discussed.
2014-01-01T00:00:00ZLi, WenchangWagner, Monica AnnePorter, Nicola JeanNeuroscience labs benefit from reliable, easily - monitored neural responses mediated by well - studied neural pathways . Xenopus laevis tadpoles have been used as a simple vertebrate model preparation in motor control studies. Most of the neuronal pathways underlying different aspects of tadpole swimming behavior have been revealed. These include the skin mechanosensory touch and pineal eye light - sensing pathways whose activation can initiate swimming , and the cement gland pressure - sensing pathway responsible for stopping swimming. A simple transection in the hindbrain can cut off the pineal eye and cement gland pathways from the swimming circuit in the spinal cord, resulting in losses of corresponding functions. Additionally, some pharmacological experiments targeting neurotransmission can be designed to affect swimming and, fluorescence - conjugated α -bungarotoxin can be used to label nicotinic receptors at neuromuscular junctions. These experiments can be readily adapted for undergraduate neuroscience teaching labs. Possible expansions of some experiments for more sophisticated pharmacological or neurophysiological labs are also discussed.Hold still, Madame: wartime gender and the photography of women in France during the Great WarHudgins, Nicolehttps://hdl.handle.net/10023/50162019-07-01T10:12:33Z2014-01-01T00:00:00ZThis study investigates French images of women during the First World War, the feminine postures and roles captured by photographers, how female images were used in the wartime media and by the state, and how captions and other textual modes strengthened an overarching message of total consent. By analysing the three most prominent genres of female imagery during the period – women in distress, feminine devotion, and women toiling for the war effort – this book seeks to demonstrate how photography assisted in the gender work of the war. Photographers and publishers showed how traditional feminine traits could contribute to a male-designed and directed war effort, while also concealing instances of female dissent, which included feminist, socialist, popular and pacifist objections to the war. Yet, although the archives contain few wartime images created by French women themselves, this work also introduces a small group of period photographs, lithographs, articles and literary works that disrupted the visual narrative of subordination.
2014-01-01T00:00:00ZHudgins, NicoleThis study investigates French images of women during the First World War, the feminine postures and roles captured by photographers, how female images were used in the wartime media and by the state, and how captions and other textual modes strengthened an overarching message of total consent. By analysing the three most prominent genres of female imagery during the period – women in distress, feminine devotion, and women toiling for the war effort – this book seeks to demonstrate how photography assisted in the gender work of the war. Photographers and publishers showed how traditional feminine traits could contribute to a male-designed and directed war effort, while also concealing instances of female dissent, which included feminist, socialist, popular and pacifist objections to the war. Yet, although the archives contain few wartime images created by French women themselves, this work also introduces a small group of period photographs, lithographs, articles and literary works that disrupted the visual narrative of subordination.Population dynamics and distribution of northern Norwegian killer whales in relation to wintering herringKuningas, Sannahttps://hdl.handle.net/10023/48782019-07-01T10:08:28Z2014-06-25T00:00:00ZThe northern Norwegian killer whale (Orcinus orca) is an important predator but little is known about its population dynamics, particular in response to changes in its main prey, the highly dynamic Norwegian spring spawning (NSS) herring (Clupea harengus). The main aims of this thesis were to estimate killer whale population parameters, to explore the future viability of the population, and to explore the response of this predator to changes in distribution and abundance of its main prey over the last 25 years. Population size was estimated as ~ 700 individuals, taking heterogeneity of capture probabilities into account and correcting for unmarked animals. Apparent survival rates of 0.974 (SE = 0.006) for adult males and 0.984 (SE = 0.006) for adult females were estimated accounting for temporary emigration, transience and trap-dependency. Temporary emigration was greater for males than females. Calving intervals ranged from 3 to 14 years (mean = 5.06); equivalent to 0.197 calves per mature female per year. Future viability of the killer whale population was evaluated under various plausible scenarios. The baseline scenario using the best available information predicted a viable population and indicated that the population may be increasing size. Analysis of data on naval sonar activity, killer whale sightings and herring abundance showed that naval sonar activity appeared to have a negative effect on killer whale presence during a period of low prey availability. A time lag of four years was found between the first sign of NSS herring changing its distribution and reduced killer whale presence inside the fjord system. Analysis of energy budgets showed that killer whales spent more time travelling/foraging in 2005/06 than the 1990s. The fjord system was inferred to be a preferred habitat for killer whales when there was a higher density of NSS herring in this area compared to offshore area.
2014-06-25T00:00:00ZKuningas, SannaThe northern Norwegian killer whale (Orcinus orca) is an important predator but little is known about its population dynamics, particular in response to changes in its main prey, the highly dynamic Norwegian spring spawning (NSS) herring (Clupea harengus). The main aims of this thesis were to estimate killer whale population parameters, to explore the future viability of the population, and to explore the response of this predator to changes in distribution and abundance of its main prey over the last 25 years. Population size was estimated as ~ 700 individuals, taking heterogeneity of capture probabilities into account and correcting for unmarked animals. Apparent survival rates of 0.974 (SE = 0.006) for adult males and 0.984 (SE = 0.006) for adult females were estimated accounting for temporary emigration, transience and trap-dependency. Temporary emigration was greater for males than females. Calving intervals ranged from 3 to 14 years (mean = 5.06); equivalent to 0.197 calves per mature female per year. Future viability of the killer whale population was evaluated under various plausible scenarios. The baseline scenario using the best available information predicted a viable population and indicated that the population may be increasing size. Analysis of data on naval sonar activity, killer whale sightings and herring abundance showed that naval sonar activity appeared to have a negative effect on killer whale presence during a period of low prey availability. A time lag of four years was found between the first sign of NSS herring changing its distribution and reduced killer whale presence inside the fjord system. Analysis of energy budgets showed that killer whales spent more time travelling/foraging in 2005/06 than the 1990s. The fjord system was inferred to be a preferred habitat for killer whales when there was a higher density of NSS herring in this area compared to offshore area.Evaluating multicenter DTI data in Huntington's disease on site specific effects : an ex post facto approachMüller, Hans-PeterGrön, GeorgSprengelmeyer, ReinerKassubek, JanLudolph, Albert C.Hobbs, NicolaCole, JamesRoos, Raymund A.C.Duerr, AlexandraTabrizi, Sarah J.Landwehrmeyer, G. BernhardSüssmuth, Sigurd D.https://hdl.handle.net/10023/47892023-04-18T09:48:23Z2013-01-01T00:00:00ZPurpose: Assessment of the feasibility to average diffusion tensor imaging (DTI) metrics of MRI data acquired in the course of a multicenter study. Materials and methods: Sixty-one early stage Huntington's disease patients and forty healthy controls were studied using four different MR scanners at four European sites with acquisition protocols as close as possible to a given standard protocol. The potential and feasibility of averaging data acquired at different sites was evaluated quantitatively by region-of-interest (ROI) based statistical comparisons of coefficients of variation (CV) across centers, as well as by testing for significant group-by-center differences on averaged fractional anisotropy (FA) values between patients and controls. In addition, a whole-brain based statistical between-group comparison was performed using FA maps. Results: The ex post facto statistical evaluation of CV and FA-values in a priori defined ROIs showed no differences between sites above chance indicating that data were not systematically biased by center specific factors. Conclusion: Averaging FA-maps from DTI data acquired at different study sites and different MR scanner types does not appear to be systematically biased. A suitable recipe for testing on the possibility to pool multicenter DTI data is provided to permit averaging of DTI-derived metrics to differentiate patients from healthy controls at a larger scale.
2013-01-01T00:00:00ZMüller, Hans-PeterGrön, GeorgSprengelmeyer, ReinerKassubek, JanLudolph, Albert C.Hobbs, NicolaCole, JamesRoos, Raymund A.C.Duerr, AlexandraTabrizi, Sarah J.Landwehrmeyer, G. BernhardSüssmuth, Sigurd D.Purpose: Assessment of the feasibility to average diffusion tensor imaging (DTI) metrics of MRI data acquired in the course of a multicenter study. Materials and methods: Sixty-one early stage Huntington's disease patients and forty healthy controls were studied using four different MR scanners at four European sites with acquisition protocols as close as possible to a given standard protocol. The potential and feasibility of averaging data acquired at different sites was evaluated quantitatively by region-of-interest (ROI) based statistical comparisons of coefficients of variation (CV) across centers, as well as by testing for significant group-by-center differences on averaged fractional anisotropy (FA) values between patients and controls. In addition, a whole-brain based statistical between-group comparison was performed using FA maps. Results: The ex post facto statistical evaluation of CV and FA-values in a priori defined ROIs showed no differences between sites above chance indicating that data were not systematically biased by center specific factors. Conclusion: Averaging FA-maps from DTI data acquired at different study sites and different MR scanner types does not appear to be systematically biased. A suitable recipe for testing on the possibility to pool multicenter DTI data is provided to permit averaging of DTI-derived metrics to differentiate patients from healthy controls at a larger scale.Shallow-water vortex equilibria and their stabilityPłotka, H.Dritschel, D.G.https://hdl.handle.net/10023/47622023-04-18T09:51:41Z2011-01-01T00:00:00ZWe first describe the equilibrium form and stability of steadily-rotating simply-connected vortex patches in the single-layer quasi-geostrophic model of geophysical fluid dynamics. This model, valid for rotating shallow-water flow in the limit of small Rossby and Froude numbers, has an intrinsic length scale L called the "Rossby deformation length" relating the strength of stratification to that of the background rotation rate. Specifically, L = c/f where c = √gH is a characteristic gravity-wave speed, g is gravity (or "reduced" gravity in a two-layer context where one layer is infinitely deep), H is the mean active layer depth, and f is the Coriolis frequency (here constant). We next introduce ageostrophic effects by using the full shallow-water model to generate what we call "quasi-equilibria". These equilibria are not strictly steady, but radiate such weak gravity waves that they are steady for all practical purposes. Through an artificial ramping procedure, we ramp up the potential vorticity anomaly of the fluid particles in our quasi-geostrophic equilibria to obtain shallow-water quasi-equilibria at finite Rossby number. We show a few examples of these states in this paper.
2011-01-01T00:00:00ZPłotka, H.Dritschel, D.G.We first describe the equilibrium form and stability of steadily-rotating simply-connected vortex patches in the single-layer quasi-geostrophic model of geophysical fluid dynamics. This model, valid for rotating shallow-water flow in the limit of small Rossby and Froude numbers, has an intrinsic length scale L called the "Rossby deformation length" relating the strength of stratification to that of the background rotation rate. Specifically, L = c/f where c = √gH is a characteristic gravity-wave speed, g is gravity (or "reduced" gravity in a two-layer context where one layer is infinitely deep), H is the mean active layer depth, and f is the Coriolis frequency (here constant). We next introduce ageostrophic effects by using the full shallow-water model to generate what we call "quasi-equilibria". These equilibria are not strictly steady, but radiate such weak gravity waves that they are steady for all practical purposes. Through an artificial ramping procedure, we ramp up the potential vorticity anomaly of the fluid particles in our quasi-geostrophic equilibria to obtain shallow-water quasi-equilibria at finite Rossby number. We show a few examples of these states in this paper.Numerical investigation of passive optical sorting of plasmon nanoparticlesPloschner, MartinMazilu, MichaelCizmar, TomasDholakia, Kishanhttps://hdl.handle.net/10023/47362023-04-18T09:44:02Z2011-07-06T00:00:00ZWe explore the passive optical sorting of plasmon nanoparticles and investigate the optimal wavelength and optimal beam shape of incident field. The condition for optimal wavelength is found by maximising the nanoparticle separation whilst minimising the temperature increase in the system. We then use the force optical eigenmode (FOEi) method to find the beam shape of incident electromagnetic field, maximising the force difference between plasmon nanoparticles. The maximum force difference is found with respect to the whole sorting region. The combination of wavelength and beam shape study is demonstrated for a specific case of gold nanoparticles of radius 40 nm and 50 nm respectively. The optimum wavelength for this particular situation is found to be above 700 nm. The optimum beam shape depends upon the size of sorting region and ranges from plane-wave illumination for infinite sorting region to a field maximising gradient force difference in a single point. (C) 2011 Optical Society of America
Funding: UK Engineering and Physical Sciences Research Council for funding, KD is a Royal Society-Wolfson Merit Award Holder.
2011-07-06T00:00:00ZPloschner, MartinMazilu, MichaelCizmar, TomasDholakia, KishanWe explore the passive optical sorting of plasmon nanoparticles and investigate the optimal wavelength and optimal beam shape of incident field. The condition for optimal wavelength is found by maximising the nanoparticle separation whilst minimising the temperature increase in the system. We then use the force optical eigenmode (FOEi) method to find the beam shape of incident electromagnetic field, maximising the force difference between plasmon nanoparticles. The maximum force difference is found with respect to the whole sorting region. The combination of wavelength and beam shape study is demonstrated for a specific case of gold nanoparticles of radius 40 nm and 50 nm respectively. The optimum wavelength for this particular situation is found to be above 700 nm. The optimum beam shape depends upon the size of sorting region and ranges from plane-wave illumination for infinite sorting region to a field maximising gradient force difference in a single point. (C) 2011 Optical Society of AmericaRapid regulation of protein activity in fission yeastBoe, Cathrine A.Garcia, IgnacioPai, Chen-ChunSharom, Jeffrey R.Skjolberg, Henriette C.Boye, ErikKearsey, StephenMacNeill, Stuart AndrewTyers, Michael D.Grallert, Beatahttps://hdl.handle.net/10023/46292023-04-18T09:40:07Z2008-05-05T00:00:00ZBackground: The fission yeast Schizosaccharomyces pombe is widely-used as a model organism for the study of a broad range of eukaryotic cellular processes such as cell cycle, genome stability and cell morphology. Despite the availability of extensive set of genetic, molecular biological, biochemical and cell biological tools for analysis of protein function in fissio n yeast, studies are often hampered by the lack of an effective method allowing for the rapid regulation of protein level or protein activity. Results: In order to be able to regulate protein function, we have made use of a previous finding that the hormone binding domain of steroid receptors can be used as a regulatory cassette to subject the activity of heterologous proteins to hormonal regulation. The approach is based on fusing the protein of interest to the hormone binding domain (HBD) of the estrogen receptor (ER). The HBD tag will attract the Hsp90 complex, which can render the fusion protein inactive. Upon addition of estradiol the protein is quickly released from the Hsp90 complex and thereby activated. We have tagged and characterised the induction of activity of four different HBD-tagged proteins. Here we show that the tag provided the means to effectively regulate the activity of two of these proteins. Conclusion: The estradiol-regulatable hormone binding do main provides a means to regulate the function of some, though not all, fission yeast proteins. This system may result in very quick and reversible activation of the protein of interest. Therefore it will be a powerful tool and it will open experimental approaches in fission yeast that have previously not been possible. Since fission yeast is a widely-used model organism, this will be valuable in many areas of research.
2008-05-05T00:00:00ZBoe, Cathrine A.Garcia, IgnacioPai, Chen-ChunSharom, Jeffrey R.Skjolberg, Henriette C.Boye, ErikKearsey, StephenMacNeill, Stuart AndrewTyers, Michael D.Grallert, BeataBackground: The fission yeast Schizosaccharomyces pombe is widely-used as a model organism for the study of a broad range of eukaryotic cellular processes such as cell cycle, genome stability and cell morphology. Despite the availability of extensive set of genetic, molecular biological, biochemical and cell biological tools for analysis of protein function in fissio n yeast, studies are often hampered by the lack of an effective method allowing for the rapid regulation of protein level or protein activity. Results: In order to be able to regulate protein function, we have made use of a previous finding that the hormone binding domain of steroid receptors can be used as a regulatory cassette to subject the activity of heterologous proteins to hormonal regulation. The approach is based on fusing the protein of interest to the hormone binding domain (HBD) of the estrogen receptor (ER). The HBD tag will attract the Hsp90 complex, which can render the fusion protein inactive. Upon addition of estradiol the protein is quickly released from the Hsp90 complex and thereby activated. We have tagged and characterised the induction of activity of four different HBD-tagged proteins. Here we show that the tag provided the means to effectively regulate the activity of two of these proteins. Conclusion: The estradiol-regulatable hormone binding do main provides a means to regulate the function of some, though not all, fission yeast proteins. This system may result in very quick and reversible activation of the protein of interest. Therefore it will be a powerful tool and it will open experimental approaches in fission yeast that have previously not been possible. Since fission yeast is a widely-used model organism, this will be valuable in many areas of research.MCM-GINS and MCM-MCM interactions in vivo visualised by bimolecular fluorescence complementation in fission yeastAkman, GoekhanMacNeill, Stuart Andrewhttps://hdl.handle.net/10023/46282023-04-18T09:40:07Z2009-02-19T00:00:00ZBackground: Each of the three individual components of the CMG complex (Cdc45, MCM and GINS) is essential for chromosomal DNA replication in eukaryotic cells, both for the initiation of replication at origins and also for normal replication fork progression. The MCM complex is a DNA helicase that most likely functions as the catalytic core of the replicative helicase, unwinding the parental duplex DNA ahead of the moving replication fork, whereas Cdc45 and the GINS complex are believed to act as accessory factors for MCM. Results:To investigate interactions between components of the CMG complex, we have used bimolecular fluorescence complementation (BiFC) in the fission yeast Schizosaccharomyces pombe for the first time, to analyse protein-protein interactions between GINS and MCM subunits expressed from their native chromosomal loci. We demonstrate interactions between GINS andMCM in the nuclei of exponentially-growing fission yeast cells and on chromatin in binucleate S-phase cells. In addition we present evidence of MCM-MCM interactions in diploid fission yeast cells. As with GINS-MCM interactions, MCM-MCM interactions also occur on chromatin in S-phase cells. Conclusion: Bimolecular fluorescence complementation can be used in fission yeast to visualise interactions between two of the three components of the CMG complex, offering the prospect that this technique could in the future be used to allow studies on replication protein dynamics in living S. pombe cells.
2009-02-19T00:00:00ZAkman, GoekhanMacNeill, Stuart AndrewBackground: Each of the three individual components of the CMG complex (Cdc45, MCM and GINS) is essential for chromosomal DNA replication in eukaryotic cells, both for the initiation of replication at origins and also for normal replication fork progression. The MCM complex is a DNA helicase that most likely functions as the catalytic core of the replicative helicase, unwinding the parental duplex DNA ahead of the moving replication fork, whereas Cdc45 and the GINS complex are believed to act as accessory factors for MCM. Results:To investigate interactions between components of the CMG complex, we have used bimolecular fluorescence complementation (BiFC) in the fission yeast Schizosaccharomyces pombe for the first time, to analyse protein-protein interactions between GINS and MCM subunits expressed from their native chromosomal loci. We demonstrate interactions between GINS andMCM in the nuclei of exponentially-growing fission yeast cells and on chromatin in binucleate S-phase cells. In addition we present evidence of MCM-MCM interactions in diploid fission yeast cells. As with GINS-MCM interactions, MCM-MCM interactions also occur on chromatin in S-phase cells. Conclusion: Bimolecular fluorescence complementation can be used in fission yeast to visualise interactions between two of the three components of the CMG complex, offering the prospect that this technique could in the future be used to allow studies on replication protein dynamics in living S. pombe cells.Functional mapping of the fission yeast DNA polymerase delta B-subunit Cdc1 by site-directed and random pentapeptide insertion mutagenesisGarcia, JSBaranovskiy, AGKnatko, EVGray, FCTahirov, THMacNeill, Stuart Andrewhttps://hdl.handle.net/10023/46272024-03-22T00:39:35Z2009-08-17T00:00:00ZBackground: DNA polymerase delta plays an essential role in chromosomal DNA replication in eukaryotic cells, being responsible for synthesising the bulk of the lagging strand. In fission yeast, Pol delta is a heterotetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1. Pol3 binds directly to the B-subunit, Cdc1, which in turn binds the C-subunit, Cdc27. Human Pol d comprises the same four subunits, and the crystal structure was recently reported of a complex of human p50 and the N-terminal domain of p66, the human orthologues of Cdc1 and Cdc27, respectively. Results: To gain insights into the structure and function of Cdc1, random and directed mutagenesis techniques were used to create a collection of thirty alleles encoding mutant Cdc1 proteins. Each allele was tested for function in fission yeast and for binding of the altered protein to Pol3 and Cdc27 using the two-hybrid system. Additionally, the locations of the amino acid changes in each protein were mapped onto the three-dimensional structure of human p50. The results obtained from these studies identify amino acid residues and regions within the Cdc1 protein that are essential for interaction with Pol3 and Cdc27 and for in vivo function. Mutations specifically defective in Pol3-Cdc1 interactions allow the identification of a possible Pol3 binding surface on Cdc1. Conclusion: In the absence of a three-dimensional structure of the entire Pol d complex, the results of this study highlight regions in Cdc1 that are vital for protein function in vivo and provide valuable clues to possible protein-protein interaction surfaces on the Cdc1 protein that will be important targets for further study.
JSG was supported by a BBSRC Research Committee studentship, EVK by the Darwin Trust of Edinburgh, and FCG and SAM by a Wellcome Trust Senior Research Fellowship in Basic Biomedical Sciences. AGB and THT research was supported by UNMC Eppley Cancer Center Pilot Project LB595 to THT.
2009-08-17T00:00:00ZGarcia, JSBaranovskiy, AGKnatko, EVGray, FCTahirov, THMacNeill, Stuart AndrewBackground: DNA polymerase delta plays an essential role in chromosomal DNA replication in eukaryotic cells, being responsible for synthesising the bulk of the lagging strand. In fission yeast, Pol delta is a heterotetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1. Pol3 binds directly to the B-subunit, Cdc1, which in turn binds the C-subunit, Cdc27. Human Pol d comprises the same four subunits, and the crystal structure was recently reported of a complex of human p50 and the N-terminal domain of p66, the human orthologues of Cdc1 and Cdc27, respectively. Results: To gain insights into the structure and function of Cdc1, random and directed mutagenesis techniques were used to create a collection of thirty alleles encoding mutant Cdc1 proteins. Each allele was tested for function in fission yeast and for binding of the altered protein to Pol3 and Cdc27 using the two-hybrid system. Additionally, the locations of the amino acid changes in each protein were mapped onto the three-dimensional structure of human p50. The results obtained from these studies identify amino acid residues and regions within the Cdc1 protein that are essential for interaction with Pol3 and Cdc27 and for in vivo function. Mutations specifically defective in Pol3-Cdc1 interactions allow the identification of a possible Pol3 binding surface on Cdc1. Conclusion: In the absence of a three-dimensional structure of the entire Pol d complex, the results of this study highlight regions in Cdc1 that are vital for protein function in vivo and provide valuable clues to possible protein-protein interaction surfaces on the Cdc1 protein that will be important targets for further study.An English lecturer, a palliative care practitioner, and an absent poet have a confabulationJones, ChrisMacpherson, Catrionahttps://hdl.handle.net/10023/46062023-04-25T23:38:26Z2014-07-09T00:00:00ZThe possibilities for developing the poet Douglas Dunn’s archive (which includes the drafts and manuscripts for his collection Elegies, dealing with the terminal illness and death of the poet’s wife from cancer) for therapeutic benefit are explored by an English lecturer (C.J.) and a palliative care practitioner (C.M.). This has led us to explore the potential benefit of this resource for health practitioners working with those affected by cancer and other life-limiting conditions. This article offers a “written conversation” (an acknowledged oxymoron of genre) about working with the themes of death and loss: a conversation which includes Douglas Dunn, who was not actually there. We reflect on the value of this “confabulation” as methodological inquiry, and its potential influence on practice. Thus, an example of “creative writing” (the confabulation) becomes a piece of research into methodology regarding the use of “creative writing” resources (the poetry archive) in palliative health care.
2014-07-09T00:00:00ZJones, ChrisMacpherson, CatrionaThe possibilities for developing the poet Douglas Dunn’s archive (which includes the drafts and manuscripts for his collection Elegies, dealing with the terminal illness and death of the poet’s wife from cancer) for therapeutic benefit are explored by an English lecturer (C.J.) and a palliative care practitioner (C.M.). This has led us to explore the potential benefit of this resource for health practitioners working with those affected by cancer and other life-limiting conditions. This article offers a “written conversation” (an acknowledged oxymoron of genre) about working with the themes of death and loss: a conversation which includes Douglas Dunn, who was not actually there. We reflect on the value of this “confabulation” as methodological inquiry, and its potential influence on practice. Thus, an example of “creative writing” (the confabulation) becomes a piece of research into methodology regarding the use of “creative writing” resources (the poetry archive) in palliative health care.The development of the legal parameters of the waqf institution in contemporary Iran and its socioeconomic impactJafar-Shaghaghi, Kayhanhttps://hdl.handle.net/10023/45092021-02-26T03:02:31Z2014-01-01T00:00:00ZThis thesis argues that the laws of waqf in Iran lack modern relevance. Such laws have never been
completely modernised, and the waqf system, no longer responsible for the delivery of public
goods, still holds a vast array of properties and resources. Many of the ongoing socioeconomic and
political disappointments of Iran, which, at the core, are the weakness of the country’s private
economic sector and its human capital deficiency, stand among the lasting consequences of the
deficiency of resources which the institution of waqf has under its control.
Traditional Islamic law laid the ground for the economic infrastructure of the Middle Eastern
countries until the late 19th century. Among the institutions that contributed to shaping the economy
of the region are the Islamic law of inheritance, which inhibited capital accumulation; the absence
in Islamic law of the concept of a corporation and the consequent weaknesses of civil society; and
the waqf, which locked vast resources into unproductive organisations for the delivery of social
services. It is often argued that many of these obstacles to economic development were largely
overcome through radical reforms initiated in the 19th century. However, the modern civil law of
Iran has kept traditional Islamic law at the core of laws of waqf, and the process of modernisation of
its laws remains incomplete.
2014-01-01T00:00:00ZJafar-Shaghaghi, KayhanThis thesis argues that the laws of waqf in Iran lack modern relevance. Such laws have never been
completely modernised, and the waqf system, no longer responsible for the delivery of public
goods, still holds a vast array of properties and resources. Many of the ongoing socioeconomic and
political disappointments of Iran, which, at the core, are the weakness of the country’s private
economic sector and its human capital deficiency, stand among the lasting consequences of the
deficiency of resources which the institution of waqf has under its control.
Traditional Islamic law laid the ground for the economic infrastructure of the Middle Eastern
countries until the late 19th century. Among the institutions that contributed to shaping the economy
of the region are the Islamic law of inheritance, which inhibited capital accumulation; the absence
in Islamic law of the concept of a corporation and the consequent weaknesses of civil society; and
the waqf, which locked vast resources into unproductive organisations for the delivery of social
services. It is often argued that many of these obstacles to economic development were largely
overcome through radical reforms initiated in the 19th century. However, the modern civil law of
Iran has kept traditional Islamic law at the core of laws of waqf, and the process of modernisation of
its laws remains incomplete.Structural studies on human dihydroxyacetone kinase (DAK) and the carbohydrate-binding domain of Streptococcus pneumoniae NanAYang, Leihttps://hdl.handle.net/10023/45062019-03-29T10:37:03Z2013-01-01T00:00:00ZA number of dihydroxyacetone kinases (DAK) have been described that can utilize
either ATP (in animals, plants and some bacteria) or phosphoenolpyruvate (PEP) (in
most bacteria) as the energy source to convert dihydroxyacetone (Dha) to
dihydroxyacetone phosphate (DhaP), which plays critical roles in many metabolic
pathways. It has also been described that Homo sapiens DAK is able to regulate the
innate immune system via its interaction with Melanoma differentiation-associated
protein 5 (MDA5), which is recognized as an RNA sensor during virus infection.
These findings make H. sapiens DAK a very noteworthy research target due to its
multiple functions in many fields. Therefore, structural studies of DAK from H.
sapiens are presented.
The initial structure of the wild type (WT) H. sapiens DAK was determined to 2.5Å
resolution and solved by molecular replacement. The structure forms a homodimer
and four dimers were shown to be present in each asymmetric unit. However, within
each monomer, most regions of the C-terminal domain were disordered, and therefore
in order to improve structure quality, multiple site-directed mutagenesis was used. The
mutated protein was then crystallized and the structure was determined to 1.4Å. The
N-terminal Dha binding domain consists of two α/β regions and the C-terminal ATP
binding domain is comprised of eight anti-parallel α-helices, which forms a deep
pocket and is filled with a phospholipid molecule. In addition, the structures of
mutated DAK in complex with ATP analogues and Dha are also described in the
current study.
The second part of the project concerned sialidases, which are glycoside hydrolases that specifically hydrolyse terminal sialic acid from various glycans. Streptococcus
pneumoniae is one of the most common pathogenic bacteria of humans, and is
reported to encode three sialidases that act as virulence factors in bacterial
colonization and infection. One of these sialidases, NanA, was reported to be present
in all clinical strains and plays a vital role during the bacterial infection.
Consequently, the structure of N-terminal Carbohydrate-binding module (CBM)
domain of NanA has been determined to 1.8Å, and reveals a β-sandwich fold. The apo
form of NanA-CBM is present as a dimer in the asymmetric unit, whereas a monomer
was detected when it is bound to sialic acid or its derivatives. Structural comparisons
between NanA-CBM and other structures of the CBM40 family were also performed.
The substrate binding sites of NanA-CBM forms a cavity that is able to accommodate
the substrates. A potential molecular binding site located beside the sialic acid binding
site was revealed, and is occupied by the side chain of a lysine from a symmetry-
related molecule. Heteronuclear single quantum coherence (HSQC) NMR
spectroscopy and fluorescent-based thermal shift assays were also carried out to
further characterise the protein.
The current results reveal the structure of both DAK from H. sapiens and NanA-CBM
from S. pneumoniae, which may contribute to a better understanding towards cell
metabolism and bacterial colonization.
2013-01-01T00:00:00ZYang, LeiA number of dihydroxyacetone kinases (DAK) have been described that can utilize
either ATP (in animals, plants and some bacteria) or phosphoenolpyruvate (PEP) (in
most bacteria) as the energy source to convert dihydroxyacetone (Dha) to
dihydroxyacetone phosphate (DhaP), which plays critical roles in many metabolic
pathways. It has also been described that Homo sapiens DAK is able to regulate the
innate immune system via its interaction with Melanoma differentiation-associated
protein 5 (MDA5), which is recognized as an RNA sensor during virus infection.
These findings make H. sapiens DAK a very noteworthy research target due to its
multiple functions in many fields. Therefore, structural studies of DAK from H.
sapiens are presented.
The initial structure of the wild type (WT) H. sapiens DAK was determined to 2.5Å
resolution and solved by molecular replacement. The structure forms a homodimer
and four dimers were shown to be present in each asymmetric unit. However, within
each monomer, most regions of the C-terminal domain were disordered, and therefore
in order to improve structure quality, multiple site-directed mutagenesis was used. The
mutated protein was then crystallized and the structure was determined to 1.4Å. The
N-terminal Dha binding domain consists of two α/β regions and the C-terminal ATP
binding domain is comprised of eight anti-parallel α-helices, which forms a deep
pocket and is filled with a phospholipid molecule. In addition, the structures of
mutated DAK in complex with ATP analogues and Dha are also described in the
current study.
The second part of the project concerned sialidases, which are glycoside hydrolases that specifically hydrolyse terminal sialic acid from various glycans. Streptococcus
pneumoniae is one of the most common pathogenic bacteria of humans, and is
reported to encode three sialidases that act as virulence factors in bacterial
colonization and infection. One of these sialidases, NanA, was reported to be present
in all clinical strains and plays a vital role during the bacterial infection.
Consequently, the structure of N-terminal Carbohydrate-binding module (CBM)
domain of NanA has been determined to 1.8Å, and reveals a β-sandwich fold. The apo
form of NanA-CBM is present as a dimer in the asymmetric unit, whereas a monomer
was detected when it is bound to sialic acid or its derivatives. Structural comparisons
between NanA-CBM and other structures of the CBM40 family were also performed.
The substrate binding sites of NanA-CBM forms a cavity that is able to accommodate
the substrates. A potential molecular binding site located beside the sialic acid binding
site was revealed, and is occupied by the side chain of a lysine from a symmetry-
related molecule. Heteronuclear single quantum coherence (HSQC) NMR
spectroscopy and fluorescent-based thermal shift assays were also carried out to
further characterise the protein.
The current results reveal the structure of both DAK from H. sapiens and NanA-CBM
from S. pneumoniae, which may contribute to a better understanding towards cell
metabolism and bacterial colonization.The effects of physical, biological and anthropogenic noise on the occurrence of dolphins in the Pacific region of the Panama CanalCampbell Castillo, Inezhttps://hdl.handle.net/10023/44842019-07-01T10:15:19Z2014-06-01T00:00:00ZThe main aim of this thesis was to investigate the occurrence of dolphins in Pacific waters adjacent to the Panama Canal in the context of biological, temporal and spatial factors. Acoustic data were collected at 101 sites at a range of distances and depths from the shipping region. Data were collected between March 2010 and April 2011 in a diurnal cycle over a total of 114 recording days. Received sound levels were split into 1/3 Octave bandwidths to study variation in sound pressure levels and then converted to spectrum density levels to show the sound components of the background noise in this region. Generalised Linear Models were used to relate dolphin whistle detections to temporal, spatial, environmental and acoustic variables.
The major sources of background noise were biological noise from soniferous fish and snapping shrimp and anthropogenic noise from vessels characterised by mid to high frequencies produced by artisanal fishing boats. There was monthly and diurnal variation with some locations characterised by loud sounds in the mid to high frequencies at night.
Whistle characteristics analysis revealed that the frequencies and range of the whistles were different to those previously reported under similar conditions. Whistles varied diurnally and in the presence of fish chorus and fishing boats. The study highlights a strong correlation between fish choruses and whistle detection.
Temporal and spatial models showed that whistle detections varied monthly and in relation to fish noise and small vessel engine noise. Dolphins were distributed throughout most of the study area; however, whistle detections varied with distance from the coast.
The results provide new knowledge about background noise composition in this region and provide the first information on the ecology of dolphin whistles in relation to this background noise, especially to fish chorus.
2014-06-01T00:00:00ZCampbell Castillo, InezThe main aim of this thesis was to investigate the occurrence of dolphins in Pacific waters adjacent to the Panama Canal in the context of biological, temporal and spatial factors. Acoustic data were collected at 101 sites at a range of distances and depths from the shipping region. Data were collected between March 2010 and April 2011 in a diurnal cycle over a total of 114 recording days. Received sound levels were split into 1/3 Octave bandwidths to study variation in sound pressure levels and then converted to spectrum density levels to show the sound components of the background noise in this region. Generalised Linear Models were used to relate dolphin whistle detections to temporal, spatial, environmental and acoustic variables.
The major sources of background noise were biological noise from soniferous fish and snapping shrimp and anthropogenic noise from vessels characterised by mid to high frequencies produced by artisanal fishing boats. There was monthly and diurnal variation with some locations characterised by loud sounds in the mid to high frequencies at night.
Whistle characteristics analysis revealed that the frequencies and range of the whistles were different to those previously reported under similar conditions. Whistles varied diurnally and in the presence of fish chorus and fishing boats. The study highlights a strong correlation between fish choruses and whistle detection.
Temporal and spatial models showed that whistle detections varied monthly and in relation to fish noise and small vessel engine noise. Dolphins were distributed throughout most of the study area; however, whistle detections varied with distance from the coast.
The results provide new knowledge about background noise composition in this region and provide the first information on the ecology of dolphin whistles in relation to this background noise, especially to fish chorus.Structural and functional characterisation of Mcb1 and the MCMᴹᶜᵇ¹ complex in Schizosaccharomyces pombeSchnick, Jasminhttps://hdl.handle.net/10023/44222019-07-01T10:19:02Z2014-06-01T00:00:00ZThe MCM helicase plays an important role in eukaryotic DNA replication, unwinding double stranded DNA ahead of the replication fork. MCM is a hetero-hexamer consisting of the six related proteins, Mcm2-Mcm7. The distantly related MCM-binding protein (MCM-BP) was first identified in a screen for proteins interacting with MCM2-7 in human cells and was found to specifically interact with Mcm3-7 but not Mcm2. It is conserved in most eukaryotes and seems to play an important role in DNA replication but its exact function is not clear yet.
This study contributes to the understanding of the fission yeast homologue of MCM-BP, named Mcb1, but also of MCM-BP in general. Results presented in this thesis document the initial biochemical characterisation of the complex Mcb1 forms with Mcm proteins, the MCMᴹᶜᵇ¹ complex. Interactions of Mcb1 with Mcm proteins, potential interaction sites between the proteins and the size of the complex were analysed using a variety of methods, including tandem affinity purification, co-immunoprecipitation, sucrose gradients and in vitro pull-down assays. Sequence analysis and structure prediction were utilised to gain some insight into Mcb1 and MCM-BP ancestry and structure. Results presented here indicate that fission yeast Mcb1 shares homology with Mcm proteins and forms a complex with Mcm3-Mcm7 but not Mcm2 and thus replaces the latter in an alternative high molecular weight complex that is likely to have an MCM-like appearance.
Deletion of mcb1⁺ showed that Mcb1 is essential in fission yeast. To examine the cellular function of the protein, temperature-sensitive mutants were generated. Inactivation of Mcb1 leads to an increase in DNA damage and cell cycle arrest in G2-phase depending on the activation of the Chk1 dependent DNA damage checkpoint. Similar observations were made when Mcb1 was overexpressed, indicating that certain levels of the protein are important for accurate DNA replication. Construction of truncated versions of Mcb1 suggested that almost the full-length protein is needed for proper function.
2014-06-01T00:00:00ZSchnick, JasminThe MCM helicase plays an important role in eukaryotic DNA replication, unwinding double stranded DNA ahead of the replication fork. MCM is a hetero-hexamer consisting of the six related proteins, Mcm2-Mcm7. The distantly related MCM-binding protein (MCM-BP) was first identified in a screen for proteins interacting with MCM2-7 in human cells and was found to specifically interact with Mcm3-7 but not Mcm2. It is conserved in most eukaryotes and seems to play an important role in DNA replication but its exact function is not clear yet.
This study contributes to the understanding of the fission yeast homologue of MCM-BP, named Mcb1, but also of MCM-BP in general. Results presented in this thesis document the initial biochemical characterisation of the complex Mcb1 forms with Mcm proteins, the MCMᴹᶜᵇ¹ complex. Interactions of Mcb1 with Mcm proteins, potential interaction sites between the proteins and the size of the complex were analysed using a variety of methods, including tandem affinity purification, co-immunoprecipitation, sucrose gradients and in vitro pull-down assays. Sequence analysis and structure prediction were utilised to gain some insight into Mcb1 and MCM-BP ancestry and structure. Results presented here indicate that fission yeast Mcb1 shares homology with Mcm proteins and forms a complex with Mcm3-Mcm7 but not Mcm2 and thus replaces the latter in an alternative high molecular weight complex that is likely to have an MCM-like appearance.
Deletion of mcb1⁺ showed that Mcb1 is essential in fission yeast. To examine the cellular function of the protein, temperature-sensitive mutants were generated. Inactivation of Mcb1 leads to an increase in DNA damage and cell cycle arrest in G2-phase depending on the activation of the Chk1 dependent DNA damage checkpoint. Similar observations were made when Mcb1 was overexpressed, indicating that certain levels of the protein are important for accurate DNA replication. Construction of truncated versions of Mcb1 suggested that almost the full-length protein is needed for proper function.Pelagic movements of pacific leatherback turtles (Dermochelys coriacea) reveal the complex role of prey and ocean currentsSchick, Robert SchillingRoberts, JasonEckert, ScottClark, JamesBailey, HelenChai, FeiShi, LiHalpin, Patrickhttps://hdl.handle.net/10023/43562023-04-25T23:37:52Z2013-11-20T00:00:00ZBackground: Leatherback turtles are renowned for their trans-oceanic migrations. However, despite numerous movement studies, the precise drivers of movement patterns in leatherbacks remain elusive. Many previous studies of leatherback turtles as well as other diving marine predators have analyzed surface movement patterns using only surface covariates. Since turtles and other marine predators spend the vast majority of their time diving under water, an analysis of movement patterns at depth should yield insight into what drives their movements. Results: We analyzed the movement paths of 15 post-nesting adult female Pacific leatherback turtles, which were caught and tagged on three nesting beaches in Mexico. The temporal length of the tracks ranged from 32 to 436 days, and the spatial distance covered ranged from 1,532 km to 13,097 km. We analyzed these tracks using a movement model designed to yield inference on the parameters driving movement. Because the telemetry data included diving depths, we extended an earlier version of the model that examined surface only movements, and here analyze movements in 3-dimensions. We tested the effect of dynamic environmental covariates from a coupled biophysical oceanographic model on patch choice in diving leatherback turtles, and compared the effects of parameters measured at the surface and at depth. The covariates included distance to future patch, temperature, salinity, meridional current velocity (current in the north–south direction), zonal current velocity (current in the east–west direction), phytoplankton density, diatom density, micro-plankton density, and meso-zooplankton density. We found significant, i.e. non-zero, correlation between movement and the parameters for oceanic covariates in 8 of the tracks. Of particular note, for one turtle we observed a lack of correlation between movements and a modeled index of zooplankton at the surface, but a significant correlation between movements and zooplankton at depth. Two of the turtles express a preference for patches at depth with elevated diatoms, and 2 turtles prefer patches with higher mezozooplankton values at depth. In contrast, 4 turtles expressed a preference for elevated zooplankton patches at the surface, but not at depth. We suggest that our understanding of a marine predator’s response to the environment may change significantly depending upon the analytical frame of reference, i.e. whether relationships are examined at the surface, at depth, or at different temporal resolutions. Lastly, we tested the effects of accounting for ocean currents on the movement patterns and found that for 13 of the 15 turtles, the parameter governing distance to the next patch decreased. Conclusions: Our results suggest that relationships derived from the analysis of surface tracks may not entirely explain movement patterns of this highly migratory species. Accounting for choices in the water column has shown that for certain individual turtles, what appears to be favourable habitat at depth is quantitatively different from that at the surface. This has implications for the analysis of the movements and diving behaviour of any top marine predator. The leatherback turtle is a deep diving reptile, and it is important to understand the subsurface variables that influence their movements if we are to precisely map the spatial dimensions of favorable leatherback habitat. These results present a new view into the drivers of diving patterns in turtles, and in particular represent a way of analyzing movements at depth that can be extended to other diving species.
APC paid through BIS OA funds.
2013-11-20T00:00:00ZSchick, Robert SchillingRoberts, JasonEckert, ScottClark, JamesBailey, HelenChai, FeiShi, LiHalpin, PatrickBackground: Leatherback turtles are renowned for their trans-oceanic migrations. However, despite numerous movement studies, the precise drivers of movement patterns in leatherbacks remain elusive. Many previous studies of leatherback turtles as well as other diving marine predators have analyzed surface movement patterns using only surface covariates. Since turtles and other marine predators spend the vast majority of their time diving under water, an analysis of movement patterns at depth should yield insight into what drives their movements. Results: We analyzed the movement paths of 15 post-nesting adult female Pacific leatherback turtles, which were caught and tagged on three nesting beaches in Mexico. The temporal length of the tracks ranged from 32 to 436 days, and the spatial distance covered ranged from 1,532 km to 13,097 km. We analyzed these tracks using a movement model designed to yield inference on the parameters driving movement. Because the telemetry data included diving depths, we extended an earlier version of the model that examined surface only movements, and here analyze movements in 3-dimensions. We tested the effect of dynamic environmental covariates from a coupled biophysical oceanographic model on patch choice in diving leatherback turtles, and compared the effects of parameters measured at the surface and at depth. The covariates included distance to future patch, temperature, salinity, meridional current velocity (current in the north–south direction), zonal current velocity (current in the east–west direction), phytoplankton density, diatom density, micro-plankton density, and meso-zooplankton density. We found significant, i.e. non-zero, correlation between movement and the parameters for oceanic covariates in 8 of the tracks. Of particular note, for one turtle we observed a lack of correlation between movements and a modeled index of zooplankton at the surface, but a significant correlation between movements and zooplankton at depth. Two of the turtles express a preference for patches at depth with elevated diatoms, and 2 turtles prefer patches with higher mezozooplankton values at depth. In contrast, 4 turtles expressed a preference for elevated zooplankton patches at the surface, but not at depth. We suggest that our understanding of a marine predator’s response to the environment may change significantly depending upon the analytical frame of reference, i.e. whether relationships are examined at the surface, at depth, or at different temporal resolutions. Lastly, we tested the effects of accounting for ocean currents on the movement patterns and found that for 13 of the 15 turtles, the parameter governing distance to the next patch decreased. Conclusions: Our results suggest that relationships derived from the analysis of surface tracks may not entirely explain movement patterns of this highly migratory species. Accounting for choices in the water column has shown that for certain individual turtles, what appears to be favourable habitat at depth is quantitatively different from that at the surface. This has implications for the analysis of the movements and diving behaviour of any top marine predator. The leatherback turtle is a deep diving reptile, and it is important to understand the subsurface variables that influence their movements if we are to precisely map the spatial dimensions of favorable leatherback habitat. These results present a new view into the drivers of diving patterns in turtles, and in particular represent a way of analyzing movements at depth that can be extended to other diving species.Boundary layer flow beneath an internal solitary wave of elevationCarr, MagdaDavies, P Ahttps://hdl.handle.net/10023/43312023-04-18T09:40:38Z2010-02-01T00:00:00ZThe wave-induced flow over a fixed bottom boundary beneath an internal solitary wave of elevation propagating in an unsheared, two-layer, stably stratified fluid is investigated experimentally. Measurements of the velocity field close to the bottom boundary are presented to illustrate that in the lower layer the fluid velocity near the bottom reverses direction as the wave decelerates while higher in the water column the fluid velocity is in the same direction as the wave propagation. The observation is similar in nature to that for wave-induced flow beneath a surface solitary wave. Contrary to theoretical predictions for internal solitary waves, no evidence for either boundary layer separation or vortex formation is found beneath the front half of the wave in the adverse pressure gradient region of the flow.
2010-02-01T00:00:00ZCarr, MagdaDavies, P AThe wave-induced flow over a fixed bottom boundary beneath an internal solitary wave of elevation propagating in an unsheared, two-layer, stably stratified fluid is investigated experimentally. Measurements of the velocity field close to the bottom boundary are presented to illustrate that in the lower layer the fluid velocity near the bottom reverses direction as the wave decelerates while higher in the water column the fluid velocity is in the same direction as the wave propagation. The observation is similar in nature to that for wave-induced flow beneath a surface solitary wave. Contrary to theoretical predictions for internal solitary waves, no evidence for either boundary layer separation or vortex formation is found beneath the front half of the wave in the adverse pressure gradient region of the flow.Human tissue in systems medicineCaie, Peter DavidSchuur, KlaasOniscu, AncaMullen, PeterReynolds, Paul AndrewHarrison, David Jameshttps://hdl.handle.net/10023/43112024-02-29T00:41:43Z2013-12-01T00:00:00ZHistopathology, the examination of an architecturally artefactual, two dimensional, static image remains a potent tool allowing diagnosis and empirical expectation of prognosis. Considerable optimism exists that the advent of molecular genetic testing and other biomarker strategies will improve or even replace this ancient technology. A number of biomarkers add considerable value for prediction of whether a treatment will work. This short review argues that a systems medicine approach to pathology will not seek to replace traditional pathology, but rather augment it. Systems approaches need to incorporate quantitative morphological, protein, mRNA and DNA. A significant challenge for clinical implementation of systems pathology is how to optimise information available from tissue, which is frequently sub-optimal in quality and amount, and yet generate useful predictive models which work. The transition of histopathology to systems pathophysiology and the use of multiscale datasets ushers in a new era in diagnosis, prognosis and prediction based on analysis of human tissue.
2013-12-01T00:00:00ZCaie, Peter DavidSchuur, KlaasOniscu, AncaMullen, PeterReynolds, Paul AndrewHarrison, David JamesHistopathology, the examination of an architecturally artefactual, two dimensional, static image remains a potent tool allowing diagnosis and empirical expectation of prognosis. Considerable optimism exists that the advent of molecular genetic testing and other biomarker strategies will improve or even replace this ancient technology. A number of biomarkers add considerable value for prediction of whether a treatment will work. This short review argues that a systems medicine approach to pathology will not seek to replace traditional pathology, but rather augment it. Systems approaches need to incorporate quantitative morphological, protein, mRNA and DNA. A significant challenge for clinical implementation of systems pathology is how to optimise information available from tissue, which is frequently sub-optimal in quality and amount, and yet generate useful predictive models which work. The transition of histopathology to systems pathophysiology and the use of multiscale datasets ushers in a new era in diagnosis, prognosis and prediction based on analysis of human tissue.Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe ÇEdwards, Thomas E.Cekan, PavolReginsson, Gunnar WidtfeldtShelke, Sandip A.Ferre D'Amare, Adrian R.Schiemann, OlavSigurdsson, Snorrihttps://hdl.handle.net/10023/42702022-04-26T10:30:07Z2011-05-01T00:00:00ZElectron Paramagnetic Resonance (EPR) spectroscopy and fluorescence spectroscopy are complementary biophysical techniques used to examine the structure and dynamics of macromolecules. We have previously described the bi-functional spectroscopic probe Ç for the study of nucleic acid structure and dynamics using EPR and fluorescence spectroscopy. As with any newly designed spectroscopic probe, the utility, functionality, and the structural effects of the probe on the nucleic acid must be examined in detail. Initial EPR, fluorescence, and thermal denaturation studies indicated that the phenoxazine-derived spin-labeled deoxycytosine analog Ç forms a structurally non-perturbing base-pair with deoxyguanosine in DNA. Here we extend the analysis of the spectroscopic probe by presenting a detailed crystallographic study of this label based on small molecule crystal structures of the nucleoside base ç and its phenoxazine analog as well as a 1.7 Å resolution crystal structure of Ç within a decamer duplex A-form DNA. The DNA crystal structure confirms that the spin-labeled deoxycytosine analog forms a non-perturbing base-pair with deoxyguanosine. Interestingly, this structure and also the one of the phenoxazine base show the label in a planar conformation, whereas the structure of the free spin label base ç has a bend at the oxazine linkage. Density function theory (DFT) calculations reveal that both conformations are very close in energy and possess both the same frequency for bending at the oxazine linkage. These results are interpreted as a small degree of bending flexibility around the oxazine linkage, which may be a consequence of the antiaromaticity in this 16-pi electron ring system. Within DNA, the amplitude of the bending motion is likely to be restricted due to steric hindrance. This detailed structural analysis shows that the spin label base ç can be used with high confidence in EPR- or fluorescence-based structural and dynamics studies of oligonucleotides.
2011-05-01T00:00:00ZEdwards, Thomas E.Cekan, PavolReginsson, Gunnar WidtfeldtShelke, Sandip A.Ferre D'Amare, Adrian R.Schiemann, OlavSigurdsson, SnorriElectron Paramagnetic Resonance (EPR) spectroscopy and fluorescence spectroscopy are complementary biophysical techniques used to examine the structure and dynamics of macromolecules. We have previously described the bi-functional spectroscopic probe Ç for the study of nucleic acid structure and dynamics using EPR and fluorescence spectroscopy. As with any newly designed spectroscopic probe, the utility, functionality, and the structural effects of the probe on the nucleic acid must be examined in detail. Initial EPR, fluorescence, and thermal denaturation studies indicated that the phenoxazine-derived spin-labeled deoxycytosine analog Ç forms a structurally non-perturbing base-pair with deoxyguanosine in DNA. Here we extend the analysis of the spectroscopic probe by presenting a detailed crystallographic study of this label based on small molecule crystal structures of the nucleoside base ç and its phenoxazine analog as well as a 1.7 Å resolution crystal structure of Ç within a decamer duplex A-form DNA. The DNA crystal structure confirms that the spin-labeled deoxycytosine analog forms a non-perturbing base-pair with deoxyguanosine. Interestingly, this structure and also the one of the phenoxazine base show the label in a planar conformation, whereas the structure of the free spin label base ç has a bend at the oxazine linkage. Density function theory (DFT) calculations reveal that both conformations are very close in energy and possess both the same frequency for bending at the oxazine linkage. These results are interpreted as a small degree of bending flexibility around the oxazine linkage, which may be a consequence of the antiaromaticity in this 16-pi electron ring system. Within DNA, the amplitude of the bending motion is likely to be restricted due to steric hindrance. This detailed structural analysis shows that the spin label base ç can be used with high confidence in EPR- or fluorescence-based structural and dynamics studies of oligonucleotides.Common HLA alleles associated with health, but not with facial attractivenessCoetzee, VinetBarrett, L.Greeff, J.M.Henzi, S.P.Perrett, David IanWadee, A.A.https://hdl.handle.net/10023/42432023-04-25T23:35:07Z2007-07-01T00:00:00ZThree adaptive hypotheses have been proposed to explain the link between the human leucocyte antigen (HLA) genes, health measures and facial attractiveness: inbreeding avoidance, heterozygote advantage and frequency-dependent selection. This paper reports findings that support a new hypothesis relating HLA to health. We suggest a new method to quantify the level of heterozygosity. HLA heterozygosity did not significantly predict health measures in women, but allele frequency did. Women with more common HLA alleles reported fewer cold and flu bouts per year, fewer illnesses in the previous year and rated themselves healthier than women with rare alleles. To our knowledge, this is the first study to show a positive correlation between HLA allele frequency and general health measures. We propose that certain common HLA alleles confer resistance to prevalent pathogens. Nevertheless, neither HLA heterozygosity nor allele frequency significantly predicted how healthy or attractive men rated the female volunteers. Three non-mutually exclusive explanations are put forward to explain this finding.
This material is based, in part, upon work supported by the National Research Foundation under Grant number 2053809 to JMG.
2007-07-01T00:00:00ZCoetzee, VinetBarrett, L.Greeff, J.M.Henzi, S.P.Perrett, David IanWadee, A.A.Three adaptive hypotheses have been proposed to explain the link between the human leucocyte antigen (HLA) genes, health measures and facial attractiveness: inbreeding avoidance, heterozygote advantage and frequency-dependent selection. This paper reports findings that support a new hypothesis relating HLA to health. We suggest a new method to quantify the level of heterozygosity. HLA heterozygosity did not significantly predict health measures in women, but allele frequency did. Women with more common HLA alleles reported fewer cold and flu bouts per year, fewer illnesses in the previous year and rated themselves healthier than women with rare alleles. To our knowledge, this is the first study to show a positive correlation between HLA allele frequency and general health measures. We propose that certain common HLA alleles confer resistance to prevalent pathogens. Nevertheless, neither HLA heterozygosity nor allele frequency significantly predicted how healthy or attractive men rated the female volunteers. Three non-mutually exclusive explanations are put forward to explain this finding.Femtosecond optoinjection of intact tobacco BY-2 cells using a reconfigurable photoporation platformMitchell, C.A.Kalies, S.Cizmár, T.Heisterkamp, A.Torrance, L.Roberts, A.G.Gunn-Moore, F.J.Dholakia, K.https://hdl.handle.net/10023/42342022-04-26T11:30:20Z2013-11-14T00:00:00ZA tightly-focused ultrashort pulsed laser beam incident upon a cell membrane has previously been shown to transiently increase cell membrane permeability while maintaining the viability of the cell, a technique known as photoporation. This permeability can be used to aid the passage of membrane-impermeable biologically-relevant substances such as dyes, proteins and nucleic acids into the cell. Ultrashort-pulsed lasers have proven to be indispensable for photoporating mammalian cells but they have rarely been applied to plant cells due to their larger sizes and rigid and thick cell walls, which significantly hinders the intracellular delivery of exogenous substances. Here we demonstrate and quantify femtosecond optical injection of membrane impermeable dyes into intact BY-2 tobacco plant cells growing in culture, investigating both optical and biological parameters. Specifically, we show that the long axial extent of a propagation invariant (“diffraction-free”) Bessel beam, which relaxes the requirements for tight focusing on the cell membrane, outperforms a standard Gaussian photoporation beam, achieving up to 70% optoinjection efficiency. Studies on the osmotic effects of culture media show that a hypertonic extracellular medium was found to be necessary to reduce turgor pressure and facilitate molecular entry into the cells.
2013-11-14T00:00:00ZMitchell, C.A.Kalies, S.Cizmár, T.Heisterkamp, A.Torrance, L.Roberts, A.G.Gunn-Moore, F.J.Dholakia, K.A tightly-focused ultrashort pulsed laser beam incident upon a cell membrane has previously been shown to transiently increase cell membrane permeability while maintaining the viability of the cell, a technique known as photoporation. This permeability can be used to aid the passage of membrane-impermeable biologically-relevant substances such as dyes, proteins and nucleic acids into the cell. Ultrashort-pulsed lasers have proven to be indispensable for photoporating mammalian cells but they have rarely been applied to plant cells due to their larger sizes and rigid and thick cell walls, which significantly hinders the intracellular delivery of exogenous substances. Here we demonstrate and quantify femtosecond optical injection of membrane impermeable dyes into intact BY-2 tobacco plant cells growing in culture, investigating both optical and biological parameters. Specifically, we show that the long axial extent of a propagation invariant (“diffraction-free”) Bessel beam, which relaxes the requirements for tight focusing on the cell membrane, outperforms a standard Gaussian photoporation beam, achieving up to 70% optoinjection efficiency. Studies on the osmotic effects of culture media show that a hypertonic extracellular medium was found to be necessary to reduce turgor pressure and facilitate molecular entry into the cells.Investigating annual diving behaviour by Hooded seals (Cystophora cristata) within the Northwest Atlantic OceanAndersen, Julie MarieSkern-Mauritzen, MetteBoehme, LarsWiersma, Yolanda F.Rosvig-Asvid, AqqaluHammill, MikeStenson, Garryhttps://hdl.handle.net/10023/42282023-04-18T09:46:31Z2013-11-25T00:00:00ZWith the exception of relatively brief periods when they reproduce and moult, hooded seals, Cystophora cristata, spend most of the year in the open ocean where they undergo feeding migrations to either recover or prepare for the next fasting period. Valuable insights into habitat use and diving behaviour during these periods have been obtained by attaching Satellite Relay Data Loggers (SRDLs) to 51 Northwest (NW) Atlantic hooded seals (33 females and 18 males) during ice-bound fasting periods (2004−2008). Using General Additive Models (GAMs) we describe habitat use in terms of First Passage Time (FPT) and analyse how bathymetry, seasonality and FPT influence the hooded seals’ diving behaviour described by maximum dive depth, dive duration and surface duration. Adult NW Atlantic hooded seals exhibit a change in diving activity in areas where they spend >20 h by increasing maximum dive depth, dive duration and surface duration, indicating a restricted search behaviour. We found that male and female hooded seals are spatially segregated and that diving behaviour varies between sexes in relation to habitat properties and seasonality. Migration periods are described by increased dive duration for both sexes with a peak in May, October and January. Males demonstrated an increase in dive depth and dive duration towards May (post-breeding/pre-moult) and August–October (post-moult/pre-breeding) but did not show any pronounced increase in surface duration. Females dived deepest and had the highest surface duration between December and January (post-moult/pre-breeding). Our results suggest that the smaller females may have a greater need to recover from dives than that of the larger males. Horizontal segregation could have evolved as a result of a resource partitioning strategy to avoid sexual competition or that the energy requirements of males and females are different due to different energy expenditure during fasting periods.
This work was funded through the Atlantic Seal Research Programme, International Governance Programme (DFO), the Greenland Institute of Natural Resources, and a CFI grant to YFW. The authors also acknowledge the support of the Marine Alliance for Science and Technology for Scotland (MASTS) pooling initiative in the completion of this study. MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
2013-11-25T00:00:00ZAndersen, Julie MarieSkern-Mauritzen, MetteBoehme, LarsWiersma, Yolanda F.Rosvig-Asvid, AqqaluHammill, MikeStenson, GarryWith the exception of relatively brief periods when they reproduce and moult, hooded seals, Cystophora cristata, spend most of the year in the open ocean where they undergo feeding migrations to either recover or prepare for the next fasting period. Valuable insights into habitat use and diving behaviour during these periods have been obtained by attaching Satellite Relay Data Loggers (SRDLs) to 51 Northwest (NW) Atlantic hooded seals (33 females and 18 males) during ice-bound fasting periods (2004−2008). Using General Additive Models (GAMs) we describe habitat use in terms of First Passage Time (FPT) and analyse how bathymetry, seasonality and FPT influence the hooded seals’ diving behaviour described by maximum dive depth, dive duration and surface duration. Adult NW Atlantic hooded seals exhibit a change in diving activity in areas where they spend >20 h by increasing maximum dive depth, dive duration and surface duration, indicating a restricted search behaviour. We found that male and female hooded seals are spatially segregated and that diving behaviour varies between sexes in relation to habitat properties and seasonality. Migration periods are described by increased dive duration for both sexes with a peak in May, October and January. Males demonstrated an increase in dive depth and dive duration towards May (post-breeding/pre-moult) and August–October (post-moult/pre-breeding) but did not show any pronounced increase in surface duration. Females dived deepest and had the highest surface duration between December and January (post-moult/pre-breeding). Our results suggest that the smaller females may have a greater need to recover from dives than that of the larger males. Horizontal segregation could have evolved as a result of a resource partitioning strategy to avoid sexual competition or that the energy requirements of males and females are different due to different energy expenditure during fasting periods.Exploring heritage through time and space : Supporting community reflection on the highland clearancesMcCaffery, John PhilipMiller, Alan Henry DavidKennedy, Sarah ElizabethDawson, TomVermehren, AnnaLefley, CStrickland, Khttps://hdl.handle.net/10023/41922024-02-25T00:38:06Z2013-10-01T00:00:00ZOn the two hundredth anniversary of the Kildonan clearances, when people were forcibly removed from their homes, the Timespan Heritage centre has created a program of community centred work aimed at challenging pre conceptions and encouraging reflection on this important historical process. This paper explores the innovative ways in which virtual world technology has facilitated community engagement, enhanced visualisation and encouraged reflection as part of this program. An installation where users navigate through a reconstruction of pre clearance Caen township is controlled through natural gestures and presented on a 300 inch six megapixel screen. This environment allows users to experience the past in new ways. The platform has value as an effective way for an educator, artist or hobbyist to create large scale virtual environments using off the shelf hardware and open source software. The result is an exhibit that also serves as a platform for experimentation into innovative ways of community co-creation and co-curation.
2013-10-01T00:00:00ZMcCaffery, John PhilipMiller, Alan Henry DavidKennedy, Sarah ElizabethDawson, TomVermehren, AnnaLefley, CStrickland, KOn the two hundredth anniversary of the Kildonan clearances, when people were forcibly removed from their homes, the Timespan Heritage centre has created a program of community centred work aimed at challenging pre conceptions and encouraging reflection on this important historical process. This paper explores the innovative ways in which virtual world technology has facilitated community engagement, enhanced visualisation and encouraged reflection as part of this program. An installation where users navigate through a reconstruction of pre clearance Caen township is controlled through natural gestures and presented on a 300 inch six megapixel screen. This environment allows users to experience the past in new ways. The platform has value as an effective way for an educator, artist or hobbyist to create large scale virtual environments using off the shelf hardware and open source software. The result is an exhibit that also serves as a platform for experimentation into innovative ways of community co-creation and co-curation.Open Virtual Worlds : A serious platform for experiential and game based learningMiller, Alan Henry DavidAllison, ColinGetchell, Kristoffer Marchttps://hdl.handle.net/10023/41822023-01-22T12:30:21Z2012-01-01T00:00:00ZThis paper presents our experiences of and reflections on five years work in using virtual worlds to support exploratory learning across a range of disciplines and educational contexts. Both educational and systems aspects are considered. Experiential learning enriches education by allowing exploration of a subject. However, often barriers of time, place, cost or scale make it difficult to conduct real world experiential learning. This paper presents experiences in utilizing virtual worlds to support experiential learning in the arts, humanities and sciences. The work presented here draws upon several years of experience in designing, developing and deploying Virtual World applications, which address the concrete needs of specific subject areas in a range of educational contexts. The work was motivated by the observation that 3D educational environments could leverage digital literacy developed playing console games and to provide an engaging learning experience where users navigate a virtual environment much as they would the real world. Furthermore developments in computer hardware and networking mean that 3D applications run on standard computers found in offices and educational institutions. The Initial application developed was a simulation of an archeological excavation. Prototypes were developed in a First Person Shooter game, a Virtual Reality environment and a Virtual World. We found that Virtual World technology offered users presence through the proxy of avatars and powerfull support for shaping and programming the environment. Initially a simulation of an archeological dig, a virtual teaching space for a management course, a virtual laboratory for wireless networking and a lab for exploring Human Computer Interaction were developed on a Second Life island. The experience was positive and students engaged in valuable learning activities that would not otherwise have been possible. However, we came up against constraints, that were not inherent in Virtual Worlds per se, but rather flowed from Second Life's service model. This lead us to migrate our development platform from Second Life to OpenSim. The ability for institutions to manage their own virtual world servers offers benefits in the areas of content creation, application development, cost and scalability. However in providing a virtual world service a number of challenges arise, which must be met if the potential of educational virtual worlds is to be realised. These challenges lie in the realms of application design, support for resource creation, and system support. The power of Open Virtual Worlds is illustrated here by presenting three exemplar applications developed on OpenSim. These are a virtual laboratory for experimenting with Internet routing protocols, a reconstruction of Scotland largest and most important religious building, St Andrews Cathedral and a tool for learning about intervention in humanitarian disasters. A number of subjects and educational contexts are considered: contexts include PhD and masters research projects, laboratory sessions as part of accredited degree programs, open days for aspiring entrants, an exhibition held in a science center attended by the “interested public”, parties of primary school students with their teachers as well as scouts and cubs on a days expedition. Subjects areas include, computer science, archeology, art history, history and management. Taken together this work demonstrates the power of virtual worlds as a platform for developing 3D applications that support heterogeneous exploratory learning. There are still challenges to be met for the potential to be realised but the potential is considerable.
2012-01-01T00:00:00ZMiller, Alan Henry DavidAllison, ColinGetchell, Kristoffer MarcThis paper presents our experiences of and reflections on five years work in using virtual worlds to support exploratory learning across a range of disciplines and educational contexts. Both educational and systems aspects are considered. Experiential learning enriches education by allowing exploration of a subject. However, often barriers of time, place, cost or scale make it difficult to conduct real world experiential learning. This paper presents experiences in utilizing virtual worlds to support experiential learning in the arts, humanities and sciences. The work presented here draws upon several years of experience in designing, developing and deploying Virtual World applications, which address the concrete needs of specific subject areas in a range of educational contexts. The work was motivated by the observation that 3D educational environments could leverage digital literacy developed playing console games and to provide an engaging learning experience where users navigate a virtual environment much as they would the real world. Furthermore developments in computer hardware and networking mean that 3D applications run on standard computers found in offices and educational institutions. The Initial application developed was a simulation of an archeological excavation. Prototypes were developed in a First Person Shooter game, a Virtual Reality environment and a Virtual World. We found that Virtual World technology offered users presence through the proxy of avatars and powerfull support for shaping and programming the environment. Initially a simulation of an archeological dig, a virtual teaching space for a management course, a virtual laboratory for wireless networking and a lab for exploring Human Computer Interaction were developed on a Second Life island. The experience was positive and students engaged in valuable learning activities that would not otherwise have been possible. However, we came up against constraints, that were not inherent in Virtual Worlds per se, but rather flowed from Second Life's service model. This lead us to migrate our development platform from Second Life to OpenSim. The ability for institutions to manage their own virtual world servers offers benefits in the areas of content creation, application development, cost and scalability. However in providing a virtual world service a number of challenges arise, which must be met if the potential of educational virtual worlds is to be realised. These challenges lie in the realms of application design, support for resource creation, and system support. The power of Open Virtual Worlds is illustrated here by presenting three exemplar applications developed on OpenSim. These are a virtual laboratory for experimenting with Internet routing protocols, a reconstruction of Scotland largest and most important religious building, St Andrews Cathedral and a tool for learning about intervention in humanitarian disasters. A number of subjects and educational contexts are considered: contexts include PhD and masters research projects, laboratory sessions as part of accredited degree programs, open days for aspiring entrants, an exhibition held in a science center attended by the “interested public”, parties of primary school students with their teachers as well as scouts and cubs on a days expedition. Subjects areas include, computer science, archeology, art history, history and management. Taken together this work demonstrates the power of virtual worlds as a platform for developing 3D applications that support heterogeneous exploratory learning. There are still challenges to be met for the potential to be realised but the potential is considerable.Ecology of the Guiana dolphin (Sotalia guianensis) in the Southern area of the Gulf of Morrosquillo, Colombia : implications for conservationDussán-Duque, Beatriz Saloméhttps://hdl.handle.net/10023/41532019-03-29T10:41:12Z2013-11-29T00:00:00ZSotalia guianensis is listed as “Data Deficient” by the IUCN and as “Vulnerable” in Colombia. This study aimed to advance understanding of the ecology of this species and its habitats, and to provide information to conservation management in the southern Gulf of Morrosquillo, Colombia. Systematic boat-based surveys were conducted during 395 days in 2002-2006 and 2009-2010, following established routes. Total survey effort was 15,199 km in an area covering ~ 310km². Fine scale habitat use and behavioural modelling, photo-identification and mark-recapture techniques were used to analyze the ecological patterns for this species. The most recent abundance estimate of dolphins using the study area during dry and rainy seasons, varied from 225 (CV = 0.34; 95% CI: 118-426) to 232 (CV = 0.32; 95% CI: 127-246). Annual survival rate is estimated at 0.948 (95% CI = 0.876-0.980). Overall density was 0.74/km². Dolphins were present year-round in the whole study area. Results indicate that they do not use the study area uniformly and that the use of particular zones is related to eco-geographic variables. Dolphins showed a preference for waters greater than 3m in depth with a slightly increased preference for waters about 5m and 15-25m deep. The average group size was nine individuals. Some individuals show long-term high site fidelity to some zones within the study site boundaries. Even though the site fidelity to feeding areas varied individually, all the individuals focused primarily on one specific area. Foraging was among one of the most predominant behaviours observed. The individual movements show that some dolphins use both bay and gulf waters. Dolphins show a range of surface cooperative foraging and feeding strategies. These cooperative behaviours were influenced by zone, group size and prey type. Based on these results an area of special management for the species will be created in Colombia.
2013-11-29T00:00:00ZDussán-Duque, Beatriz SaloméSotalia guianensis is listed as “Data Deficient” by the IUCN and as “Vulnerable” in Colombia. This study aimed to advance understanding of the ecology of this species and its habitats, and to provide information to conservation management in the southern Gulf of Morrosquillo, Colombia. Systematic boat-based surveys were conducted during 395 days in 2002-2006 and 2009-2010, following established routes. Total survey effort was 15,199 km in an area covering ~ 310km². Fine scale habitat use and behavioural modelling, photo-identification and mark-recapture techniques were used to analyze the ecological patterns for this species. The most recent abundance estimate of dolphins using the study area during dry and rainy seasons, varied from 225 (CV = 0.34; 95% CI: 118-426) to 232 (CV = 0.32; 95% CI: 127-246). Annual survival rate is estimated at 0.948 (95% CI = 0.876-0.980). Overall density was 0.74/km². Dolphins were present year-round in the whole study area. Results indicate that they do not use the study area uniformly and that the use of particular zones is related to eco-geographic variables. Dolphins showed a preference for waters greater than 3m in depth with a slightly increased preference for waters about 5m and 15-25m deep. The average group size was nine individuals. Some individuals show long-term high site fidelity to some zones within the study site boundaries. Even though the site fidelity to feeding areas varied individually, all the individuals focused primarily on one specific area. Foraging was among one of the most predominant behaviours observed. The individual movements show that some dolphins use both bay and gulf waters. Dolphins show a range of surface cooperative foraging and feeding strategies. These cooperative behaviours were influenced by zone, group size and prey type. Based on these results an area of special management for the species will be created in Colombia.Female rose bitterling prefer MHC-dissimilar males : experimental evidenceReichard, MartinSpence, Rowena Grace AlisonBryjova, AnnaBryja, PepaSmith, Carlhttps://hdl.handle.net/10023/41432023-04-18T09:45:23Z2012-07-18T00:00:00ZThe role of genetic benefits in female mate choice remains a controversial aspect of sexual selection theory. In contrast to “good allele” models of sexual selection, “compatible allele” models of mate choice predict that females prefer mates with alleles complementary to their own rather than conferring additive effects. While correlative results suggest complementary genetic effects to be plausible, direct experimental evidence is scarce. A previous study on the Chinese rose bitterling (Rhodeus ocellatus) demonstrated a positive correlation between female mate choice, offspring growth and survival, and the functional dissimilarity between the Major Histocompatibility Complex (MHC) alleles of males and females. Here we directly tested whether females used cues associated with MHC genes to select genetically compatible males in an experimental framework. By sequentially pairing females with MHC similar and dissimilar males, based on a priori known MHC profiles, we showed that females discriminated between similar and dissimilar males and deposited significantly more eggs with MHC dissimilar males. Notably, the degree of dissimilarity was an important factor for female decision to mate, possibly indicating a potential threshold value of dissimilarity for decision making, or of an indirect effect of the MHC.
2012-07-18T00:00:00ZReichard, MartinSpence, Rowena Grace AlisonBryjova, AnnaBryja, PepaSmith, CarlThe role of genetic benefits in female mate choice remains a controversial aspect of sexual selection theory. In contrast to “good allele” models of sexual selection, “compatible allele” models of mate choice predict that females prefer mates with alleles complementary to their own rather than conferring additive effects. While correlative results suggest complementary genetic effects to be plausible, direct experimental evidence is scarce. A previous study on the Chinese rose bitterling (Rhodeus ocellatus) demonstrated a positive correlation between female mate choice, offspring growth and survival, and the functional dissimilarity between the Major Histocompatibility Complex (MHC) alleles of males and females. Here we directly tested whether females used cues associated with MHC genes to select genetically compatible males in an experimental framework. By sequentially pairing females with MHC similar and dissimilar males, based on a priori known MHC profiles, we showed that females discriminated between similar and dissimilar males and deposited significantly more eggs with MHC dissimilar males. Notably, the degree of dissimilarity was an important factor for female decision to mate, possibly indicating a potential threshold value of dissimilarity for decision making, or of an indirect effect of the MHC.Propaganda and persuasion in the early Scottish Reformation, c.1527-1557Tapscott, Elizabeth L.https://hdl.handle.net/10023/41152019-07-01T10:12:21Z2013-11-30T00:00:00ZThe decades before the Scottish Reformation Parliament of 1560 witnessed the unprecedented use of a range of different media to disseminate the Protestant message and to shape beliefs and attitudes. By placing these works within their historical context, this thesis explores the ways in which various media – academic discourse, courtly entertainments, printed poetry, public performances, preaching and pedagogical tools – were employed by evangelical and Protestant reformers to persuade and/or educate different audiences within sixteenth-century Scottish society. The thematic approach examines not only how the reformist message was packaged, but how the movement itself and its persuasive agenda developed, revealing the ways in which it appealed to ever broader circles of Scottish society.
In their efforts to bring about religious change, the reformers capitalised on a number of traditional media, while using different media to address different audiences. Hoping to initiate reform from within Church institutions, the reformers first addressed their appeals to the kingdom’s educated elite. When their attempts at reasoned academic discourse met with resistance, they turned their attention to the monarch, James V, and the royal court. Reformers within the court utilised courtly entertainments intended to amuse the royal circle and to influence the young king to oversee the reformation of religion within his realm. When, following James’s untimely death in 1542, the throne passed to his infant daughter, the reformers took advantage of the period of uncertainty that accompanied the minority. Through the relatively new technology of print, David Lindsay’s poetry and English propaganda presented the reformist message to audiences beyond the kingdom’s elite. Lindsay and other reformers also exploited the oral media of religious theatre in public spaces, while preaching was one of the most theologically significant, though under-researched, means of disseminating the reformist message. In addition to works intended to convert, the reformers also recognised the need for literature to edify the already converted. To this end, they produced pedagogical tools for use in individual and group devotions. Through the examination of these various media of persuasion, this study contributes to our understanding of the means by which reformed ideas were disseminated in Scotland, as well as the development of the reformist movement before 1560.
2013-11-30T00:00:00ZTapscott, Elizabeth L.The decades before the Scottish Reformation Parliament of 1560 witnessed the unprecedented use of a range of different media to disseminate the Protestant message and to shape beliefs and attitudes. By placing these works within their historical context, this thesis explores the ways in which various media – academic discourse, courtly entertainments, printed poetry, public performances, preaching and pedagogical tools – were employed by evangelical and Protestant reformers to persuade and/or educate different audiences within sixteenth-century Scottish society. The thematic approach examines not only how the reformist message was packaged, but how the movement itself and its persuasive agenda developed, revealing the ways in which it appealed to ever broader circles of Scottish society.
In their efforts to bring about religious change, the reformers capitalised on a number of traditional media, while using different media to address different audiences. Hoping to initiate reform from within Church institutions, the reformers first addressed their appeals to the kingdom’s educated elite. When their attempts at reasoned academic discourse met with resistance, they turned their attention to the monarch, James V, and the royal court. Reformers within the court utilised courtly entertainments intended to amuse the royal circle and to influence the young king to oversee the reformation of religion within his realm. When, following James’s untimely death in 1542, the throne passed to his infant daughter, the reformers took advantage of the period of uncertainty that accompanied the minority. Through the relatively new technology of print, David Lindsay’s poetry and English propaganda presented the reformist message to audiences beyond the kingdom’s elite. Lindsay and other reformers also exploited the oral media of religious theatre in public spaces, while preaching was one of the most theologically significant, though under-researched, means of disseminating the reformist message. In addition to works intended to convert, the reformers also recognised the need for literature to edify the already converted. To this end, they produced pedagogical tools for use in individual and group devotions. Through the examination of these various media of persuasion, this study contributes to our understanding of the means by which reformed ideas were disseminated in Scotland, as well as the development of the reformist movement before 1560.Geographically weighted spatial interaction (GWSI)Kordi, Maryamhttps://hdl.handle.net/10023/41122020-09-28T17:52:30Z2013-11-30T00:00:00ZOne of the key concerns in spatial analysis and modelling is to study and analyse similarities or dissimilarities between places over geographical space. However, ”global“ spatial models may fail to identify spatial variations of relationships (spatial heterogeneity) by assuming spatial stationarity of relationships. In many real-life situations spatial variation in relationships possibly exists and the assumption of global stationarity might be highly unrealistic leading to ignorance of a large amount of spatial information. In contrast, local spatial models emphasise differences or dissimilarity over space and focus on identifying spatial variations in relationships. These models allow the parameters of models to vary locally and can provide more useful information on the processes generating the data in different parts of the study area.
In this study, a framework for localising spatial interaction models, based on geographically weighted (GW) techniques, has been developed. This framework can help in detecting, visualising and analysing spatial heterogeneity in spatial interaction systems. In order to apply the GW concept to spatial interaction models, we investigate several approaches differing mainly in the way calibration points (flows) are defined and spatial separation (distance) between flows is calculated. As a result, a series of localised geographically weighted spatial interaction (GWSI) models are developed.
Using custom-built algorithms and computer code, we apply the GWSI models to a journey-to-work dataset in Switzerland for validation and comparison with the related global models. The results of the model calibrations are visualised using a series of conventional and flow maps along with some matrix visualisations. The comparison of the results indicates that in most cases local GWSI models exhibit an improvement over the global models both in providing more useful local information and also in model performance and goodness-of-fit.
2013-11-30T00:00:00ZKordi, MaryamOne of the key concerns in spatial analysis and modelling is to study and analyse similarities or dissimilarities between places over geographical space. However, ”global“ spatial models may fail to identify spatial variations of relationships (spatial heterogeneity) by assuming spatial stationarity of relationships. In many real-life situations spatial variation in relationships possibly exists and the assumption of global stationarity might be highly unrealistic leading to ignorance of a large amount of spatial information. In contrast, local spatial models emphasise differences or dissimilarity over space and focus on identifying spatial variations in relationships. These models allow the parameters of models to vary locally and can provide more useful information on the processes generating the data in different parts of the study area.
In this study, a framework for localising spatial interaction models, based on geographically weighted (GW) techniques, has been developed. This framework can help in detecting, visualising and analysing spatial heterogeneity in spatial interaction systems. In order to apply the GW concept to spatial interaction models, we investigate several approaches differing mainly in the way calibration points (flows) are defined and spatial separation (distance) between flows is calculated. As a result, a series of localised geographically weighted spatial interaction (GWSI) models are developed.
Using custom-built algorithms and computer code, we apply the GWSI models to a journey-to-work dataset in Switzerland for validation and comparison with the related global models. The results of the model calibrations are visualised using a series of conventional and flow maps along with some matrix visualisations. The comparison of the results indicates that in most cases local GWSI models exhibit an improvement over the global models both in providing more useful local information and also in model performance and goodness-of-fit.The seasonal movements and dynamics of migrating humpback whales off the east coast of AfricaBanks, Aaron M.https://hdl.handle.net/10023/41092019-03-29T10:37:07Z2013-11-29T00:00:00ZData collected during boat-based and aerial surveys were used to describe population structure, movements, temporal patterns of migration and skin condition of humpback whales in breeding sub-stock C1-S off southern Africa. Results confirmed that the migration route along the south coast of South Africa is linked to the winter ground off Mozambique. A lack of exchange between breeding sub-stocks C1-N and C1-S was found, suggesting that these are independent of each other. Molecular analysis revealed unexpected levels of population structure between the migration route and the winter ground of C1-S, as well as the possibility that this migration route is also utilised by some individuals from breeding sub-stock C3. A skin condition of unknown aetiology that primarily affects humpback whale mother-calf pairs was identified. The first assessment of its prevalence and severity was made, providing a baseline for future monitoring. Humpback whale abundance in an inshore region of Bazaruto Archipelago, Mozambique was estimated and attempts were also made to use the limited information off Plettenberg Bay/Knysna, South Africa. In addition to improving our understanding of humpback whales from Breeding Stock C, knowledge about another baleen whale species utilising the southwest Indian Ocean was extended. The first evidence of southern right whale presence off the coast of Mozambique since the cessation of whaling was documented. It remains unknown whether this is a remnant sub-stock or the recovering South African sub-stock reoccupying its historical range.
2013-11-29T00:00:00ZBanks, Aaron M.Data collected during boat-based and aerial surveys were used to describe population structure, movements, temporal patterns of migration and skin condition of humpback whales in breeding sub-stock C1-S off southern Africa. Results confirmed that the migration route along the south coast of South Africa is linked to the winter ground off Mozambique. A lack of exchange between breeding sub-stocks C1-N and C1-S was found, suggesting that these are independent of each other. Molecular analysis revealed unexpected levels of population structure between the migration route and the winter ground of C1-S, as well as the possibility that this migration route is also utilised by some individuals from breeding sub-stock C3. A skin condition of unknown aetiology that primarily affects humpback whale mother-calf pairs was identified. The first assessment of its prevalence and severity was made, providing a baseline for future monitoring. Humpback whale abundance in an inshore region of Bazaruto Archipelago, Mozambique was estimated and attempts were also made to use the limited information off Plettenberg Bay/Knysna, South Africa. In addition to improving our understanding of humpback whales from Breeding Stock C, knowledge about another baleen whale species utilising the southwest Indian Ocean was extended. The first evidence of southern right whale presence off the coast of Mozambique since the cessation of whaling was documented. It remains unknown whether this is a remnant sub-stock or the recovering South African sub-stock reoccupying its historical range.Maximum likelihood estimation of mark-recapture-recovery models in the presence of continuous covariatesLangrock, RolandKing, Ruthhttps://hdl.handle.net/10023/40732023-04-18T09:46:34Z2013-01-01T00:00:00ZWe consider mark-recapture-recovery (MRR) data of animals where the model parameters are a function of individual time-varying continuous covariates. For such covariates, the covariate value is unobserved if the corresponding individual is unobserved, in which case the survival probability cannot be evaluated. For continuous-valued covariates, the corresponding likelihood can only be expressed in the form of an integral that is analytically intractable, and, to date, no maximum likelihood approach that uses all the information in the data has been developed. Assuming a first-order Markov process for the covariate values, we accomplish this task by formulating the MRR setting in a state-space framework and considering an approximate likelihood approach which essentially discretizes the range of covariate values, reducing the integral to a summation. The likelihood can then be efficiently calculated and maximized using standard techniques for hidden Markov models. We initially assess the approach using simulated data before applying to real data relating to Soay sheep, specifying the survival probability as a function of body mass. Models that have previously been suggested for the corresponding covariate process are typically of the form of di.usive random walks. We consider an alternative non-di.usive AR(1)-type model which appears to provide a significantly better fit to the Soay sheep data.
Supplementary material: R code for model fitting. Sample R code for simulating MRR data and fitting the corresponding model using the HMM-based approach (with MRR model as described in Section 3). Digital Object Identifier: doi:10.1214/13-AOAS644SUPP
2013-01-01T00:00:00ZLangrock, RolandKing, RuthWe consider mark-recapture-recovery (MRR) data of animals where the model parameters are a function of individual time-varying continuous covariates. For such covariates, the covariate value is unobserved if the corresponding individual is unobserved, in which case the survival probability cannot be evaluated. For continuous-valued covariates, the corresponding likelihood can only be expressed in the form of an integral that is analytically intractable, and, to date, no maximum likelihood approach that uses all the information in the data has been developed. Assuming a first-order Markov process for the covariate values, we accomplish this task by formulating the MRR setting in a state-space framework and considering an approximate likelihood approach which essentially discretizes the range of covariate values, reducing the integral to a summation. The likelihood can then be efficiently calculated and maximized using standard techniques for hidden Markov models. We initially assess the approach using simulated data before applying to real data relating to Soay sheep, specifying the survival probability as a function of body mass. Models that have previously been suggested for the corresponding covariate process are typically of the form of di.usive random walks. We consider an alternative non-di.usive AR(1)-type model which appears to provide a significantly better fit to the Soay sheep data.The Legacy of Iconoclasm: religious war and the relic landscape of Tours, Blois and Vendôme, 1550-1750Nelson, Erichttps://hdl.handle.net/10023/40382019-04-01T11:10:07Z2013-09-01T00:00:00ZThis study explores the process of physically rebuilding, renewing and reinventing the relic landscape in the regions around Tours, Blois and Vendôme following the widespread iconoclastic damage of the French religious wars. The author takes a long-term perspective exploring developments over two hundred years, from the mid-sixteenth through to the mid-eighteenth centuries. The book explores what the physical renewal of the landscape can tell us about evolving beliefs and practices concerning relics during the Catholic Reformation and what reconstruction activities reveal about the meaning and experience of relic veneration. It pays particular attention to how the relic landscape evolved through relic translations and how communities that oversaw relic shrines remembered the iconoclastic acts of the religious wars through liturgical and ritual commemorations, memorials, artistic renderings, oral traditions and written accounts.
2013-09-01T00:00:00ZNelson, EricThis study explores the process of physically rebuilding, renewing and reinventing the relic landscape in the regions around Tours, Blois and Vendôme following the widespread iconoclastic damage of the French religious wars. The author takes a long-term perspective exploring developments over two hundred years, from the mid-sixteenth through to the mid-eighteenth centuries. The book explores what the physical renewal of the landscape can tell us about evolving beliefs and practices concerning relics during the Catholic Reformation and what reconstruction activities reveal about the meaning and experience of relic veneration. It pays particular attention to how the relic landscape evolved through relic translations and how communities that oversaw relic shrines remembered the iconoclastic acts of the religious wars through liturgical and ritual commemorations, memorials, artistic renderings, oral traditions and written accounts.Prostitution and subjectivity in late mediaeval Germany and SwitzerlandPage, Jamiehttps://hdl.handle.net/10023/40372023-11-15T03:02:35Z2013-11-30T00:00:00ZThis thesis is a study of the problem of subjectivity and prostitution in the Middle Ages. Three legal case studies of unpublished archival material and one chapter focussing on fictional texts from late mediaeval Germany and Switzerland are used to investigate the conditions of prostitutes’ subjectification in law and literature. The thesis takes impetus from Ruth Karras’s recent articulation of the problem of prostitution and sexuality, seeking to engage critically with her notion of “prostitute” as a medieval sexual identity that might be applied to any woman who had extra-marital sex. In dealing with trial records, it also aims to make a methodological contribution to the study of crime and the problem of locating the individual.
Chapters I-III examine the records of criminal cases featuring the testimony of prostitutes, or women who risked such categorisation, to consider the available subject positions both within and outwith the context of municipal regulation. Whilst acknowledging the force of normative ideas about prostitutes as lustful women, these chapters argue that prostitutes’ subject positions in legal cases were adopted according to local conditions, and depended upon the immediate circumstances of the women involved. They also consider trial records as a form of masculine discourse, arguing that an anxious masculine subject can be seen to emerge in response to the phenomenon of prostitution. Chapter IV expands this discussion by drawing on literary texts showing how prostitutes prompted concern on the part of male poets and audiences, for whom their sexual agency was a threat which belied their theoretical status as sexual objects.
Note: Transcriptions of the legal cases making up chapters I-III are provided in Appendices A, B, and C.
2013-11-30T00:00:00ZPage, JamieThis thesis is a study of the problem of subjectivity and prostitution in the Middle Ages. Three legal case studies of unpublished archival material and one chapter focussing on fictional texts from late mediaeval Germany and Switzerland are used to investigate the conditions of prostitutes’ subjectification in law and literature. The thesis takes impetus from Ruth Karras’s recent articulation of the problem of prostitution and sexuality, seeking to engage critically with her notion of “prostitute” as a medieval sexual identity that might be applied to any woman who had extra-marital sex. In dealing with trial records, it also aims to make a methodological contribution to the study of crime and the problem of locating the individual.
Chapters I-III examine the records of criminal cases featuring the testimony of prostitutes, or women who risked such categorisation, to consider the available subject positions both within and outwith the context of municipal regulation. Whilst acknowledging the force of normative ideas about prostitutes as lustful women, these chapters argue that prostitutes’ subject positions in legal cases were adopted according to local conditions, and depended upon the immediate circumstances of the women involved. They also consider trial records as a form of masculine discourse, arguing that an anxious masculine subject can be seen to emerge in response to the phenomenon of prostitution. Chapter IV expands this discussion by drawing on literary texts showing how prostitutes prompted concern on the part of male poets and audiences, for whom their sexual agency was a threat which belied their theoretical status as sexual objects.
Note: Transcriptions of the legal cases making up chapters I-III are provided in Appendices A, B, and C.Time is of the essence for ParaHox homeobox gene clustering.Garstang, Myles GrantFerrier, David Ellard Keithhttps://hdl.handle.net/10023/39972023-04-18T09:48:53Z2013-06-01T00:00:00ZParaHox genes, and their evolutionary sisters the Hox genes, are integral to patterning the anterior-posterior axis of most animals. Like the Hox genes, ParaHox genes can be clustered and exhibit the phenomenon of colinearity - gene order within the cluster matching gene activation. Two new instances of ParaHox clustering provide the first examples of intact clusters outside chordates, with gene expression lending weight to the argument that temporal colinearity is the key to understanding clustering.
2013-06-01T00:00:00ZGarstang, Myles GrantFerrier, David Ellard KeithParaHox genes, and their evolutionary sisters the Hox genes, are integral to patterning the anterior-posterior axis of most animals. Like the Hox genes, ParaHox genes can be clustered and exhibit the phenomenon of colinearity - gene order within the cluster matching gene activation. Two new instances of ParaHox clustering provide the first examples of intact clusters outside chordates, with gene expression lending weight to the argument that temporal colinearity is the key to understanding clustering.Structural studies of CRISPR-associated proteinsReeks, Judithhttps://hdl.handle.net/10023/39652019-03-29T11:19:48Z2013-11-29T00:00:00ZClustered regularly interspaced short palindromic repeats (CRISPRs) act to prevent viral infection and horizontal gene transfer in prokaryotes. The genomic CRISPR array contains short sequences (“spacers”) that are derived from foreign genetic elements. The CRISPR array is transcribed and processed into CRISPR RNAs (crRNAs) used in the sequence-specific degradation of foreign nucleic acids. This process is called interference and is mediated by CRISPR-associated (Cas) proteins.
This thesis has focused on the structural and functional characterisation of four Cas proteins from the CRISPR/Cas system of Sulfolobus solfataricus. The crystal structure of Cmr7 (Sso1725), a Sulfolobales-specific subunit of the ssRNA-degrading CMR complex, allowed for the identification of a putative protein-binding site, though no specific function could be ascribed to the protein. Cas6 (Sso1437) is the enzyme responsible for crRNA maturation and the characterisation of this protein allowed for the molecular rationalisation of its atypical RNA cleavage mechanism. Csa5 and Cas8a2 are subunits of the aCascade complex that targets dsDNA. Csa5 (Sso1398) was shown to have a putative role in R-loop stabilisation during interference while the role of Cas8a2 (Sso1401) was not determined. The structures of these two proteins were used to define relationships between the subunits of interference complexes from various CRISPR/Cas systems.
A second aspect of this work has been the expression and purification of eukaryotic ion channels for structural studies. The acid sensing ion channel (ASIC) and FMRFamide-gated sodium channel (FaNaC) are gated ion channels with unknown mechanisms of channel activation. These ion channels must be expressed in eukaryotic systems and so human embryonic kidney (HEK) cells and baculovirus-insect cell expression systems were developed to express ASIC and FaNaC constructs. The expression and purification protocols have been optimised to allow for the preparation of soluble protein that will in future be used for crystallography and electron paramagnetic resonance (EPR) studies.
2013-11-29T00:00:00ZReeks, JudithClustered regularly interspaced short palindromic repeats (CRISPRs) act to prevent viral infection and horizontal gene transfer in prokaryotes. The genomic CRISPR array contains short sequences (“spacers”) that are derived from foreign genetic elements. The CRISPR array is transcribed and processed into CRISPR RNAs (crRNAs) used in the sequence-specific degradation of foreign nucleic acids. This process is called interference and is mediated by CRISPR-associated (Cas) proteins.
This thesis has focused on the structural and functional characterisation of four Cas proteins from the CRISPR/Cas system of Sulfolobus solfataricus. The crystal structure of Cmr7 (Sso1725), a Sulfolobales-specific subunit of the ssRNA-degrading CMR complex, allowed for the identification of a putative protein-binding site, though no specific function could be ascribed to the protein. Cas6 (Sso1437) is the enzyme responsible for crRNA maturation and the characterisation of this protein allowed for the molecular rationalisation of its atypical RNA cleavage mechanism. Csa5 and Cas8a2 are subunits of the aCascade complex that targets dsDNA. Csa5 (Sso1398) was shown to have a putative role in R-loop stabilisation during interference while the role of Cas8a2 (Sso1401) was not determined. The structures of these two proteins were used to define relationships between the subunits of interference complexes from various CRISPR/Cas systems.
A second aspect of this work has been the expression and purification of eukaryotic ion channels for structural studies. The acid sensing ion channel (ASIC) and FMRFamide-gated sodium channel (FaNaC) are gated ion channels with unknown mechanisms of channel activation. These ion channels must be expressed in eukaryotic systems and so human embryonic kidney (HEK) cells and baculovirus-insect cell expression systems were developed to express ASIC and FaNaC constructs. The expression and purification protocols have been optimised to allow for the preparation of soluble protein that will in future be used for crystallography and electron paramagnetic resonance (EPR) studies.Categories, concepts, and calls : auditory perceptual mechanisms and cognitive abilities across different types of birds.Hahn, AllisonGuillette, LaurenHoeschele, MarisaCook, RobertSturdy, Christopherhttps://hdl.handle.net/10023/39612023-07-25T10:30:02Z2013-06-01T00:00:00ZAlthough involving different animals, preparations, and objectives, our laboratories (Sturdy's and Cook's) are mutually interested in category perception and concept formation. The Sturdy laboratory has a history of studying perceptual categories in songbirds, while Cook laboratory has a history of studying abstract concept formation in pigeons. Recently, we undertook a suite of collaborative projects to combine our investigations to examine abstract concept formation in songbirds, and perception of songbird vocalizations in pigeons. This talk will include our recent findings of songbird category perception, songbird abstract concept formation (same/different task), and early results from pigeons' processing of songbird vocalizations in a same/different task. Our findings indicate that (1) categorization in birds seems to be most heavily influenced by acoustic, rather than genetic or experiential factors (2) songbirds treat their vocalizations as perceptual categories, both at the level of the note and species/whole call, (3) chickadees, like pigeons, can perceive abstract, same-different relations, and (4) pigeons are not as good at discriminating chickadee vocalizations as songbirds (chickadees and finches). Our findings suggest that although there are commonalities in complex auditory processing among birds, there are potentially important comparative differences between songbirds and non-songbirds in their treatment of certain types of auditory objects.
2013-06-01T00:00:00ZHahn, AllisonGuillette, LaurenHoeschele, MarisaCook, RobertSturdy, ChristopherAlthough involving different animals, preparations, and objectives, our laboratories (Sturdy's and Cook's) are mutually interested in category perception and concept formation. The Sturdy laboratory has a history of studying perceptual categories in songbirds, while Cook laboratory has a history of studying abstract concept formation in pigeons. Recently, we undertook a suite of collaborative projects to combine our investigations to examine abstract concept formation in songbirds, and perception of songbird vocalizations in pigeons. This talk will include our recent findings of songbird category perception, songbird abstract concept formation (same/different task), and early results from pigeons' processing of songbird vocalizations in a same/different task. Our findings indicate that (1) categorization in birds seems to be most heavily influenced by acoustic, rather than genetic or experiential factors (2) songbirds treat their vocalizations as perceptual categories, both at the level of the note and species/whole call, (3) chickadees, like pigeons, can perceive abstract, same-different relations, and (4) pigeons are not as good at discriminating chickadee vocalizations as songbirds (chickadees and finches). Our findings suggest that although there are commonalities in complex auditory processing among birds, there are potentially important comparative differences between songbirds and non-songbirds in their treatment of certain types of auditory objects.Reverberlocation in chickadees?Mercado, EduardoWisniewski, MatthewGuillette, LaurenMcIntosh, BrittanySturdy, Christopherhttps://hdl.handle.net/10023/39602023-07-25T10:30:02Z2013-06-01T00:00:00ZChickadee songs provide conspecifics with information about the locations of singers. Song amplitude, frequency, and reverberation all vary with distance, and it is thought that chickadees use such cues to estimate distance. The current study examined transmission of chickadee songs in an open field to assess whether other cues such as relative changes in inter-note timing or relative differences in spectral energy might also provide useful information about a singer's location. Surprisingly, the difference between direct signal energy and reverberant spectral energy provided clear indications of how far a song had traveled. Preliminary analyses suggest that this cue may be robust to variations in source level, note duration, note frequency, and transmission loss. If chickadees use this cue to judge auditory distance, then this may explain why they maintain specific spectral ratios between the notes within their songs. Specifically, the spectral spacing of notes within songs appears to be directly related to chickadee auditory filter bandwidth. We describe ranging of a singing chickadee based on the spectral profile of its songs as reverberlocation (construed as an instance of passive echolocation) because it involves comparisons between a direct signal and echoes of a signal.
2013-06-01T00:00:00ZMercado, EduardoWisniewski, MatthewGuillette, LaurenMcIntosh, BrittanySturdy, ChristopherChickadee songs provide conspecifics with information about the locations of singers. Song amplitude, frequency, and reverberation all vary with distance, and it is thought that chickadees use such cues to estimate distance. The current study examined transmission of chickadee songs in an open field to assess whether other cues such as relative changes in inter-note timing or relative differences in spectral energy might also provide useful information about a singer's location. Surprisingly, the difference between direct signal energy and reverberant spectral energy provided clear indications of how far a song had traveled. Preliminary analyses suggest that this cue may be robust to variations in source level, note duration, note frequency, and transmission loss. If chickadees use this cue to judge auditory distance, then this may explain why they maintain specific spectral ratios between the notes within their songs. Specifically, the spectral spacing of notes within songs appears to be directly related to chickadee auditory filter bandwidth. We describe ranging of a singing chickadee based on the spectral profile of its songs as reverberlocation (construed as an instance of passive echolocation) because it involves comparisons between a direct signal and echoes of a signal.Exploring the ultrashort pulse laser parameter space for membrane permeabilisation in mammalian cells.Rudhall, Andrew PeterAntkowiak, MaciejTsampoula, XanthiMazilu, MichaelMetzger, N KlausGunn-Moore, Frank JDholakia, Kishanhttps://hdl.handle.net/10023/39192023-04-18T09:46:20Z2012-01-01T00:00:00ZThe use of ultrashort femtosecond pulsed lasers to effect membrane permeabilisation and initiate both optoinjection and transfection of cells has recently seen immense interest. We investigate femtosecond laser-induced membrane permeabilisation in mammalian cells as a function of pulse duration, pulse energy and number of pulses, by quantifying the efficiency of optoinjection for these parameters. Depending on pulse duration and pulse energy we identify two distinct membrane permeabilisation regimes. In the first regime a nonlinear dependence of order 3.4-9.6 is exhibited below a threshold peak power of at least 6 kW. Above this threshold peak power, the nonlinear dependence is saturated resulting in linear behaviour. This indicates that the membrane permeabilisation mechanism requires efficient multiphoton absorption to produce free electrons but once this process saturates, linear absorption dominates. Our experimental findings support a previously proposed theoretical model and provide a step towards the optimisation of laser-mediated gene delivery into mammalian cells.
2012-01-01T00:00:00ZRudhall, Andrew PeterAntkowiak, MaciejTsampoula, XanthiMazilu, MichaelMetzger, N KlausGunn-Moore, Frank JDholakia, KishanThe use of ultrashort femtosecond pulsed lasers to effect membrane permeabilisation and initiate both optoinjection and transfection of cells has recently seen immense interest. We investigate femtosecond laser-induced membrane permeabilisation in mammalian cells as a function of pulse duration, pulse energy and number of pulses, by quantifying the efficiency of optoinjection for these parameters. Depending on pulse duration and pulse energy we identify two distinct membrane permeabilisation regimes. In the first regime a nonlinear dependence of order 3.4-9.6 is exhibited below a threshold peak power of at least 6 kW. Above this threshold peak power, the nonlinear dependence is saturated resulting in linear behaviour. This indicates that the membrane permeabilisation mechanism requires efficient multiphoton absorption to produce free electrons but once this process saturates, linear absorption dominates. Our experimental findings support a previously proposed theoretical model and provide a step towards the optimisation of laser-mediated gene delivery into mammalian cells.Characterization and downstream mannose phosphorylation of human recombinant α-L-iduronidase produced in Arabidopsis complex glycan-deficient (cgl) seedsHe, XuPierce, OwenHaselhorst, ThomasKolarich, DanielPacker, Nicolle H.Gloster, TraceyVocadlo, David J.Qian, YiBrooks, DougKermode, Allison R.https://hdl.handle.net/10023/39102024-02-27T00:41:32Z2013-12-01T00:00:00ZMucopolysaccharidosis (MPS) I is a lysosomal storage disease caused by a deficiency of α-L-iduronidase (IDUA) (EC 3.2.1.76); enzyme replacement therapy is the conventional treatment for this genetic disease. Arabidopsis cgl mutants are characterized by a deficiency of the activity of N-acetylglucosaminyl transferase I (EC 2.4.1.101), the first enzyme in the pathway of hybrid and complex N-glycan biosynthesis. To develop a seed-based platform for the production of recombinant IDUA for potential treatment of MPS I, cgl mutant seeds were generated to express human IDUA at high yields and to avoid maturation of the N-linked glycans on the recombinant human enzyme. Enzyme kinetic data showed that cgl-IDUA has similar enzymatic properties to the commercial recombinant IDUA derived from cultured Chinese hamster ovary (CHO) cells (AldurazymeTM). The N-glycan profile showed that cgl-derived IDUA contained predominantly high-mannose-type N-glycans (94.5%), and the residual complex/hybrid N-glycan-containing enzyme was efficiently removed by an additional affinity chromatography step. Furthermore, purified cgl-IDUA was amenable to sequential in vitro processing by soluble recombinant forms of the two enzymes that mediate the addition of the mannose-6-phosphate (M6P) tag in mammalian cells—UDP-GlcNAc:lysosomal enzyme N−acetylglucosamine (GlcNAc)−1−phosphotransferase—and GlcNAc−1−phosphodiester α−N−acetylglucosaminidase (the ‘uncovering enzyme’). Arabidopsis seeds provide an alternative system for producing recombinant lysosomal enzymes for enzyme replacement therapy; the purified enzymes can be subjected to downstream processing to create the M6P, a recognition marker essential for efficient receptor-mediated uptake into lysosomes of human cells.
This work was supported by a Wellcome Trust award to TMG.
2013-12-01T00:00:00ZHe, XuPierce, OwenHaselhorst, ThomasKolarich, DanielPacker, Nicolle H.Gloster, TraceyVocadlo, David J.Qian, YiBrooks, DougKermode, Allison R.Mucopolysaccharidosis (MPS) I is a lysosomal storage disease caused by a deficiency of α-L-iduronidase (IDUA) (EC 3.2.1.76); enzyme replacement therapy is the conventional treatment for this genetic disease. Arabidopsis cgl mutants are characterized by a deficiency of the activity of N-acetylglucosaminyl transferase I (EC 2.4.1.101), the first enzyme in the pathway of hybrid and complex N-glycan biosynthesis. To develop a seed-based platform for the production of recombinant IDUA for potential treatment of MPS I, cgl mutant seeds were generated to express human IDUA at high yields and to avoid maturation of the N-linked glycans on the recombinant human enzyme. Enzyme kinetic data showed that cgl-IDUA has similar enzymatic properties to the commercial recombinant IDUA derived from cultured Chinese hamster ovary (CHO) cells (AldurazymeTM). The N-glycan profile showed that cgl-derived IDUA contained predominantly high-mannose-type N-glycans (94.5%), and the residual complex/hybrid N-glycan-containing enzyme was efficiently removed by an additional affinity chromatography step. Furthermore, purified cgl-IDUA was amenable to sequential in vitro processing by soluble recombinant forms of the two enzymes that mediate the addition of the mannose-6-phosphate (M6P) tag in mammalian cells—UDP-GlcNAc:lysosomal enzyme N−acetylglucosamine (GlcNAc)−1−phosphotransferase—and GlcNAc−1−phosphodiester α−N−acetylglucosaminidase (the ‘uncovering enzyme’). Arabidopsis seeds provide an alternative system for producing recombinant lysosomal enzymes for enzyme replacement therapy; the purified enzymes can be subjected to downstream processing to create the M6P, a recognition marker essential for efficient receptor-mediated uptake into lysosomes of human cells.Wintertime water mass modification near an Antarctic Ice Shelf frontArthun, MariusNicholls, KeithBoehme, Larshttps://hdl.handle.net/10023/39032023-04-18T09:46:23Z2013-02-01T00:00:00ZUnder ice measurements by seals carrying a miniaturized conductivity–temperature–depth (CTD) instrument fill an important gap in existing observations. Here we present data from an instrumented Weddell seal that spent 8 consecutive months (February–September) for aging in close proximity to Filchner Ice Shelf, thus providing detailed information about the evolution of mixed layer hydrography during the austral autumn and winter. The resultant time series of hydrography shows strong seasonal water mass modification, dominated by an upper–ocean (0–300 m) salinity increase of 0.31, corresponding to 3.1 m sea ice growth, and the development of a 500 m thick winter mixed layer. Observations furthermore highlight a gradual salinity increase in a slow (3–5 cms−1 ) southward flow on the continental shelf, to wards the site, and suggest that the inferred ice production is better considered as a regional average rather than being purely local. No clear seasonality is observed in the properties of the underlying Ice Shelf Water.
2013-02-01T00:00:00ZArthun, MariusNicholls, KeithBoehme, LarsUnder ice measurements by seals carrying a miniaturized conductivity–temperature–depth (CTD) instrument fill an important gap in existing observations. Here we present data from an instrumented Weddell seal that spent 8 consecutive months (February–September) for aging in close proximity to Filchner Ice Shelf, thus providing detailed information about the evolution of mixed layer hydrography during the austral autumn and winter. The resultant time series of hydrography shows strong seasonal water mass modification, dominated by an upper–ocean (0–300 m) salinity increase of 0.31, corresponding to 3.1 m sea ice growth, and the development of a 500 m thick winter mixed layer. Observations furthermore highlight a gradual salinity increase in a slow (3–5 cms−1 ) southward flow on the continental shelf, to wards the site, and suggest that the inferred ice production is better considered as a regional average rather than being purely local. No clear seasonality is observed in the properties of the underlying Ice Shelf Water.Interactions between luminance and colour signals : effects on shapeClery, StephaneBloj, MarinaHarris, Juliehttps://hdl.handle.net/10023/38612022-04-26T08:30:12Z2013-04-18T00:00:00ZAlthough luminance and color are thought to be processed independently at early stages of visual processing, there is evidence that they interact at later stages. For example, chromatic information has been shown to enhance or suppress depth from luminance depending on whether chromatic edges are aligned or orthogonal with luminance edges. Here we explored more generally how chromatic information interacts with luminance information that specifies shape from shading. Using a depth-matching task, we measured perceived depth in sinusoidal and square-wave gratings (specifying close-to sinusoidal and triangle-wave depth profiles, respectively) in three conditions. In the first, as we varied luminance contrast in the presence of an orthogonal chromatic grating, perceived depth increased (consistent with classical shape from shading). When we held the luminance at a fixed contrast and varied the chromatic grating in the other two conditions (orthogonal or aligned), we found large and inconsistent individual differences. Some participants exhibited the expected pattern of enhancement and suppression, but most did not, either for the sinusoidal or square-wave stimuli. Our results cast doubt on the idea that the interaction demonstrates a single high-level heuristic linked to depth perception. Instead, we speculate that interactions are more likely due to early cross-channel masking
This research was supported by the Engineering and Physical Sciences Research Council (EPSRC).
2013-04-18T00:00:00ZClery, StephaneBloj, MarinaHarris, JulieAlthough luminance and color are thought to be processed independently at early stages of visual processing, there is evidence that they interact at later stages. For example, chromatic information has been shown to enhance or suppress depth from luminance depending on whether chromatic edges are aligned or orthogonal with luminance edges. Here we explored more generally how chromatic information interacts with luminance information that specifies shape from shading. Using a depth-matching task, we measured perceived depth in sinusoidal and square-wave gratings (specifying close-to sinusoidal and triangle-wave depth profiles, respectively) in three conditions. In the first, as we varied luminance contrast in the presence of an orthogonal chromatic grating, perceived depth increased (consistent with classical shape from shading). When we held the luminance at a fixed contrast and varied the chromatic grating in the other two conditions (orthogonal or aligned), we found large and inconsistent individual differences. Some participants exhibited the expected pattern of enhancement and suppression, but most did not, either for the sinusoidal or square-wave stimuli. Our results cast doubt on the idea that the interaction demonstrates a single high-level heuristic linked to depth perception. Instead, we speculate that interactions are more likely due to early cross-channel maskingEnter the dragon : the emerging Chinese approach to peacebuilding in LiberiaKuo, Steven Chiun-Yihttps://hdl.handle.net/10023/38162020-04-01T02:02:41Z2013-01-01T00:00:00ZCritics of the liberal peace point out that the imposition of liberal democratic structures of governance through United Nations Peacekeeping Operations has not led to a sustainable peace being built. In reply, supporters of the liberal peace argue that even though the liberal peace is imperfect, there are no better alternatives. The objective of this thesis is to examine the Chinese approach to peacebuilding and explore the possibility that it may be a potential alternative to the liberal peace. The thesis examines the Chinese understanding of the causes of insecurity in Africa, what the Chinese position is with regards to United Nations peacekeeping and peacebuilding missions in Africa; and what role China see itself playing vis-à-vis United Nations Peacekeeping Operations in Africa.
The Chinese approach to peacebuilding recognises poverty alleviation as the foundation upon which sustainable peace can be built in post-conflict countries. Beijing does not believe the external imposition of a political ruling superstructure can succeed, and sees the liberal peace as neo-colonialism and liberal hubris. However, there is no set Chinese model of peacebuilding which can replace the liberal peace, or which African countries might follow. This is because the Chinese developmental model respects the local context, is based on pragmatism, and relies on trial and error to find the way forward.
The Chinese have been keeping a low profile in the United Nations Mission in Liberia (UNMIL) and have focused on providing transportation and logistical support to UNMIL. The Chinese focus on infrastructure rehabilitation is appreciated by Liberians and is making a positive contribution to the life of ordinary people. On the deep societal divide that lies at the heart of the Liberian civil war and continues to cause instability, both the Chinese approach to peacebuilding and the liberal peace remain silent.
2013-01-01T00:00:00ZKuo, Steven Chiun-YiCritics of the liberal peace point out that the imposition of liberal democratic structures of governance through United Nations Peacekeeping Operations has not led to a sustainable peace being built. In reply, supporters of the liberal peace argue that even though the liberal peace is imperfect, there are no better alternatives. The objective of this thesis is to examine the Chinese approach to peacebuilding and explore the possibility that it may be a potential alternative to the liberal peace. The thesis examines the Chinese understanding of the causes of insecurity in Africa, what the Chinese position is with regards to United Nations peacekeeping and peacebuilding missions in Africa; and what role China see itself playing vis-à-vis United Nations Peacekeeping Operations in Africa.
The Chinese approach to peacebuilding recognises poverty alleviation as the foundation upon which sustainable peace can be built in post-conflict countries. Beijing does not believe the external imposition of a political ruling superstructure can succeed, and sees the liberal peace as neo-colonialism and liberal hubris. However, there is no set Chinese model of peacebuilding which can replace the liberal peace, or which African countries might follow. This is because the Chinese developmental model respects the local context, is based on pragmatism, and relies on trial and error to find the way forward.
The Chinese have been keeping a low profile in the United Nations Mission in Liberia (UNMIL) and have focused on providing transportation and logistical support to UNMIL. The Chinese focus on infrastructure rehabilitation is appreciated by Liberians and is making a positive contribution to the life of ordinary people. On the deep societal divide that lies at the heart of the Liberian civil war and continues to cause instability, both the Chinese approach to peacebuilding and the liberal peace remain silent.Aesthesis and ascesis : the relationship between the arts and spiritual formationMcCullough, James J.https://hdl.handle.net/10023/37552019-11-19T03:06:04Z2013-01-01T00:00:00ZThe general claim of the thesis is that the exercise and development of skills and capacities related to sensory perception can contribute positively to the process commonly referred to as spiritual formation. The dynamics of aesthesis and ascesis can be perceived as existing in a symbiotic
relationship, encouraging and reinforcing the potentials of the other toward the development of a vibrant, discerning Christian spirituality. The arts can help mediate this relationship, and in doing so can be said to catalyze these dynamics.
In order to maximize the catalytic potentials of the arts for lay formation, a definition of art is employed that identifies art as the result of a combination of craft, content and context. Accent is placed on the communicability and cognitive cogency of art in this analysis. In order to argue for the moral and spiritual efficacy of the arts, resources from aesthetics, ethics and human development
theory as appropriated within practical theology are explored. A variant on virtue ethics that emphasizes the morally-formative potential of narrative is highlighted as the correlative to the claim that works of
art can be seen as conveyers through which an ‘inhabitable’ sense of worldview, the truth-claims of which are insinuated effectively or ineffectively according to the relative strength of the artistic
utterance. It is through the inhabitation or indwelling of the story so conveyed that art exerts its spiritually formative influence.
2013-01-01T00:00:00ZMcCullough, James J.The general claim of the thesis is that the exercise and development of skills and capacities related to sensory perception can contribute positively to the process commonly referred to as spiritual formation. The dynamics of aesthesis and ascesis can be perceived as existing in a symbiotic
relationship, encouraging and reinforcing the potentials of the other toward the development of a vibrant, discerning Christian spirituality. The arts can help mediate this relationship, and in doing so can be said to catalyze these dynamics.
In order to maximize the catalytic potentials of the arts for lay formation, a definition of art is employed that identifies art as the result of a combination of craft, content and context. Accent is placed on the communicability and cognitive cogency of art in this analysis. In order to argue for the moral and spiritual efficacy of the arts, resources from aesthetics, ethics and human development
theory as appropriated within practical theology are explored. A variant on virtue ethics that emphasizes the morally-formative potential of narrative is highlighted as the correlative to the claim that works of
art can be seen as conveyers through which an ‘inhabitable’ sense of worldview, the truth-claims of which are insinuated effectively or ineffectively according to the relative strength of the artistic
utterance. It is through the inhabitation or indwelling of the story so conveyed that art exerts its spiritually formative influence.Syria's authoritarian upgrading, 2000-2010 : Bashar al-Asad's promotion of foreign-educated returnees as transnational agents of changeZintl, Tinahttps://hdl.handle.net/10023/37452019-04-01T08:18:40Z2013-01-01T00:00:00ZThis thesis analyses the political role of highly-educated Syrian return migrants between 2000 and 2010 and their significance for the regime’s authoritarian upgrading. It
critically engages with the expectations raised by different bodies of literature, first, that returnees facilitate the development of their home country and, second, that, in the Syrian case, a foreign-trained president promoted the influence of highly-skilled technocrats. The study is based on qualitative interviews with foreign-educated returnees and conceptualizes their unique background as ‘transnationality’, which encompasses diverse foreign and local cultural, social, economic and symbolic capitals.
‘Transnationality’ can have a political impact only if it is linked up with the political status quo and, in Syria, this process was characterized by selectivity and elitism that coincided with strategies of authoritarian upgrading. Thus, there was a delicate balance between returnees’ modernizing influence and the pressure for them to re-adapt exerted by their environment. On the one hand, the socio-economic circumstances of migration
and return, the need to re-adapt as well as the logic of co-opting the most influential
parts of society led to a ‘bourgeois bias’ that privileged well-connected members of
society and hampered upward social mobility. On the other hand, although returnees
exerted a notable influence on some reforms areas, this influence was often weakened
by indirect and temporary agreements and confined to particular policy areas which the
authoritarian regime prioritized for reforms. By scrutinizing returnees’ influence in the areas of economy and finance, civil society, the media and tertiary education, it becomes clear that their political impact exemplifies and explains the Syrian regime’s outsourcing strategy to the private sector. The study concludes that Syrian returnees were mostly ‘agents of status quo’ who – whether consciously or not – helped to bolster
authoritarian politics and, especially, the legitimizing discourse that reinforced the
image of Bashar al-Asad as a modernizer struggling against ‘old guard’ hardliners.
2013-01-01T00:00:00ZZintl, TinaThis thesis analyses the political role of highly-educated Syrian return migrants between 2000 and 2010 and their significance for the regime’s authoritarian upgrading. It
critically engages with the expectations raised by different bodies of literature, first, that returnees facilitate the development of their home country and, second, that, in the Syrian case, a foreign-trained president promoted the influence of highly-skilled technocrats. The study is based on qualitative interviews with foreign-educated returnees and conceptualizes their unique background as ‘transnationality’, which encompasses diverse foreign and local cultural, social, economic and symbolic capitals.
‘Transnationality’ can have a political impact only if it is linked up with the political status quo and, in Syria, this process was characterized by selectivity and elitism that coincided with strategies of authoritarian upgrading. Thus, there was a delicate balance between returnees’ modernizing influence and the pressure for them to re-adapt exerted by their environment. On the one hand, the socio-economic circumstances of migration
and return, the need to re-adapt as well as the logic of co-opting the most influential
parts of society led to a ‘bourgeois bias’ that privileged well-connected members of
society and hampered upward social mobility. On the other hand, although returnees
exerted a notable influence on some reforms areas, this influence was often weakened
by indirect and temporary agreements and confined to particular policy areas which the
authoritarian regime prioritized for reforms. By scrutinizing returnees’ influence in the areas of economy and finance, civil society, the media and tertiary education, it becomes clear that their political impact exemplifies and explains the Syrian regime’s outsourcing strategy to the private sector. The study concludes that Syrian returnees were mostly ‘agents of status quo’ who – whether consciously or not – helped to bolster
authoritarian politics and, especially, the legitimizing discourse that reinforced the
image of Bashar al-Asad as a modernizer struggling against ‘old guard’ hardliners.Making a place on Earth : participation in creation and redemption through placemaking and the artsCraft, Jennifer Allenhttps://hdl.handle.net/10023/37322019-07-01T10:05:11Z2013-06-25T00:00:00ZThis thesis will explore a theology of place and placemaking that is focused on the participatory role of humans in both creation and redemption, while suggesting the central and paradigmatic role of artistry in our construction of and identification with place. Building on the most recent theological and philosophical engagement with place, this thesis will argue for a theology of place that takes seriously the doctrines of creation and incarnation, focusing on a particularly redemptive understanding of placemaking in the material world. In its study of scripture and theology, it will focus on God’s blessing of people to participate in the making of places, along with the role this human making has in relationship to divine presence and the divine plan for creation and redemption. After developing a theology of place and placemaking more generally, the second half of this thesis will consider the practical, constructive, and transformative capabilities of placemaking as witnessed through the arts. Relying on theological engagement with the arts, it will argue that artistic making of all kinds and attention to place go hand in hand. Exploring a selection of artistic genres, including the photography of Marlene Creates, the quilts of Gee’s Bend, and the literature of Wendell Berry, this thesis will suggest that imaginative and “artistic” placemaking practices can give us a deeper understanding of the creative, redemptive, and transformative work of Christ in Creation, while also elucidating our calling to participate in it.
2013-06-25T00:00:00ZCraft, Jennifer AllenThis thesis will explore a theology of place and placemaking that is focused on the participatory role of humans in both creation and redemption, while suggesting the central and paradigmatic role of artistry in our construction of and identification with place. Building on the most recent theological and philosophical engagement with place, this thesis will argue for a theology of place that takes seriously the doctrines of creation and incarnation, focusing on a particularly redemptive understanding of placemaking in the material world. In its study of scripture and theology, it will focus on God’s blessing of people to participate in the making of places, along with the role this human making has in relationship to divine presence and the divine plan for creation and redemption. After developing a theology of place and placemaking more generally, the second half of this thesis will consider the practical, constructive, and transformative capabilities of placemaking as witnessed through the arts. Relying on theological engagement with the arts, it will argue that artistic making of all kinds and attention to place go hand in hand. Exploring a selection of artistic genres, including the photography of Marlene Creates, the quilts of Gee’s Bend, and the literature of Wendell Berry, this thesis will suggest that imaginative and “artistic” placemaking practices can give us a deeper understanding of the creative, redemptive, and transformative work of Christ in Creation, while also elucidating our calling to participate in it.Available actors, appropriate action : theodramatic formation and performanceVander Lugt, Wesleyhttps://hdl.handle.net/10023/37282019-03-29T13:43:00Z2013-06-25T00:00:00ZSituated within the theatrical turn in Christian theology, this project explores theatre as a model for theological ethics, looking particularly at the dynamic interplay between formation as disponibility (availability) and performance as fittingness (appropriateness). A primary goal is to demonstrate how disponible formation and fitting performance are multi-dimensional realities oriented simultaneously toward the triune God (as playwright-producer-protagonist), Scripture (as transcript and prescript), the church (as characters in company), tradition (as performance paradigms), unbelievers (as audience), and local context (as theatrical environment and place). As a result, this theodramatic approach seeks to integrate theology and ethics, describing and resourcing everyday Christian practice with reflection on the theodrama. In addition, focusing on the dynamic interplay between formation and performance represents an attempt to unify agent-oriented with action-oriented theological ethics within a holistic, theodramatic framework. Finally, through attentive interaction with theatrical theory and practice, this project contributes to a fruitful and growing dialogue between Christian theology and the arts, particularly how theatre provides imaginative, heuristic models for theological ethics pursued within the liberating constraints of confessional Christianity.
2013-06-25T00:00:00ZVander Lugt, WesleySituated within the theatrical turn in Christian theology, this project explores theatre as a model for theological ethics, looking particularly at the dynamic interplay between formation as disponibility (availability) and performance as fittingness (appropriateness). A primary goal is to demonstrate how disponible formation and fitting performance are multi-dimensional realities oriented simultaneously toward the triune God (as playwright-producer-protagonist), Scripture (as transcript and prescript), the church (as characters in company), tradition (as performance paradigms), unbelievers (as audience), and local context (as theatrical environment and place). As a result, this theodramatic approach seeks to integrate theology and ethics, describing and resourcing everyday Christian practice with reflection on the theodrama. In addition, focusing on the dynamic interplay between formation and performance represents an attempt to unify agent-oriented with action-oriented theological ethics within a holistic, theodramatic framework. Finally, through attentive interaction with theatrical theory and practice, this project contributes to a fruitful and growing dialogue between Christian theology and the arts, particularly how theatre provides imaginative, heuristic models for theological ethics pursued within the liberating constraints of confessional Christianity.Estimating wildlife distribution and abundance from line transect surveys conducted from platforms of opportunityMarques, Fernanda F. C.https://hdl.handle.net/10023/37272019-04-01T08:36:08Z2001-01-01T00:00:00ZLine transect data obtained from 'platforms of opportunity' are useful for the monitoring
of long term trends in dolphin populations which occur over vast areas, yet analyses of
such data axe problematic due to violation of fundamental assumptions of line transect
methodology. In this thesis we develop methods which allow estimates of dolphin relative
abundance to be obtained when certain assumptions of line transect sampling are violated.
Generalised additive models are used to model encounter rate and mean school size as
a function of spatially and temporally referenced covariates. The estimated relationship
between the response and the environmental and locational covariates is then used to
obtain a predicted surface for the response over the entire survey region. Given those
predicted surfaces, a density surface can then be obtained and an estimate of abundance
computed by numerically integrating over the entire survey region. This approach is
particularly useful when search effort is not random, in which case standard line transect
methods would yield biased estimates.
Estimates of f (0) (the inverse of the effective strip (half-)width), an essential component
of the line transect estimator, may also be biased due to heterogeneity in detection probabilities.
We developed a conditional likelihood approach in which covariate effects are
directly incorporated into the estimation procedure. Simulation results indicated that the
method performs well in the presence of size-bias. When multiple covariates are used, it
is important that covariate selection be carried out.
As an example we applied the methods described above to eastern tropical Pacific dolphin
stocks. However, uncertainty in stock identification has never been directly incorporated
into methods used to obtain estimates of relative or absolute abundance. Therefore we
illustrate an approach in which trends in dolphin relative abundance axe monitored by
small areas, rather than stocks.
2001-01-01T00:00:00ZMarques, Fernanda F. C.Line transect data obtained from 'platforms of opportunity' are useful for the monitoring
of long term trends in dolphin populations which occur over vast areas, yet analyses of
such data axe problematic due to violation of fundamental assumptions of line transect
methodology. In this thesis we develop methods which allow estimates of dolphin relative
abundance to be obtained when certain assumptions of line transect sampling are violated.
Generalised additive models are used to model encounter rate and mean school size as
a function of spatially and temporally referenced covariates. The estimated relationship
between the response and the environmental and locational covariates is then used to
obtain a predicted surface for the response over the entire survey region. Given those
predicted surfaces, a density surface can then be obtained and an estimate of abundance
computed by numerically integrating over the entire survey region. This approach is
particularly useful when search effort is not random, in which case standard line transect
methods would yield biased estimates.
Estimates of f (0) (the inverse of the effective strip (half-)width), an essential component
of the line transect estimator, may also be biased due to heterogeneity in detection probabilities.
We developed a conditional likelihood approach in which covariate effects are
directly incorporated into the estimation procedure. Simulation results indicated that the
method performs well in the presence of size-bias. When multiple covariates are used, it
is important that covariate selection be carried out.
As an example we applied the methods described above to eastern tropical Pacific dolphin
stocks. However, uncertainty in stock identification has never been directly incorporated
into methods used to obtain estimates of relative or absolute abundance. Therefore we
illustrate an approach in which trends in dolphin relative abundance axe monitored by
small areas, rather than stocks.Bayesian point process modelling of ecological communitiesNightingale, Glenna Faithhttps://hdl.handle.net/10023/37102019-04-01T08:36:02Z2013-06-28T00:00:00ZThe modelling of biological communities is important to further the understanding
of species coexistence and the mechanisms involved in maintaining
biodiversity. This involves considering not only interactions between individual
biological organisms, but also the incorporation of covariate information,
if available, in the modelling process. This thesis explores the use
of point processes to model interactions in bivariate point patterns within
a Bayesian framework, and, where applicable, in conjunction with covariate
data. Specifically, we distinguish between symmetric and asymmetric species
interactions and model these using appropriate point processes. In this thesis
we consider both pairwise and area interaction point processes to allow for
inhibitory interactions and both inhibitory and attractive interactions.
It is envisaged that the analyses and innovations presented in this thesis
will contribute to the parsimonious modelling of biological communities.
2013-06-28T00:00:00ZNightingale, Glenna FaithThe modelling of biological communities is important to further the understanding
of species coexistence and the mechanisms involved in maintaining
biodiversity. This involves considering not only interactions between individual
biological organisms, but also the incorporation of covariate information,
if available, in the modelling process. This thesis explores the use
of point processes to model interactions in bivariate point patterns within
a Bayesian framework, and, where applicable, in conjunction with covariate
data. Specifically, we distinguish between symmetric and asymmetric species
interactions and model these using appropriate point processes. In this thesis
we consider both pairwise and area interaction point processes to allow for
inhibitory interactions and both inhibitory and attractive interactions.
It is envisaged that the analyses and innovations presented in this thesis
will contribute to the parsimonious modelling of biological communities.Two-dimensional magnetohydrodynamic turbulence in the small magnetic Prandtl number limitDritschel, David GerardTobias, Stevehttps://hdl.handle.net/10023/36982022-04-14T15:30:43Z2012-07-01T00:00:00ZIn this paper we introduce a new method for computations of two-dimensional magnetohydrodynamic (MHD) turbulence at low magnetic Prandtl number $\Pra=\nu/\eta$. When $\Pra \ll 1$, the magnetic field dissipates at a scale much larger than the velocity field. The method we utilise is a novel hybrid contour--spectral method, the ``Combined Lagrangian Advection Method'', formally to integrate the equations with zero viscous dissipation. The method is compared with a standard pseudo-spectral method for decreasing $\Pra$ for the problem of decaying two-dimensional MHD turbulence. The method is shown to agree well for a wide range of imposed magnetic field strengths. Examples of problems for which such a method may prove invaluable are also given.
2012-07-01T00:00:00ZDritschel, David GerardTobias, SteveIn this paper we introduce a new method for computations of two-dimensional magnetohydrodynamic (MHD) turbulence at low magnetic Prandtl number $\Pra=\nu/\eta$. When $\Pra \ll 1$, the magnetic field dissipates at a scale much larger than the velocity field. The method we utilise is a novel hybrid contour--spectral method, the ``Combined Lagrangian Advection Method'', formally to integrate the equations with zero viscous dissipation. The method is compared with a standard pseudo-spectral method for decreasing $\Pra$ for the problem of decaying two-dimensional MHD turbulence. The method is shown to agree well for a wide range of imposed magnetic field strengths. Examples of problems for which such a method may prove invaluable are also given.Distance measurements using pulsed EPR : noncovalently bound nitroxide and trityl spin labelsReginsson, Gunnar Widtfeldthttps://hdl.handle.net/10023/36802019-03-29T10:41:20Z2013-06-26T00:00:00ZThe function of biomacromolecules is controlled by their structure and conformational flexibility. Investigating the structure of biologically important macromolecules can, therefore, yield information that could explain their complex biological function. In addition to X ray crystallography and nuclear magnetic resonance (NMR) methods, pulsed electron paramagnetic resonance (EPR) methods, in particular the pulsed electron electron double resonance (PELDOR) technique has, during the last decade, become a valuable tool for structural determination of macromolecules. Long range distance constraints obtained from pulsed EPR measurements, make it possible to carry out structural refinements on structures from NMR and X ray methods. In addition, EPR yields distance distributions that give information about structural flexibility.
The use of EPR for structural studies of biomacromolecules requires in most cases site specific incorporation of paramagnetic centres known as spin labelling. To date, spin labelling nucleic acids has required complex spin labelling chemistry. The first application of a site directed and noncovalent spin labelling method for distance measurements on DNA is described. It is demonstrated that noncovalent spin labelling with a rigid spin label can afford detailed information on internal DNA dynamics using PELDOR. Furthermore, it is shown that noncovalent spin labelling can be used to study DNA protein complexes.
PELDOR can also yield information about spin label orientation. Therefore, spin labels with limited flexibility can be used to measure the relative orientation of the spin labelled sites. Although information on orientation can be obtained from 9.7 GHz PELDOR measurements in selected applications, measurements at 97 GHz or higher, increases orientation selection. It is shown that PELDOR measurements on semi rigid and rigid nitroxide biradicals using a home built high power 97 GHz EPR spectrometer (Hiper) and model based simulations yield quantitative information on spin label orientations and dynamics.
The most widely used spin labels for EPR studies on biomacromolecules are the aminoxyl (nitroxide) radicals. The major drawbacks of nitroxide spin labels include low sensitivity for distance measurements, fast spin spin relaxation in solution and limited stability in reducing environments. Carbon centered triarylmethyl (trityl) radicals have properties that could eliminate some of the limitations of nitroxide spin labels. To evaluate the use of trityl spin labels for nanometer distance measurements, models systems with trityl and nitroxide spin labels were measured using PELDOR and Double Quantum Coherence (DQC). This study shows that trityl spin labels yield reliable information on interlabel distances and dynamics, establishing the trityl radical as a viable spin label for structural studies on biomacromolecules.
2013-06-26T00:00:00ZReginsson, Gunnar WidtfeldtThe function of biomacromolecules is controlled by their structure and conformational flexibility. Investigating the structure of biologically important macromolecules can, therefore, yield information that could explain their complex biological function. In addition to X ray crystallography and nuclear magnetic resonance (NMR) methods, pulsed electron paramagnetic resonance (EPR) methods, in particular the pulsed electron electron double resonance (PELDOR) technique has, during the last decade, become a valuable tool for structural determination of macromolecules. Long range distance constraints obtained from pulsed EPR measurements, make it possible to carry out structural refinements on structures from NMR and X ray methods. In addition, EPR yields distance distributions that give information about structural flexibility.
The use of EPR for structural studies of biomacromolecules requires in most cases site specific incorporation of paramagnetic centres known as spin labelling. To date, spin labelling nucleic acids has required complex spin labelling chemistry. The first application of a site directed and noncovalent spin labelling method for distance measurements on DNA is described. It is demonstrated that noncovalent spin labelling with a rigid spin label can afford detailed information on internal DNA dynamics using PELDOR. Furthermore, it is shown that noncovalent spin labelling can be used to study DNA protein complexes.
PELDOR can also yield information about spin label orientation. Therefore, spin labels with limited flexibility can be used to measure the relative orientation of the spin labelled sites. Although information on orientation can be obtained from 9.7 GHz PELDOR measurements in selected applications, measurements at 97 GHz or higher, increases orientation selection. It is shown that PELDOR measurements on semi rigid and rigid nitroxide biradicals using a home built high power 97 GHz EPR spectrometer (Hiper) and model based simulations yield quantitative information on spin label orientations and dynamics.
The most widely used spin labels for EPR studies on biomacromolecules are the aminoxyl (nitroxide) radicals. The major drawbacks of nitroxide spin labels include low sensitivity for distance measurements, fast spin spin relaxation in solution and limited stability in reducing environments. Carbon centered triarylmethyl (trityl) radicals have properties that could eliminate some of the limitations of nitroxide spin labels. To evaluate the use of trityl spin labels for nanometer distance measurements, models systems with trityl and nitroxide spin labels were measured using PELDOR and Double Quantum Coherence (DQC). This study shows that trityl spin labels yield reliable information on interlabel distances and dynamics, establishing the trityl radical as a viable spin label for structural studies on biomacromolecules.Propositions : an essay on linguistic contentHodgson, Thomas William Stricklandhttps://hdl.handle.net/10023/36772019-07-01T10:13:36Z2013-06-27T00:00:00ZThis thesis presents an account of the nature of structured propositions and addresses a series of questions that arise from that proposal. Chapter 1 presents the account and explains how it meets standard objections to such views. Chapter 2 responds to the objection that this version of propositionalism is really a form of sententialism by arguing for the distinct advantages of the propositionalist view. Chapter 3 argues against a closely related view of propositions by way of general principles about how to construct such theories. Chapter 4 illustrates how a theory of propositions of the sort proposed can be defended against a recent argument that propositions need not play a central role in linguistic theory.
2013-06-27T00:00:00ZHodgson, Thomas William StricklandThis thesis presents an account of the nature of structured propositions and addresses a series of questions that arise from that proposal. Chapter 1 presents the account and explains how it meets standard objections to such views. Chapter 2 responds to the objection that this version of propositionalism is really a form of sententialism by arguing for the distinct advantages of the propositionalist view. Chapter 3 argues against a closely related view of propositions by way of general principles about how to construct such theories. Chapter 4 illustrates how a theory of propositions of the sort proposed can be defended against a recent argument that propositions need not play a central role in linguistic theory.Female putty-nosed monkeys use experimentally altered contextual information to disambiguate the cause of male alarm callsArnold, KateZuberbuehler, Klaushttps://hdl.handle.net/10023/36742023-04-18T09:47:54Z2013-06-05T00:00:00ZMany animal vocal signals are given in a wide range of contexts which can sometimes have little in common. Yet, to respond adaptively, listeners must find ways to identify the cause of a signal, or at least rule out alternatives. Here, we investigate the nature of this process in putty-nosed monkeys, a forest primate. In this species, adult males have a very restricted repertoire of vocalizations which are given in response to a wide variety of events occurring under conditions of limited visibility. We carried out a series of field playback experiments on females (N = 6) in a habituated group in Gashaka Gumti National Park, Nigeria, in which male alarm/loud calls were presented either alone, or following acoustic information that simulated the occurrence of natural disturbances. We demonstrate that listeners appear to integrate contextual information in order to distinguish among possible causes of calls. We conclude that, in many cases, pragmatic aspects of communication play a crucial role in call interpretation and place a premium on listeners' abilities to integrate information from different sources.
Funding was provided by The Leverhulme Trust (http://www.leverhulme.ac.uk/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
2013-06-05T00:00:00ZArnold, KateZuberbuehler, KlausMany animal vocal signals are given in a wide range of contexts which can sometimes have little in common. Yet, to respond adaptively, listeners must find ways to identify the cause of a signal, or at least rule out alternatives. Here, we investigate the nature of this process in putty-nosed monkeys, a forest primate. In this species, adult males have a very restricted repertoire of vocalizations which are given in response to a wide variety of events occurring under conditions of limited visibility. We carried out a series of field playback experiments on females (N = 6) in a habituated group in Gashaka Gumti National Park, Nigeria, in which male alarm/loud calls were presented either alone, or following acoustic information that simulated the occurrence of natural disturbances. We demonstrate that listeners appear to integrate contextual information in order to distinguish among possible causes of calls. We conclude that, in many cases, pragmatic aspects of communication play a crucial role in call interpretation and place a premium on listeners' abilities to integrate information from different sources.Acoustic mechanisms of a species-based discrimination of the chick-a-dee call in sympatric black-capped (Poecile atricapillus) and mountain chickadees (P. gambeli)Guillette, LaurenFarrell, TaraHoeschele, MarisaSturdy, Christopherhttps://hdl.handle.net/10023/35662022-04-14T20:31:48Z2010-01-01T00:00:00ZPrevious perceptual research with black-capped and mountain chickadees has demonstrated that these species treat each other’s namesake chick-a-dee calls as belonging to separate, open-ended categories. Further, the terminal dee portion of the call has been implicated as the most prominent species marker. However, statistical classification using acoustic summary features suggests that all note-types contained within the chick-a-dee call should be sufficient for species classification. The current study seeks to better understand the note-type based mechanisms underlying species-based classification of the chick-a-dee call by black-capped and mountain chickadees. In two, complementary, operant discrimination experiments, both species were trained to discriminate the species of the signaler using either entire chick-a-dee calls, or individual note-types from chick-a-dee calls. In agreement with previous perceptual work we find that the D note had significant stimulus control over species-based discrimination. However, in line with statistical classifications, we find that all note-types carry species information. We discuss reasons why the most easily discriminated note-types are likely candidates to carry species-based cues.
2010-01-01T00:00:00ZGuillette, LaurenFarrell, TaraHoeschele, MarisaSturdy, ChristopherPrevious perceptual research with black-capped and mountain chickadees has demonstrated that these species treat each other’s namesake chick-a-dee calls as belonging to separate, open-ended categories. Further, the terminal dee portion of the call has been implicated as the most prominent species marker. However, statistical classification using acoustic summary features suggests that all note-types contained within the chick-a-dee call should be sufficient for species classification. The current study seeks to better understand the note-type based mechanisms underlying species-based classification of the chick-a-dee call by black-capped and mountain chickadees. In two, complementary, operant discrimination experiments, both species were trained to discriminate the species of the signaler using either entire chick-a-dee calls, or individual note-types from chick-a-dee calls. In agreement with previous perceptual work we find that the D note had significant stimulus control over species-based discrimination. However, in line with statistical classifications, we find that all note-types carry species information. We discuss reasons why the most easily discriminated note-types are likely candidates to carry species-based cues.Biodiversity assessment of freshwater fishes : Thailand as a case studyKhachonpisitsak, Salineehttps://hdl.handle.net/10023/35592017-10-27T16:04:40Z2012-11-29T00:00:00ZA key challenge in biodiversity is: How many species are there on earth? This issue is especially acute in poorly surveyed regions with high diversity, particularly Southeast Asia that also experiences many limitations such as lack of funds, documents and experts. To help meet this challenge, I have developed a five-tiered approach for diversity measurement of freshwater fish for use in Thailand. This is: (1) the creation of a newly updated species inventory that uses existing data; (2) exploration of the patterns of species richness, endemism, and uniqueness; (3) estimation of the total species richness; (4) investigation of patterns of rarity; and (5) integration of this knowledge into conservation practice. The system should be applicable to other regions and other taxa where a similar challenge exists.
My work shows that eight hundred and seventy-two species in 17 orders, 55 families and 255 genera of freshwater fishes, accounting for roughly 10% of the world’s freshwater fish diversity, have been reported for Thailand to date. This number was derived from information in the museum collections, literature and all other available sources, including reports written in Thai as well as in English. During this work I uncovered many gaps in biodiversity information, in terms of taxonomic and spatial records, though some families and basins are better represented than others. Taxonomic uncertainty also continues to be a challenge for taxonomists and users.
The high diversity of freshwater fishes in Thailand is the result of both high alpha (α) diversity (diversity within a particular locality) and beta (β) diversity (diversity differences between localities). I concluded that the substantial beta diversity I detected is associated with the geographical separation of the six river basins in Thailand. For example, the species composition of freshwater fishes in the Salween Basin dramatically differs from all other basins of Thailand. In contrast, the Chao Phraya Basin and the Mekong Basin contain the greatest number of shared species. Approximately 55% of species have a wide distribution range (being reported from more than two basins), whereas 45% are highly restricted within a single basin.
Analyses using species richness estimators suggest that the figure of 872 species is an underestimate and that there may be between 1000 and 1300 fish species in Thailand, in other words an increase of between 14.7% and 49.1% over the list I compiled (which is itself an increase of 52.2% over the last report in 1997). Freshwater fish have become increasingly vulnerable to anthropogenic activities. Of the 872 Thai fish species, 6.8% and 15.1% are globally and nationally threatened, respectively. Nonetheless, a striking feature of the database is that the conservation status of the vast majority of species has not so far been assessed, either globally or nationally. Scientists and policy makers will find these results useful in appreciating the magnitude of the tasks involved in surveying, describing and conserving the country’s freshwater fish biota. My work highlights localities and taxa where conservation is a priority and is thus an important resource for policy makers and conservation planners concerned with the management of freshwater fish in Thailand.
2012-11-29T00:00:00ZKhachonpisitsak, SalineeA key challenge in biodiversity is: How many species are there on earth? This issue is especially acute in poorly surveyed regions with high diversity, particularly Southeast Asia that also experiences many limitations such as lack of funds, documents and experts. To help meet this challenge, I have developed a five-tiered approach for diversity measurement of freshwater fish for use in Thailand. This is: (1) the creation of a newly updated species inventory that uses existing data; (2) exploration of the patterns of species richness, endemism, and uniqueness; (3) estimation of the total species richness; (4) investigation of patterns of rarity; and (5) integration of this knowledge into conservation practice. The system should be applicable to other regions and other taxa where a similar challenge exists.
My work shows that eight hundred and seventy-two species in 17 orders, 55 families and 255 genera of freshwater fishes, accounting for roughly 10% of the world’s freshwater fish diversity, have been reported for Thailand to date. This number was derived from information in the museum collections, literature and all other available sources, including reports written in Thai as well as in English. During this work I uncovered many gaps in biodiversity information, in terms of taxonomic and spatial records, though some families and basins are better represented than others. Taxonomic uncertainty also continues to be a challenge for taxonomists and users.
The high diversity of freshwater fishes in Thailand is the result of both high alpha (α) diversity (diversity within a particular locality) and beta (β) diversity (diversity differences between localities). I concluded that the substantial beta diversity I detected is associated with the geographical separation of the six river basins in Thailand. For example, the species composition of freshwater fishes in the Salween Basin dramatically differs from all other basins of Thailand. In contrast, the Chao Phraya Basin and the Mekong Basin contain the greatest number of shared species. Approximately 55% of species have a wide distribution range (being reported from more than two basins), whereas 45% are highly restricted within a single basin.
Analyses using species richness estimators suggest that the figure of 872 species is an underestimate and that there may be between 1000 and 1300 fish species in Thailand, in other words an increase of between 14.7% and 49.1% over the list I compiled (which is itself an increase of 52.2% over the last report in 1997). Freshwater fish have become increasingly vulnerable to anthropogenic activities. Of the 872 Thai fish species, 6.8% and 15.1% are globally and nationally threatened, respectively. Nonetheless, a striking feature of the database is that the conservation status of the vast majority of species has not so far been assessed, either globally or nationally. Scientists and policy makers will find these results useful in appreciating the magnitude of the tasks involved in surveying, describing and conserving the country’s freshwater fish biota. My work highlights localities and taxa where conservation is a priority and is thus an important resource for policy makers and conservation planners concerned with the management of freshwater fish in Thailand.Living like the laity? : The negotiation of religious status in the cities of late medieval ItalyAndrews, Franceshttps://hdl.handle.net/10023/35052023-04-18T09:40:03Z2010-12-01T00:00:00ZFramed by consideration of images of treasurers on the books of the treasury in thirteenth-century Siena, this article uses evidence for the employment of men of religion in city offices in central and northern Italy to show how religious status (treated as a subset of ‘clerical culture’) could become an important object of negotiation between city and churchmen, a tool in the repertoire of power relations. It focuses on the employment of men of religion as urban treasurers and takes Florence in the late thirteenth and early fourteenth centuries as a principal case study, but also touches on the other tasks assigned to men of religion and, very briefly, on evidence from other cities (Bologna, Brescia, Como, Milan, Padua, Perugia and Siena). It outlines some of the possible arguments deployed for this use of men of religion in order to demonstrate that religious status was, like gender, more contingent and fluid than the norm-based models often relied on as a shorthand by historians. Despite the powerful rhetoric of lay–clerical separation in this period, the engagement of men of religion in paid, term-bound urban offices inevitably brought them closer to living like the laity.
2010-12-01T00:00:00ZAndrews, FrancesFramed by consideration of images of treasurers on the books of the treasury in thirteenth-century Siena, this article uses evidence for the employment of men of religion in city offices in central and northern Italy to show how religious status (treated as a subset of ‘clerical culture’) could become an important object of negotiation between city and churchmen, a tool in the repertoire of power relations. It focuses on the employment of men of religion as urban treasurers and takes Florence in the late thirteenth and early fourteenth centuries as a principal case study, but also touches on the other tasks assigned to men of religion and, very briefly, on evidence from other cities (Bologna, Brescia, Como, Milan, Padua, Perugia and Siena). It outlines some of the possible arguments deployed for this use of men of religion in order to demonstrate that religious status was, like gender, more contingent and fluid than the norm-based models often relied on as a shorthand by historians. Despite the powerful rhetoric of lay–clerical separation in this period, the engagement of men of religion in paid, term-bound urban offices inevitably brought them closer to living like the laity.Development of a contact call in black-capped chickadees (Poecile atricapillus) hand-reared in different acoustic environmentsGuillette, LaurenBloomfiled, LaurieBatty, EmilyDawson, MichaelSturdy, Chrishttps://hdl.handle.net/10023/34722024-02-20T00:40:13Z2011-01-01T00:00:00ZThe tseet contact call, common to black-capped (Poecile atricapillus) and mountain chickadees (P. gambeli), is the most frequently produced vocalization of each species. Previous work has characterized the tseet call of black-capped and mountain chickadees from different geographic locations in terms of nine acoustic features. In the current study, using similar methods, the tseet call of black-capped chickadees that were hand reared with either conspecifics, heterospecifics (mountain chickadees), or in isolation from adult chickadees are described. Analysis of call features examined which acoustic features were most affected by rearing environment, and revealed that starting frequency and the slope of the descending portion of the tseet call differed between black-capped chickadees reared with either conspecific or heterospecific adults. Birds reared in isolation from adults differed from the other hand-reared groups on almost every acoustic feature. Chickadee tseet calls are more individualized when they are reared with adult conspecifics or heterospecifics compared to chickadees that are reared in isolation from adults. The current results suggest a role of learning in this commonly used contact call.
2011-01-01T00:00:00ZGuillette, LaurenBloomfiled, LaurieBatty, EmilyDawson, MichaelSturdy, ChrisThe tseet contact call, common to black-capped (Poecile atricapillus) and mountain chickadees (P. gambeli), is the most frequently produced vocalization of each species. Previous work has characterized the tseet call of black-capped and mountain chickadees from different geographic locations in terms of nine acoustic features. In the current study, using similar methods, the tseet call of black-capped chickadees that were hand reared with either conspecifics, heterospecifics (mountain chickadees), or in isolation from adult chickadees are described. Analysis of call features examined which acoustic features were most affected by rearing environment, and revealed that starting frequency and the slope of the descending portion of the tseet call differed between black-capped chickadees reared with either conspecific or heterospecific adults. Birds reared in isolation from adults differed from the other hand-reared groups on almost every acoustic feature. Chickadee tseet calls are more individualized when they are reared with adult conspecifics or heterospecifics compared to chickadees that are reared in isolation from adults. The current results suggest a role of learning in this commonly used contact call.Estimating whale abundance using sparse hydrophone arraysHarris, Danielle Veronicahttps://hdl.handle.net/10023/34632019-07-01T10:12:25Z2012-06-20T00:00:00ZPassive acoustic monitoring has been used to investigate many aspects of marine mammal ecology, although methods to estimate absolute abundance and density using acoustic data have only been developed in recent years. The instrument configuration in an acoustic survey determines which abundance estimation methods can be used. Sparsely distributed arrays of instruments are useful because wide geographic areas can be covered. However, instrument spacing in sparse arrays is such that the same vocalisation will not be detected on multiple instruments, excluding the use of some abundance estimation methods. The aim of this thesis was to explore cetacean abundance and density estimation using novel sparse array datasets, applying existing methods where possible, or developing new approaches.
The wealth of data collected by sparse arrays was demonstrated by analysing a 10-year dataset collected by the U.S. Navy’s Sound Surveillance System in the north-east Atlantic. Spatial and temporal patterns of blue (Balaenoptera musculus) and fin whale (Balaenoptera physalus) vocal activity were investigated using generalised additive models.
Distance sampling-based methods were applied to fin whale calls recorded by an array of Ocean Bottom Seismometers in the north-east Atlantic. Estimated call density was 993 calls/1000 km².hr⁻¹ (CV: 0.39). Animal density could not be estimated because the call rate was unknown. Further development of the call localisation method is required so the current density estimate may be biased. Furthermore, analysing a single day of data resulted in a high variance estimate.
Finally, a new simulation-based method developed to estimate density from single hydrophones was applied to blue whale calls recorded in the northern Indian Ocean. Estimated call density was 3 calls/1000 km².hr⁻¹ (CV: 0.17). Again, density of whales could not be estimated as the vocalisation rate was unknown. Lack of biological knowledge poses the greatest limitation to abundance and density estimation using acoustic data.
2012-06-20T00:00:00ZHarris, Danielle VeronicaPassive acoustic monitoring has been used to investigate many aspects of marine mammal ecology, although methods to estimate absolute abundance and density using acoustic data have only been developed in recent years. The instrument configuration in an acoustic survey determines which abundance estimation methods can be used. Sparsely distributed arrays of instruments are useful because wide geographic areas can be covered. However, instrument spacing in sparse arrays is such that the same vocalisation will not be detected on multiple instruments, excluding the use of some abundance estimation methods. The aim of this thesis was to explore cetacean abundance and density estimation using novel sparse array datasets, applying existing methods where possible, or developing new approaches.
The wealth of data collected by sparse arrays was demonstrated by analysing a 10-year dataset collected by the U.S. Navy’s Sound Surveillance System in the north-east Atlantic. Spatial and temporal patterns of blue (Balaenoptera musculus) and fin whale (Balaenoptera physalus) vocal activity were investigated using generalised additive models.
Distance sampling-based methods were applied to fin whale calls recorded by an array of Ocean Bottom Seismometers in the north-east Atlantic. Estimated call density was 993 calls/1000 km².hr⁻¹ (CV: 0.39). Animal density could not be estimated because the call rate was unknown. Further development of the call localisation method is required so the current density estimate may be biased. Furthermore, analysing a single day of data resulted in a high variance estimate.
Finally, a new simulation-based method developed to estimate density from single hydrophones was applied to blue whale calls recorded in the northern Indian Ocean. Estimated call density was 3 calls/1000 km².hr⁻¹ (CV: 0.17). Again, density of whales could not be estimated as the vocalisation rate was unknown. Lack of biological knowledge poses the greatest limitation to abundance and density estimation using acoustic data.Concepts in contextOnofri, Andreahttps://hdl.handle.net/10023/34622019-04-01T09:27:22Z2013-01-01T00:00:00ZMy thesis tackles two related problems that have taken center stage in the recent
literature on concepts:
• What are the individuation conditions of concepts? Under what conditions is a
concept C₁ the same concept as a concept C₂?
• What are the possession conditions of concepts? What conditions must be satisfied
for a thinker to have a concept C?
I will develop a pluralist and contextualist theory of concept individuation and
possession: different concepts have different individuation and possession conditions,
and contextual factors play a crucial role in determining what concepts we attribute to
other subjects when we ascribe propositional attitudes to them.
In chapters 1-3, I defend a contextualist, non-Millian theory of propositional attitude
ascriptions. Then, I suggest contextualist theories of ascriptions can be applied to the
problem of concept individuation/possession. In particular, I use contextualism to
provide a new, more effective argument for Fodor’s “publicity principle”, according to
which concepts must be shared in order for interpersonally applicable psychological
generalizations to be possible.
Publicity has important implications: in particular, it is inconsistent with existing
versions of holism, on which concepts cannot be shared by ordinary thinkers.
Nonetheless, in chapters 4-5 I show how holism can still play an important role in our
best theory of concepts. More specifically, I argue that the tradition of appealing to
modes of presentation in order to give an account of “Frege cases” is in fact committed
to holism. To develop a version of holism that will give a successful account of Frege
cases without violating publicity, I suggest we should adopt my pluralist-contextualist
picture: on that picture, the concepts involved in a Frege case will be holistically
individuated and not public, while other concepts will be more coarsely individuated
and widely shared. In chapter 6, I will develop this view further by contrasting it with
other pluralist theories (Weiskopf) and with rival theories of concepts, such as the
localist views defended by Peacocke, Rey and Jackson.
2013-01-01T00:00:00ZOnofri, AndreaMy thesis tackles two related problems that have taken center stage in the recent
literature on concepts:
• What are the individuation conditions of concepts? Under what conditions is a
concept C₁ the same concept as a concept C₂?
• What are the possession conditions of concepts? What conditions must be satisfied
for a thinker to have a concept C?
I will develop a pluralist and contextualist theory of concept individuation and
possession: different concepts have different individuation and possession conditions,
and contextual factors play a crucial role in determining what concepts we attribute to
other subjects when we ascribe propositional attitudes to them.
In chapters 1-3, I defend a contextualist, non-Millian theory of propositional attitude
ascriptions. Then, I suggest contextualist theories of ascriptions can be applied to the
problem of concept individuation/possession. In particular, I use contextualism to
provide a new, more effective argument for Fodor’s “publicity principle”, according to
which concepts must be shared in order for interpersonally applicable psychological
generalizations to be possible.
Publicity has important implications: in particular, it is inconsistent with existing
versions of holism, on which concepts cannot be shared by ordinary thinkers.
Nonetheless, in chapters 4-5 I show how holism can still play an important role in our
best theory of concepts. More specifically, I argue that the tradition of appealing to
modes of presentation in order to give an account of “Frege cases” is in fact committed
to holism. To develop a version of holism that will give a successful account of Frege
cases without violating publicity, I suggest we should adopt my pluralist-contextualist
picture: on that picture, the concepts involved in a Frege case will be holistically
individuated and not public, while other concepts will be more coarsely individuated
and widely shared. In chapter 6, I will develop this view further by contrasting it with
other pluralist theories (Weiskopf) and with rival theories of concepts, such as the
localist views defended by Peacocke, Rey and Jackson.Male mating tactics in the rose bitterling (Rhodeus ocellatus) and European bitterling (Rhodeus amarus)Casalini, Marahttps://hdl.handle.net/10023/34472019-03-29T10:38:49Z2013-06-26T00:00:00ZThe aim of this study was to investigate the basis to male mating decisions in two related species of bitterling: Rhodeus ocellatus and R. amarus. Bitterling have a resource-based mating system; females lay eggs in the gills of live freshwater mussels and males fertilize the eggs by releasing sperm into the inhalant syphon of the mussel. Male bitterling perform courtship behaviour and aggressively defend mussels in a territory from which they exclude other males. Using laboratory and field experiments it was shown that male aggressive behaviour is inherited through additive maternal genes. Male aggression is also influenced by the number of conspecific males encountered in competition for a mussel, and by the degree of clustering of mussels. Limited availability of mussels results in stronger selection on traits males use in mating context: hence they are more aggressive, larger and more colourful. The differences in mating behaviours in different environments may indicate a conflict between male dominance and female choice, but have not led to reproductive isolation. Resource availability during ontogenesis and male density during embryogenesis, however, do not exert an effect on male aggressive behaviour. Red carotenoid-based nuptial coloration functions as an inter- and intra-sexual signal and undergoes rapid variation in response to changes in mating context. Male bitterling do not modulate their courtship and aggressive behaviour in response to variation in female size, and their choice of mussel species is influenced by, and consistent with, female oviposition choice.
2013-06-26T00:00:00ZCasalini, MaraThe aim of this study was to investigate the basis to male mating decisions in two related species of bitterling: Rhodeus ocellatus and R. amarus. Bitterling have a resource-based mating system; females lay eggs in the gills of live freshwater mussels and males fertilize the eggs by releasing sperm into the inhalant syphon of the mussel. Male bitterling perform courtship behaviour and aggressively defend mussels in a territory from which they exclude other males. Using laboratory and field experiments it was shown that male aggressive behaviour is inherited through additive maternal genes. Male aggression is also influenced by the number of conspecific males encountered in competition for a mussel, and by the degree of clustering of mussels. Limited availability of mussels results in stronger selection on traits males use in mating context: hence they are more aggressive, larger and more colourful. The differences in mating behaviours in different environments may indicate a conflict between male dominance and female choice, but have not led to reproductive isolation. Resource availability during ontogenesis and male density during embryogenesis, however, do not exert an effect on male aggressive behaviour. Red carotenoid-based nuptial coloration functions as an inter- and intra-sexual signal and undergoes rapid variation in response to changes in mating context. Male bitterling do not modulate their courtship and aggressive behaviour in response to variation in female size, and their choice of mussel species is influenced by, and consistent with, female oviposition choice.Quantifying biodiversity trends in time and spaceStudeny, Angelika C.https://hdl.handle.net/10023/34142019-04-01T08:36:01Z2012-11-30T00:00:00ZThe global loss of biodiversity calls for robust large-scale diversity assessment. Biological diversity is a multi-faceted concept; defined as the “variety of life”, answering questions such as “How much is there?” or more precisely “Have we succeeded in reducing the rate of its decline?” is not straightforward. While various aspects of biodiversity give rise to numerous ways of quantification, we focus on temporal (and spatial) trends and their changes in species diversity.
Traditional diversity indices summarise information contained in the species abundance distribution, i.e. each species' proportional contribution to total abundance. Estimated from data, these indices can be biased if variation in detection probability is ignored. We discuss differences between diversity indices and demonstrate possible adjustments for detectability.
Additionally, most indices focus on the most abundant species in ecological communities. We introduce a new set of diversity measures, based on a family of goodness-of-fit statistics. A function of a free parameter, this family allows us to vary the sensitivity of these measures to dominance and rarity of species.
Their performance is studied by assessing temporal trends in diversity for five communities of British breeding birds based on 14 years of survey data, where they are applied alongside the current headline index, a geometric mean of relative abundances. Revealing the contributions of both rare and common species to biodiversity trends, these "goodness-of-fit" measures provide novel insights into how ecological communities change over time.
Biodiversity is not only subject to temporal changes, but it also varies across space. We take first steps towards estimating spatial diversity trends. Finally, processes maintaining biodiversity act locally, at specific spatial scales. Contrary to abundance-based summary statistics, spatial characteristics of ecological communities may distinguish these processes. We suggest a generalisation to a spatial summary, the cross-pair overlap distribution, to render it more flexible to spatial scale.
2012-11-30T00:00:00ZStudeny, Angelika C.The global loss of biodiversity calls for robust large-scale diversity assessment. Biological diversity is a multi-faceted concept; defined as the “variety of life”, answering questions such as “How much is there?” or more precisely “Have we succeeded in reducing the rate of its decline?” is not straightforward. While various aspects of biodiversity give rise to numerous ways of quantification, we focus on temporal (and spatial) trends and their changes in species diversity.
Traditional diversity indices summarise information contained in the species abundance distribution, i.e. each species' proportional contribution to total abundance. Estimated from data, these indices can be biased if variation in detection probability is ignored. We discuss differences between diversity indices and demonstrate possible adjustments for detectability.
Additionally, most indices focus on the most abundant species in ecological communities. We introduce a new set of diversity measures, based on a family of goodness-of-fit statistics. A function of a free parameter, this family allows us to vary the sensitivity of these measures to dominance and rarity of species.
Their performance is studied by assessing temporal trends in diversity for five communities of British breeding birds based on 14 years of survey data, where they are applied alongside the current headline index, a geometric mean of relative abundances. Revealing the contributions of both rare and common species to biodiversity trends, these "goodness-of-fit" measures provide novel insights into how ecological communities change over time.
Biodiversity is not only subject to temporal changes, but it also varies across space. We take first steps towards estimating spatial diversity trends. Finally, processes maintaining biodiversity act locally, at specific spatial scales. Contrary to abundance-based summary statistics, spatial characteristics of ecological communities may distinguish these processes. We suggest a generalisation to a spatial summary, the cross-pair overlap distribution, to render it more flexible to spatial scale.Locations of envy : an ethnography of Aguabuena pottersCastellanos Montes, Danielahttps://hdl.handle.net/10023/34042019-04-01T09:28:38Z2012-12-04T00:00:00ZThis thesis is an anthropological exploration of the envy of Aguabuena people, a small rural community of potters in the village of Ráquira, in the Boyacá region of Andean Colombia. Based on long-term ethnographic fieldwork among these potters, I propose an understanding of envy in Aguabuena as an existential experience, shaping relationships between the self and others in the world, crosscutting metaphysical and physical spheres, and balancing between corrosive and more empathetic ways of co-existence. Disclosing the multipresence of envy in Aguabuena’s world, its effects on people (including the ethnographer), and the way envy is embodied, performed, reciprocated and circumvented by the potters, I locate envy in various contexts where it is said to be manifested. Furthermore, I discuss the complex spectrum of envy and its multivalent meanings, or oscillations, in the life of Aguabuena people. I also present interactions with people surrounding potters, such as Augustinian monks, crafts middlemen, and municipal authorities, all of whom recount the envy of potters. My research challenges previous anthropological interpretations on envy and provides an alternative reading of this phenomenon. Moving away from labelling and regulatory explanations of envy, performative models, or pathological interpretations of the subject, I analyse the lived experience of envy and how it encompasses different realms of experience as well as flows of social relations. While focusing on the tensions and entanglements that envy brings to potters, as it constrains social life but also activates and reinforces social bonds, I examine the channels through which envy circulates and how it is put into motion by potters. Additionally, my thesis intends to contribute to anthropological studies of rural pottery communities in Andean Colombia. I present my unfolding understanding of envy by using both the potters’ concept and material detail, punto, location, referring to a spot from where Aguabuena people enter different vistas of the world, or denoting a precise time when things or materials change their physical qualities. Through this device, I disclose realms of envy, while seeking to immerse the reader in the lived experience of envy.
2012-12-04T00:00:00ZCastellanos Montes, DanielaThis thesis is an anthropological exploration of the envy of Aguabuena people, a small rural community of potters in the village of Ráquira, in the Boyacá region of Andean Colombia. Based on long-term ethnographic fieldwork among these potters, I propose an understanding of envy in Aguabuena as an existential experience, shaping relationships between the self and others in the world, crosscutting metaphysical and physical spheres, and balancing between corrosive and more empathetic ways of co-existence. Disclosing the multipresence of envy in Aguabuena’s world, its effects on people (including the ethnographer), and the way envy is embodied, performed, reciprocated and circumvented by the potters, I locate envy in various contexts where it is said to be manifested. Furthermore, I discuss the complex spectrum of envy and its multivalent meanings, or oscillations, in the life of Aguabuena people. I also present interactions with people surrounding potters, such as Augustinian monks, crafts middlemen, and municipal authorities, all of whom recount the envy of potters. My research challenges previous anthropological interpretations on envy and provides an alternative reading of this phenomenon. Moving away from labelling and regulatory explanations of envy, performative models, or pathological interpretations of the subject, I analyse the lived experience of envy and how it encompasses different realms of experience as well as flows of social relations. While focusing on the tensions and entanglements that envy brings to potters, as it constrains social life but also activates and reinforces social bonds, I examine the channels through which envy circulates and how it is put into motion by potters. Additionally, my thesis intends to contribute to anthropological studies of rural pottery communities in Andean Colombia. I present my unfolding understanding of envy by using both the potters’ concept and material detail, punto, location, referring to a spot from where Aguabuena people enter different vistas of the world, or denoting a precise time when things or materials change their physical qualities. Through this device, I disclose realms of envy, while seeking to immerse the reader in the lived experience of envy.Instability in internal solitary waves with trapped coresCarr, MagdaKing, Stuart EdwardDritschel, David Gerardhttps://hdl.handle.net/10023/33972023-04-18T09:44:51Z2012-01-01T00:00:00ZA numerical method that employs a combination of contour advection and pseudo-spectral techniques is used to investigate instability in internal solitary waves with trapped cores. A three-layer configuration for the background stratification in which the top two layers are linearly stratified and the lower layer is homogeneous is considered throughout. The strength of the stratification in the very top layer is chosen to be sufficient so that waves of depression with trapped cores can be generated. The flow is assumed to satisfy the Dubriel-Jacotin-Long equation both inside and outside of the core region. The Brunt-Vaisala frequency is modelled such that it varies from a constant value outside of the core to zero inside the core over a sharp but continuous transition length. This results in a stagnant core in which the vorticity is zero and the density is homogeneous and approximately equal to that at the core boundary. The time dependent simulations show that instability occurs on the boundary of the core. The instability takes the form of Kelvin-Helmholtz billows. If the instability in the vorticity field is energetic enough, disturbance in the buoyancy field is also seen and fluid exchange takes place across the core boundary. Occurrence of the Kelvin-Helmholtz billows is attributed to the sharp change in the vorticity field at the boundary between the core and the pycnocline. The numerical scheme is not limited by small Richardson number unlike the other alternatives currently available in the literature which appear to be.
2012-01-01T00:00:00ZCarr, MagdaKing, Stuart EdwardDritschel, David GerardA numerical method that employs a combination of contour advection and pseudo-spectral techniques is used to investigate instability in internal solitary waves with trapped cores. A three-layer configuration for the background stratification in which the top two layers are linearly stratified and the lower layer is homogeneous is considered throughout. The strength of the stratification in the very top layer is chosen to be sufficient so that waves of depression with trapped cores can be generated. The flow is assumed to satisfy the Dubriel-Jacotin-Long equation both inside and outside of the core region. The Brunt-Vaisala frequency is modelled such that it varies from a constant value outside of the core to zero inside the core over a sharp but continuous transition length. This results in a stagnant core in which the vorticity is zero and the density is homogeneous and approximately equal to that at the core boundary. The time dependent simulations show that instability occurs on the boundary of the core. The instability takes the form of Kelvin-Helmholtz billows. If the instability in the vorticity field is energetic enough, disturbance in the buoyancy field is also seen and fluid exchange takes place across the core boundary. Occurrence of the Kelvin-Helmholtz billows is attributed to the sharp change in the vorticity field at the boundary between the core and the pycnocline. The numerical scheme is not limited by small Richardson number unlike the other alternatives currently available in the literature which appear to be.Genetic analysis of life-history constraint and evolution in a wild ungulate populationMorrissey, Michael BlairWalling, CraigWilson, AlastairPemberton, JosephineClutton-Brock, TimKruuk, Loeskehttps://hdl.handle.net/10023/33632023-04-18T09:45:14Z2012-04-01T00:00:00ZTrade-offs among life-history traits are central to evolutionary theory. In quantitative genetic terms, trade-offs may be manifested as negative genetic covariances relative to the direction of selection on phenotypic traits. Although the expression and selection of ecologically important phenotypic variation are fundamentally multivariate phenomena, the in situ quantification of genetic covariances is challenging. Even for life-history traits, where well-developed theory exists with which to relate phenotypic variation to fitness variation, little evidence exists from in situ studies that negative genetic covariances are an important aspect of the genetic architecture of life-history traits. In fact, the majority of reported estimates of genetic covariances among life-history traits are positive. Here we apply theory of the genetics and selection of life histories in organisms with complex life cycles to provide a framework for quantifying the contribution of multivariate genetically based relationships among traits to evolutionary constraint. We use a Bayesian framework to link pedigree-based inference of the genetic basis of variation in life-history traits to evolutionary demography theory regarding how life histories are selected. Our results suggest that genetic covariances may be acting to constrain the evolution of female life-history traits in a wild population of red deer Cervus elaphus: genetic covariances are estimated to reduce the rate of adaptation by about 40%, relative to predicted evolutionary change in the absence of genetic covariances. Furthermore, multivariate phenotypic (rather than genetic) relationships among female life-history traits do not reveal this constraint.
2012-04-01T00:00:00ZMorrissey, Michael BlairWalling, CraigWilson, AlastairPemberton, JosephineClutton-Brock, TimKruuk, LoeskeTrade-offs among life-history traits are central to evolutionary theory. In quantitative genetic terms, trade-offs may be manifested as negative genetic covariances relative to the direction of selection on phenotypic traits. Although the expression and selection of ecologically important phenotypic variation are fundamentally multivariate phenomena, the in situ quantification of genetic covariances is challenging. Even for life-history traits, where well-developed theory exists with which to relate phenotypic variation to fitness variation, little evidence exists from in situ studies that negative genetic covariances are an important aspect of the genetic architecture of life-history traits. In fact, the majority of reported estimates of genetic covariances among life-history traits are positive. Here we apply theory of the genetics and selection of life histories in organisms with complex life cycles to provide a framework for quantifying the contribution of multivariate genetically based relationships among traits to evolutionary constraint. We use a Bayesian framework to link pedigree-based inference of the genetic basis of variation in life-history traits to evolutionary demography theory regarding how life histories are selected. Our results suggest that genetic covariances may be acting to constrain the evolution of female life-history traits in a wild population of red deer Cervus elaphus: genetic covariances are estimated to reduce the rate of adaptation by about 40%, relative to predicted evolutionary change in the absence of genetic covariances. Furthermore, multivariate phenotypic (rather than genetic) relationships among female life-history traits do not reveal this constraint.On the contrary: disagreement, context, and relative truthHuvenes, Torfinn Thomesenhttps://hdl.handle.net/10023/33602019-04-01T09:23:41Z2012-11-30T00:00:00Z2012-11-30T00:00:00ZHuvenes, Torfinn ThomesenPublic information use in ninespine sticklebacks (Pungitius pungitius) : isolating the mechanisms using computer-animated stimuliChouinard-Thuly, Laurahttps://hdl.handle.net/10023/33492021-10-12T09:10:24Z2012-01-01T00:00:00ZMany studies demonstrated the use, and strategies of use, of public information -or the ability of an observer to assess a resource’s quality by watching inadvertent behavioural cues- in the ninespine stickleback (Pungitius pungitius) presented with a foraging patch assessment problem. Many aspects of behaviour were seen to vary with an increased feeding rate and identifying the one responsible for transmission of information is difficult with live demonstrators. This project created and utilized computer-animated ninespine sticklebacks to isolate behaviours and test which ones are used by observers to gain information. We predicted and found that out of six different behaviours associated with an increase in feeding rate, strike rate is the one used to assess foraging patches’ quality. Observer ninespine sticklebacks preferred to associate with sides that were formerly associated with an animated shoal of conspecifics different only in the amount of strikes per demonstration period, in a ratio of six versus two.
2012-01-01T00:00:00ZChouinard-Thuly, LauraMany studies demonstrated the use, and strategies of use, of public information -or the ability of an observer to assess a resource’s quality by watching inadvertent behavioural cues- in the ninespine stickleback (Pungitius pungitius) presented with a foraging patch assessment problem. Many aspects of behaviour were seen to vary with an increased feeding rate and identifying the one responsible for transmission of information is difficult with live demonstrators. This project created and utilized computer-animated ninespine sticklebacks to isolate behaviours and test which ones are used by observers to gain information. We predicted and found that out of six different behaviours associated with an increase in feeding rate, strike rate is the one used to assess foraging patches’ quality. Observer ninespine sticklebacks preferred to associate with sides that were formerly associated with an animated shoal of conspecifics different only in the amount of strikes per demonstration period, in a ratio of six versus two.On disjoint unions of finitely many copies of the free monogenic semigroupAbughazalah, NabilahRuskuc, Nikhttps://hdl.handle.net/10023/33412023-04-18T09:47:16Z2013-08-01T00:00:00ZEvery semigroup which is a finite disjoint union of copies of the free monogenic semigroup (natural numbers under addition) is finitely presented and residually finite.
2013-08-01T00:00:00ZAbughazalah, NabilahRuskuc, NikEvery semigroup which is a finite disjoint union of copies of the free monogenic semigroup (natural numbers under addition) is finitely presented and residually finite.Excavating the borders of literary Anglo-Saxonism in nineteenth-century Britain and AustraliaD'Arcens, LouiseJones, Chrishttps://hdl.handle.net/10023/33372023-04-18T09:46:41Z2013-12-01T00:00:00ZComparing nineteenth-century British and Australian Anglo-Saxonist literature enables a "decentered" exploration of Anglo-Saxonism's intersections with national, imperial, and colonial discourses, challenging assumption that this discourse was an uncritical vehicle of English nationalism and British manifest destiny. Far from reflecting a stable imperial center, evocations of 'ancient Englishness' in British literature were polyvalent and self-contesting, while in Australian literature they offered a response to colonization and emerging knowledge about the vast age of Indigenous Australian cultures.
2013-12-01T00:00:00ZD'Arcens, LouiseJones, ChrisComparing nineteenth-century British and Australian Anglo-Saxonist literature enables a "decentered" exploration of Anglo-Saxonism's intersections with national, imperial, and colonial discourses, challenging assumption that this discourse was an uncritical vehicle of English nationalism and British manifest destiny. Far from reflecting a stable imperial center, evocations of 'ancient Englishness' in British literature were polyvalent and self-contesting, while in Australian literature they offered a response to colonization and emerging knowledge about the vast age of Indigenous Australian cultures.While crowding memories came : Edwin Morgan, Old English and nostalgiaJones, Chrishttps://hdl.handle.net/10023/33192023-04-18T09:47:04Z2012-01-01T00:00:00Z2012-01-01T00:00:00ZJones, ChrisFluorescence suppression using wavelength modulated Raman spectroscopy in fiber-probe-based tissue analysisBalagopal, BavishnaAshok, Praveen CheriyanMazilu, MichaelRiches, Andrew CliveHerrington, C SimonDholakia, Kishanhttps://hdl.handle.net/10023/33032024-02-17T00:40:25Z2012-07-09T00:00:00ZIn the field of biomedical optics, Raman spectroscopy is a powerful tool for probing the chemical composition of biological samples. In particular, fiber Raman probes play a crucial role for in vivo and ex vivo tissue analysis. However, the high-fluorescence background typically contributed by the auto fluorescence from both a tissue sample and the fiber-probe interferes strongly with the relatively weak Raman signal. Here we demonstrate the implementation of wavelength-modulated Raman spectroscopy (WMRS) to suppress the fluorescence background while analyzing tissues using fiber Raman probes. We have observed a significant signal-to-noise ratio enhancement in the Raman bands of bone tissue, which have a relatively high fluorescence background. Implementation of WMRS in fiber-probe-based bone tissue study yielded usable Raman spectra in a relatively short acquisition time (∼30 s), notably without any special sample preparation stage. Finally, we have validated its capability to suppress fluorescence on other tissue samples such as adipose tissue derived from four different species.
The work was funded by CR-UK/EPSRC/MRC/DoH (England) imaging programme.
2012-07-09T00:00:00ZBalagopal, BavishnaAshok, Praveen CheriyanMazilu, MichaelRiches, Andrew CliveHerrington, C SimonDholakia, KishanIn the field of biomedical optics, Raman spectroscopy is a powerful tool for probing the chemical composition of biological samples. In particular, fiber Raman probes play a crucial role for in vivo and ex vivo tissue analysis. However, the high-fluorescence background typically contributed by the auto fluorescence from both a tissue sample and the fiber-probe interferes strongly with the relatively weak Raman signal. Here we demonstrate the implementation of wavelength-modulated Raman spectroscopy (WMRS) to suppress the fluorescence background while analyzing tissues using fiber Raman probes. We have observed a significant signal-to-noise ratio enhancement in the Raman bands of bone tissue, which have a relatively high fluorescence background. Implementation of WMRS in fiber-probe-based bone tissue study yielded usable Raman spectra in a relatively short acquisition time (∼30 s), notably without any special sample preparation stage. Finally, we have validated its capability to suppress fluorescence on other tissue samples such as adipose tissue derived from four different species.Tunicates push the limits of animal evo-devoFerrier, David Ellard Keithhttps://hdl.handle.net/10023/32502023-04-18T09:43:12Z2011-01-20T00:00:00ZThe phylum to which humans belong, Chordata, takes its name from one of the major shared derived features of the group, the notochord. All chordates have a notochord, at least during embryogenesis, and there is little doubt about notochord homology at the morphological level. A study in BMC Evolutionary Biology now shows that there is greater variability in the molecular genetics underlying notochord development than previously appreciated.
2011-01-20T00:00:00ZFerrier, David Ellard KeithThe phylum to which humans belong, Chordata, takes its name from one of the major shared derived features of the group, the notochord. All chordates have a notochord, at least during embryogenesis, and there is little doubt about notochord homology at the morphological level. A study in BMC Evolutionary Biology now shows that there is greater variability in the molecular genetics underlying notochord development than previously appreciated.Attenuation of bunyavirus replication by modification of genomic untranslated regionsMazel-Sanchez, Berylhttps://hdl.handle.net/10023/32302019-03-29T10:37:43Z2012-11-30T00:00:00ZBunyamwera orthobunyavirus (BUNV) is the prototype for the family Bunyaviridae.
BUNV has a tripartite RNA genome of negative polarity composed of the large(L),medium (M)and small(S)segments. Each segment contains an open reading frame (ORF) flanked by untranslated regions (UTRs). The eleven terminal nucleotides are conserved between the three segments while the internal regions are unique. The UTRs play an important role in the virus life cycle by promoting transcription, replication and encapsidation of the viral genome.The work presented in this thesis explores UTRs plasticity and examines ways to engineere attenuated viruses by modifying only their UTRs. Using reverse genetics, mainly two ways of attenuation were explored: rescue of viruses either carrying deletions within their 3’ and/or 5’ UTRs in all three segments, or of viruses carrying one segment bearing heterologous UTRs. Both approaches resulted in virus attenuation in tissue culture, with viruses producing smaller plaques or even no plaques, and growing to lower titres than wild-type BUNV. Through serial passage, viruses were shown to
regain some level of fitness while the mutations introduced in the UTRs proved to be stable. Thus, to investigate the mechanism behind fitness recovery, the nucleotide sequence of the entire genome of viruses with deletions in their UTRs was determined. Amino acid changes were observed in the viral polymerase (L protein) of most mutant viruses and the vast majority of the amino acid changes occured in the C-terminal region. The function of this domain is unclear to date, however data obtained using a mini-replicon assay suggest that the
C-terminal domain of the L protein might be involved in UTR recognition. Full genome
sequencing also allowed the identification of an amino acid mutation within the polymerase that resulted in a temperature sensitive phenotype when introduced in an otherwise wild-type BUNV. Thus, it was shown that mutations introduced within the UTR regions of the genome were stable through serial passage and resulted in attenuation. Such a strategy could be used in
combination with mutations of the ORF to design live-attenuated vaccines against serious pathogens within the family Bunyaviridae.
2012-11-30T00:00:00ZMazel-Sanchez, BerylBunyamwera orthobunyavirus (BUNV) is the prototype for the family Bunyaviridae.
BUNV has a tripartite RNA genome of negative polarity composed of the large(L),medium (M)and small(S)segments. Each segment contains an open reading frame (ORF) flanked by untranslated regions (UTRs). The eleven terminal nucleotides are conserved between the three segments while the internal regions are unique. The UTRs play an important role in the virus life cycle by promoting transcription, replication and encapsidation of the viral genome.The work presented in this thesis explores UTRs plasticity and examines ways to engineere attenuated viruses by modifying only their UTRs. Using reverse genetics, mainly two ways of attenuation were explored: rescue of viruses either carrying deletions within their 3’ and/or 5’ UTRs in all three segments, or of viruses carrying one segment bearing heterologous UTRs. Both approaches resulted in virus attenuation in tissue culture, with viruses producing smaller plaques or even no plaques, and growing to lower titres than wild-type BUNV. Through serial passage, viruses were shown to
regain some level of fitness while the mutations introduced in the UTRs proved to be stable. Thus, to investigate the mechanism behind fitness recovery, the nucleotide sequence of the entire genome of viruses with deletions in their UTRs was determined. Amino acid changes were observed in the viral polymerase (L protein) of most mutant viruses and the vast majority of the amino acid changes occured in the C-terminal region. The function of this domain is unclear to date, however data obtained using a mini-replicon assay suggest that the
C-terminal domain of the L protein might be involved in UTR recognition. Full genome
sequencing also allowed the identification of an amino acid mutation within the polymerase that resulted in a temperature sensitive phenotype when introduced in an otherwise wild-type BUNV. Thus, it was shown that mutations introduced within the UTR regions of the genome were stable through serial passage and resulted in attenuation. Such a strategy could be used in
combination with mutations of the ORF to design live-attenuated vaccines against serious pathogens within the family Bunyaviridae.The influence of mid-ocean ridges on euphausiid and pelagic ecologyLetessier, Tom Bechhttps://hdl.handle.net/10023/32292019-03-29T10:41:08Z2012-06-19T00:00:00ZChapters 1 & 2. Euphausiids comprise a major component of ecosystems in the pelagic realm, the
world’s largest habitat, but basin scale drivers of euphausiids diversity and abundance
are poorly understood. Mid-Ocean Ridges are the largest topographical feature in the
pelagic realm and their benthic and pelagic fauna have only just recently become the
focus of research. This thesis present new analyses on the drivers of euphausiids species
richness in the Atlantic and the Pacific, giving specific attention to the influence of Mid-Ocean Ridges. New information is given on the biogeography of euphausiids and
pelagic food-web trophology of the Mid-Atlantic Ridge, and on the biogeography of
pelagic decapods on the South-West Indian Ocean ridge.
3. A Generalized Additive Model framework was used to explore spatial patterns of
variability in euphausiid species richness (from recognized areas of occurrence) and in
numerical abundance (from the Continuous Plankton Recorder survey) in conjunction
with variability in a suite of biological, physical and environmental parameters on, and
at either side of, the Mid-Atlantic Ridge. Euphausiid species richness peaked in mid-latitudes
and was significantly higher on the ridge than in adjacent waters, but the ridge
did not influence numerical abundance in the top 10 m significantly. Sea surface
temperature (SST) was the most important single factor influencing both euphausiid
numerical abundance (-76.7%) and species richness (34.44%). Dissolved silicate
concentration, a proxy for diatom abundance, significantly increased species richness
(29.46%). Increases in sea surface height variance, a proxy for mixing, increased the
numerical abundance of euphausiids. GAM predictions of variability in species richness
as a function of SST and depth of the mixed layer were consistent with present theories,
which suggest that pelagic niche-availability is related to the thermal structure of the
near surface water.
4. Using a Generalized Additive Model in the Pacific, the main drivers of species
richness, in order of decreasing importance, were found to be sea surface temperature
(explaining 29.53% in species variability), salinity (20.29%), longitude (-15.01%,
species richness decreased from West to East), distance to coast (10.99%), and
dissolved silicate concentration (9.03%). An additional linear model poorly predicted
numerical abundance. The practical differences in drivers of species richness in the
Atlantic and Pacific Ocean were compared. Predictions of future species richness
changes in the Pacific and Atlantic were made using projected environmental change
from the IPCC A1B climate scenario, suggesting an increase in species richness in
temperature latitudes (30° to 60° N and S) and little to no change in low latitudes (20° N
to 20° S).
5. New baseline information is presented on biogeography, abundance and vertical
distribution of euphausiids along the Mid-Atlantic Ridge (40° to 62° N). 18 species
were recorded, with Euphausia krohni and Thysanoessa longicaudata being most
abundant. Eight species had not been recorded in the area previously. The Subpolar
Front is a northern boundary to some southern species, but not a southern boundary to
northern ubiquitous species that show submergence. Four major species assemblages
were identified and characterised in terms of spatial distribution and species
composition. Numerical abundance was highly variable but decreased by orders of
magnitude with depth. The Mid-Atlantic Ridge showed only a marginal effect on
euphausiid distribution and abundance patterns.
6. Zooplankton and micronektic invertebrate epi- and mesopelagic (0-200 and 200-800 m) vertical distribution (e.g. Euphausiacea, Decapoda, Amphipoda, Thecosomata,
Lophogastrida) on either side of the Subpolar Front of the Mid-Atlantic Ridge is
described. Dietary relationships are explored, using stable isotope ratios and fatty acid
trophic marker (FATM) composition. An increase in trophic level with size was
observed. Individuals from southern stations were higher in dinoflagellate Fatty Acid
Trophic Markers (FATM) (22:6(n-3)) and individuals from northern stations were
higher in Calanus spp and storage FATMs (20:1(n-9) and 22:1(n-9)) reflecting primary
production patterns in the two survey sectors. Observations on the geographical and
vertical variability in trophodynamics are discussed.
7. New baseline information is presented on the biogeography, abundance, and vertical
distribution of mesopelagic (200-1000 m), crustacean micronekton on- and offseamounts
of the South-West Indian Ocean Ridge (26° to 42° S). Species richness and
numerical abundance were typically higher near seamounts and lower over the abyssal
plains, with several species being caught uniquely on seamounts. Observations suggest
that the ‘oasis effect’ of seamounts conventionally associated with higher trophic levels
is also applicable to pelagic micronektic crustaceans at lower trophic levels. Biophysical
coupling of micronekton to seamounts may be an important factor controlling
benthopelagic coupling in seamount food-webs.
8. Euphausiid and pelagic diversity is driven primarily by geographical variability in
temperature, by longitudinal patterns in upwellings, and by variability in nutrient
concentration. Mid-Ocean Ridges modify pelagic ecology, by raising the seafloor and
by bringing in proximity true pelagic and bathypelagic predators associated with the
seabed. The increase in specialized fauna and biomass associated with ridges and
seamounts serves to deplete zooplankton in the near bottom layer (0-200 m) and affect
systems in and above the benthic boundary layer (<200 m from the seafloor), and the
benthopelagic faunal layer. Mid-Ocean Ridges may serve to structure pelagic faunal
distribution, and increase the overall diversity of the world ocean. The influence of
ridges in the ocean basin may be comparable to that of hedges in a farmland; whilst
delimiting the extent of crops (or zooplankton assemblages), hedges serve as local
hotspots of mammal and avian diversity.
2012-06-19T00:00:00ZLetessier, Tom BechChapters 1 & 2. Euphausiids comprise a major component of ecosystems in the pelagic realm, the
world’s largest habitat, but basin scale drivers of euphausiids diversity and abundance
are poorly understood. Mid-Ocean Ridges are the largest topographical feature in the
pelagic realm and their benthic and pelagic fauna have only just recently become the
focus of research. This thesis present new analyses on the drivers of euphausiids species
richness in the Atlantic and the Pacific, giving specific attention to the influence of Mid-Ocean Ridges. New information is given on the biogeography of euphausiids and
pelagic food-web trophology of the Mid-Atlantic Ridge, and on the biogeography of
pelagic decapods on the South-West Indian Ocean ridge.
3. A Generalized Additive Model framework was used to explore spatial patterns of
variability in euphausiid species richness (from recognized areas of occurrence) and in
numerical abundance (from the Continuous Plankton Recorder survey) in conjunction
with variability in a suite of biological, physical and environmental parameters on, and
at either side of, the Mid-Atlantic Ridge. Euphausiid species richness peaked in mid-latitudes
and was significantly higher on the ridge than in adjacent waters, but the ridge
did not influence numerical abundance in the top 10 m significantly. Sea surface
temperature (SST) was the most important single factor influencing both euphausiid
numerical abundance (-76.7%) and species richness (34.44%). Dissolved silicate
concentration, a proxy for diatom abundance, significantly increased species richness
(29.46%). Increases in sea surface height variance, a proxy for mixing, increased the
numerical abundance of euphausiids. GAM predictions of variability in species richness
as a function of SST and depth of the mixed layer were consistent with present theories,
which suggest that pelagic niche-availability is related to the thermal structure of the
near surface water.
4. Using a Generalized Additive Model in the Pacific, the main drivers of species
richness, in order of decreasing importance, were found to be sea surface temperature
(explaining 29.53% in species variability), salinity (20.29%), longitude (-15.01%,
species richness decreased from West to East), distance to coast (10.99%), and
dissolved silicate concentration (9.03%). An additional linear model poorly predicted
numerical abundance. The practical differences in drivers of species richness in the
Atlantic and Pacific Ocean were compared. Predictions of future species richness
changes in the Pacific and Atlantic were made using projected environmental change
from the IPCC A1B climate scenario, suggesting an increase in species richness in
temperature latitudes (30° to 60° N and S) and little to no change in low latitudes (20° N
to 20° S).
5. New baseline information is presented on biogeography, abundance and vertical
distribution of euphausiids along the Mid-Atlantic Ridge (40° to 62° N). 18 species
were recorded, with Euphausia krohni and Thysanoessa longicaudata being most
abundant. Eight species had not been recorded in the area previously. The Subpolar
Front is a northern boundary to some southern species, but not a southern boundary to
northern ubiquitous species that show submergence. Four major species assemblages
were identified and characterised in terms of spatial distribution and species
composition. Numerical abundance was highly variable but decreased by orders of
magnitude with depth. The Mid-Atlantic Ridge showed only a marginal effect on
euphausiid distribution and abundance patterns.
6. Zooplankton and micronektic invertebrate epi- and mesopelagic (0-200 and 200-800 m) vertical distribution (e.g. Euphausiacea, Decapoda, Amphipoda, Thecosomata,
Lophogastrida) on either side of the Subpolar Front of the Mid-Atlantic Ridge is
described. Dietary relationships are explored, using stable isotope ratios and fatty acid
trophic marker (FATM) composition. An increase in trophic level with size was
observed. Individuals from southern stations were higher in dinoflagellate Fatty Acid
Trophic Markers (FATM) (22:6(n-3)) and individuals from northern stations were
higher in Calanus spp and storage FATMs (20:1(n-9) and 22:1(n-9)) reflecting primary
production patterns in the two survey sectors. Observations on the geographical and
vertical variability in trophodynamics are discussed.
7. New baseline information is presented on the biogeography, abundance, and vertical
distribution of mesopelagic (200-1000 m), crustacean micronekton on- and offseamounts
of the South-West Indian Ocean Ridge (26° to 42° S). Species richness and
numerical abundance were typically higher near seamounts and lower over the abyssal
plains, with several species being caught uniquely on seamounts. Observations suggest
that the ‘oasis effect’ of seamounts conventionally associated with higher trophic levels
is also applicable to pelagic micronektic crustaceans at lower trophic levels. Biophysical
coupling of micronekton to seamounts may be an important factor controlling
benthopelagic coupling in seamount food-webs.
8. Euphausiid and pelagic diversity is driven primarily by geographical variability in
temperature, by longitudinal patterns in upwellings, and by variability in nutrient
concentration. Mid-Ocean Ridges modify pelagic ecology, by raising the seafloor and
by bringing in proximity true pelagic and bathypelagic predators associated with the
seabed. The increase in specialized fauna and biomass associated with ridges and
seamounts serves to deplete zooplankton in the near bottom layer (0-200 m) and affect
systems in and above the benthic boundary layer (<200 m from the seafloor), and the
benthopelagic faunal layer. Mid-Ocean Ridges may serve to structure pelagic faunal
distribution, and increase the overall diversity of the world ocean. The influence of
ridges in the ocean basin may be comparable to that of hedges in a farmland; whilst
delimiting the extent of crops (or zooplankton assemblages), hedges serve as local
hotspots of mammal and avian diversity.Examining the response of top marine predators to ecological change using stable isotope proxiesHanson, Nora Nellhttps://hdl.handle.net/10023/32212019-03-29T10:33:58Z2012-11-30T00:00:00ZMonitoring the response of upper trophic level animals to ecological change is important
to understanding the state and stability of ecosystems. Marine predators
integrate information over large geographical scales and are relatively long-lived; furthermore,
many of these organisms are restricted to terrestrial or freshwater habitats
at certain times during their life history and are accessible to researchers. This thesis
investigated the response of marine predators to ecological change at a variety
of spatial and temporal scales using stable isotope ratio methods with the aims of
developing meaningful proxies, or indices, of variability in marine ecosystems.
The first study explored the intrinsic (i.e. ontogenetic) and extrinsic (i.e. environmental)
factors important to modulating variation in the stable isotope ratios of
C and N in tooth dentin of male Antarctic fur seals (Arctocephalus gazella) in the
Southern Ocean. In the second study, long-term records of variation in δ¹⁵N and δ¹³C values of Atlantic salmon (Salmo salar) scales and grey seal (Halichoerus grypus)
tooth dentin provided evidence for large-scale climate forcing across the eastern
North Atlantic. In the following study, a more detailed examination of intra- and
inter-individual stable isotope variation in Atlantic salmon within a single year was
undertaken in an attempt to better understand recent declines in somatic condition
of these fish.
The last two studies were concerned with the development of high resolution sampling
of fish otoliths using secondary mass spectrometry (SIMS) and the application
of this technique to reconstructing the thermal and metabolic histories of individual
Atlantic salmon from intra-otolith δ¹³C and δ¹⁸O values.
Stable isotope proxies can be used to document shifts in trophic dynamics and
animal movement that may be associated with ecological change. Using multiple
tissues, elements and species, such studies provide unique monitoring tools at a
range of spatial and temporal scales.
2012-11-30T00:00:00ZHanson, Nora NellMonitoring the response of upper trophic level animals to ecological change is important
to understanding the state and stability of ecosystems. Marine predators
integrate information over large geographical scales and are relatively long-lived; furthermore,
many of these organisms are restricted to terrestrial or freshwater habitats
at certain times during their life history and are accessible to researchers. This thesis
investigated the response of marine predators to ecological change at a variety
of spatial and temporal scales using stable isotope ratio methods with the aims of
developing meaningful proxies, or indices, of variability in marine ecosystems.
The first study explored the intrinsic (i.e. ontogenetic) and extrinsic (i.e. environmental)
factors important to modulating variation in the stable isotope ratios of
C and N in tooth dentin of male Antarctic fur seals (Arctocephalus gazella) in the
Southern Ocean. In the second study, long-term records of variation in δ¹⁵N and δ¹³C values of Atlantic salmon (Salmo salar) scales and grey seal (Halichoerus grypus)
tooth dentin provided evidence for large-scale climate forcing across the eastern
North Atlantic. In the following study, a more detailed examination of intra- and
inter-individual stable isotope variation in Atlantic salmon within a single year was
undertaken in an attempt to better understand recent declines in somatic condition
of these fish.
The last two studies were concerned with the development of high resolution sampling
of fish otoliths using secondary mass spectrometry (SIMS) and the application
of this technique to reconstructing the thermal and metabolic histories of individual
Atlantic salmon from intra-otolith δ¹³C and δ¹⁸O values.
Stable isotope proxies can be used to document shifts in trophic dynamics and
animal movement that may be associated with ecological change. Using multiple
tissues, elements and species, such studies provide unique monitoring tools at a
range of spatial and temporal scales.Workshop on new developments in cetacean survey methodsBorchers, David LouisThomas, LenBuckland, Stephen TerrenceSkaug, HansBarlow, Jayhttps://hdl.handle.net/10023/32162023-04-26T00:22:12Z2011-01-01T00:00:00ZThis report contains the slides from a workshop on New Developments in Cetacean Survey Methods held on 27th November 2011 at the 19th Biennial Conference on the Biology of Marine Mammals, Tampa, Florida. Review talks were given on Passive Acoustic Density Estimation (Len Thomas); Dealing with g(0)<1: Perception Bias (Stephen Buckland); Dealing with g(0)<1: Availability Bias (Hans Skaug); Dealing with Measurement Error (David Borchers); and Density Surface Modelling (Jay Barlow). The sessions were followed by a discussion, and this is summarized at the end of the report.
2011-01-01T00:00:00ZBorchers, David LouisThomas, LenBuckland, Stephen TerrenceSkaug, HansBarlow, JayThis report contains the slides from a workshop on New Developments in Cetacean Survey Methods held on 27th November 2011 at the 19th Biennial Conference on the Biology of Marine Mammals, Tampa, Florida. Review talks were given on Passive Acoustic Density Estimation (Len Thomas); Dealing with g(0)<1: Perception Bias (Stephen Buckland); Dealing with g(0)<1: Availability Bias (Hans Skaug); Dealing with Measurement Error (David Borchers); and Density Surface Modelling (Jay Barlow). The sessions were followed by a discussion, and this is summarized at the end of the report.Interfacing Coq + SSReflect with GAPKomendantsky, VladimirKonovalov, AlexanderLinton, Stephen Alexanderhttps://hdl.handle.net/10023/31752023-04-18T09:46:36Z2012-09-19T00:00:00ZWe report on an extendable implementation of the communication interface connecting Coq proof assistant to the computational algebra system GAP using the Symbolic Computation Software Composability Protocol (SCSCP). It allows Coq to issue OpenMath requests to a local or remote GAP instances and represent server responses as Coq terms.
Presentation slides and preprint both provided by author. Preprint published in Electronic Notes in Theoretical Computer Science: Proceedings of the 9th International Workshop On User Interfaces for Theorem Provers (UITP10).
2012-09-19T00:00:00ZKomendantsky, VladimirKonovalov, AlexanderLinton, Stephen AlexanderWe report on an extendable implementation of the communication interface connecting Coq proof assistant to the computational algebra system GAP using the Symbolic Computation Software Composability Protocol (SCSCP). It allows Coq to issue OpenMath requests to a local or remote GAP instances and represent server responses as Coq terms.Statistical developments for understanding anthropogenic impacts on marine ecosystemsMarshall, Laurahttps://hdl.handle.net/10023/31722019-07-01T10:08:55Z2012-06-20T00:00:00ZOver the past decades technological developments have both changed and increased
human influence on the marine environment. We now have greater potential than ever before to introduce disturbance and deplete marine resources. Two of the issues currently under public scrutiny are the exploitation of fish stocks worldwide and
levels of anthropogenic noise in the marine environment. The aim of this thesis is to investigate and develop novel analyses and simulations to provide additional insight into some of the challenges facing the marine ecosystem today. These methodologies
will improve the management of these risks to marine ecosystems. This thesis first addresses the issue of competition between humans and grey seals
(Halichoerus grypus) for marine resources, providing compelling evidence that a substantial proportion of the sandeels consumed by grey seals in the North Sea are in fact H. lanceolatus, which is not commercially exploited, rather than the commercially important A. marinus. In addition, we present quantitative results regarding sources of bias when estimating the total biomass of sandeels consumed by grey seals. Secondly, we investigate spatially adaptive 2-dimensional smoothing to improve the prediction of both the presence and density of marine species, information that is often key in the management of marine ecosystems. Particularly, we demonstrate the benefits of
such methods in the prediction of sandeel occurrence. Lastly this thesis provides a
quantitative assessment of the protocols for real-time monitoring of marine mammal presence, which require that acoustic operations cease when an animal is detected
within a certain distance (i.e. the "monitoring zone") of the sound source. We assess monitoring zones of different sizes with regards to their effectiveness in reducing the risks of temporary and permanent damage to the animals' hearing, and demonstrate that a monitoring zone of 2 km is generally recommendable.
2012-06-20T00:00:00ZMarshall, LauraOver the past decades technological developments have both changed and increased
human influence on the marine environment. We now have greater potential than ever before to introduce disturbance and deplete marine resources. Two of the issues currently under public scrutiny are the exploitation of fish stocks worldwide and
levels of anthropogenic noise in the marine environment. The aim of this thesis is to investigate and develop novel analyses and simulations to provide additional insight into some of the challenges facing the marine ecosystem today. These methodologies
will improve the management of these risks to marine ecosystems. This thesis first addresses the issue of competition between humans and grey seals
(Halichoerus grypus) for marine resources, providing compelling evidence that a substantial proportion of the sandeels consumed by grey seals in the North Sea are in fact H. lanceolatus, which is not commercially exploited, rather than the commercially important A. marinus. In addition, we present quantitative results regarding sources of bias when estimating the total biomass of sandeels consumed by grey seals. Secondly, we investigate spatially adaptive 2-dimensional smoothing to improve the prediction of both the presence and density of marine species, information that is often key in the management of marine ecosystems. Particularly, we demonstrate the benefits of
such methods in the prediction of sandeel occurrence. Lastly this thesis provides a
quantitative assessment of the protocols for real-time monitoring of marine mammal presence, which require that acoustic operations cease when an animal is detected
within a certain distance (i.e. the "monitoring zone") of the sound source. We assess monitoring zones of different sizes with regards to their effectiveness in reducing the risks of temporary and permanent damage to the animals' hearing, and demonstrate that a monitoring zone of 2 km is generally recommendable.Impact of environmental change on primary production in model marine coastal ecosystemsHicks, Nataliehttps://hdl.handle.net/10023/31432019-04-01T11:12:31Z2011-01-01T00:00:00ZCoastal ecosystems, including estuaries, provide a range of services to humans,
mediated by the species within these ecosystems. Microphytobenthos (MPB) play a
vital role in many key processes within estuarine ecosystems, and provide a food
source for higher trophic levels. Anthropogenic activity is already causing changes to
ecosystems, through pollution, overexploitation and, more recently, climate change.
Increasing temperature and carbon dioxide levels, and altered biodiversity, are likely
to affect species, and their interactions, within these ecosystems. Much ecological
research has focused on the effects of a single stressor on specific species or
ecosystems, with relatively little work examining the effects of multiple stressors.
The research in this thesis investigates the effects of altered environmental variables
(light, tidal regime, temperature and carbon dioxide) and different macrofaunal
diversity on primary production (MPB biomass) through a series of manipulative lab-based mesocosm experiments. This work also examines the temporal variability of
environmental stressors on species across two trophic levels. Results demonstrate how
multiple environmental stressors interact in a complex and non-additive way to
determine an ecosystem response (MPB biomass, nutrient concentration), and the
effects of altered biodiversity were underpinned by strong species effects. Temporal
variation of stressors had a strong effect on ecosystem response. In marine coastal
ecosystems, environmental changes through ocean acidification will have economic
and social repercussions, directly impacting the human services and livelihoods that
these systems provide. As such, future research should be focused on identifying and
mitigating the inevitable multiple effects that future global change may have on
coastal ecosystems.
2011-01-01T00:00:00ZHicks, NatalieCoastal ecosystems, including estuaries, provide a range of services to humans,
mediated by the species within these ecosystems. Microphytobenthos (MPB) play a
vital role in many key processes within estuarine ecosystems, and provide a food
source for higher trophic levels. Anthropogenic activity is already causing changes to
ecosystems, through pollution, overexploitation and, more recently, climate change.
Increasing temperature and carbon dioxide levels, and altered biodiversity, are likely
to affect species, and their interactions, within these ecosystems. Much ecological
research has focused on the effects of a single stressor on specific species or
ecosystems, with relatively little work examining the effects of multiple stressors.
The research in this thesis investigates the effects of altered environmental variables
(light, tidal regime, temperature and carbon dioxide) and different macrofaunal
diversity on primary production (MPB biomass) through a series of manipulative lab-based mesocosm experiments. This work also examines the temporal variability of
environmental stressors on species across two trophic levels. Results demonstrate how
multiple environmental stressors interact in a complex and non-additive way to
determine an ecosystem response (MPB biomass, nutrient concentration), and the
effects of altered biodiversity were underpinned by strong species effects. Temporal
variation of stressors had a strong effect on ecosystem response. In marine coastal
ecosystems, environmental changes through ocean acidification will have economic
and social repercussions, directly impacting the human services and livelihoods that
these systems provide. As such, future research should be focused on identifying and
mitigating the inevitable multiple effects that future global change may have on
coastal ecosystems.The genetic basis of flesh quality traits in farmed Atlantic salmonAshton, Thomas Jameshttps://hdl.handle.net/10023/31072016-08-09T09:09:45Z2011-11-30T00:00:00ZThe aim was to develop new methods for measuring texture of Atlantic salmon (Salmo salar L.) fillets and investigate the genetic basis of flesh quality traits.
Firstly, a new tensile strength method was developed to quantify the force required to tear a standardized block of salmon muscle with the aim of identifying those samples more prone to factory downgrading as a result of gaping. The repeatability, sensitivity and predictability of the new technique was evaluated against other common instrumental texture measurement methods. Data from the new method were shown to have the strongest correlations with gaping severity r=-0.514, P<0.001) and the highest level of repeatability of data when analysing cold-smoked samples. The Warner Bratzler shear method gave the most repeatable data from fresh samples and had the highest correlations between fresh and smoked product from the same fish (r=0.811, P<0.001). It is therefore recommended that the new method be adopted for measuring gaping potential and the Warner Bratzler method become the standard for firmness assessment.
Genes associated with post mortem softening in mammals were characterised in Atlantic salmon. A previously unknown ancient paralogue of calpastatin (here named CAST2) was identified. Evidence was provided for the existence of highly homologous recent paralogues of CAST2 and CTSD1. Evidence for the ancestral history of these paralogues was provided by phylogenetic analysis. Recent gene duplicates of 6 further genes were identified. In all cases, homology between recent paralogues was greater than 94%. Analysis of synonymous vs non-synonymous nucleotide substitution between the observed paralogue pairs shows a significant purifying selection in most cases. The CTSD1 gene shows significant purifying selection in a pairwise analysis between 12 teleost species (all cases P<0.0001) but a similar analysis of CTSD2 revealed no significant occurrence of purifying selection. The present study provides further support for the idea of asymmetrical selective pressure on paralogues.
Genetic markers were developed that can distinguish individuals with above average fillet yield and texture. A database of firmness, tensile strength and fillet yield was made from 254 individuals from 5 batches of farmed salmon and these fish were genotyped at 7 novel SNP loci. Individuals with the combined favourable genotype at CAPN1a and MYOD1b were associated with an average increase in fillet yield of 2.7% above batch average. A combined genotype of CAPN1a, MYOD1b and MYF5 was significantly associated with an average increase in tensile strength of 9.8% above batch average (P=0.015). In both cases individuals with the combined favourable genotype occurred with a frequency of c. 6% across all batches. The favourable genotypes had no unfavourable effects on other traits.
Highly polymorphic microsatellite loci were used to perform tests of assignment, which revealed an overall correct assignment rate of 92.7% to batch of origin and a minimum reference sample number of 25 was empirically determined. A phylogenetic analysis supported the results of the assignment tests. Given that 7 microsatellites is a relatively small number for a study of this nature, these results suggest that reliable assignment of unknown fish to the true batch of origin is potentially rapid and cost effective.
Overall, the thesis presents molecular markers for broodstock selection, new genes of relevance to flesh quality, a new method of texture analysis and a proposal for an escapee traceability project.
2011-11-30T00:00:00ZAshton, Thomas JamesThe aim was to develop new methods for measuring texture of Atlantic salmon (Salmo salar L.) fillets and investigate the genetic basis of flesh quality traits.
Firstly, a new tensile strength method was developed to quantify the force required to tear a standardized block of salmon muscle with the aim of identifying those samples more prone to factory downgrading as a result of gaping. The repeatability, sensitivity and predictability of the new technique was evaluated against other common instrumental texture measurement methods. Data from the new method were shown to have the strongest correlations with gaping severity r=-0.514, P<0.001) and the highest level of repeatability of data when analysing cold-smoked samples. The Warner Bratzler shear method gave the most repeatable data from fresh samples and had the highest correlations between fresh and smoked product from the same fish (r=0.811, P<0.001). It is therefore recommended that the new method be adopted for measuring gaping potential and the Warner Bratzler method become the standard for firmness assessment.
Genes associated with post mortem softening in mammals were characterised in Atlantic salmon. A previously unknown ancient paralogue of calpastatin (here named CAST2) was identified. Evidence was provided for the existence of highly homologous recent paralogues of CAST2 and CTSD1. Evidence for the ancestral history of these paralogues was provided by phylogenetic analysis. Recent gene duplicates of 6 further genes were identified. In all cases, homology between recent paralogues was greater than 94%. Analysis of synonymous vs non-synonymous nucleotide substitution between the observed paralogue pairs shows a significant purifying selection in most cases. The CTSD1 gene shows significant purifying selection in a pairwise analysis between 12 teleost species (all cases P<0.0001) but a similar analysis of CTSD2 revealed no significant occurrence of purifying selection. The present study provides further support for the idea of asymmetrical selective pressure on paralogues.
Genetic markers were developed that can distinguish individuals with above average fillet yield and texture. A database of firmness, tensile strength and fillet yield was made from 254 individuals from 5 batches of farmed salmon and these fish were genotyped at 7 novel SNP loci. Individuals with the combined favourable genotype at CAPN1a and MYOD1b were associated with an average increase in fillet yield of 2.7% above batch average. A combined genotype of CAPN1a, MYOD1b and MYF5 was significantly associated with an average increase in tensile strength of 9.8% above batch average (P=0.015). In both cases individuals with the combined favourable genotype occurred with a frequency of c. 6% across all batches. The favourable genotypes had no unfavourable effects on other traits.
Highly polymorphic microsatellite loci were used to perform tests of assignment, which revealed an overall correct assignment rate of 92.7% to batch of origin and a minimum reference sample number of 25 was empirically determined. A phylogenetic analysis supported the results of the assignment tests. Given that 7 microsatellites is a relatively small number for a study of this nature, these results suggest that reliable assignment of unknown fish to the true batch of origin is potentially rapid and cost effective.
Overall, the thesis presents molecular markers for broodstock selection, new genes of relevance to flesh quality, a new method of texture analysis and a proposal for an escapee traceability project.Metafreedom? The carnivalesque of freedom in a Brazilian favelaLino e Silva, Moiseshttps://hdl.handle.net/10023/30952019-04-01T09:30:48Z2012-05-15T00:00:00ZThis thesis dwells on the existence of freedom in the life of people in a Brazilian favela (shantytown). The ethnography presents the dance of freedom with the full intensity of a carnivalesque. The exploration also ponders the existence of metafreedom (proposed as the freedom necessary for the expression of freedom) as a form of control over iterations of freedom. At the same time that it argues for a radical carnivalization of narratives of freedom, it flirts with the very limits of freedom as a concept and as a practice. One of the main contributions is in avoiding a reductive analysis of the concept of freedom, narrowing it to a simpler or alternative notion. Instead, the project presents the complex relations of five experienced objects – livre; livre-arbítrio; libertação; liberada and liberdade – to one another and to the life situations in which they come to existence in Favela da Rocinha in Rio de Janeiro. In methodological terms, the research argues that one of the ways to approach the topic of freedom from an ethnographic perspective is through the occurrences of linguistic expressions of freedom as objects that can be empirically experienced and registered by the ethnographer. It is mainly by making the complexities of freedom visible ethnographically, by tracing freedoms in their daily existence and by connecting these different kinds of freedom to diverse lived experiences and social contexts that the thesis advances the debate on freedom. The discussion of a carnivalesque of freedom in a Brazilian favela is also a call for a reflection on what ethnography as an empirical method, and anthropology more broadly, can offer to the understanding of freedom.
2012-05-15T00:00:00ZLino e Silva, MoisesThis thesis dwells on the existence of freedom in the life of people in a Brazilian favela (shantytown). The ethnography presents the dance of freedom with the full intensity of a carnivalesque. The exploration also ponders the existence of metafreedom (proposed as the freedom necessary for the expression of freedom) as a form of control over iterations of freedom. At the same time that it argues for a radical carnivalization of narratives of freedom, it flirts with the very limits of freedom as a concept and as a practice. One of the main contributions is in avoiding a reductive analysis of the concept of freedom, narrowing it to a simpler or alternative notion. Instead, the project presents the complex relations of five experienced objects – livre; livre-arbítrio; libertação; liberada and liberdade – to one another and to the life situations in which they come to existence in Favela da Rocinha in Rio de Janeiro. In methodological terms, the research argues that one of the ways to approach the topic of freedom from an ethnographic perspective is through the occurrences of linguistic expressions of freedom as objects that can be empirically experienced and registered by the ethnographer. It is mainly by making the complexities of freedom visible ethnographically, by tracing freedoms in their daily existence and by connecting these different kinds of freedom to diverse lived experiences and social contexts that the thesis advances the debate on freedom. The discussion of a carnivalesque of freedom in a Brazilian favela is also a call for a reflection on what ethnography as an empirical method, and anthropology more broadly, can offer to the understanding of freedom.Learning to use illumination gradients as an unambiguous cue to three dimensional shapeHarding, GlenHarris, JulieBloj, Marinahttps://hdl.handle.net/10023/30772022-04-26T08:30:04Z2012-04-30T00:00:00ZThe luminance and colour gradients across an image are the result of complex interactions between object shape, material and illumination. Using such variations to infer object shape or surface colour is therefore a difficult problem for the visual system. We know that changes to the shape of an object can affect its perceived colour, and that shading gradients confer a sense of shape. Here we investigate if the visual system is able to effectively utilise these gradients as a cue to shape perception, even when additional cues are not available. We tested shape perception of a folded card object that contained illumination gradients in the form of shading and more subtle effects such as inter-reflections. Our results suggest that observers are able to use the gradients to make consistent shape judgements. In order to do this, observers must be given the opportunity to learn suitable assumptions about the lighting and scene. Using a variety of different training conditions, we demonstrate that learning can occur quickly and requires only coarse information. We also establish that learning does not deliver a trivial mapping between gradient and shape; rather learning leads to the acquisition of assumptions about lighting and scene parameters that subsequently allow for gradients to be used as a shape cue. The perceived shape is shown to be consistent for convex and concave versions of the object that exhibit very different shading, and also similar to that delivered by outline, a largely unrelated cue to shape. Overall our results indicate that, although gradients are less reliable than some other cues, the relationship between gradients and shape can be quickly assessed and the gradients therefore used effectively as a visual shape cue.
2012-04-30T00:00:00ZHarding, GlenHarris, JulieBloj, MarinaThe luminance and colour gradients across an image are the result of complex interactions between object shape, material and illumination. Using such variations to infer object shape or surface colour is therefore a difficult problem for the visual system. We know that changes to the shape of an object can affect its perceived colour, and that shading gradients confer a sense of shape. Here we investigate if the visual system is able to effectively utilise these gradients as a cue to shape perception, even when additional cues are not available. We tested shape perception of a folded card object that contained illumination gradients in the form of shading and more subtle effects such as inter-reflections. Our results suggest that observers are able to use the gradients to make consistent shape judgements. In order to do this, observers must be given the opportunity to learn suitable assumptions about the lighting and scene. Using a variety of different training conditions, we demonstrate that learning can occur quickly and requires only coarse information. We also establish that learning does not deliver a trivial mapping between gradient and shape; rather learning leads to the acquisition of assumptions about lighting and scene parameters that subsequently allow for gradients to be used as a shape cue. The perceived shape is shown to be consistent for convex and concave versions of the object that exhibit very different shading, and also similar to that delivered by outline, a largely unrelated cue to shape. Overall our results indicate that, although gradients are less reliable than some other cues, the relationship between gradients and shape can be quickly assessed and the gradients therefore used effectively as a visual shape cue."For the salvation of my soul": women and wills in medieval and early modern Francehttps://hdl.handle.net/10023/30522019-04-01T11:10:07Z2012-01-01T00:00:00ZThis volume seeks to investigate the testamentary practices of women in medieval and early modern France, examining the experience of a cross-section of the population, from artisans to the elite, in Aix-en-Provence, Avignon, Marseille, Montpellier, La Rochelle, Brittany, and Burgundy. The making of a will was perhaps the single most prominent moment in women’s lives for the assertion of agency. Though constrained to some degree by customary practice and the increasing influence of Roman law, women demonstrated remarkable initiative in the formulation of their last wishes. Wills permitted women to reward friendship and loyalty, to designate universal heirs as major beneficiaries, to stipulate conditions of inheritance so that last wishes were carried out, and, perhaps most importantly, to make pious donations to the Church for the salvation of the testators’ souls. They chose their burial sites and arranged for funeral processions, and they endowed anniversary masses for their souls in perpetuity. Individual testamentary decisions differed, as did spousal strategies, but the reinforcement of family ties, even the assertion of relationship, was possible in wills.
2012-01-01T00:00:00ZThis volume seeks to investigate the testamentary practices of women in medieval and early modern France, examining the experience of a cross-section of the population, from artisans to the elite, in Aix-en-Provence, Avignon, Marseille, Montpellier, La Rochelle, Brittany, and Burgundy. The making of a will was perhaps the single most prominent moment in women’s lives for the assertion of agency. Though constrained to some degree by customary practice and the increasing influence of Roman law, women demonstrated remarkable initiative in the formulation of their last wishes. Wills permitted women to reward friendship and loyalty, to designate universal heirs as major beneficiaries, to stipulate conditions of inheritance so that last wishes were carried out, and, perhaps most importantly, to make pious donations to the Church for the salvation of the testators’ souls. They chose their burial sites and arranged for funeral processions, and they endowed anniversary masses for their souls in perpetuity. Individual testamentary decisions differed, as did spousal strategies, but the reinforcement of family ties, even the assertion of relationship, was possible in wills.Conservation ecology and phylogenetics of the Indus River dolphin (Platanista gangetica minor)Braulik, Gillian T.https://hdl.handle.net/10023/30362019-07-01T10:16:59Z2012-06-20T00:00:00ZThe historical range of the Indus River dolphin has declined by 80% since the 19th
century and has been fragmented into 17 river sections by construction of irrigation
barrages. Dolphin sighting and interview surveys showed that river dolphins persist in
six river sections, have been extirpated from ten, and are of unknown status in the
remaining section. Logistic regression and survival modelling showed that low dry
season river discharge was the primary factor responsible for the Indus dolphins range decline.
Abundance of the three largest Indus dolphin subpopulations was estimated using tandem vessel-based direct counts, corrected for missed animals using conditional likelihood
capture-recapture models. The entire subspecies was estimated to number between 1550-1750 in 2006. Dolphin encounter rates within the Guddu-Sukkur subpopulation (10.35/km) were the highest reported for any river dolphin and direct counts suggest that this subpopulation may have been increasing in abundance since the 1970s when hunting was banned.
The dry season habitat selection of Indus dolphins was explored using Generalised
Linear Models of dolphin distribution and abundance in relation to river geomorphology,
and channel geometry in cross-section. Channel cross-sectional area was shown to be
the most important factor determining dolphin presence. Indus dolphins avoided
channels with small cross-sectional area <700m2, presumably due to the risk of
entrapment and reduced foraging opportunities.
The phylogenetics of Indus and Ganges River dolphins was explored using Mitochondrial control region sequences. Genetic diversity was low, and all 20 Indus River dolphin samples were identical. There were no haplotypes shared by Indus and Ganges River dolphins, phylogenetic trees demonstrated reciprocal monophyletic separation and Bayesian modelling suggested that the two dolphin populations diverged approximately 0.66 million years ago.
Declining river flows threaten Indus dolphins especially at the upstream end of their range, and it is important to determine how much water is required to sustain a dolphin population through the dry season. Fisheries interactions are an increasing problem that will be best addressed through localised, community-based conservation activities.
2012-06-20T00:00:00ZBraulik, Gillian T.The historical range of the Indus River dolphin has declined by 80% since the 19th
century and has been fragmented into 17 river sections by construction of irrigation
barrages. Dolphin sighting and interview surveys showed that river dolphins persist in
six river sections, have been extirpated from ten, and are of unknown status in the
remaining section. Logistic regression and survival modelling showed that low dry
season river discharge was the primary factor responsible for the Indus dolphins range decline.
Abundance of the three largest Indus dolphin subpopulations was estimated using tandem vessel-based direct counts, corrected for missed animals using conditional likelihood
capture-recapture models. The entire subspecies was estimated to number between 1550-1750 in 2006. Dolphin encounter rates within the Guddu-Sukkur subpopulation (10.35/km) were the highest reported for any river dolphin and direct counts suggest that this subpopulation may have been increasing in abundance since the 1970s when hunting was banned.
The dry season habitat selection of Indus dolphins was explored using Generalised
Linear Models of dolphin distribution and abundance in relation to river geomorphology,
and channel geometry in cross-section. Channel cross-sectional area was shown to be
the most important factor determining dolphin presence. Indus dolphins avoided
channels with small cross-sectional area <700m2, presumably due to the risk of
entrapment and reduced foraging opportunities.
The phylogenetics of Indus and Ganges River dolphins was explored using Mitochondrial control region sequences. Genetic diversity was low, and all 20 Indus River dolphin samples were identical. There were no haplotypes shared by Indus and Ganges River dolphins, phylogenetic trees demonstrated reciprocal monophyletic separation and Bayesian modelling suggested that the two dolphin populations diverged approximately 0.66 million years ago.
Declining river flows threaten Indus dolphins especially at the upstream end of their range, and it is important to determine how much water is required to sustain a dolphin population through the dry season. Fisheries interactions are an increasing problem that will be best addressed through localised, community-based conservation activities.Evolution of signal multiplexing by 14-3-3-binding 2R-ohnologue protein families in the vertebratesTinti, MicheleJohnson, CatherineToth, RachelFerrier, David Ellard KeithMacKintosh, Carolhttps://hdl.handle.net/10023/30222022-04-07T08:30:34Z2012-07-01T00:00:00Z14-3-3 proteins regulate cellular responses to stimuli by docking onto pairs of phosphorylated residues on target proteins. The present study shows that the human 14-3-3-binding phosphoproteome is highly enriched in 2R-ohnologues, which are proteins in families of two to four members that were generated by two rounds of whole genome duplication at the origin of the vertebrates. We identify 2R-ohnologue families whose members share a ‘lynchpin’, defined as a 14-3-3-binding phosphosite that is conserved across members of a given family, and aligns with a Ser/Thr residue in pro-orthologues from the invertebrate chordates. For example, the human receptor expression enhancing protein (REEP) 1–4 family has the commonest type of lynchpin motif in current datasets, with a phosphorylatable serine in the –2 position relative to the 14-3-3-binding phosphosite. In contrast, the second 14-3-3-binding sites of REEPs 1–4 differ and are phosphorylated by different kinases, and hence the REEPs display different affinities for 14-3-3 dimers. We suggest a conceptual model for intracellular regulation involving protein families whose evolution into signal multiplexing systems was facilitated by 14-3-3 dimer binding to lynchpins, which gave freedom for other regulatory sites to evolve. While increased signalling complexity was needed for vertebrate life, these systems also generate vulnerability to genetic disorders.
This work was supported by the UK Medical Research Council via a Developmental Pathway Funding Scheme award and a Research Councils UK fellowship in marine biology.
2012-07-01T00:00:00ZTinti, MicheleJohnson, CatherineToth, RachelFerrier, David Ellard KeithMacKintosh, Carol14-3-3 proteins regulate cellular responses to stimuli by docking onto pairs of phosphorylated residues on target proteins. The present study shows that the human 14-3-3-binding phosphoproteome is highly enriched in 2R-ohnologues, which are proteins in families of two to four members that were generated by two rounds of whole genome duplication at the origin of the vertebrates. We identify 2R-ohnologue families whose members share a ‘lynchpin’, defined as a 14-3-3-binding phosphosite that is conserved across members of a given family, and aligns with a Ser/Thr residue in pro-orthologues from the invertebrate chordates. For example, the human receptor expression enhancing protein (REEP) 1–4 family has the commonest type of lynchpin motif in current datasets, with a phosphorylatable serine in the –2 position relative to the 14-3-3-binding phosphosite. In contrast, the second 14-3-3-binding sites of REEPs 1–4 differ and are phosphorylated by different kinases, and hence the REEPs display different affinities for 14-3-3 dimers. We suggest a conceptual model for intracellular regulation involving protein families whose evolution into signal multiplexing systems was facilitated by 14-3-3 dimer binding to lynchpins, which gave freedom for other regulatory sites to evolve. While increased signalling complexity was needed for vertebrate life, these systems also generate vulnerability to genetic disorders.Polarities of difference : how Wapichannao negotiate identities within a creole stateHope, Stacy A. A.https://hdl.handle.net/10023/30182019-04-01T11:09:54Z2011-01-01T00:00:00ZThis thesis is an ethnographic account of how the Wapichannao, who are situated in the
Rupununi of Guyana perceive themselves within the nation-state. This is also an account
of how non-Amerindian Guyanese envisage Amerindians as ‘past’ peoples. Hence,
distinctions are made between Amerindian and non-Amerindian—us vs. them—where
both identities become placed as opposite poles within a continuum.
Emphasis is placed on the shifting relationships between these poles, but more
specifically, the cultural paradigm through which these relationships are made possible.
This paradigm, I suggest, may be understood in terms of polarities of difference, with
regard to which Amerindians are constantly ambiguating/negotiating, disjoining, and
resignifying notions of ‘who they are’.
This thesis evidences this paradigm through an ethnography of some of those aspects of
Wapichannao culture—village work, the shop, joking activity, culture shows—that are
considered to be traditional on the one hand, and modern on the other. In doing so, an
incongruous trend emerges, on which makes the classic imagery of Amerindian
ontological homogeneity much more complex. Therefore, this thesis moves from the
more traditional aspects of Wapichannao culture towards the nation-state, in order to
take into account aspects of Amerindian experience absent from classic ethnographic
accounts.
2011-01-01T00:00:00ZHope, Stacy A. A.This thesis is an ethnographic account of how the Wapichannao, who are situated in the
Rupununi of Guyana perceive themselves within the nation-state. This is also an account
of how non-Amerindian Guyanese envisage Amerindians as ‘past’ peoples. Hence,
distinctions are made between Amerindian and non-Amerindian—us vs. them—where
both identities become placed as opposite poles within a continuum.
Emphasis is placed on the shifting relationships between these poles, but more
specifically, the cultural paradigm through which these relationships are made possible.
This paradigm, I suggest, may be understood in terms of polarities of difference, with
regard to which Amerindians are constantly ambiguating/negotiating, disjoining, and
resignifying notions of ‘who they are’.
This thesis evidences this paradigm through an ethnography of some of those aspects of
Wapichannao culture—village work, the shop, joking activity, culture shows—that are
considered to be traditional on the one hand, and modern on the other. In doing so, an
incongruous trend emerges, on which makes the classic imagery of Amerindian
ontological homogeneity much more complex. Therefore, this thesis moves from the
more traditional aspects of Wapichannao culture towards the nation-state, in order to
take into account aspects of Amerindian experience absent from classic ethnographic
accounts.Neural events underlying escape swimming behaviour in the squat lobster 'Galathea strigosa' (Crustacea, Anomura)Sillar, Keith T. (Keith Thomas)https://hdl.handle.net/10023/29752019-04-01T11:10:42Z1984-01-01T00:00:00Z1. The anatomy and physiology of escape swimming behaviour in the
squat lobster, Galathea strigosa, have been investigated and
the results discussed in the context of comparative mechanisms
of escape in rela~ed species.
2. In contrast to many other decapods, G. strigosa, does not possess
a giant-fibre system which underlies escape.
3. In terms of the number, size and position of neuronal somata,
the fast flexor motorneuron pools in Galathea and crayfish are
homologous.
4. A neuron, homologous with the crayfish MeG, has been studied.
Unlike the crayfish neuron, MoGH is a typical, unspecialized
fast flexor motorneuron.
5. The anatomy of afferent and efferent neurons involved in abdominal
extension has been investigated. The extensor motorneuron and
accessory neuron pools in crayfish and Galathea are largely
homologous.
6. A small degree of intersegmental and interspecific variation
in abdominal flexor and extensor motorneuron pools is reported.
7. The anatomy and physiology of the abdominal MRO's has been examined.
These are found to be homologous in structure and function with
other decapod MRO's.
8. The considerable differences between the phasic and tonic MRO
sensory dendrites may account for their different response characteristics.
9. The MRO's excite both extensor motorneurons and the flexor inhibitor
motorneuron via an apparently monosynaptic pathway. Similar
input properties have been described for the crayfish MHO's .
10. The MRO's, which are shown to fire in response to abdominal flexion,
produce EPSP's in extensor motorneurons which both summate and
facilitate. This feature has not been decribed previously and
may be important in the reflex function of the MHO's during escape
swimming behaviour.
11. The relative roles of proprioceptive and exteroceptive feedback
on the generation of the swimming rhythm have been studied using
a variety of preparations involving restraint and deafferenta-
tion.
12. Sensory feedback both excites and inhibits swimming. It is deduced
that proprioceptive feedback has excitatory effects and extero-
ceptive feedback inhibits swimming behaviour.
13. It is suggested that the MHO's may playa role in exciting the
neural circuits underlying swimming bewvbur via both direct
connections with the thoracic nervous system and a restricted
portion of the abdominal motorneuron pool.
14. A deafferented preparation has been used to analyse the motor
programme underlying swimming behaviour. The ability to record
swimming activity, identical with that recorded in the intact
animal, in the absence of sensory feedback from the abdomen,
suggests that swimming behaviour is controlled by a central pattern
generator (CPG).
15. A method of inducing swimming activity by high frequency electrical-
stimulation of abdominal sensori-motor roots is described.
16. The CPG for swimming behaviour is shown to be most likely to
reside in the suboesophageal or thoracic ganglion.
17. The activity of flexor and extensor motorneurons in abdominal
ganglia has been analysed at the cellular level using both extra-
cellular and intracellular recording techniques.
18. Fast flexor motorneurons are driven by a combination of brief
unitary synaptic potentials and a large underlying oscillatory
slow wave depolarization.
19. Current injection into the somata of fast flexor motorneurons
during swimming has dramatic effects on slow wave amplitude and
suggests that motorneuron drive results from powerful periodic
excitation via chemical synapses.
20. In contrast to the fast flexor motorneurons, fast extensor
motorneurons are driven by only brief unitary synaptic potentials
and not by an underlying slow wave depolarization. The contrasting
mechanisms for excitation in antagonistic sets of motorneurons
is documented and a possible explanation presented.
21. Among the fast extensor motorneurons there is an apparent gradation
in spike thresholds which can be correlated with a gradation
in soma diameter. The largest of the available pool of extensor
motorneurons has the highest spike threshold.
22. The activity of the phasic inhibitors of the extensor and flexor
muscles has been analysed. The extensor inhibitor, which fires
in antiphase with other extensor motorneurons during the flexion
phase of the swim cycle, appears to receive the same slow wave
depolarization as fast flexor motorneurons. The extensor inibitor
motorneuron burst is terminated by a high frequency barrage of
IPSP's superimposed upon the membrane slow wave. The flexor
inhibitor motorneuron receives complex excitation and inhibition
during swimming, involving both unitary events and membrane waves.
23. The coordination of segmented limb structures during swimming
has been investigated. The walking legs are physically protracted
during flexion while the unmodified male swimmerets are flicked
posteriorly.
24. Swimmeret retraction during swimming is controlled by the activity
of a single swimmeret motorneuron which appears to be part of
the swimming circuit and which may also be a primitive homologue
of the Segmental Giant neuron in crayfish.
25. It is concluded that escape swimming behaviour is homologous
with non-giant backwards swimming in crayfish and may also be
homologous with swimming in certain sand crab species. The
evolutionary relationships of a number of decapods is discussed
on the basis of escape circuitry and it is suggested that Galathea
may represent an ancestral type of swimming decapod.
1984-01-01T00:00:00ZSillar, Keith T. (Keith Thomas)1. The anatomy and physiology of escape swimming behaviour in the
squat lobster, Galathea strigosa, have been investigated and
the results discussed in the context of comparative mechanisms
of escape in rela~ed species.
2. In contrast to many other decapods, G. strigosa, does not possess
a giant-fibre system which underlies escape.
3. In terms of the number, size and position of neuronal somata,
the fast flexor motorneuron pools in Galathea and crayfish are
homologous.
4. A neuron, homologous with the crayfish MeG, has been studied.
Unlike the crayfish neuron, MoGH is a typical, unspecialized
fast flexor motorneuron.
5. The anatomy of afferent and efferent neurons involved in abdominal
extension has been investigated. The extensor motorneuron and
accessory neuron pools in crayfish and Galathea are largely
homologous.
6. A small degree of intersegmental and interspecific variation
in abdominal flexor and extensor motorneuron pools is reported.
7. The anatomy and physiology of the abdominal MRO's has been examined.
These are found to be homologous in structure and function with
other decapod MRO's.
8. The considerable differences between the phasic and tonic MRO
sensory dendrites may account for their different response characteristics.
9. The MRO's excite both extensor motorneurons and the flexor inhibitor
motorneuron via an apparently monosynaptic pathway. Similar
input properties have been described for the crayfish MHO's .
10. The MRO's, which are shown to fire in response to abdominal flexion,
produce EPSP's in extensor motorneurons which both summate and
facilitate. This feature has not been decribed previously and
may be important in the reflex function of the MHO's during escape
swimming behaviour.
11. The relative roles of proprioceptive and exteroceptive feedback
on the generation of the swimming rhythm have been studied using
a variety of preparations involving restraint and deafferenta-
tion.
12. Sensory feedback both excites and inhibits swimming. It is deduced
that proprioceptive feedback has excitatory effects and extero-
ceptive feedback inhibits swimming behaviour.
13. It is suggested that the MHO's may playa role in exciting the
neural circuits underlying swimming bewvbur via both direct
connections with the thoracic nervous system and a restricted
portion of the abdominal motorneuron pool.
14. A deafferented preparation has been used to analyse the motor
programme underlying swimming behaviour. The ability to record
swimming activity, identical with that recorded in the intact
animal, in the absence of sensory feedback from the abdomen,
suggests that swimming behaviour is controlled by a central pattern
generator (CPG).
15. A method of inducing swimming activity by high frequency electrical-
stimulation of abdominal sensori-motor roots is described.
16. The CPG for swimming behaviour is shown to be most likely to
reside in the suboesophageal or thoracic ganglion.
17. The activity of flexor and extensor motorneurons in abdominal
ganglia has been analysed at the cellular level using both extra-
cellular and intracellular recording techniques.
18. Fast flexor motorneurons are driven by a combination of brief
unitary synaptic potentials and a large underlying oscillatory
slow wave depolarization.
19. Current injection into the somata of fast flexor motorneurons
during swimming has dramatic effects on slow wave amplitude and
suggests that motorneuron drive results from powerful periodic
excitation via chemical synapses.
20. In contrast to the fast flexor motorneurons, fast extensor
motorneurons are driven by only brief unitary synaptic potentials
and not by an underlying slow wave depolarization. The contrasting
mechanisms for excitation in antagonistic sets of motorneurons
is documented and a possible explanation presented.
21. Among the fast extensor motorneurons there is an apparent gradation
in spike thresholds which can be correlated with a gradation
in soma diameter. The largest of the available pool of extensor
motorneurons has the highest spike threshold.
22. The activity of the phasic inhibitors of the extensor and flexor
muscles has been analysed. The extensor inhibitor, which fires
in antiphase with other extensor motorneurons during the flexion
phase of the swim cycle, appears to receive the same slow wave
depolarization as fast flexor motorneurons. The extensor inibitor
motorneuron burst is terminated by a high frequency barrage of
IPSP's superimposed upon the membrane slow wave. The flexor
inhibitor motorneuron receives complex excitation and inhibition
during swimming, involving both unitary events and membrane waves.
23. The coordination of segmented limb structures during swimming
has been investigated. The walking legs are physically protracted
during flexion while the unmodified male swimmerets are flicked
posteriorly.
24. Swimmeret retraction during swimming is controlled by the activity
of a single swimmeret motorneuron which appears to be part of
the swimming circuit and which may also be a primitive homologue
of the Segmental Giant neuron in crayfish.
25. It is concluded that escape swimming behaviour is homologous
with non-giant backwards swimming in crayfish and may also be
homologous with swimming in certain sand crab species. The
evolutionary relationships of a number of decapods is discussed
on the basis of escape circuitry and it is suggested that Galathea
may represent an ancestral type of swimming decapod.Physical, biological and cultural factors influencing the formation, stabilisation and protection of archaeological deposits in U.K. coastal watersFerrari, Benhttps://hdl.handle.net/10023/29712019-04-01T11:10:43Z1995-01-01T00:00:00ZA considerable corpus of information regarding the formation of
terrestrial archaeological deposits exists which is not matched by
studies of deposit formation in coastal waters. Similarly, there is a
disjunction between strident calls for minimal disturbance
investigation, with conservation in situ, and knowledge of how this
might actually be achieved in the marine environment.
The manner in which the investigation of deposit formation can
complement the study of in situ conservation is considered An
approach is proposed which combines selected elements of Schiffer's
Transformation Theory with a method of studying changes to
deposits outlined by Wildesen. It is suggested that, although
sufficient regularities can be detected in the influence of formation
processes to allow their influence to be recognised and inference
refined accordingly, there are case specific limitations on the extent
to which the precise influence of each process can be described and
evaluated.
A case study is presented which investigates casual depredation as a
formation process. Commercial fishing activity and marine
burrowing activity are the subject of detailed consideration. New
insights into these processes result from this study and specific
recommendations concerning in situ conservation of deposits subject
to their influence are made. The need to consider fishing practice as
well as the mechanical properties of fishing gear in the study of
deposit formation and protection is emphasised. The excavation of a
16th century wreck in Studland Bay, Dorset, is used to demonstrate
the pervasive influence of burrowing activity and the problems
associated with mitigation of this process. Recommendations are
made regarding future study of formation processes and the
development of policy related to the management of the submerged
archaeological resource.
1995-01-01T00:00:00ZFerrari, BenA considerable corpus of information regarding the formation of
terrestrial archaeological deposits exists which is not matched by
studies of deposit formation in coastal waters. Similarly, there is a
disjunction between strident calls for minimal disturbance
investigation, with conservation in situ, and knowledge of how this
might actually be achieved in the marine environment.
The manner in which the investigation of deposit formation can
complement the study of in situ conservation is considered An
approach is proposed which combines selected elements of Schiffer's
Transformation Theory with a method of studying changes to
deposits outlined by Wildesen. It is suggested that, although
sufficient regularities can be detected in the influence of formation
processes to allow their influence to be recognised and inference
refined accordingly, there are case specific limitations on the extent
to which the precise influence of each process can be described and
evaluated.
A case study is presented which investigates casual depredation as a
formation process. Commercial fishing activity and marine
burrowing activity are the subject of detailed consideration. New
insights into these processes result from this study and specific
recommendations concerning in situ conservation of deposits subject
to their influence are made. The need to consider fishing practice as
well as the mechanical properties of fishing gear in the study of
deposit formation and protection is emphasised. The excavation of a
16th century wreck in Studland Bay, Dorset, is used to demonstrate
the pervasive influence of burrowing activity and the problems
associated with mitigation of this process. Recommendations are
made regarding future study of formation processes and the
development of policy related to the management of the submerged
archaeological resource.A taste of movement : an exploration of the social ethics of the Tsimanes of lowland BoliviaEllis, Rebeccahttps://hdl.handle.net/10023/29012019-04-01T11:09:52Z1997-01-01T00:00:00ZThis thesis explores Tsimane understandings and creations of varying forms of sociality. Each chapter addresses different but related issues concerning sociality. Fieldwork was carried out in three riverine settlements over the period from December 1991 to August 1994.
The thesis shows that sociality is created and perpetuated by individuals as a processual endeavour, and does not amount to a tangible structure predicated upon fixed social relationships. Community in a physically bound sense is not found amongst the Tsimanes. Given forms of sociality are shown to rest more upon an appropriateness or inappropriateness of mood or affectivity. These are created and effected by subtle details of each individual’s presence amongst others. Social presence is understood by the Tsimanes as both potentially nurturant and predatory.
Tsimanes are explicit about their ideas of preferred and abhorred social presence and behaviour of human and non-human others. This thesis explores ways in which such ideas are articulated to create a discourse on social ethics. A Tsimane aesthetics of social living carries with it practical implications for creating and perpetuating forms of sociality.
An underlying theme of the thesis is one of mobility and the oscillating nature of Tsimane movements between different groups of kin and affines, and between moods and forms of sociality. I demonstrate that the high value placed by the Tsimanes upon movement, and the enjoyment they experience from it, most efficiently enable the achievement of correct social existence. A lack of knowledge and intention, ultimately resulting in illness and death, are principally deemed to occur as a result of immobility.
1997-01-01T00:00:00ZEllis, RebeccaThis thesis explores Tsimane understandings and creations of varying forms of sociality. Each chapter addresses different but related issues concerning sociality. Fieldwork was carried out in three riverine settlements over the period from December 1991 to August 1994.
The thesis shows that sociality is created and perpetuated by individuals as a processual endeavour, and does not amount to a tangible structure predicated upon fixed social relationships. Community in a physically bound sense is not found amongst the Tsimanes. Given forms of sociality are shown to rest more upon an appropriateness or inappropriateness of mood or affectivity. These are created and effected by subtle details of each individual’s presence amongst others. Social presence is understood by the Tsimanes as both potentially nurturant and predatory.
Tsimanes are explicit about their ideas of preferred and abhorred social presence and behaviour of human and non-human others. This thesis explores ways in which such ideas are articulated to create a discourse on social ethics. A Tsimane aesthetics of social living carries with it practical implications for creating and perpetuating forms of sociality.
An underlying theme of the thesis is one of mobility and the oscillating nature of Tsimane movements between different groups of kin and affines, and between moods and forms of sociality. I demonstrate that the high value placed by the Tsimanes upon movement, and the enjoyment they experience from it, most efficiently enable the achievement of correct social existence. A lack of knowledge and intention, ultimately resulting in illness and death, are principally deemed to occur as a result of immobility.Space, time and harmony : symbolic aspects of language in Andean textiles with special reference to those from Bolivar Province (Cochabamba, Bolivia).Crickmay, Lindseyhttps://hdl.handle.net/10023/28762019-04-01T11:09:59Z1992-01-01T00:00:00ZThe thesis investigates how the designs woven in Andean textiles make up a symbolic language which both communicates information about those who wear them and demonstrates their desire to balance the opposing forces which are believed to govern their world. All textile elements share this communicative function and the thesis examines the significance of spin, colour and layout in the textile as a whole and in the individual designs. Textile terminology is drawn from fieldwork, the literature and from early Aymara and Quechua lexicons. The contemporary designs examined were personally observed in Bolivar in 1982/3 and 1986; the thesis suggests their derivation from colonial designs and discusses their possible iconographic content.
Part one shows the significance of clothing as a statement of identity and describes briefly the weaving techniques and figures typical of the Bolivar area. Part two shows how cloth is seen as a vital, three-dimensional object and how in weaving as in the other plastic arts designs are encoded with abstract concepts fundamental to the traditions of a social group.
Part three examines how certain colour combinations represent social, political or cosmic tensions and how their arrangement attempts to manipulate and control the energy generated by them. In particular it investigates how colour represents the circulation of suerte, or fortune, many of the names of which are also terms for colour combinations similar to those used in textiles. It also shows how specific elements such as stripes and figured designs act as metaphors through which the textile becomes a map or record of social, ritual and cosmic space.
1992-01-01T00:00:00ZCrickmay, LindseyThe thesis investigates how the designs woven in Andean textiles make up a symbolic language which both communicates information about those who wear them and demonstrates their desire to balance the opposing forces which are believed to govern their world. All textile elements share this communicative function and the thesis examines the significance of spin, colour and layout in the textile as a whole and in the individual designs. Textile terminology is drawn from fieldwork, the literature and from early Aymara and Quechua lexicons. The contemporary designs examined were personally observed in Bolivar in 1982/3 and 1986; the thesis suggests their derivation from colonial designs and discusses their possible iconographic content.
Part one shows the significance of clothing as a statement of identity and describes briefly the weaving techniques and figures typical of the Bolivar area. Part two shows how cloth is seen as a vital, three-dimensional object and how in weaving as in the other plastic arts designs are encoded with abstract concepts fundamental to the traditions of a social group.
Part three examines how certain colour combinations represent social, political or cosmic tensions and how their arrangement attempts to manipulate and control the energy generated by them. In particular it investigates how colour represents the circulation of suerte, or fortune, many of the names of which are also terms for colour combinations similar to those used in textiles. It also shows how specific elements such as stripes and figured designs act as metaphors through which the textile becomes a map or record of social, ritual and cosmic space.The implications of manioc cultivation in the culture and mythology of the Machiguenga of South Eastern PeruLewington, Annahttps://hdl.handle.net/10023/28682019-07-01T10:11:31Z1986-01-01T00:00:00ZThe aim of this thesis is to effect an introduction to the place of manioc (Manihot esculenta Crantz) in the culture of the Machiguenga Indians of the Peruvian rain forest. The main substance of my work finds its focus in a myth, the narrative of which was recorded during fieldwork on location in the Urubamba region of south east Peru. My thesis will attempt to examine the role of manioc and the justification of its description as a ‘sacred plant’ to the Machiguenga.
The evidence I put forward to demonstrate the significance of manioc comes under the following headings:
a) manioc cultivation and dietary uses,
b) manioc plant taxonomy,
c) the manioc myth itself, which I have transcribed and translated from my recordings.
Whilst the anthropological structures of the myth are examined, no attempt will be made to deal in detail with the vocabulary and morphology of the Machiguenga language. Whilst conceding that it is vital to show the connection between the material use of manioc and the belief structure surrounding it, material already collected would suggest a more ambitious piece of work than a Master of Philosophy degree would allow, and I hope in the future to undertake full-scale investigation into this largely untouched aspect of Machiguenga social and religious organization. The present work aims only at an introduction to the people and their use of manioc, and the presentation of the manioc myth.
1986-01-01T00:00:00ZLewington, AnnaThe aim of this thesis is to effect an introduction to the place of manioc (Manihot esculenta Crantz) in the culture of the Machiguenga Indians of the Peruvian rain forest. The main substance of my work finds its focus in a myth, the narrative of which was recorded during fieldwork on location in the Urubamba region of south east Peru. My thesis will attempt to examine the role of manioc and the justification of its description as a ‘sacred plant’ to the Machiguenga.
The evidence I put forward to demonstrate the significance of manioc comes under the following headings:
a) manioc cultivation and dietary uses,
b) manioc plant taxonomy,
c) the manioc myth itself, which I have transcribed and translated from my recordings.
Whilst the anthropological structures of the myth are examined, no attempt will be made to deal in detail with the vocabulary and morphology of the Machiguenga language. Whilst conceding that it is vital to show the connection between the material use of manioc and the belief structure surrounding it, material already collected would suggest a more ambitious piece of work than a Master of Philosophy degree would allow, and I hope in the future to undertake full-scale investigation into this largely untouched aspect of Machiguenga social and religious organization. The present work aims only at an introduction to the people and their use of manioc, and the presentation of the manioc myth.Green index in semigroups : generators, presentations and automatic structuresCain, A.J.Gray, RRuskuc, Nikhttps://hdl.handle.net/10023/27602023-04-18T09:42:52Z2012-01-01T00:00:00ZThe Green index of a subsemigroup T of a semigroup S is given by counting strong orbits in the complement S n T under the natural actions of T on S via right and left multiplication. This partitions the complement S nT into T-relative H -classes, in the sense of Wallace, and with each such class there is a naturally associated group called the relative Schützenberger group. If the Rees index ΙS n TΙ is finite, T also has finite Green index in S. If S is a group and T a subgroup then T has finite Green index in S if and only if it has finite group index in S. Thus Green index provides a common generalisation of Rees index and group index. We prove a rewriting theorem which shows how generating sets for S may be used to obtain generating sets for T and the Schützenberger groups, and vice versa. We also give a method for constructing a presentation for S from given presentations of T and the Schützenberger groups. These results are then used to show that several important properties are preserved when passing to finite Green index subsemigroups or extensions, including: finite generation, solubility of the word problem, growth type, automaticity (for subsemigroups), finite presentability (for extensions) and finite Malcev presentability (in the case of group-embeddable semigroups).
2012-01-01T00:00:00ZCain, A.J.Gray, RRuskuc, NikThe Green index of a subsemigroup T of a semigroup S is given by counting strong orbits in the complement S n T under the natural actions of T on S via right and left multiplication. This partitions the complement S nT into T-relative H -classes, in the sense of Wallace, and with each such class there is a naturally associated group called the relative Schützenberger group. If the Rees index ΙS n TΙ is finite, T also has finite Green index in S. If S is a group and T a subgroup then T has finite Green index in S if and only if it has finite group index in S. Thus Green index provides a common generalisation of Rees index and group index. We prove a rewriting theorem which shows how generating sets for S may be used to obtain generating sets for T and the Schützenberger groups, and vice versa. We also give a method for constructing a presentation for S from given presentations of T and the Schützenberger groups. These results are then used to show that several important properties are preserved when passing to finite Green index subsemigroups or extensions, including: finite generation, solubility of the word problem, growth type, automaticity (for subsemigroups), finite presentability (for extensions) and finite Malcev presentability (in the case of group-embeddable semigroups).Perception of relative depth interval : Systematic biases in perceived depthHarris, JulieChopin, AdrienZeiner, Katharina MariaHibbard, Paul Barryhttps://hdl.handle.net/10023/27492022-07-08T10:30:03Z2012-01-01T00:00:00ZGiven an estimate of the binocular disparity between a pair of points and an estimate of the viewing distance, or knowledge of eye position, it should be possible to obtain an estimate of their depth separation. Here we show that, when points are arranged in different vertical geometric configurations across two intervals, many observers find this task difficult. Those who can do the task tend to perceive the depth interval in one configuration as very different from depth in the other configuration. We explore two plausible explanations for this effect. The first is the tilt of the empirical vertical horopter: Points perceived along an apparently vertical line correspond to a physical line of points tilted backwards in space. Second, the eyes can rotate in response to a particular stimulus. Without compensation for this rotation, biases in depth perception would result. We measured cyclovergence indirectly, using a standard psychophysical task, while observers viewed our depth configuration. Biases predicted from error due either to cyclovergence or to the tilted vertical horopter were not consistent with the depth configuration results. Our data suggest that, even for the simplest scenes, we do not have ready access to metric depth from binocular disparity.
2012-01-01T00:00:00ZHarris, JulieChopin, AdrienZeiner, Katharina MariaHibbard, Paul BarryGiven an estimate of the binocular disparity between a pair of points and an estimate of the viewing distance, or knowledge of eye position, it should be possible to obtain an estimate of their depth separation. Here we show that, when points are arranged in different vertical geometric configurations across two intervals, many observers find this task difficult. Those who can do the task tend to perceive the depth interval in one configuration as very different from depth in the other configuration. We explore two plausible explanations for this effect. The first is the tilt of the empirical vertical horopter: Points perceived along an apparently vertical line correspond to a physical line of points tilted backwards in space. Second, the eyes can rotate in response to a particular stimulus. Without compensation for this rotation, biases in depth perception would result. We measured cyclovergence indirectly, using a standard psychophysical task, while observers viewed our depth configuration. Biases predicted from error due either to cyclovergence or to the tilted vertical horopter were not consistent with the depth configuration results. Our data suggest that, even for the simplest scenes, we do not have ready access to metric depth from binocular disparity.What visual information is used for stereoscopic depth displacement discrimination?Nefs, HaroldHarris, Juliehttps://hdl.handle.net/10023/27462023-04-18T09:43:04Z2010-01-01T00:00:00ZThere are two ways to detect a displacement in stereoscopic depth, namely by monitoring the change in disparity over time (CDOT) or by monitoring the inter-ocular velocity difference (IOVD). Though previous studies have attempted to understand which cue is most significant for the visual system, none have designed stimuli that provide a comparison in terms of relative efficiency between them. Here we used two-frame motion and random dot noise to deliver equivalent strengths of CDOT and IOVD information to the visual system. Using three kinds of random dot stimuli, we were able to isolate CDOT or IOVD or deliver both simultaneously. The proportion of dots delivering CDOT or IOVD signals could be varied, and we defined discrimination threshold as the proportion needed to detect the direction of displacement (towards or away)1. Thresholds were similar for stimuli containing CDOT only, and containing both CDOT and IOVD, but only one participant was able to consistently perceive the displacement for stimuli containing only IOVD. We also investigated the effect of disparity pedestals on discrimination. Performance was best when the displacement crossed the reference plane, but was not significantly different for stimuli containing CDOT only, or containing both CDOT and IOVD. When stimuli are specifically designed to provide equivalent two-frame motion or disparity-change, few participants can reliably detect displacement when IOVD is the only cue. This challenges the notion that IOVD is involved in the discrimination of direction of displacement in two-frame motion displays.
2010-01-01T00:00:00ZNefs, HaroldHarris, JulieThere are two ways to detect a displacement in stereoscopic depth, namely by monitoring the change in disparity over time (CDOT) or by monitoring the inter-ocular velocity difference (IOVD). Though previous studies have attempted to understand which cue is most significant for the visual system, none have designed stimuli that provide a comparison in terms of relative efficiency between them. Here we used two-frame motion and random dot noise to deliver equivalent strengths of CDOT and IOVD information to the visual system. Using three kinds of random dot stimuli, we were able to isolate CDOT or IOVD or deliver both simultaneously. The proportion of dots delivering CDOT or IOVD signals could be varied, and we defined discrimination threshold as the proportion needed to detect the direction of displacement (towards or away)1. Thresholds were similar for stimuli containing CDOT only, and containing both CDOT and IOVD, but only one participant was able to consistently perceive the displacement for stimuli containing only IOVD. We also investigated the effect of disparity pedestals on discrimination. Performance was best when the displacement crossed the reference plane, but was not significantly different for stimuli containing CDOT only, or containing both CDOT and IOVD. When stimuli are specifically designed to provide equivalent two-frame motion or disparity-change, few participants can reliably detect displacement when IOVD is the only cue. This challenges the notion that IOVD is involved in the discrimination of direction of displacement in two-frame motion displays.Pictures and interpretations : towards an applied semioticsBoot, Katiehttps://hdl.handle.net/10023/27102019-04-01T11:11:09Z1994-01-01T00:00:00ZThis is a study about the ways in which pictures can be interpreted and the
ways in which they are interpreted; the latter, specifically, in a relatively remote
part of Peru.
Chapter II reviews an assortment of picture tests which bring to light
differences in the ways pictures are perceived. Chapter III examines the specific
cultural context in which a fairly informal picture test was administered.
Chapter IV presents some results and asks what cultural and situational factors
may have contributed to the variety in interpretations evident.
The drawing of firm conclusions is precluded by the absence of any systematic
approach to the interpretations or to the pictures themselves, and it is this which
the second half of the study attempts to remedy; by providing a theoretical
framework for the assessment of verbalized responses to pictures.
Chapter V offers a definition of "picture" and locates it within a typology of
indices. It also examines the notion of "visual resemblance", eventually
adopting the view that any picture is infinitely ambiguous. Chapter VI
introduces two methodological necessities consequent on this ambiguity: a
stipulation as to the identity and the taxonomic specificity of any signified
object; and a stipulation as to the spatial extension of its signifier. No other
methodological content is presented. Chapter VII classifies types of verbalized
responses in terms of their visual motivation, and the degree to which they
interrelate the stipulated pictorial units. Chapter VIII acknowledges that
signification may continue beyond the representational level. Further, postrepresentational,
types of responses are classified in terms of the nature of the
link maintained with the representational signified.
1994-01-01T00:00:00ZBoot, KatieThis is a study about the ways in which pictures can be interpreted and the
ways in which they are interpreted; the latter, specifically, in a relatively remote
part of Peru.
Chapter II reviews an assortment of picture tests which bring to light
differences in the ways pictures are perceived. Chapter III examines the specific
cultural context in which a fairly informal picture test was administered.
Chapter IV presents some results and asks what cultural and situational factors
may have contributed to the variety in interpretations evident.
The drawing of firm conclusions is precluded by the absence of any systematic
approach to the interpretations or to the pictures themselves, and it is this which
the second half of the study attempts to remedy; by providing a theoretical
framework for the assessment of verbalized responses to pictures.
Chapter V offers a definition of "picture" and locates it within a typology of
indices. It also examines the notion of "visual resemblance", eventually
adopting the view that any picture is infinitely ambiguous. Chapter VI
introduces two methodological necessities consequent on this ambiguity: a
stipulation as to the identity and the taxonomic specificity of any signified
object; and a stipulation as to the spatial extension of its signifier. No other
methodological content is presented. Chapter VII classifies types of verbalized
responses in terms of their visual motivation, and the degree to which they
interrelate the stipulated pictorial units. Chapter VIII acknowledges that
signification may continue beyond the representational level. Further, postrepresentational,
types of responses are classified in terms of the nature of the
link maintained with the representational signified.The use of active sonar to study cetaceansBernasconi, Matteohttps://hdl.handle.net/10023/25802019-07-01T10:18:44Z2012-06-01T00:00:00ZCetacean species face serious challenges worldwide due to the increasing noise pollution brought to their environment by human activities such as seismic exploration. Regulation of these activities is vaguely defined and uncoordinated. Visual observations and passive listening devices, aimed at preventing conflicts between human wealth and cetaceans’ health have some fundamental limitations and may consequently fail their mitigation purposes. Active sonar technology could be the optimal solution to implement mitigation of such human activities. In my thesis, the proper sonar unit was used to test the feasibility to detect cetaceans in situ. Omnidirectional sonars could be the optimal solution to monitor the presence of cetaceans in the proximity of potential danger areas. To use this class of sonar in a quantitative manner, the first step was to develop a calibration method. This thesis links in situ measurements of target strength (TS) with variation trends linked to the behavior, morphology and physiology of cetacean. The butterfly effect of a cetacean’s body was described for a fin whale insonified from different angles. A relationship between whale respiration and TS energy peaks was tested through a simple prediction model which seems very promising for further implementation. The effect of lung compression on cetacean TS due to increasing depth was tested through a basic mathematical model. The model fit the in situ TS measurements. TS measurements at depth of a humpback whale, when post-processed, correspond to TS measurements recorded at the surface. Sonar technology is clearly capable of detecting whale foot prints around an operating vessel. Sonar frequency response shows that frequencies between 18 and 38 kHz should be employed. This work has established a baseline and raised new questions so that active sonar can be developed and employed in the best interest for the whales involved in potentially harmful conflicts with man.
2012-06-01T00:00:00ZBernasconi, MatteoCetacean species face serious challenges worldwide due to the increasing noise pollution brought to their environment by human activities such as seismic exploration. Regulation of these activities is vaguely defined and uncoordinated. Visual observations and passive listening devices, aimed at preventing conflicts between human wealth and cetaceans’ health have some fundamental limitations and may consequently fail their mitigation purposes. Active sonar technology could be the optimal solution to implement mitigation of such human activities. In my thesis, the proper sonar unit was used to test the feasibility to detect cetaceans in situ. Omnidirectional sonars could be the optimal solution to monitor the presence of cetaceans in the proximity of potential danger areas. To use this class of sonar in a quantitative manner, the first step was to develop a calibration method. This thesis links in situ measurements of target strength (TS) with variation trends linked to the behavior, morphology and physiology of cetacean. The butterfly effect of a cetacean’s body was described for a fin whale insonified from different angles. A relationship between whale respiration and TS energy peaks was tested through a simple prediction model which seems very promising for further implementation. The effect of lung compression on cetacean TS due to increasing depth was tested through a basic mathematical model. The model fit the in situ TS measurements. TS measurements at depth of a humpback whale, when post-processed, correspond to TS measurements recorded at the surface. Sonar technology is clearly capable of detecting whale foot prints around an operating vessel. Sonar frequency response shows that frequencies between 18 and 38 kHz should be employed. This work has established a baseline and raised new questions so that active sonar can be developed and employed in the best interest for the whales involved in potentially harmful conflicts with man.Replication of Bunyamwera virus in mosquito cellsSzemiel, Agnieszka M.https://hdl.handle.net/10023/25702019-07-01T10:11:49Z2011-01-01T00:00:00ZThe Bunyaviridae family is one of the largest among RNA viruses, comprising more
than 350 serologically distinct viruses. The family is classified into five genera,
Orthobunyavirus, Hantavirus, Nairovirus, Phlebovirus, and Tospovirus.
Orthobunyaviruses, nairoviruses and phleboviruses are maintained in nature by a
propagative cycle involving blood-feeding arthropods and susceptible vertebrate hosts.
Like most arthropod-borne viruses, bunyavirus replication causes little damage to the
vector, whereas infection of the mammalian host may lead to death. This situation is
mimicked in the laboratory: in cultured mosquito cells no cytopathology is observed
and a persistent infection is established, whereas in cultured mammalian cells
orthobunyavirus infection is lytic and leads to cell death.
Bunyaviruses encode four common structural proteins: an RNA-dependent RNA
polymerase, two glycoproteins (Gc and Gn), and a nucleoprotein N. Some viruses also
code for nonstructural proteins called NSm and NSs. The NSs protein of the prototype
bunyavirus, Bunyamwera virus, seems to be one of the factors responsible for the
different outcomes of infection in mammalian and mosquito cell lines. However, only
limited information is available on the growth of bunyaviruses in cultured mosquito cell
lines other than Aedes albopictus C6/36 cells. Here, I compared the replication of
Bunyamwera virus in two additional Aedes albopictus cell clones, C7-10 and U4.4, and
two Aedes aegypti cell clones, Ae and A20, and investigated the impact of virus
replication on cell function. In addition, whereas the vertebrate innate immune
response to arbovirus infection is well studied, relatively little is known about
mosquitoes’ reaction to these infections. I investigated the immune responses of the
different mosquito cells to Bunyamwera virus infection, in particular antimicrobial
signaling pathways (Toll and IMD) and RNA interference (RNAi). The data obtained in
U4.4 cells suggest that NSs plays an important role in the infection of mosquitoes.
Moreover infection of U4.4 cells more closely resembles infection in Ae and A20 cells
and live Aedes aegypti mosquitoes. My data showed that the investigated cell lines
have various properties, and therefore they can be used to study different aspects of
mosquito-virus interactions.
2011-01-01T00:00:00ZSzemiel, Agnieszka M.The Bunyaviridae family is one of the largest among RNA viruses, comprising more
than 350 serologically distinct viruses. The family is classified into five genera,
Orthobunyavirus, Hantavirus, Nairovirus, Phlebovirus, and Tospovirus.
Orthobunyaviruses, nairoviruses and phleboviruses are maintained in nature by a
propagative cycle involving blood-feeding arthropods and susceptible vertebrate hosts.
Like most arthropod-borne viruses, bunyavirus replication causes little damage to the
vector, whereas infection of the mammalian host may lead to death. This situation is
mimicked in the laboratory: in cultured mosquito cells no cytopathology is observed
and a persistent infection is established, whereas in cultured mammalian cells
orthobunyavirus infection is lytic and leads to cell death.
Bunyaviruses encode four common structural proteins: an RNA-dependent RNA
polymerase, two glycoproteins (Gc and Gn), and a nucleoprotein N. Some viruses also
code for nonstructural proteins called NSm and NSs. The NSs protein of the prototype
bunyavirus, Bunyamwera virus, seems to be one of the factors responsible for the
different outcomes of infection in mammalian and mosquito cell lines. However, only
limited information is available on the growth of bunyaviruses in cultured mosquito cell
lines other than Aedes albopictus C6/36 cells. Here, I compared the replication of
Bunyamwera virus in two additional Aedes albopictus cell clones, C7-10 and U4.4, and
two Aedes aegypti cell clones, Ae and A20, and investigated the impact of virus
replication on cell function. In addition, whereas the vertebrate innate immune
response to arbovirus infection is well studied, relatively little is known about
mosquitoes’ reaction to these infections. I investigated the immune responses of the
different mosquito cells to Bunyamwera virus infection, in particular antimicrobial
signaling pathways (Toll and IMD) and RNA interference (RNAi). The data obtained in
U4.4 cells suggest that NSs plays an important role in the infection of mosquitoes.
Moreover infection of U4.4 cells more closely resembles infection in Ae and A20 cells
and live Aedes aegypti mosquitoes. My data showed that the investigated cell lines
have various properties, and therefore they can be used to study different aspects of
mosquito-virus interactions.The Bernese disputations of 1532 and 1538 : a historical and theological analysisEccher, Stephen Bretthttps://hdl.handle.net/10023/25662019-04-01T11:12:34Z2011-11-01T00:00:00ZGiven the relative paucity of treatments relating to both the 1532 and 1538 Bern Gespräche, alongside a growing historiography which has offered a clearer understanding of the backdrop around which these two debates were held, the focus of this research project will be to provide a comparative analysis of the recorded dialogues from the debates at Bern. This ecclesiologically focused comparison aims to discern whether the debate relating to the nature of the church at the 1538 session was merely a redundant exercise and continuation of the earlier 1532 disputation or whether the latter debate offered anything substantively new to the ongoing religious dialogue between these two groups. Furthermore, all of the respective views on the nature of the church manifest in these debates will be examined in light of the preceding Anabaptist/Reformed dialogue of the period to determine their place contextually.
Having embarked upon the aforementioned goals several conclusions may be definitively drawn. First, the major ecclesiological suppositions expressed by both the Anabaptist and Reformed participants at the 1538 debate were, in fact, retained using the same core theological elements employed by their predecessors at the 1532 debate. Yet, despite this striking similarity, the independent nature of these debates must also be acknowledged. This may primarily be found in that both groups expressed their retained ecclesiologies with notable variation in things such as language, argumentative content, biblical corroboration, and illustrative evidence. Finally, both the similar and independent nature of these events will be shown to have been largely derived from the Anabaptist/Reformed dialogue already begun as the Swiss Brethren movement emerged from under Zwingli’s reform efforts in Zürich. Each of these conclusions should help to paint a more accurate portrait of not only what was accomplished through these debates, but where each stands contextually during the period.
2011-11-01T00:00:00ZEccher, Stephen BrettGiven the relative paucity of treatments relating to both the 1532 and 1538 Bern Gespräche, alongside a growing historiography which has offered a clearer understanding of the backdrop around which these two debates were held, the focus of this research project will be to provide a comparative analysis of the recorded dialogues from the debates at Bern. This ecclesiologically focused comparison aims to discern whether the debate relating to the nature of the church at the 1538 session was merely a redundant exercise and continuation of the earlier 1532 disputation or whether the latter debate offered anything substantively new to the ongoing religious dialogue between these two groups. Furthermore, all of the respective views on the nature of the church manifest in these debates will be examined in light of the preceding Anabaptist/Reformed dialogue of the period to determine their place contextually.
Having embarked upon the aforementioned goals several conclusions may be definitively drawn. First, the major ecclesiological suppositions expressed by both the Anabaptist and Reformed participants at the 1538 debate were, in fact, retained using the same core theological elements employed by their predecessors at the 1532 debate. Yet, despite this striking similarity, the independent nature of these debates must also be acknowledged. This may primarily be found in that both groups expressed their retained ecclesiologies with notable variation in things such as language, argumentative content, biblical corroboration, and illustrative evidence. Finally, both the similar and independent nature of these events will be shown to have been largely derived from the Anabaptist/Reformed dialogue already begun as the Swiss Brethren movement emerged from under Zwingli’s reform efforts in Zürich. Each of these conclusions should help to paint a more accurate portrait of not only what was accomplished through these debates, but where each stands contextually during the period.Evidence for weak or linear conformity but not for hyper-conformity in an everyday social learning contextClaidiere, NicolasBowler, Mark TimothyWhiten, Andrewhttps://hdl.handle.net/10023/25552023-04-18T09:44:58Z2012-02-20T00:00:00ZConformity is thought to be an important force in cultural evolution because it has the potential to stabilize cooperation in large groups, potentiate group selection and thus explain uniquely human behaviors. However, the effects of such conformity on cultural and biological evolution will depend much on the way individuals are influenced by the frequency of alternative behavioral options witnessed. Theoretical modeling has suggested that only what we refer to as ‘hyper-conformity’, an exaggerated tendency to perform the most frequent behavior witnessed in other individuals, is able to increase within-group homogeneity and between-group diversity, for instance. Empirically however, few experiments have addressed how the frequency of behavior witnessed affects behavior. Accordingly we performed an experiment to test for the presence of conformity in a natural situation with humans. Visitors to a Zoo exhibit were invited to write or draw answers to questions on A5 cards and potentially win a small prize. We manipulated the proportion of existing writings versus drawings visible to visitors and measured the proportion of written cards submitted. We found a strong and significant effect of the proportion of text displayed on the proportion of text in the answers, thus demonstrating social learning. We show that this effect is approximately linear, with potentially a small, weak-conformist component but no hyper-conformist one. The present experiment therefore provides evidence for linear conformity in humans in a very natural context.
2012-02-20T00:00:00ZClaidiere, NicolasBowler, Mark TimothyWhiten, AndrewConformity is thought to be an important force in cultural evolution because it has the potential to stabilize cooperation in large groups, potentiate group selection and thus explain uniquely human behaviors. However, the effects of such conformity on cultural and biological evolution will depend much on the way individuals are influenced by the frequency of alternative behavioral options witnessed. Theoretical modeling has suggested that only what we refer to as ‘hyper-conformity’, an exaggerated tendency to perform the most frequent behavior witnessed in other individuals, is able to increase within-group homogeneity and between-group diversity, for instance. Empirically however, few experiments have addressed how the frequency of behavior witnessed affects behavior. Accordingly we performed an experiment to test for the presence of conformity in a natural situation with humans. Visitors to a Zoo exhibit were invited to write or draw answers to questions on A5 cards and potentially win a small prize. We manipulated the proportion of existing writings versus drawings visible to visitors and measured the proportion of written cards submitted. We found a strong and significant effect of the proportion of text displayed on the proportion of text in the answers, thus demonstrating social learning. We show that this effect is approximately linear, with potentially a small, weak-conformist component but no hyper-conformist one. The present experiment therefore provides evidence for linear conformity in humans in a very natural context.Unary FA-presentable semigroupsCain, Alan JamesRuskuc, NikThomas, R.M.https://hdl.handle.net/10023/23752024-03-04T00:40:53Z2012-06-08T00:00:00ZAutomatic presentations, also called FA-presentations, were introduced to extend nite model theory to innite structures whilst retaining the solubility of interesting decision problems. A particular focus of research has been the classication of those structures of some species that admit automatic presentations. Whilst some successes have been obtained, this appears to be a dicult problem in general. A restricted problem, also of signicant interest, is to ask this question for unary automatic presentations: auto-matic presentations over a one-letter alphabet. This paper studies unary FA-presentable semigroups. We prove the following: Every unary FA-presentable structure admits an injective unary automatic presentation where the language of representatives consists of every word over a one-letter alphabet. Unary FA-presentable semigroups are locally nite, but non-nitely generated unary FA-presentable semigroups may be innite. Every unary FA-presentable semigroup satises some Burnside identity.We describe the Green's relations in unary FA-presentable semigroups. We investigate the relationship between the class of unary FA-presentable semigroups and various semigroup constructions. A classication is given of the unary FA-presentable completely simple semigroups.
2012-06-08T00:00:00ZCain, Alan JamesRuskuc, NikThomas, R.M.Automatic presentations, also called FA-presentations, were introduced to extend nite model theory to innite structures whilst retaining the solubility of interesting decision problems. A particular focus of research has been the classication of those structures of some species that admit automatic presentations. Whilst some successes have been obtained, this appears to be a dicult problem in general. A restricted problem, also of signicant interest, is to ask this question for unary automatic presentations: auto-matic presentations over a one-letter alphabet. This paper studies unary FA-presentable semigroups. We prove the following: Every unary FA-presentable structure admits an injective unary automatic presentation where the language of representatives consists of every word over a one-letter alphabet. Unary FA-presentable semigroups are locally nite, but non-nitely generated unary FA-presentable semigroups may be innite. Every unary FA-presentable semigroup satises some Burnside identity.We describe the Green's relations in unary FA-presentable semigroups. We investigate the relationship between the class of unary FA-presentable semigroups and various semigroup constructions. A classication is given of the unary FA-presentable completely simple semigroups."No word for it" : Postcolonial Anglo-Saxon in John Haynes' Letter to PatienceJones, Chrishttps://hdl.handle.net/10023/22852024-03-11T00:40:56Z2010-01-01T00:00:00ZThis article examines a number of allusions to Old English, especially to the poem The Wanderer, in John Haynes’s award winning poem Letter to Patience (2006). A broad historical contextualisation of the use of Anglo-Saxon in modern poetry is offered first, against which Haynes’s specific poetic Anglo-Saxonism is then analysed in detail. Consideration is given to the sources – editions and translations – that Haynes used, and a sustained close reading of sections of his poem is offered in the light of this source study. The representation of English as an instrument of imperialism is discussed and juxtaposed with the use and status of early English to offer a long historical view of the politics of the vernacular. It is argued that Haynes’s poem, set partly in Nigeria, represents a new departure in the use it finds for Old English poetry, in effect constituting a kind of ‘postcolonial Anglo-Saxonism’.
2010-01-01T00:00:00ZJones, ChrisThis article examines a number of allusions to Old English, especially to the poem The Wanderer, in John Haynes’s award winning poem Letter to Patience (2006). A broad historical contextualisation of the use of Anglo-Saxon in modern poetry is offered first, against which Haynes’s specific poetic Anglo-Saxonism is then analysed in detail. Consideration is given to the sources – editions and translations – that Haynes used, and a sustained close reading of sections of his poem is offered in the light of this source study. The representation of English as an instrument of imperialism is discussed and juxtaposed with the use and status of early English to offer a long historical view of the politics of the vernacular. It is argued that Haynes’s poem, set partly in Nigeria, represents a new departure in the use it finds for Old English poetry, in effect constituting a kind of ‘postcolonial Anglo-Saxonism’.A critical review of the literature on population modellingCabrelli, AbigailHarwood, JohnMatthiopoulos, JasonNew, Leslie FrancesThomas, Lenhttps://hdl.handle.net/10023/22412023-04-26T00:22:10Z2009-01-01T00:00:00ZThe 2005 report of the National Research Council’s ‘Committee on Characterizing Biologically Significant Marine Mammal Behavior’ proposed a framework, which they called PCAD - Population Consequences of Acoustic Disturbance, that uses a series of transfer functions to link behavioural responses to sound with life functions, vital rates, and population change. The Committee suggested that the best understood transfer functions are those linking vital rates to population change. One of the main aims of this report is to document that understanding. However, we also show how the existing frameworks for modelling the dynamics of marine mammal populations can be extended to include the effects of behavioural responses on vital rates. In Chapter 1 we introduce the central concept of the rate of increase (lambda) of a population, which we believe is the most useful measure of the effects of behavioural responses on the dynamics of a population. If the value of lambda exceeds one, then thepopulation will increase over time; if it is less than one it will decrease. We show how changes in lambda provide a measure of the impact of human activities (such as exploitation, conservation, or disturbance) on a population. We also introduce structured population models, which take account of the fact that all individuals in a population are not identical, and show how the dynamics of different parts of a population can be modelled using a population projection matrix. The mathematical properties of this projection matrix can be used to determine the sensitivity of lambda to small changes in vital rates. Finally, we provide a very brief introduction to the concept of stochasticity, and the use of lambda to predict when (and if) a population might be driven to extinction. Chapter 2 describes how lambda also provides a measure of the Darwinian fitness of the individual members of a population. An individual’s fitness, the contribution it will make to future generations, depends to a large extent on its body condition and on the risks of mortality to which it is exposed. Both of these could be affected by behaviour responses to sound. We also explain current theories about the relationship between an individual’s feeding behaviour and the abundance and distribution of prey, and how this can affect body condition. Chapter 3 provides a more detailed description of how elasticity analysis can be used to investigate the impact of changes in vital rates on lambda . Elasticity analysis is a useful tool for detecting which vital rates are most important in determining the dynamics of a population. However, its value is limited because it does not take account of random variations (stochasticity) and, in theory, it can only predict the effect of small changes in vital rates. Chapter 4 describes the fundamental concept of density dependence: the way in which vital rates change with population size or the availability of resources, such as prey. Not only is density dependence an essential prerequisite for population stability and sustainable use, but the form it takes will also determine how a population responds to behavioural changes. This is because behaviour, and particularly the effect of behavioural change on body condition, plays a central role in many of the mechanistic models of density dependence. Chapters 5 and 6 explore the way in which additional complexities, such as social structure and the way in which populations are distributed in space, can affect the dynamics of populations. Models that account for these complexities behave in a much less predictable way than the relatively simple structured models that form the core of Chapters 1-4. So far, the models of population dynamics that we have reviewed have been deterministic. That is, they have assumed that the only way in which vital rates can vary is in response to a change in abundance, via density dependent mechanisms. In Chapters 7 and 8 we investigate the effect of random variation (stochasticity) on population dynamics. We distinguish the effects of demographic stochasticity, chance variations in the number of animals that die or give birth in a time interval that occur even if vital rates do not vary over time, and environmental stochasticity, which is the result of variations in vital rates across years. Variation in abundance may also occur as a result of environmental change and changes in the ecological community of which a population is a part. The effect of all these sources of variation is to reduce the realised growth rate of a population, and therefore its risk of extinction. In Chapter 9 we consider how the basic population modelling framework described in Chapters 1-8 might be extended to take account of the life functions identified by the NRC Committee. We suggest that these life functions are useful for defining the context in which behavioural responses might affect vital rates, but that they do not need to be modelled explicitly. Removing vital functions from the PCAD framework results in a much simpler structure, which is compatible with existing population modelling frameworks. However, these will have to be extended to allow population states, like body condition, that vary continuously to be modelled. Chapter 10 describes how changes in lambda can be detected. The simple analytical frameworks that are available for this are all vulnerable to the effects of variability that we introduced in Chapter 7. However, there is a framework (state-space and hidden Markov process modelling) that can account for the effects of this variability, and we recommend its use for detecting trends. The additional benefit of this approach is that its use results in a detailed model of the dynamics of the population that is under investigation. Chapter 11 reviews the different model structures that can be used to describe the dynamics of a population, and explains when different forms of population models (e.g. discrete vs. continuous time, deterministic vs. stochastic) are most appropriate. We also discuss how these different frameworks can be extended to account for continuous population states, as recommended in Chapter 8. The final focus is on how state-space models can be fitted to time series of abundance estimates and information on vital rates. Chapter 12 looks at the relevance of the different modelling approaches described in the previous chapters for analysing the potential effects of behavioural responses to sound on population dynamics, particularly the kinds of sounds that may be generated by the oil and gas industry. We conclude that lambda , the population rate of increase, and its variation provides a useful measure of these effects. We also believe that the models used for this purpose will certainly have to account for the effects of variability and density dependence. They will probably also have to account for the effects of social structure and the way in which populations use space. The state-space modelling framework outlined in Chapter 11 can, in principle, be extended to capture all of these features although work on this is still in its infancy.
Final Report to the Joint Industry Project of the International Association of Oil & Gas Producers on contract JIP22 07_20
2009-01-01T00:00:00ZCabrelli, AbigailHarwood, JohnMatthiopoulos, JasonNew, Leslie FrancesThomas, LenThe 2005 report of the National Research Council’s ‘Committee on Characterizing Biologically Significant Marine Mammal Behavior’ proposed a framework, which they called PCAD - Population Consequences of Acoustic Disturbance, that uses a series of transfer functions to link behavioural responses to sound with life functions, vital rates, and population change. The Committee suggested that the best understood transfer functions are those linking vital rates to population change. One of the main aims of this report is to document that understanding. However, we also show how the existing frameworks for modelling the dynamics of marine mammal populations can be extended to include the effects of behavioural responses on vital rates. In Chapter 1 we introduce the central concept of the rate of increase (lambda) of a population, which we believe is the most useful measure of the effects of behavioural responses on the dynamics of a population. If the value of lambda exceeds one, then thepopulation will increase over time; if it is less than one it will decrease. We show how changes in lambda provide a measure of the impact of human activities (such as exploitation, conservation, or disturbance) on a population. We also introduce structured population models, which take account of the fact that all individuals in a population are not identical, and show how the dynamics of different parts of a population can be modelled using a population projection matrix. The mathematical properties of this projection matrix can be used to determine the sensitivity of lambda to small changes in vital rates. Finally, we provide a very brief introduction to the concept of stochasticity, and the use of lambda to predict when (and if) a population might be driven to extinction. Chapter 2 describes how lambda also provides a measure of the Darwinian fitness of the individual members of a population. An individual’s fitness, the contribution it will make to future generations, depends to a large extent on its body condition and on the risks of mortality to which it is exposed. Both of these could be affected by behaviour responses to sound. We also explain current theories about the relationship between an individual’s feeding behaviour and the abundance and distribution of prey, and how this can affect body condition. Chapter 3 provides a more detailed description of how elasticity analysis can be used to investigate the impact of changes in vital rates on lambda . Elasticity analysis is a useful tool for detecting which vital rates are most important in determining the dynamics of a population. However, its value is limited because it does not take account of random variations (stochasticity) and, in theory, it can only predict the effect of small changes in vital rates. Chapter 4 describes the fundamental concept of density dependence: the way in which vital rates change with population size or the availability of resources, such as prey. Not only is density dependence an essential prerequisite for population stability and sustainable use, but the form it takes will also determine how a population responds to behavioural changes. This is because behaviour, and particularly the effect of behavioural change on body condition, plays a central role in many of the mechanistic models of density dependence. Chapters 5 and 6 explore the way in which additional complexities, such as social structure and the way in which populations are distributed in space, can affect the dynamics of populations. Models that account for these complexities behave in a much less predictable way than the relatively simple structured models that form the core of Chapters 1-4. So far, the models of population dynamics that we have reviewed have been deterministic. That is, they have assumed that the only way in which vital rates can vary is in response to a change in abundance, via density dependent mechanisms. In Chapters 7 and 8 we investigate the effect of random variation (stochasticity) on population dynamics. We distinguish the effects of demographic stochasticity, chance variations in the number of animals that die or give birth in a time interval that occur even if vital rates do not vary over time, and environmental stochasticity, which is the result of variations in vital rates across years. Variation in abundance may also occur as a result of environmental change and changes in the ecological community of which a population is a part. The effect of all these sources of variation is to reduce the realised growth rate of a population, and therefore its risk of extinction. In Chapter 9 we consider how the basic population modelling framework described in Chapters 1-8 might be extended to take account of the life functions identified by the NRC Committee. We suggest that these life functions are useful for defining the context in which behavioural responses might affect vital rates, but that they do not need to be modelled explicitly. Removing vital functions from the PCAD framework results in a much simpler structure, which is compatible with existing population modelling frameworks. However, these will have to be extended to allow population states, like body condition, that vary continuously to be modelled. Chapter 10 describes how changes in lambda can be detected. The simple analytical frameworks that are available for this are all vulnerable to the effects of variability that we introduced in Chapter 7. However, there is a framework (state-space and hidden Markov process modelling) that can account for the effects of this variability, and we recommend its use for detecting trends. The additional benefit of this approach is that its use results in a detailed model of the dynamics of the population that is under investigation. Chapter 11 reviews the different model structures that can be used to describe the dynamics of a population, and explains when different forms of population models (e.g. discrete vs. continuous time, deterministic vs. stochastic) are most appropriate. We also discuss how these different frameworks can be extended to account for continuous population states, as recommended in Chapter 8. The final focus is on how state-space models can be fitted to time series of abundance estimates and information on vital rates. Chapter 12 looks at the relevance of the different modelling approaches described in the previous chapters for analysing the potential effects of behavioural responses to sound on population dynamics, particularly the kinds of sounds that may be generated by the oil and gas industry. We conclude that lambda , the population rate of increase, and its variation provides a useful measure of these effects. We also believe that the models used for this purpose will certainly have to account for the effects of variability and density dependence. They will probably also have to account for the effects of social structure and the way in which populations use space. The state-space modelling framework outlined in Chapter 11 can, in principle, be extended to capture all of these features although work on this is still in its infancy.Revisiting Geneva: Robert Kingdon and the coming of the French Wars of Religionhttps://hdl.handle.net/10023/21592019-04-01T11:10:08Z2012-01-01T00:00:00ZThe late Robert Kingdon’s Geneva and the Coming of the Wars of Religion in France, 1555-1563 (1956) was not merely an engaging and challenging piece of scholarship, it came to dominate the study of Genevan Protestantism and the city’s relationship with other Reformed communities, particularly those in France. Based on the rich archival records in Geneva, Kingdon’s work would inspire many subsequent scholars to investigate the questions he first raised in the 1950s. This volume is testament to the breadth of material he first covered, and demonstrates the variety of fields in which he came to have influence, including printing history, the role of the nobility in the Reformation, the functioning of the Consistory and the lives of pastors. Born out of a conference celebrating the fiftieth anniversary of his original book, this volume now stands as a memorial to a life of exemplary scholarship.
2012-01-01T00:00:00ZThe late Robert Kingdon’s Geneva and the Coming of the Wars of Religion in France, 1555-1563 (1956) was not merely an engaging and challenging piece of scholarship, it came to dominate the study of Genevan Protestantism and the city’s relationship with other Reformed communities, particularly those in France. Based on the rich archival records in Geneva, Kingdon’s work would inspire many subsequent scholars to investigate the questions he first raised in the 1950s. This volume is testament to the breadth of material he first covered, and demonstrates the variety of fields in which he came to have influence, including printing history, the role of the nobility in the Reformation, the functioning of the Consistory and the lives of pastors. Born out of a conference celebrating the fiftieth anniversary of his original book, this volume now stands as a memorial to a life of exemplary scholarship.An update to the methods in Endangered Species Research 2011 paper "Estimating North Pacific right whale Eubalaena japonica density using passive acoustic cue counting"Marques, Tiago A.Munger, LisaThomas, LenWiggins, SeanHildebrand, Johnhttps://hdl.handle.net/10023/21582023-04-18T09:36:45Z2012-01-01T00:00:00Z2012-01-01T00:00:00ZMarques, Tiago A.Munger, LisaThomas, LenWiggins, SeanHildebrand, JohnGrowth rates for subclasses of Av(321)Albert, M.H.Atkinson, M.D.Brignall, RRuskuc, NikSmith, RWest, Jhttps://hdl.handle.net/10023/21372023-04-18T09:42:57Z2010-10-22T00:00:00ZPattern classes which avoid 321 and other patterns are shown to have the same growth rates as similar (but strictly larger) classes obtained by adding articulation points to any or all of the other patterns. The method of proof is to show that the elements of the latter classes can be represented as bounded merges of elements of the original class, and that the bounded merge construction does not change growth rates.
2010-10-22T00:00:00ZAlbert, M.H.Atkinson, M.D.Brignall, RRuskuc, NikSmith, RWest, JPattern classes which avoid 321 and other patterns are shown to have the same growth rates as similar (but strictly larger) classes obtained by adding articulation points to any or all of the other patterns. The method of proof is to show that the elements of the latter classes can be represented as bounded merges of elements of the original class, and that the bounded merge construction does not change growth rates.Generators and relations for subsemigroups via boundaries in Cayley graphsGray, RRuskuc, Nikhttps://hdl.handle.net/10023/21312023-04-18T09:42:52Z2011-11-01T00:00:00ZGiven a finitely generated semigroup S and subsemigroup T of S we define the notion of the boundary of T in S which, intuitively, describes the position of T inside the left and right Cayley graphs of S. We prove that if S is finitely generated and T has a finite boundary in S then T is finitely generated. We also prove that if S is finitely presented and T has a finite boundary in S then T is finitely presented. Several corollaries and examples are given.
2011-11-01T00:00:00ZGray, RRuskuc, NikGiven a finitely generated semigroup S and subsemigroup T of S we define the notion of the boundary of T in S which, intuitively, describes the position of T inside the left and right Cayley graphs of S. We prove that if S is finitely generated and T has a finite boundary in S then T is finitely generated. We also prove that if S is finitely presented and T has a finite boundary in S then T is finitely presented. Several corollaries and examples are given.Kametsa asaiki : the pursuit of the 'good life' in an Ashaninka village (Peruvian Amazonia)Sarmiento Barletti, Juan Pablohttps://hdl.handle.net/10023/21142019-04-01T09:32:18Z2011-01-01T00:00:00ZThis thesis is an ethnographic study of the pursuit of kametsa asaiki (‘the good life’) in
an Ashaninka village by the Bajo Urubamba River (Peruvian Amazonia). My study
centres on Ashaninka social organization in a context made difficult by the wake of
the Peruvian Internal War, the activities of extractive industries, and a series of
despotic decrees that have been passed by the Peruvian government. This is all
framed by a change in their social organization from living in small, separated
family-based settlements to one of living in villages.
This shift presents them with great problems when internal conflicts arise.
Whilst in the past settlements would have fissioned in order to avoid conflict, today
there are two related groups of reasons that lead them to want to live in centralised
communities. The first is their great desire for their children to go to school and the
importance they place on long-term cash-crops. The second is the encroachment of
the Peruvian State and private companies on their territory and lives which forces
them to stay together in order to resist and protect their territory and way of life.
I suggest that this change in organisation changes the rules of the game of
sociality. Contemporary Ashaninka life is centred on the pursuit of kametsa asaiki, a
philosophy of life they believe to have inherited from their ancestors that teaches
emotional restraint and the sharing of food in order to create the right type of
Ashaninka person. Yet, at present it also has new factors they believe allow them to
become ‘civilised’: school education, new forms of leadership and conflict resolution,
money, new forms of conflict resolution, intercultural health, and a strong political
federation to defend their right to pursue kametsa asaiki.
My thesis is an anthropological analysis of the 'audacious innovations' they
have developed to retake the pursuit of kametsa asaiki in the aftermath of the war. I
show that this ethos of living is not solely a communal project of conviviality but it
has become a symbol of resistance in their fight for the right to have rights in Peru.
2011-01-01T00:00:00ZSarmiento Barletti, Juan PabloThis thesis is an ethnographic study of the pursuit of kametsa asaiki (‘the good life’) in
an Ashaninka village by the Bajo Urubamba River (Peruvian Amazonia). My study
centres on Ashaninka social organization in a context made difficult by the wake of
the Peruvian Internal War, the activities of extractive industries, and a series of
despotic decrees that have been passed by the Peruvian government. This is all
framed by a change in their social organization from living in small, separated
family-based settlements to one of living in villages.
This shift presents them with great problems when internal conflicts arise.
Whilst in the past settlements would have fissioned in order to avoid conflict, today
there are two related groups of reasons that lead them to want to live in centralised
communities. The first is their great desire for their children to go to school and the
importance they place on long-term cash-crops. The second is the encroachment of
the Peruvian State and private companies on their territory and lives which forces
them to stay together in order to resist and protect their territory and way of life.
I suggest that this change in organisation changes the rules of the game of
sociality. Contemporary Ashaninka life is centred on the pursuit of kametsa asaiki, a
philosophy of life they believe to have inherited from their ancestors that teaches
emotional restraint and the sharing of food in order to create the right type of
Ashaninka person. Yet, at present it also has new factors they believe allow them to
become ‘civilised’: school education, new forms of leadership and conflict resolution,
money, new forms of conflict resolution, intercultural health, and a strong political
federation to defend their right to pursue kametsa asaiki.
My thesis is an anthropological analysis of the 'audacious innovations' they
have developed to retake the pursuit of kametsa asaiki in the aftermath of the war. I
show that this ethos of living is not solely a communal project of conviviality but it
has become a symbol of resistance in their fight for the right to have rights in Peru.The dramatising of theology : humanity’s participation in God’s drama with particular reference to the theologies of Hans Urs von Balthasar and Karl BarthFarlow, Matthew S.https://hdl.handle.net/10023/21022019-07-01T10:13:52Z2011-11-30T00:00:00ZThe aim of this project is to investigate the proper response of theology to the Christian God who, as revealed through revelation, is Being-in-act. This project takes seriously the idea posited by Shakespeare, that totus mundus agit histrionem, and upon this stage ‘all the men and women merely players: They have their exits and their entrances; and one man in his time plays many parts.’ If, then, God’s Being is in act, and as so many have deduced, life and death are enveloped within the drama of everyday, then, might it be possible that our theological endeavours would prosper through a dramatic rendering? In light of this, the project seeks to illumine that it is beneficial for both the Church and society, to realise how drama can be, and is, fruitful for our theological endeavours. God is Being-in-act, and through His revelation, He invites humanity to enter into and participate in His action. In light of the aforementioned, then, theology must contend with the implications for its practices, which, as is being argued, are benefited most through a full embrace of the dramatising of theology.
The thesis is situated in the recent movement of our theological endeavours that recognise the profundity of the dramatic and its ability to illuminate God’s action and call to action from theology, the Church and society. Moving forward from the seminal work of Hans Urs von Balthasar, and set forth in the context of the theologies of Balthasar and Karl Barth, this project argues that it is through the dramatising of theology that theology is best equipped to illumine God’s desire for humanity’s participation in His Theo-drama. The dramatising of theology is a natural response to God’s Being-in-act; it is the natural movement of theology’s response to God’s action which calls for an active response on our part. Current examples of today’s theological movement towards the dramatic can be seen in such authors as Max Harris, Trevor Hart, Stanley Hauerwas, Michael Horton, Todd Johnson and Dale Savidge, Ben Quash, Kevin Vanhoozer, Samuel Wells and N.T. Wright. This project hopes to contribute to the movement towards the dramatising of theology.
2011-11-30T00:00:00ZFarlow, Matthew S.The aim of this project is to investigate the proper response of theology to the Christian God who, as revealed through revelation, is Being-in-act. This project takes seriously the idea posited by Shakespeare, that totus mundus agit histrionem, and upon this stage ‘all the men and women merely players: They have their exits and their entrances; and one man in his time plays many parts.’ If, then, God’s Being is in act, and as so many have deduced, life and death are enveloped within the drama of everyday, then, might it be possible that our theological endeavours would prosper through a dramatic rendering? In light of this, the project seeks to illumine that it is beneficial for both the Church and society, to realise how drama can be, and is, fruitful for our theological endeavours. God is Being-in-act, and through His revelation, He invites humanity to enter into and participate in His action. In light of the aforementioned, then, theology must contend with the implications for its practices, which, as is being argued, are benefited most through a full embrace of the dramatising of theology.
The thesis is situated in the recent movement of our theological endeavours that recognise the profundity of the dramatic and its ability to illuminate God’s action and call to action from theology, the Church and society. Moving forward from the seminal work of Hans Urs von Balthasar, and set forth in the context of the theologies of Balthasar and Karl Barth, this project argues that it is through the dramatising of theology that theology is best equipped to illumine God’s desire for humanity’s participation in His Theo-drama. The dramatising of theology is a natural response to God’s Being-in-act; it is the natural movement of theology’s response to God’s action which calls for an active response on our part. Current examples of today’s theological movement towards the dramatic can be seen in such authors as Max Harris, Trevor Hart, Stanley Hauerwas, Michael Horton, Todd Johnson and Dale Savidge, Ben Quash, Kevin Vanhoozer, Samuel Wells and N.T. Wright. This project hopes to contribute to the movement towards the dramatising of theology.Complex Region Spatial Smoother (CReSS)Scott Hayward, Lindesay Alexandra SarahMacKenzie, Monique LeaDonovan, Carl RobertWalker, CameronAshe, Erinhttps://hdl.handle.net/10023/20482022-04-15T10:30:13Z2011-01-01T00:00:00ZConventional smoothing over complicated coastal and island regions may result in errors across boundaries, due to the use of Euclidean distances to represent inter-point similarity. The new Complex Region Spatial Smoother (CReSS) method presented here, uses estimated geodesic distances, model averaging and a local radial basis function to provide improved smoothing over complex domains. CReSS is compared, via simulation, to recent related smoothing techniques, Thin Plate Splines (TPS, Harder and Desmarais, 1972), geodesic low rank TPS [Wang and Ranalli, 2007] and the Soap film smoother [Wood et al., 2008]. The GLTPS method cannot be used in areas with islands and SOAP can be hard to parameterize. CReSS is comparable with, if not better than, all considered methods on a range of simulations. Supplementary materials for this article are available online.
This work is supported with funding from NERC UK
2011-01-01T00:00:00ZScott Hayward, Lindesay Alexandra SarahMacKenzie, Monique LeaDonovan, Carl RobertWalker, CameronAshe, ErinConventional smoothing over complicated coastal and island regions may result in errors across boundaries, due to the use of Euclidean distances to represent inter-point similarity. The new Complex Region Spatial Smoother (CReSS) method presented here, uses estimated geodesic distances, model averaging and a local radial basis function to provide improved smoothing over complex domains. CReSS is compared, via simulation, to recent related smoothing techniques, Thin Plate Splines (TPS, Harder and Desmarais, 1972), geodesic low rank TPS [Wang and Ranalli, 2007] and the Soap film smoother [Wood et al., 2008]. The GLTPS method cannot be used in areas with islands and SOAP can be hard to parameterize. CReSS is comparable with, if not better than, all considered methods on a range of simulations. Supplementary materials for this article are available online.Comparing pre- and post-construction distributions of long-tailed ducks Clangula hyemalis in and around the Nysted offshore wind farm, Denmark : a quasi-designed experiment accounting for imperfect detection, local surface features and autocorrelationPetersen, Ib KragMacKenzie, Monique LeaRexstad, EricWisz, Mary S.Fox, Anthony D.https://hdl.handle.net/10023/20082024-02-28T00:47:04Z2011-01-01T00:00:00ZWe report a novel technique to model abundance patterns of wintering seaducks in relation to the construction of an offshore wind farm (OWF) based on seven years of aerial survey transect data. Distance sampling was used to estimate seaduck densities adjusted for covariates affecting detection probabilities. A generalized additive model (GAM) generated seaduck densities in sampling units in relation to spatially explicit covariates, using bootstrapping to account for uncertainties in both processes. Generalized estimating equations generated precision measures for the GAM robust to spatial and temporal autocorrelation. Comparison of pre- and post-construction model generated surfaces showed significant reductions in long-tailed duck numbers only within the OWF (despite the fact that the model was uninformed about the OWF location), although the absolute numbers involved were trivial in a flyway population context. This method provides quantification of distributional effects on organisms over a gradient in space and time that offers an alternative to Before-After/Control-Impact designs in environmental impact assessment.
2011-01-01T00:00:00ZPetersen, Ib KragMacKenzie, Monique LeaRexstad, EricWisz, Mary S.Fox, Anthony D.We report a novel technique to model abundance patterns of wintering seaducks in relation to the construction of an offshore wind farm (OWF) based on seven years of aerial survey transect data. Distance sampling was used to estimate seaduck densities adjusted for covariates affecting detection probabilities. A generalized additive model (GAM) generated seaduck densities in sampling units in relation to spatially explicit covariates, using bootstrapping to account for uncertainties in both processes. Generalized estimating equations generated precision measures for the GAM robust to spatial and temporal autocorrelation. Comparison of pre- and post-construction model generated surfaces showed significant reductions in long-tailed duck numbers only within the OWF (despite the fact that the model was uninformed about the OWF location), although the absolute numbers involved were trivial in a flyway population context. This method provides quantification of distributional effects on organisms over a gradient in space and time that offers an alternative to Before-After/Control-Impact designs in environmental impact assessment.Between the Ayllu and the nation-state : intertextuality and ambiguities of identity in San Pablo de LípezBolton, Margarethttps://hdl.handle.net/10023/20052019-04-01T11:09:53Z2001-01-01T00:00:00ZThis thesis is based on fieldwork carried out in San Pablo de Lípez province, Bolivia. Through an examination of the history of the region, economic activities, ritual and oral histories, it seeks to understand the sorts of relations that have come to exist between a rural Andean group and the Bolivian nation-state and, in particular, the ways in which rural people understand themselves in the face of the state’s nation-building activities. The thesis is thus situated within the framework of studies of mestizaje, or of hybridity of peoples and cultures, and of nation-state and Indian in Latin America.
The thesis proposes a model to account for the ways in which contemporary people in Sud Lípez understand themselves and others. This takes into account the historical dimension and attempts to avoid reifications of such groupings as ‘Indian’, mestizo and Spaniard, and of ethnic groups in the more abstract sense. Central to it is the concept of intertextuality, a term borrowed from linguistic theory and literary criticism that derives largely from Bakhtin’s ideas of dialogue. Intertextuality emphasises the heterogeneity of texts and the diverse elements from which they are made.
The thesis is concerned primarily with discourses that surround categories of people. In contemporary Bolivia, such discourses include a current official discourse of pluralism and ethnic diversity which, it could be said, is in dialogue with ideas of homogenisation, assimilation of the Indian population, and the mestizo nation that became prominent following the National Revolution of 1952. This dialogue between contemporary discourses can be held to constitute a ‘horizontal axis’ of intertextuality. A ‘vertical axis’, which forms the context for the present-day dialogue, is in turn constituted by the discourses and dialogues surrounding categories of people throughout the colonial and early republican eras. The historical focus of the thesis allows a consideration of these past discourses.
The central chapters of the thesis focus on the relation between discourse and material practices. Chapters 5 and 6 show how discourses concerning identity are reflected in everyday life in San Pablo. Chapters 7 and 8 concern ritual, and focus on local and national identity. These chapters start by attempting to divide rituals of the state from rituals of the locality and introduce the idea that people are cast as ‘consumers’ for rituals of the state, while they are the ‘producers’ of rituals of their own locality (c.f. de Certeau 1984). Ultimately, however, the chapters conclude that such a division is not as clear as it might at first appear, and that it is not a simple matter to separate productive from consumptive practices and the tactics of consumers from the strategies of producers. The chapters end by suggesting that local people have a greater degree of agency than the initial model allowed, and with the proposition that through ritual they produce a locality (Appadurai 1995) that incorporates belonging to the nation.
The thesis concludes that agency is essential to the process through which the people of San Pablo arrive at an understanding of themselves and the nation-state. Agency enables them to put themselves beyond the categories that others imagine, that is, to adopt a strategy of making themselves indeterminate. Local people may inherit discourses from the past, and are aware of those of the present, but they do not merely adhere to them, nor do they simply rearrange their elements. They may adopt elements from the different discourses that surround them, but in so doing, they transform them.
2001-01-01T00:00:00ZBolton, MargaretThis thesis is based on fieldwork carried out in San Pablo de Lípez province, Bolivia. Through an examination of the history of the region, economic activities, ritual and oral histories, it seeks to understand the sorts of relations that have come to exist between a rural Andean group and the Bolivian nation-state and, in particular, the ways in which rural people understand themselves in the face of the state’s nation-building activities. The thesis is thus situated within the framework of studies of mestizaje, or of hybridity of peoples and cultures, and of nation-state and Indian in Latin America.
The thesis proposes a model to account for the ways in which contemporary people in Sud Lípez understand themselves and others. This takes into account the historical dimension and attempts to avoid reifications of such groupings as ‘Indian’, mestizo and Spaniard, and of ethnic groups in the more abstract sense. Central to it is the concept of intertextuality, a term borrowed from linguistic theory and literary criticism that derives largely from Bakhtin’s ideas of dialogue. Intertextuality emphasises the heterogeneity of texts and the diverse elements from which they are made.
The thesis is concerned primarily with discourses that surround categories of people. In contemporary Bolivia, such discourses include a current official discourse of pluralism and ethnic diversity which, it could be said, is in dialogue with ideas of homogenisation, assimilation of the Indian population, and the mestizo nation that became prominent following the National Revolution of 1952. This dialogue between contemporary discourses can be held to constitute a ‘horizontal axis’ of intertextuality. A ‘vertical axis’, which forms the context for the present-day dialogue, is in turn constituted by the discourses and dialogues surrounding categories of people throughout the colonial and early republican eras. The historical focus of the thesis allows a consideration of these past discourses.
The central chapters of the thesis focus on the relation between discourse and material practices. Chapters 5 and 6 show how discourses concerning identity are reflected in everyday life in San Pablo. Chapters 7 and 8 concern ritual, and focus on local and national identity. These chapters start by attempting to divide rituals of the state from rituals of the locality and introduce the idea that people are cast as ‘consumers’ for rituals of the state, while they are the ‘producers’ of rituals of their own locality (c.f. de Certeau 1984). Ultimately, however, the chapters conclude that such a division is not as clear as it might at first appear, and that it is not a simple matter to separate productive from consumptive practices and the tactics of consumers from the strategies of producers. The chapters end by suggesting that local people have a greater degree of agency than the initial model allowed, and with the proposition that through ritual they produce a locality (Appadurai 1995) that incorporates belonging to the nation.
The thesis concludes that agency is essential to the process through which the people of San Pablo arrive at an understanding of themselves and the nation-state. Agency enables them to put themselves beyond the categories that others imagine, that is, to adopt a strategy of making themselves indeterminate. Local people may inherit discourses from the past, and are aware of those of the present, but they do not merely adhere to them, nor do they simply rearrange their elements. They may adopt elements from the different discourses that surround them, but in so doing, they transform them.Finite groups are big as semigroupsDolinka, IgorRuskuc, Nikhttps://hdl.handle.net/10023/20042023-04-18T09:43:52Z2011-09-01T00:00:00ZWe prove that a finite group G occurs as a maximal proper subsemigroup of an infinite semigroup (in the terminology of Freese, Ježek, and Nation, G is a big semigroup) if and only if |G| ≥ 3. In fact, any finite semigroup whose minimal ideal contains a subgroup with at least three elements is big.
2011-09-01T00:00:00ZDolinka, IgorRuskuc, NikWe prove that a finite group G occurs as a maximal proper subsemigroup of an infinite semigroup (in the terminology of Freese, Ježek, and Nation, G is a big semigroup) if and only if |G| ≥ 3. In fact, any finite semigroup whose minimal ideal contains a subgroup with at least three elements is big.Presentations of inverse semigroups, their kernels and extensionsCarvalho, C.A.Gray, RRuskuc, Nikhttps://hdl.handle.net/10023/19982023-04-18T09:42:54Z2011-06-01T00:00:00ZLet S be an inverse semigroup and let π:S→T be a surjective homomorphism with kernel K. We show how to obtain a presentation for K from a presentation for S, and vice versa. We then investigate the relationship between the properties of S, K and T, focusing mainly on finiteness conditions. In particular we consider finite presentability, solubility of the word problem, residual finiteness, and the homological finiteness property FPn. Our results extend several classical results from combinatorial group theory concerning group extensions to inverse semigroups. Examples are also provided that highlight the differences with the special case of groups.
"Part of this work was done while Gray was an EPSRC Postdoctoral Research Fellow at the University of St Andrews, Scotland"
2011-06-01T00:00:00ZCarvalho, C.A.Gray, RRuskuc, NikLet S be an inverse semigroup and let π:S→T be a surjective homomorphism with kernel K. We show how to obtain a presentation for K from a presentation for S, and vice versa. We then investigate the relationship between the properties of S, K and T, focusing mainly on finiteness conditions. In particular we consider finite presentability, solubility of the word problem, residual finiteness, and the homological finiteness property FPn. Our results extend several classical results from combinatorial group theory concerning group extensions to inverse semigroups. Examples are also provided that highlight the differences with the special case of groups.Simple extensions of combinatorial structuresBrignall, RRuskuc, NikVatter, Vhttps://hdl.handle.net/10023/19972024-03-24T00:40:25Z2011-07-01T00:00:00ZAn interval in a combinatorial structure R is a set I of points which are related to every point in R \ I in the same way. A structure is simple if it has no proper intervals. Every combinatorial structure can be expressed as an inflation of a simple structure by structures of smaller sizes — this is called the substitution (or modular) decomposition. In this paper we prove several results of the following type: An arbitrary structure S of size n belonging to a class C can be embedded into a simple structure from C by adding at most f (n) elements. We prove such results when C is the class of all tournaments, graphs, permutations, posets, digraphs, oriented graphs and general relational structures containing a relation of arity greater than 2. The function f (n) in these cases is 2, ⌈log2(n + 1)⌉, ⌈(n + 1)/2⌉, ⌈(n + 1)/2⌉, ⌈log4(n + 1)⌉, ⌈log3(n + 1)⌉ and 1, respectively. In each case these bounds are the best possible.
2011-07-01T00:00:00ZBrignall, RRuskuc, NikVatter, VAn interval in a combinatorial structure R is a set I of points which are related to every point in R \ I in the same way. A structure is simple if it has no proper intervals. Every combinatorial structure can be expressed as an inflation of a simple structure by structures of smaller sizes — this is called the substitution (or modular) decomposition. In this paper we prove several results of the following type: An arbitrary structure S of size n belonging to a class C can be embedded into a simple structure from C by adding at most f (n) elements. We prove such results when C is the class of all tournaments, graphs, permutations, posets, digraphs, oriented graphs and general relational structures containing a relation of arity greater than 2. The function f (n) in these cases is 2, ⌈log2(n + 1)⌉, ⌈(n + 1)/2⌉, ⌈(n + 1)/2⌉, ⌈log4(n + 1)⌉, ⌈log3(n + 1)⌉ and 1, respectively. In each case these bounds are the best possible.Symbolic arrangement and communication in the despachoArmstrong, Gwenethhttps://hdl.handle.net/10023/19932019-04-01T11:09:55Z1990-01-01T00:00:00ZThe thesis investigates the content and composition of the despacho, the ritual offering used to propitiate principal earth deities in the Bolivian mining town of Oruro (Department of Oruro). The despacho is also designed to increase suerte which is viewed not only in terms of material fortune, but also personal well-being and harmony with the cosmos. The concepts and terminology of the despacho are discussed, as well as the different types of despacho used, and particular features of their content, composition and presentation. The first part of the thesis shows how the content and arrangement of the despacho constitute a symbolic language, communicating what is important about suerte, and creating a miniature picture of life on earth in all its abundance. The despacho’s symbolic language is particularly meaningful in terms of suerte and the Quechua and Aymara peoples’ worldview.
The second part of the thesis investigates the use of six different curing mesas used in a ritual ceremony to restore suerte following a coca divination ceremony. Both ceremonies were performed by an Aymara ritual specialist from a village south of Oruro. The content and function of each mesa is discussed, and I show how the six mesas were used in a sequence to describe a transition from mala suerte to suerte, and as part of a broader sequence of ritual events. In this part of the thesis I demonstrate how symbolic language is also used in healing mesas to describe and bring about changes between different states, and to create access to suerte in ritual.
1990-01-01T00:00:00ZArmstrong, GwenethThe thesis investigates the content and composition of the despacho, the ritual offering used to propitiate principal earth deities in the Bolivian mining town of Oruro (Department of Oruro). The despacho is also designed to increase suerte which is viewed not only in terms of material fortune, but also personal well-being and harmony with the cosmos. The concepts and terminology of the despacho are discussed, as well as the different types of despacho used, and particular features of their content, composition and presentation. The first part of the thesis shows how the content and arrangement of the despacho constitute a symbolic language, communicating what is important about suerte, and creating a miniature picture of life on earth in all its abundance. The despacho’s symbolic language is particularly meaningful in terms of suerte and the Quechua and Aymara peoples’ worldview.
The second part of the thesis investigates the use of six different curing mesas used in a ritual ceremony to restore suerte following a coca divination ceremony. Both ceremonies were performed by an Aymara ritual specialist from a village south of Oruro. The content and function of each mesa is discussed, and I show how the six mesas were used in a sequence to describe a transition from mala suerte to suerte, and as part of a broader sequence of ritual events. In this part of the thesis I demonstrate how symbolic language is also used in healing mesas to describe and bring about changes between different states, and to create access to suerte in ritual.A first survey of the global population size and distribution of the Scottish Crossbill Loxia scoticaSummers, Ron WBuckland, Stephen Terrencehttps://hdl.handle.net/10023/19572022-04-14T09:30:16Z2011-06-01T00:00:00ZA survey of Scottish Crossbills Loxia scotica was carried out in 3,506 km2 of conifer woodland in northern Scotland during January to April 2008 to provide the first estimate of the global population size for this endemic bird. Population estimates were also made for Common Crossbills L. curvirostra and Parrot Crossbills L. pytyopsittacus within this range. Crossbills were lured to systematically selected survey points for counting, sexing and recording their calls for later call-type (species) identification from sonograms. Crossbills were located at 451 of the 852 survey points, and adequate tape-recordings made at 387 of these. The Scottish Crossbill had a disjunct distribution, occurring largely within the eastern part of the study area, but also in the northwest. Common Crossbills had a mainly westerly distribution. The population size of postjuvenile Scottish Crossbills was estimated as 13,600 (95%C.I. 8,130–22,700), which will approximate to 6,800 (4,065–11,350) pairs. Common Crossbills were more abundant within this range (27,100, 95% C.I. 14,700–38,400) and Parrot Crossbills rare (about 100). The sex ratio was not significantly different from parity for Scottish Crossbills. The modal number at survey points was two but numbers were larger in January than later in the survey. The numbers and distribution of all crossbill species are likely to vary between years, depending upon the size of the cone crops of the different conifers: all were coning in 2008. Common Crossbill and Parrot Crossbill numbers will also be affected by irruptions from continental Europe. A monitoring scheme is required to detect any population trend, and further work on their habitat requirement (e.g. conifer selection at different seasons) is needed to inform habitat management of native and planted conifer forests to ensure a secure future for this endemic bird.
"The survey was part-financed by Scottish Natural Heritage"
2011-06-01T00:00:00ZSummers, Ron WBuckland, Stephen TerrenceA survey of Scottish Crossbills Loxia scotica was carried out in 3,506 km2 of conifer woodland in northern Scotland during January to April 2008 to provide the first estimate of the global population size for this endemic bird. Population estimates were also made for Common Crossbills L. curvirostra and Parrot Crossbills L. pytyopsittacus within this range. Crossbills were lured to systematically selected survey points for counting, sexing and recording their calls for later call-type (species) identification from sonograms. Crossbills were located at 451 of the 852 survey points, and adequate tape-recordings made at 387 of these. The Scottish Crossbill had a disjunct distribution, occurring largely within the eastern part of the study area, but also in the northwest. Common Crossbills had a mainly westerly distribution. The population size of postjuvenile Scottish Crossbills was estimated as 13,600 (95%C.I. 8,130–22,700), which will approximate to 6,800 (4,065–11,350) pairs. Common Crossbills were more abundant within this range (27,100, 95% C.I. 14,700–38,400) and Parrot Crossbills rare (about 100). The sex ratio was not significantly different from parity for Scottish Crossbills. The modal number at survey points was two but numbers were larger in January than later in the survey. The numbers and distribution of all crossbill species are likely to vary between years, depending upon the size of the cone crops of the different conifers: all were coning in 2008. Common Crossbill and Parrot Crossbill numbers will also be affected by irruptions from continental Europe. A monitoring scheme is required to detect any population trend, and further work on their habitat requirement (e.g. conifer selection at different seasons) is needed to inform habitat management of native and planted conifer forests to ensure a secure future for this endemic bird.Los urbanizadores de Arequipa : a study of the effects of urbanization on Quechua folklore, language and traditions in a southern Peruvian cityAdams, Stewart I. M.https://hdl.handle.net/10023/19372019-04-01T11:09:58Z1980-01-01T00:00:00ZThe thesis endeavours to assess the changes which have taken place, due to urbanization, in certain fundamental aspects of Quechua culture among migrants from the Southern Peruvian Sierra who have settled in the pueblos jóvenes, “shanty towns” of Arequipa, Peru.
In 7 chapters, based on material taped from 45 Quechua informants, the thesis discusses the urban milieu, evidence for the continuance of a riddling tradition, a folk song tradition, and traditional Quechua belief systems in the city. The thesis also examines the linguistic aspect of Quechua in the urban environment, whether it still constitutes a functional means of communication, and whether the closer proximity to Spanish in the city has resulted in what might be classed as an urban dialect of Quechua.
The thesis concludes that whereas Quechua immigrants to the city have been willing to adapt to city life in its more material aspects, in the more symbolic aspects of their culture, they have been less willing to change. Consequently, many features of Quechua culture appear, for the present, to be thriving in the city. Evidence for the survival of the symbolic aspects of Quechua culture are contained throughout the main body of the thesis in the Quechua transcriptions and English/Spanish translations of interviews given by informants, in the English translations of the riddles, in the synopses of the folktales narrated by the informants, and in the appendices, where the full Quechua transcriptions of some 32 folktales, 36 riddles and 24 songs are contained.
The thesis maintains that the Quechua immigrants to Arequipa constitute a new subculture which looks to the city for material support, but which is still heavily based on Quechua linguistic and cultural values. There has been a weakening of Quechua language and cultural traits in the city as a result of urbanization, but there does not appear to be the wholesale adoption of “western” ways to the detriment of Indian language and culture as was once suspected.
1980-01-01T00:00:00ZAdams, Stewart I. M.The thesis endeavours to assess the changes which have taken place, due to urbanization, in certain fundamental aspects of Quechua culture among migrants from the Southern Peruvian Sierra who have settled in the pueblos jóvenes, “shanty towns” of Arequipa, Peru.
In 7 chapters, based on material taped from 45 Quechua informants, the thesis discusses the urban milieu, evidence for the continuance of a riddling tradition, a folk song tradition, and traditional Quechua belief systems in the city. The thesis also examines the linguistic aspect of Quechua in the urban environment, whether it still constitutes a functional means of communication, and whether the closer proximity to Spanish in the city has resulted in what might be classed as an urban dialect of Quechua.
The thesis concludes that whereas Quechua immigrants to the city have been willing to adapt to city life in its more material aspects, in the more symbolic aspects of their culture, they have been less willing to change. Consequently, many features of Quechua culture appear, for the present, to be thriving in the city. Evidence for the survival of the symbolic aspects of Quechua culture are contained throughout the main body of the thesis in the Quechua transcriptions and English/Spanish translations of interviews given by informants, in the English translations of the riddles, in the synopses of the folktales narrated by the informants, and in the appendices, where the full Quechua transcriptions of some 32 folktales, 36 riddles and 24 songs are contained.
The thesis maintains that the Quechua immigrants to Arequipa constitute a new subculture which looks to the city for material support, but which is still heavily based on Quechua linguistic and cultural values. There has been a weakening of Quechua language and cultural traits in the city as a result of urbanization, but there does not appear to be the wholesale adoption of “western” ways to the detriment of Indian language and culture as was once suspected.Of life and happiness : morality, aesthetics, and social life among the southeastern Amazonian Mebengokré (Kayapó), as seen from the margins of ritualOliveira, Adolfo dehttps://hdl.handle.net/10023/19292019-07-01T10:05:24Z2003-01-01T00:00:00ZThis thesis deals with different aspects of the processes of production of sociability
among the Xikrin-Mebengokré of the Cateté River, central Brazil. I focus on ceremonies and their performance, as ways of access to Mebengokré conceptions concerning the morality and aesthetics of social life. I analyse the semiotics of
‘kin’-ship production, the performative aspects of emotion as a sociability tool, the
use of song and dance for the co-ordination of collective technical tasks, and a
Mebengokré ‘theory of language’ as social agency. In the conclusion I focus on the
criticism of some of the key theoretical aspects of Ge ethnology, in the light of my
previous analysis.
2003-01-01T00:00:00ZOliveira, Adolfo deThis thesis deals with different aspects of the processes of production of sociability
among the Xikrin-Mebengokré of the Cateté River, central Brazil. I focus on ceremonies and their performance, as ways of access to Mebengokré conceptions concerning the morality and aesthetics of social life. I analyse the semiotics of
‘kin’-ship production, the performative aspects of emotion as a sociability tool, the
use of song and dance for the co-ordination of collective technical tasks, and a
Mebengokré ‘theory of language’ as social agency. In the conclusion I focus on the
criticism of some of the key theoretical aspects of Ge ethnology, in the light of my
previous analysis.Education and episcopacy : the universities of Scotland in the fifteenth centuryWoodman, Islahttps://hdl.handle.net/10023/18822019-07-01T10:14:51Z2011-06-23T00:00:00ZEducational provision in Scotland was revolutionised in the fifteenth century through the foundation of three universities, or studia generale, at St Andrews, Glasgow and Aberdeen. These institutions can be viewed as part of the general expansion in higher education across Europe from the late-fourteenth century, which saw the establishment of many new centres of learning, often intended to serve local needs. Their impact on Scotland ought to have been profound; in theory, they removed the need for its scholars to continue to seek higher education at the universities of England or the continent.
Scotland’s fifteenth-century universities were essentially episcopal foundations, formally instituted by bishops within the cathedral cities of their dioceses, designed to meet the educational needs and career aspirations of the clergy. They are not entirely neglected subjects; the previous generation of university historians – including A. Dunlop, J. Durkan and L. J. Macfarlane – did much to recover the institutional, organisational and curricular developments that shaped their character. Less well explored, are the over-arching political themes that influenced the evolution of university provision in fifteenth-century Scotland as a whole. Similarly under-researched, is the impact of these foundations on the scholarly community, and society more generally.
This thesis explores these comparatively neglected themes in two parts. Part I presents a short narrative, offering a more politically sensitive interpretation of the introduction and expansion of higher educational provision in Scotland. Part II explores the impact of these foundations on Scottish scholars. The nature of extant sources inhibits reconstruction of the full extent of their influence on student numbers and patterns of university attendance. Instead, Part II presents a thorough quantitative and qualitative prosopographical study of the Scottish episcopate within the context of this embryonic era of university provision in Scotland. In so doing, this thesis offers new insights into a neglected aspect of contemporary clerical culture as well as the politics of fifteenth-century academic learning.
2011-06-23T00:00:00ZWoodman, IslaEducational provision in Scotland was revolutionised in the fifteenth century through the foundation of three universities, or studia generale, at St Andrews, Glasgow and Aberdeen. These institutions can be viewed as part of the general expansion in higher education across Europe from the late-fourteenth century, which saw the establishment of many new centres of learning, often intended to serve local needs. Their impact on Scotland ought to have been profound; in theory, they removed the need for its scholars to continue to seek higher education at the universities of England or the continent.
Scotland’s fifteenth-century universities were essentially episcopal foundations, formally instituted by bishops within the cathedral cities of their dioceses, designed to meet the educational needs and career aspirations of the clergy. They are not entirely neglected subjects; the previous generation of university historians – including A. Dunlop, J. Durkan and L. J. Macfarlane – did much to recover the institutional, organisational and curricular developments that shaped their character. Less well explored, are the over-arching political themes that influenced the evolution of university provision in fifteenth-century Scotland as a whole. Similarly under-researched, is the impact of these foundations on the scholarly community, and society more generally.
This thesis explores these comparatively neglected themes in two parts. Part I presents a short narrative, offering a more politically sensitive interpretation of the introduction and expansion of higher educational provision in Scotland. Part II explores the impact of these foundations on Scottish scholars. The nature of extant sources inhibits reconstruction of the full extent of their influence on student numbers and patterns of university attendance. Instead, Part II presents a thorough quantitative and qualitative prosopographical study of the Scottish episcopate within the context of this embryonic era of university provision in Scotland. In so doing, this thesis offers new insights into a neglected aspect of contemporary clerical culture as well as the politics of fifteenth-century academic learning.“Proven patriots”: the French diplomatic corps, 1789-1799Frey, Linda S.Frey, Marsha L.https://hdl.handle.net/10023/18812019-04-01T11:10:08Z2011-01-01T00:00:00ZThis study analyzes a hitherto unexamined group, the French diplomatic corps during the Revolution (1789 to 1799), and focuses on the question of loyalty and conscience. For some diplomats choice was an illusion as their status often determined their fate. Some supported the king and continued to do so in spite of the high cost, often creatively sabotaging the Revolution. Others put nation, as they defined it, above king. Because the definition of loyalty constantly shifted the corps, like the army and the bureaucracy, was periodically purged. Those who had worked for or been sympathetic to the old regime or those who had allied with a certain political faction came under scrutiny. The turmoil in the diplomatic corps not only had international repercussions but also reflects larger societal trends, such as the attack on the aristocracy and the displacement of one elite by another. The French diplomatic corps was thus emblematic of many issues surrounding the revolutionary struggle of this decade.
2011-01-01T00:00:00ZFrey, Linda S.Frey, Marsha L.This study analyzes a hitherto unexamined group, the French diplomatic corps during the Revolution (1789 to 1799), and focuses on the question of loyalty and conscience. For some diplomats choice was an illusion as their status often determined their fate. Some supported the king and continued to do so in spite of the high cost, often creatively sabotaging the Revolution. Others put nation, as they defined it, above king. Because the definition of loyalty constantly shifted the corps, like the army and the bureaucracy, was periodically purged. Those who had worked for or been sympathetic to the old regime or those who had allied with a certain political faction came under scrutiny. The turmoil in the diplomatic corps not only had international repercussions but also reflects larger societal trends, such as the attack on the aristocracy and the displacement of one elite by another. The French diplomatic corps was thus emblematic of many issues surrounding the revolutionary struggle of this decade.Living in the past : Thebes, periodization, and The Two Noble KinsmenDavis, Alexander Leehttps://hdl.handle.net/10023/18522023-04-18T09:40:36Z2010-01-01T00:00:00ZOur sense of the distinction between the "medieval" and the "early modern" is structured by two notions: that the early modern period is characterized by the death of a chivalric culture that is dominant in the medieval period; and that the early modern is distinguished from the medieval by its superior historical self-awareness. This essay reassesses these themes through a reading of Shakespeare and Fletcher's The Two Noble Kinsmen (1634). This is a play of knighthood and chivalric spectacle, adapted from Chaucer's Knight's Tale, which brings Chaucer on stage in the play's prologue. Reading the play through a tradition of "Theban" narratives that proliferated from antiquity through the Middle Ages shows that the representation of chivalric culture in The Two Noble Kinsmen constructs a vision of the past very different from how modern accounts distinguish between medieval and early modern cultures.
2010-01-01T00:00:00ZDavis, Alexander LeeOur sense of the distinction between the "medieval" and the "early modern" is structured by two notions: that the early modern period is characterized by the death of a chivalric culture that is dominant in the medieval period; and that the early modern is distinguished from the medieval by its superior historical self-awareness. This essay reassesses these themes through a reading of Shakespeare and Fletcher's The Two Noble Kinsmen (1634). This is a play of knighthood and chivalric spectacle, adapted from Chaucer's Knight's Tale, which brings Chaucer on stage in the play's prologue. Reading the play through a tradition of "Theban" narratives that proliferated from antiquity through the Middle Ages shows that the representation of chivalric culture in The Two Noble Kinsmen constructs a vision of the past very different from how modern accounts distinguish between medieval and early modern cultures.Scottish medieval parish churches : the evidence from the dioceses of Dunblane and DunkeldFawcett, RichardOram, RichardLuxford, Julian Marcushttps://hdl.handle.net/10023/18272023-04-18T09:43:27Z2010-02-01T00:00:00ZAn account of a research project into the architectural and historical evidence for the survival of medieval fabric in the parish churches of the dioceses of Dunblane and Dunkeld.
2010-02-01T00:00:00ZFawcett, RichardOram, RichardLuxford, Julian MarcusAn account of a research project into the architectural and historical evidence for the survival of medieval fabric in the parish churches of the dioceses of Dunblane and Dunkeld.Variation in habitat preference and distribution of harbour porpoises west of ScotlandBooth, Cormac Ghttps://hdl.handle.net/10023/17012019-07-01T10:11:34Z2010-11-30T00:00:00ZThe waters off the west coast of Scotland have one of the highest densities of harbour porpoise
(Phocoena phocoena) in Europe. Harbour porpoise are listed under Annex II of the EU Habitats
Directive, requiring the designation of Special Areas of Conservation (SACs) for the species’
protection and conservation.
The main aim of this thesis is to identify habitat preferences for harbour porpoise, and key
regions that embody these preferences, which could therefore be suitable as SACs; and to
determine how harbour porpoise use these regions over time and space. Designed visual and
acoustic line-transect surveys were conducted between 2003 and 2008. Generalised Estimating
Equations (GEEs) were used to determine relationships between the relative density of harbour
porpoise and temporally and spatially variable oceanographic covariates.
Predictive models showed that depth, slope, distance to land and spring tidal range were all
important in explaining porpoise distribution. There were also significant temporal variations in
habitat use. However, whilst some variation was observed among years and months, consistent
preferences for water depths between 50 and 150 m and highly sloped regions were observed
across the temporal models. Predicted surfaces revealed a consistent inshore distribution for the
species throughout the west coast of Scotland. Regional models revealed similar habitat
preferences to the full-extent models, and indicated that the Small Isles and Sound of Jura were
the most consistently important regions for harbour porpoise, and that these regions could be
suitable as SACs.
The impacts of seal scarers on distribution and habitat use were also investigated, and there
were indications that these devices have the potential to displace harbour porpoise.
These results should be considered in the assessment of sites for SAC designation, and in
implementing appropriate conservation measures for harbour porpoise.
2010-11-30T00:00:00ZBooth, Cormac GThe waters off the west coast of Scotland have one of the highest densities of harbour porpoise
(Phocoena phocoena) in Europe. Harbour porpoise are listed under Annex II of the EU Habitats
Directive, requiring the designation of Special Areas of Conservation (SACs) for the species’
protection and conservation.
The main aim of this thesis is to identify habitat preferences for harbour porpoise, and key
regions that embody these preferences, which could therefore be suitable as SACs; and to
determine how harbour porpoise use these regions over time and space. Designed visual and
acoustic line-transect surveys were conducted between 2003 and 2008. Generalised Estimating
Equations (GEEs) were used to determine relationships between the relative density of harbour
porpoise and temporally and spatially variable oceanographic covariates.
Predictive models showed that depth, slope, distance to land and spring tidal range were all
important in explaining porpoise distribution. There were also significant temporal variations in
habitat use. However, whilst some variation was observed among years and months, consistent
preferences for water depths between 50 and 150 m and highly sloped regions were observed
across the temporal models. Predicted surfaces revealed a consistent inshore distribution for the
species throughout the west coast of Scotland. Regional models revealed similar habitat
preferences to the full-extent models, and indicated that the Small Isles and Sound of Jura were
the most consistently important regions for harbour porpoise, and that these regions could be
suitable as SACs.
The impacts of seal scarers on distribution and habitat use were also investigated, and there
were indications that these devices have the potential to displace harbour porpoise.
These results should be considered in the assessment of sites for SAC designation, and in
implementing appropriate conservation measures for harbour porpoise.Character and symbol in José Lezama Lima's 'Paradiso'Ritchie, Fiona M.https://hdl.handle.net/10023/16842019-04-01T11:09:47Z1982-01-01T00:00:00ZThis thesis explores the
possibility of some
degree
of unity
in
Paradiso,
which appears
initially to be
a work of poetic self-indulgence,
lacking
a coherent plot, credible characters and causality, and possessing
seemingly extraneous chapters.
In
particular,
the characters, with
their
one shared voice
(Lezama’s)
and apparently arbitrary appearances
in
independent
scenarios,
demand
scrutiny.
Lezama Lima's earlier works are
devoted to his
sistema poético, a
working method aimed at a material representation of
the
mystical world of
the Spirit in the "incarnate Word". Since the
writer
himself has defined
Paradiso
as a novela-poema,
the
novel
is here
examined as a poem, with
the
characters
(recurring
images)
fulfilling
symbolic roles.
Luis Fernández
Sosa’s reading of some of
Lezama’s poems
"anagogically"
(following
the
terminology of
Northrop Frye) is
equally applicable
to Paradiso, with
its
multiple
levels
of meaning.
In Paradiso each act or
incident is
ritualized, suggesting
that the
characters are
indeed
symbolic and may attain
the
stature of archetypes.
Characters derived from
members of
Lezama’s family
circle acquire symbolic
names and
layer
upon
layer
of additional
imagery until
they
are expanded
into
archetypes.
The
recurring
image of
the
(family) tree linking heaven
and earth, continual emphasis on
the cycle of
birth/death/renewal and
the
main configurations, such as
hero/princess/dragon/treasure, assist
in the
identification of
the principal symbolic characters:
Great Mother Goddess,
Son/Lover, Dionysiac sacrifice,
the questing
Orpheus and
the
magnificent
doomed Icarus.
Each
concept or character
is
a stepping-stone
for the central auto-
biographical figure, inspired by
personal
tragedy to
seek self-perfection
and accept
his vocation.
The
stages on
the journey
--family
relationships,
the discovery and mastery of sexuality and creativity,
the pursuit of
infinite knowledge-- are presided over
by
a variety of
tutors, not
least
Rialta, Cemí’s
anima, poetic
Muse
and spiritual guide.
Within Cemí’s heroic
conquest of
the Unconscious, the imagery of
the quest yields much when
interpreted in terms
of
Jungian archetypes.
With his eventual assimilation
of opposites,
Cemí becomes
actively contemplative, attuned
to ritmo
hesicástico and obedient
to his calling.
'The analysis of character
is the
key to Lezama’s fictionalized autobiography, which emerges as a
finely
structured novel given precise
form by its symbolic characters.
1982-01-01T00:00:00ZRitchie, Fiona M.This thesis explores the
possibility of some
degree
of unity
in
Paradiso,
which appears
initially to be
a work of poetic self-indulgence,
lacking
a coherent plot, credible characters and causality, and possessing
seemingly extraneous chapters.
In
particular,
the characters, with
their
one shared voice
(Lezama’s)
and apparently arbitrary appearances
in
independent
scenarios,
demand
scrutiny.
Lezama Lima's earlier works are
devoted to his
sistema poético, a
working method aimed at a material representation of
the
mystical world of
the Spirit in the "incarnate Word". Since the
writer
himself has defined
Paradiso
as a novela-poema,
the
novel
is here
examined as a poem, with
the
characters
(recurring
images)
fulfilling
symbolic roles.
Luis Fernández
Sosa’s reading of some of
Lezama’s poems
"anagogically"
(following
the
terminology of
Northrop Frye) is
equally applicable
to Paradiso, with
its
multiple
levels
of meaning.
In Paradiso each act or
incident is
ritualized, suggesting
that the
characters are
indeed
symbolic and may attain
the
stature of archetypes.
Characters derived from
members of
Lezama’s family
circle acquire symbolic
names and
layer
upon
layer
of additional
imagery until
they
are expanded
into
archetypes.
The
recurring
image of
the
(family) tree linking heaven
and earth, continual emphasis on
the cycle of
birth/death/renewal and
the
main configurations, such as
hero/princess/dragon/treasure, assist
in the
identification of
the principal symbolic characters:
Great Mother Goddess,
Son/Lover, Dionysiac sacrifice,
the questing
Orpheus and
the
magnificent
doomed Icarus.
Each
concept or character
is
a stepping-stone
for the central auto-
biographical figure, inspired by
personal
tragedy to
seek self-perfection
and accept
his vocation.
The
stages on
the journey
--family
relationships,
the discovery and mastery of sexuality and creativity,
the pursuit of
infinite knowledge-- are presided over
by
a variety of
tutors, not
least
Rialta, Cemí’s
anima, poetic
Muse
and spiritual guide.
Within Cemí’s heroic
conquest of
the Unconscious, the imagery of
the quest yields much when
interpreted in terms
of
Jungian archetypes.
With his eventual assimilation
of opposites,
Cemí becomes
actively contemplative, attuned
to ritmo
hesicástico and obedient
to his calling.
'The analysis of character
is the
key to Lezama’s fictionalized autobiography, which emerges as a
finely
structured novel given precise
form by its symbolic characters.Cashinahua cosmovision : a perspectival approach to identity and alterityLagrou, Elsje Mariahttps://hdl.handle.net/10023/16762019-04-01T11:09:51Z1998-01-01T00:00:00ZThis thesis explores the interface of social and cosmogonic thought in an indigenous society of the southwestern Brazilian Amazon. The first part sets out the Cashinahua ontological framework, describes key concepts and places the Cashinahua in the broader context of an Amerindian worldview where perspectivism and a special philosophical interest in the questions of alterity and identity are central issues. These questions are dealt with by means of a complex dualistic symbolism that pervades the fields of ethnicity, gender, social life and ritual. The second part of the thesis is divided into two chapters (chapters III and IV). Chapter three sets out the mythological framework in which the key concepts previously described gain a narrative form, while chapter IV describes the Nixpu pima initiation ritual of girls and boys and shows how this ritual represents an important moment of synthesis and actualisation of the Cashinahua worldview. The initiation ritual illustrates how the Cashinahua basic ontological distinctions between the embodied and rooted self as opposed to free-floating images and spirits are expressed in a graphic way and guide ritual action. Throughout the thesis references are also made to the intimate association and mutual illumination between, on the one hand, the Cashinahua worldview, social life and ontology, and, on the other, eschatology and indigenous conceptions of death.
1998-01-01T00:00:00ZLagrou, Elsje MariaThis thesis explores the interface of social and cosmogonic thought in an indigenous society of the southwestern Brazilian Amazon. The first part sets out the Cashinahua ontological framework, describes key concepts and places the Cashinahua in the broader context of an Amerindian worldview where perspectivism and a special philosophical interest in the questions of alterity and identity are central issues. These questions are dealt with by means of a complex dualistic symbolism that pervades the fields of ethnicity, gender, social life and ritual. The second part of the thesis is divided into two chapters (chapters III and IV). Chapter three sets out the mythological framework in which the key concepts previously described gain a narrative form, while chapter IV describes the Nixpu pima initiation ritual of girls and boys and shows how this ritual represents an important moment of synthesis and actualisation of the Cashinahua worldview. The initiation ritual illustrates how the Cashinahua basic ontological distinctions between the embodied and rooted self as opposed to free-floating images and spirits are expressed in a graphic way and guide ritual action. Throughout the thesis references are also made to the intimate association and mutual illumination between, on the one hand, the Cashinahua worldview, social life and ontology, and, on the other, eschatology and indigenous conceptions of death.Becoming similar : knowledge, sociality and the aesthetics of relatedness amongst the Nivacle of the Paraguayan ChacoGrant, Suzannehttps://hdl.handle.net/10023/16722019-07-01T10:06:27Z2006-01-01T00:00:00ZThis thesis is an exploration of the concepts of knowledge, sociality and relatedness amongst the Nivacle indigenous people of the Paraguayan Chaco, concentrating particularly on the community of Jotoicha in the Mennonite Colonies of the Central Chaco region. A central issue in this thesis is the concept of "knowledge" as a relational capacity and the ways in which knowledgeable behaviour can be constitutive of aesthetically pleasing forms of sociality. Such practices can be generative of increased similarity between individuals over time. The thesis begins with an exploration of Nivacle understandings of "knowledge" and shows it to be an eminently social concept that is created in an organ located in the stomach known as the cachi. "Knowledge" for the Nivacle is the basis for an individual's social conscience, their productive and reproductive skills, as well as their inter-personal relationships. "Knowledge" is also a central aspect of Nivacle understandings of relatedness. Rather than being based on a static genealogical structure, relatedness is best understood within the context of lived relationships that are constantly evolving. These relationships are generated through the practices of feeding and caring for one's "close" kin, with such practices also being generative of sociality itself. However,"close" relationships are neither static nor geographically bounded and are always open to the possibility of re-activation through visiting and gift giving. The Nivacle have been inserted into the market economy for several decades. Wage labour is conceptualised alongside other "subsistence activities" and productive activities are generative both of gender relations and sociality itself. In the final chapter I discuss Nivacle notions of reciprocity within the context of team-based sporting events. I show that whilst such community-based divisions appear to be premised on relations of "sameness" and "difference," they are best understood within the context of an overarching desire for people to generate similarity between different kinds of people in a variety of contexts.
2006-01-01T00:00:00ZGrant, SuzanneThis thesis is an exploration of the concepts of knowledge, sociality and relatedness amongst the Nivacle indigenous people of the Paraguayan Chaco, concentrating particularly on the community of Jotoicha in the Mennonite Colonies of the Central Chaco region. A central issue in this thesis is the concept of "knowledge" as a relational capacity and the ways in which knowledgeable behaviour can be constitutive of aesthetically pleasing forms of sociality. Such practices can be generative of increased similarity between individuals over time. The thesis begins with an exploration of Nivacle understandings of "knowledge" and shows it to be an eminently social concept that is created in an organ located in the stomach known as the cachi. "Knowledge" for the Nivacle is the basis for an individual's social conscience, their productive and reproductive skills, as well as their inter-personal relationships. "Knowledge" is also a central aspect of Nivacle understandings of relatedness. Rather than being based on a static genealogical structure, relatedness is best understood within the context of lived relationships that are constantly evolving. These relationships are generated through the practices of feeding and caring for one's "close" kin, with such practices also being generative of sociality itself. However,"close" relationships are neither static nor geographically bounded and are always open to the possibility of re-activation through visiting and gift giving. The Nivacle have been inserted into the market economy for several decades. Wage labour is conceptualised alongside other "subsistence activities" and productive activities are generative both of gender relations and sociality itself. In the final chapter I discuss Nivacle notions of reciprocity within the context of team-based sporting events. I show that whilst such community-based divisions appear to be premised on relations of "sameness" and "difference," they are best understood within the context of an overarching desire for people to generate similarity between different kinds of people in a variety of contexts.Density estimation implications of increasing ambient noise on beaked whale click detection and classificationMarques, Tiago A.Ward, JessicaJarvis, SusanMoretti, DavidMorrissey, RonaldDiMarzio, NancyThomas, Lenhttps://hdl.handle.net/10023/16522023-04-18T09:36:24Z2010-01-01T00:00:00ZAcoustic based density estimates are being increasingly used. Usually density estimation methods require one to evaluate the effective survey area of the acoustic sensors, or equivalently estimate the mean detection probability of detecting the animals or cues of interest. This is often done based on an estimated detection function, the probability of detecting an object of interest as a function of covariates, usually distance and additional covariates. If the actual survey data and the data used to estimate a detection function are not collected simultaneously, as in Marques et al. (2009), the estimated detection function might not correspond to the detection process that generated the survey data. This would lead to biaseddensity estimates. Here we evaluate the influence of ambient noise in the detection and classification of beaked whale clicks at the Atlantic Undersea Test and Evaluation Center (AUTEC) hydrophones, to assess if the density estimates reported in Marques et al. (2009) might have been biased. To do so we contaminated a data set with increasing levels of ambient noise, and then estimated the detection function accounting for the noise level as an additional covariate. The results obtained suggest that for the particular results obtained at AUTEC’s deep water hydrophones the influence of ambient noise on the beaked whale’s click detection probability might have been minor, and hence unlikely to have had an impact on density estimates. However, we do not exclude the possibility that the results could be different under other scenarios.
2010-01-01T00:00:00ZMarques, Tiago A.Ward, JessicaJarvis, SusanMoretti, DavidMorrissey, RonaldDiMarzio, NancyThomas, LenAcoustic based density estimates are being increasingly used. Usually density estimation methods require one to evaluate the effective survey area of the acoustic sensors, or equivalently estimate the mean detection probability of detecting the animals or cues of interest. This is often done based on an estimated detection function, the probability of detecting an object of interest as a function of covariates, usually distance and additional covariates. If the actual survey data and the data used to estimate a detection function are not collected simultaneously, as in Marques et al. (2009), the estimated detection function might not correspond to the detection process that generated the survey data. This would lead to biaseddensity estimates. Here we evaluate the influence of ambient noise in the detection and classification of beaked whale clicks at the Atlantic Undersea Test and Evaluation Center (AUTEC) hydrophones, to assess if the density estimates reported in Marques et al. (2009) might have been biased. To do so we contaminated a data set with increasing levels of ambient noise, and then estimated the detection function accounting for the noise level as an additional covariate. The results obtained suggest that for the particular results obtained at AUTEC’s deep water hydrophones the influence of ambient noise on the beaked whale’s click detection probability might have been minor, and hence unlikely to have had an impact on density estimates. However, we do not exclude the possibility that the results could be different under other scenarios.Estimating gopher tortoise abundance through design-based and model-based methodsBal, Payalhttps://hdl.handle.net/10023/16362019-07-01T10:19:45Z2010-01-01T00:00:00ZGopher tortoises are a small land tortoise that inhabit south-eastern United States and
are listed as threatened due to habitat loss. They are rather hard to survey, since they
occur at low density. This project was based on extensive data from systematic line
transect surveys for gopher tortoises at Fort Gordon and Ichauway in Georgia, USA,
collected by the Joseph W. Jones Ecological Research Centre. Despite excellent survey
designs and field methods, the resulting estimates of abundance have shown high
variance. Alternate methods for abundance and variance estimation that could lower
the variance were explored. Both, design-based and model-based approaches to
abundance estimation were attempted. For the design-based approach, abundance and
associated variance estimates were obtained using the CDS/MCDS analysis engines in
DISTANCE (Version 6.0). The cluster size estimation technique to scale burrow to tortoise
abundance was used. Variance of the encounter rate component, that usually dominates
the overall variance estimate for line transect data was originally calculated using the R2
estimator (used in DISTANCE 6.0 as the default) that is suited for random line placement.
This was compared against encounter rate variance estimators developed for systematic
designs (Fewster et al. 2009). As expected, the latter produced substantially lower
variance estimates. For the model-based approach, abundance as well as occupancy was
modelled by specifying GAMs using environmental covariates (where available) for the
study sites. Resulting predictions were subjected to non-parametric and parametric
bootstrapping for variance estimation. Parametric bootstrap suited to the model-based
approach did not perform well because the underlying GAMs specified for burrow
occupancy were found to be inaccurate. Due to the excellent design of the survey and
the lack of sufficient information to model burrow occupancy accurately, design-based
methods appeared to do better than the model-based methods for the data. The final
estimates for both the study sites and the surface maps (only for Ichauway) produced
need to be reviewed and must be considered in conjunction with the accompanying
uncertainty.
2010-01-01T00:00:00ZBal, PayalGopher tortoises are a small land tortoise that inhabit south-eastern United States and
are listed as threatened due to habitat loss. They are rather hard to survey, since they
occur at low density. This project was based on extensive data from systematic line
transect surveys for gopher tortoises at Fort Gordon and Ichauway in Georgia, USA,
collected by the Joseph W. Jones Ecological Research Centre. Despite excellent survey
designs and field methods, the resulting estimates of abundance have shown high
variance. Alternate methods for abundance and variance estimation that could lower
the variance were explored. Both, design-based and model-based approaches to
abundance estimation were attempted. For the design-based approach, abundance and
associated variance estimates were obtained using the CDS/MCDS analysis engines in
DISTANCE (Version 6.0). The cluster size estimation technique to scale burrow to tortoise
abundance was used. Variance of the encounter rate component, that usually dominates
the overall variance estimate for line transect data was originally calculated using the R2
estimator (used in DISTANCE 6.0 as the default) that is suited for random line placement.
This was compared against encounter rate variance estimators developed for systematic
designs (Fewster et al. 2009). As expected, the latter produced substantially lower
variance estimates. For the model-based approach, abundance as well as occupancy was
modelled by specifying GAMs using environmental covariates (where available) for the
study sites. Resulting predictions were subjected to non-parametric and parametric
bootstrapping for variance estimation. Parametric bootstrap suited to the model-based
approach did not perform well because the underlying GAMs specified for burrow
occupancy were found to be inaccurate. Due to the excellent design of the survey and
the lack of sufficient information to model burrow occupancy accurately, design-based
methods appeared to do better than the model-based methods for the data. The final
estimates for both the study sites and the surface maps (only for Ichauway) produced
need to be reviewed and must be considered in conjunction with the accompanying
uncertainty.Bayesian modelling of integrated data and its application to seabird populationsReynolds, Toby J.https://hdl.handle.net/10023/16352019-07-01T10:10:01Z2010-11-30T00:00:00ZIntegrated data analyses are becoming increasingly popular in studies of wild animal populations where two or more separate sources of data contain information about common parameters. Here we develop an integrated population model using abundance and demographic data from a study of common guillemots (Uria aalge) on the Isle of May, southeast Scotland. A state-space model for the count data is supplemented by three demographic time series (productivity and two mark-recapture-recovery (MRR)), enabling the estimation of prebreeder emigration rate - a parameter for which there is no direct observational data, and which is unidentifiable in the separate analysis of MRR data. A Bayesian approach using MCMC provides a flexible and powerful analysis framework.
This model is extended to provide predictions of future population trajectories. Adopting random effects models for the survival and productivity parameters, we implement the MCMC algorithm to obtain a posterior sample of the underlying process means and variances (and population sizes) within the study period. Given this sample, we predict future demographic parameters, which in turn allows us to predict future population sizes and obtain the corresponding posterior distribution. Under the assumption that recent, unfavourable conditions persist in the future, we obtain a posterior probability of 70% that there is a population decline of >25% over a 10-year period.
Lastly, using MRR data we test for spatial, temporal and age-related correlations in guillemot survival among three widely separated Scottish colonies that have varying overlap in nonbreeding distribution. We show that survival is highly correlated over time for colonies/age classes sharing wintering areas, and essentially uncorrelated for those with separate wintering areas. These results strongly suggest that one or more aspects of winter environment are responsible for spatiotemporal variation in survival of British guillemots, and provide insight into the factors driving multi-population dynamics of the species.
2010-11-30T00:00:00ZReynolds, Toby J.Integrated data analyses are becoming increasingly popular in studies of wild animal populations where two or more separate sources of data contain information about common parameters. Here we develop an integrated population model using abundance and demographic data from a study of common guillemots (Uria aalge) on the Isle of May, southeast Scotland. A state-space model for the count data is supplemented by three demographic time series (productivity and two mark-recapture-recovery (MRR)), enabling the estimation of prebreeder emigration rate - a parameter for which there is no direct observational data, and which is unidentifiable in the separate analysis of MRR data. A Bayesian approach using MCMC provides a flexible and powerful analysis framework.
This model is extended to provide predictions of future population trajectories. Adopting random effects models for the survival and productivity parameters, we implement the MCMC algorithm to obtain a posterior sample of the underlying process means and variances (and population sizes) within the study period. Given this sample, we predict future demographic parameters, which in turn allows us to predict future population sizes and obtain the corresponding posterior distribution. Under the assumption that recent, unfavourable conditions persist in the future, we obtain a posterior probability of 70% that there is a population decline of >25% over a 10-year period.
Lastly, using MRR data we test for spatial, temporal and age-related correlations in guillemot survival among three widely separated Scottish colonies that have varying overlap in nonbreeding distribution. We show that survival is highly correlated over time for colonies/age classes sharing wintering areas, and essentially uncorrelated for those with separate wintering areas. These results strongly suggest that one or more aspects of winter environment are responsible for spatiotemporal variation in survival of British guillemots, and provide insight into the factors driving multi-population dynamics of the species.The language of Quechua rural teachers in Bolivia: a study of bilingualism - interlingualism among rural Quechua native speakersYraola-Burgos, Ana-Mariahttps://hdl.handle.net/10023/16312019-07-01T10:09:57Z1995-01-01T00:00:00ZThis is a study of the linguistic situation of contemporary Bolivia carried out between 1990 and 1993. It attempts to delimit a particular speech community (that of bilingual rural school teachers in the Quechua speaking region).
It started as a study for delimiting the Spanish dialects spoken in Bolivia, seeking explanations for possible deviations from standard Spanish in the influence and actions of the mother tongue, Quechua. However, as the analysis progressed, I found increasingly a certain systematicity in the characteristics of the presumed Spanish dialect. Although there existed a determined structural transference, this did not reflect merely a direct transcription from the mother tongue Quechua, since it was not always possible to determine whether it was the result of transference from this language, or if it could be explained in terms of the non-native language. Finding some analogy with the conclusions of Labov concerning the English spoken by blacks in New York, I considered that the best explaination would be to interpret the speech in question as the expression of a distinct code.
In summary, this thesis comes down specifically to the demonstration, by means of the analysis of the characteristic structures of the Spanish spoken by rural school teachers in the Quechua speaking areas of Bolivia, that the code they use as their habitual medium of communication is an interlanguage in the process of forming itself into a new code of the creole type, what we call a semilanguage.
The existence of the semilanguage could also be proved in the observation of a series of social and psycological factors which affect its speakers. We could see that the teachers form an intermediate group, which is the product of a process of adaptation, and in which the confluence of certain values and attitudes has provoked the rise of hybrid values and behaviour, tending to create a new order which involves a new culture and thus a new code of expression.
1995-01-01T00:00:00ZYraola-Burgos, Ana-MariaThis is a study of the linguistic situation of contemporary Bolivia carried out between 1990 and 1993. It attempts to delimit a particular speech community (that of bilingual rural school teachers in the Quechua speaking region).
It started as a study for delimiting the Spanish dialects spoken in Bolivia, seeking explanations for possible deviations from standard Spanish in the influence and actions of the mother tongue, Quechua. However, as the analysis progressed, I found increasingly a certain systematicity in the characteristics of the presumed Spanish dialect. Although there existed a determined structural transference, this did not reflect merely a direct transcription from the mother tongue Quechua, since it was not always possible to determine whether it was the result of transference from this language, or if it could be explained in terms of the non-native language. Finding some analogy with the conclusions of Labov concerning the English spoken by blacks in New York, I considered that the best explaination would be to interpret the speech in question as the expression of a distinct code.
In summary, this thesis comes down specifically to the demonstration, by means of the analysis of the characteristic structures of the Spanish spoken by rural school teachers in the Quechua speaking areas of Bolivia, that the code they use as their habitual medium of communication is an interlanguage in the process of forming itself into a new code of the creole type, what we call a semilanguage.
The existence of the semilanguage could also be proved in the observation of a series of social and psycological factors which affect its speakers. We could see that the teachers form an intermediate group, which is the product of a process of adaptation, and in which the confluence of certain values and attitudes has provoked the rise of hybrid values and behaviour, tending to create a new order which involves a new culture and thus a new code of expression.The N-terminus of Bunyamwera orthobunyavirus NSs protein is essential for interferon antagonismVan Knippenberg, Ingeborg ChristineCarlton-Smith, CharlesElliott, Richard Michaelhttps://hdl.handle.net/10023/11482023-04-18T09:42:04Z2010-04-01T00:00:00ZBunyamwera virus NSs protein is involved in the inhibition of cellular transcription and the interferon (IFN) response, and it interacts with the Med8 component of Mediator. A spontaneous mutant of a recombinant NSs-deleted Bunyamwera virus (rBUNdelNSs2) was identified and characterized. This mutant virus, termed mBUNNSs22, expresses a 21 aa N-terminally truncated form of NSs. Like rBUNdelNSs2, mBUNNSs22 is attenuated in IFN-deficient cells, and to a greater extent in IFN-competent cells. Both rBUNdelNSs2 and mBUNNSs22 are potent IFN inducers and their growth can be rescued by depleting cellular IRF3. Strikingly, despite encoding an NSs protein that contains the Med8 interaction domain, mBUNNSs22 fails to block RNA polymerase II activity during infection. Overall, our data suggest that both the interaction of NSs with Med8 and a novel unidentified function of the NSs N-terminus, seem necessary for Bunyamwera virus to counteract host antiviral responses.
This work is supported by UK MRC and BBRC
2010-04-01T00:00:00ZVan Knippenberg, Ingeborg ChristineCarlton-Smith, CharlesElliott, Richard MichaelBunyamwera virus NSs protein is involved in the inhibition of cellular transcription and the interferon (IFN) response, and it interacts with the Med8 component of Mediator. A spontaneous mutant of a recombinant NSs-deleted Bunyamwera virus (rBUNdelNSs2) was identified and characterized. This mutant virus, termed mBUNNSs22, expresses a 21 aa N-terminally truncated form of NSs. Like rBUNdelNSs2, mBUNNSs22 is attenuated in IFN-deficient cells, and to a greater extent in IFN-competent cells. Both rBUNdelNSs2 and mBUNNSs22 are potent IFN inducers and their growth can be rescued by depleting cellular IRF3. Strikingly, despite encoding an NSs protein that contains the Med8 interaction domain, mBUNNSs22 fails to block RNA polymerase II activity during infection. Overall, our data suggest that both the interaction of NSs with Med8 and a novel unidentified function of the NSs N-terminus, seem necessary for Bunyamwera virus to counteract host antiviral responses.The archaeo-eukaryotic GINS proteins and the archaeal primase catalytic subunit PriS share a common domainSwiatek, AgnieszkaMacNeill, Stuart Andrewhttps://hdl.handle.net/10023/10472024-02-26T00:40:45Z2010-04-12T00:00:00ZPrimase and GINS are essential factors for chromosomal DNA replication in eukaryotic and archaeal cells. Here we describe a previously undetected relationship between the C-terminal domain of the catalytic subunit (PriS) of archaeal primase and the B-domains of the archaeo-eukaryotic GINS proteins in the form of a conserved structural domain comprising a three-stranded antiparallel beta-sheet adjacent to an alpha-helix and a two-stranded beta-sheet or hairpin. The presence of a shared domain in archaeal PriS and GINS proteins, the genes for which are often found adjacent on the chromosome, suggests simple mechanisms for the evolution of these proteins.
This work was funded by the Scottish Universities Life Sciences Alliance (SULSA).
2010-04-12T00:00:00ZSwiatek, AgnieszkaMacNeill, Stuart AndrewPrimase and GINS are essential factors for chromosomal DNA replication in eukaryotic and archaeal cells. Here we describe a previously undetected relationship between the C-terminal domain of the catalytic subunit (PriS) of archaeal primase and the B-domains of the archaeo-eukaryotic GINS proteins in the form of a conserved structural domain comprising a three-stranded antiparallel beta-sheet adjacent to an alpha-helix and a two-stranded beta-sheet or hairpin. The presence of a shared domain in archaeal PriS and GINS proteins, the genes for which are often found adjacent on the chromosome, suggests simple mechanisms for the evolution of these proteins.Assessing the effectiveness of conservation measures : resolving the "wicked" problem of the Steller sea lionBoyd, Ian Lamonthttps://hdl.handle.net/10023/10342024-03-05T00:40:33Z2010-07-01T00:00:00Z“Wicked” problems are those that are complex and that change when solutions are applied. Many conflicts in conservation fall in to this category. The study approached the problem of how to constrain the apparent wickedness of a problem in the conservation management of a species by using simple empirical indicators to carry out iterative assessment of the risk to a population and to document how this risk evolves in relation to the addition of new data and the implementation of management actions. Effects of high levels of uncertainty within data and also concerning population structure were examined through stochastic simulation and by exploration of scenarios. Historical trends in the example used, the Steller sea lion, showed rapid declines in abundance in some regions during the 1980s. The current total population is 130,000-150,000 Steller sea lions through Alaska and British Columbia and this number has been stable since about 1990 in spite of regional differences in population dynamics. Regional differences in the sequence of changes in the number of pups and non-pups, suggested that an internal re-distribution of juveniles could have happened between 1980 and 1990. Current productivity also appears close to the long term mean. Stochastic population projection using various scenarios showed that, based upon this history, the risk of extinction for the population has declined and is below reasonable thresholds for considering the population to be endangered.
2010-07-01T00:00:00ZBoyd, Ian Lamont“Wicked” problems are those that are complex and that change when solutions are applied. Many conflicts in conservation fall in to this category. The study approached the problem of how to constrain the apparent wickedness of a problem in the conservation management of a species by using simple empirical indicators to carry out iterative assessment of the risk to a population and to document how this risk evolves in relation to the addition of new data and the implementation of management actions. Effects of high levels of uncertainty within data and also concerning population structure were examined through stochastic simulation and by exploration of scenarios. Historical trends in the example used, the Steller sea lion, showed rapid declines in abundance in some regions during the 1980s. The current total population is 130,000-150,000 Steller sea lions through Alaska and British Columbia and this number has been stable since about 1990 in spite of regional differences in population dynamics. Regional differences in the sequence of changes in the number of pups and non-pups, suggested that an internal re-distribution of juveniles could have happened between 1980 and 1990. Current productivity also appears close to the long term mean. Stochastic population projection using various scenarios showed that, based upon this history, the risk of extinction for the population has declined and is below reasonable thresholds for considering the population to be endangered.A grammar of ResígaroAllin, Trevor R.https://hdl.handle.net/10023/10122019-04-01T09:31:15Z1976-01-01T00:00:00ZThe thesis gives a description within the framework of tagmemic theory of Resigaro, a South American Indian language
of the Huitoto group, spoken in the region between the Amazon and the Putumayo, in north-eastern Peru.
The Introduction reviews critically previous work on the language, and sets out modifications in tagmemic theory which
it is claimed avoid circularity and repetition and improve the
description. Principal among these is a strict separation of
the three modes of Contrast, Variation and Distribution, and the use of multiplication of derive structures.
Part I of the thesis describes the first two levels of the
Phonological Hierarchy - Phoneme level and Syllable level.
Part II describes the grammatical hierarchy, in which the following levels are set up:
Root
Stem
Word
(Group)
(Piece)
Phrase
Clause
Sentence
(Group and Piece are sub-levels affecting only the Verb class.) Each Level is described in a separate chapter, starting at the lowest level (Root). Each class (Verb, Noun, Pronoun, etc.) is described in turn at each level at which it has elements. At Phrase level, Phrases are described as being either Endocentric or Axis-Relator. Endocentric Phrases (Verb, Noun, and Numeral) are described first. At Clause level, the description of Clause structure is preceded by a description of Clause-level tagmemes - first the nuclear, and then the peripheral tagmemes. It is indicated that this simplifies the presentation of Clause structure. Under Clause structure, the Declarative clause is described first, and other Clause classes are derived from this, viz.: Interrogative, Imperative, Nominalized and Relativized. The description of the Contrast and Variation modes of Sentence level is followed by an analysis of the first section of a text.
Appendix I presents a lexicon of Resigaro in two parts: Part I is Resigaro-Spanish-English, and Part II is Spanish-Resigaro.
Appendix II presents a 376-word four-language comparative word list for Resigaro, Bora, Ocaina and Huitoto Muinane
1976-01-01T00:00:00ZAllin, Trevor R.The thesis gives a description within the framework of tagmemic theory of Resigaro, a South American Indian language
of the Huitoto group, spoken in the region between the Amazon and the Putumayo, in north-eastern Peru.
The Introduction reviews critically previous work on the language, and sets out modifications in tagmemic theory which
it is claimed avoid circularity and repetition and improve the
description. Principal among these is a strict separation of
the three modes of Contrast, Variation and Distribution, and the use of multiplication of derive structures.
Part I of the thesis describes the first two levels of the
Phonological Hierarchy - Phoneme level and Syllable level.
Part II describes the grammatical hierarchy, in which the following levels are set up:
Root
Stem
Word
(Group)
(Piece)
Phrase
Clause
Sentence
(Group and Piece are sub-levels affecting only the Verb class.) Each Level is described in a separate chapter, starting at the lowest level (Root). Each class (Verb, Noun, Pronoun, etc.) is described in turn at each level at which it has elements. At Phrase level, Phrases are described as being either Endocentric or Axis-Relator. Endocentric Phrases (Verb, Noun, and Numeral) are described first. At Clause level, the description of Clause structure is preceded by a description of Clause-level tagmemes - first the nuclear, and then the peripheral tagmemes. It is indicated that this simplifies the presentation of Clause structure. Under Clause structure, the Declarative clause is described first, and other Clause classes are derived from this, viz.: Interrogative, Imperative, Nominalized and Relativized. The description of the Contrast and Variation modes of Sentence level is followed by an analysis of the first section of a text.
Appendix I presents a lexicon of Resigaro in two parts: Part I is Resigaro-Spanish-English, and Part II is Spanish-Resigaro.
Appendix II presents a 376-word four-language comparative word list for Resigaro, Bora, Ocaina and Huitoto MuinaneThe astronomy of Andean myth : the history of a cosmologySullivan, William F.https://hdl.handle.net/10023/10112019-04-01T09:30:54Z1986-01-01T00:00:00ZThe paper aims to show that Andean myth, on one level, represents a technical language recording astronomical observations of precession and, at the same time, an historical record of simultaneous social and celestial transformations.
Topographic and architectural terms of Andean myth are interpreted as a metaphor for the organisation of and locations on the celestial sphere. Via ethnoastronmical data, mythical animals are identified as stars and placed on the celestial sphere according to their "topographical " location. Tested in the planetarium, these "arrays" generate clusters of dates - 200 B.C. and 650. A. D. Analysis of the names of Wiraqocha and Manco Capac indicates they represent Saturn and Jupiter and that their mythical meeting represents their conjunction in 650 A.D.
The astronomy of Andean myth is then used as an historical tool to examine how the Andean priest-astronomers recorded the simultaneous creation of the ayllu and of this distinctive astronomical system about 200 B.C. The idea that the agricultural ayllu, with its double descent system stressing the importance of paternity, represents a transformation of society from an earlier matrilineal/horticultural era is examined in light of the sexual
imagery employed in myth. Wiraqocha’s androgyny and the division of the celestial sphere
into male (ecliptic) and -female(celestial equator = “earth” ) are interpreted as cosmological validations of the new social structure.
1986-01-01T00:00:00ZSullivan, William F.The paper aims to show that Andean myth, on one level, represents a technical language recording astronomical observations of precession and, at the same time, an historical record of simultaneous social and celestial transformations.
Topographic and architectural terms of Andean myth are interpreted as a metaphor for the organisation of and locations on the celestial sphere. Via ethnoastronmical data, mythical animals are identified as stars and placed on the celestial sphere according to their "topographical " location. Tested in the planetarium, these "arrays" generate clusters of dates - 200 B.C. and 650. A. D. Analysis of the names of Wiraqocha and Manco Capac indicates they represent Saturn and Jupiter and that their mythical meeting represents their conjunction in 650 A.D.
The astronomy of Andean myth is then used as an historical tool to examine how the Andean priest-astronomers recorded the simultaneous creation of the ayllu and of this distinctive astronomical system about 200 B.C. The idea that the agricultural ayllu, with its double descent system stressing the importance of paternity, represents a transformation of society from an earlier matrilineal/horticultural era is examined in light of the sexual
imagery employed in myth. Wiraqocha’s androgyny and the division of the celestial sphere
into male (ecliptic) and -female(celestial equator = “earth” ) are interpreted as cosmological validations of the new social structure.The making of real people : an interpretation of a morality-centred theory of sociality, livelihood and selfhood among the Muinane (Colombian Amazon)Londoño Sulkin, Carlos Davidhttps://hdl.handle.net/10023/10102019-04-01T09:30:41Z2000-01-01T00:00:00ZIn this monograph I interpret a wide-ranging native theory of sociality of
the Muinane, an indigenous group of the Colombian Amazon. This theory
simultaneously addresses their livelihood activities, some aspects of their
phenomenological experience, their bodily form, their group identity, and their
views on the achievement of a uniquely human, morally sociable way of life.
The Muinane understand their thoughts/emotions as well as their bodies to be
material in origin and character. Proper bodies and thoughts/emotions are
made out of ritual substances and foodstuffs, which have divine subjectivities
and agencies of their own, and which ‘sound’ through people, establishing
people's subjectivities and agencies. Such subjectivities and agencies lead to
the communal achievement of `coolness', the state of convivial sociability,
tranquility, abundance and generalised good health that constitutes ideal
community life. Because they share substances, kin are also understood to
share bodily features and thoughts/emotions. Their consubstantiality leads to
mutual love and to an intersubjectivity that enables them to live well together,
without unseemly contestations or differences in ultimate moral purposes.
However, the material character of bodies and thoughts/emotions is
also a source of danger. Animals and other evil beings can sabotage proper
community life by replacing people's moral substances with their own false
ones, causing people to experience mad, envious, angry and even sorcerous
thoughts/emotions, and to suffer from weakening or lethal bodily diseases.
It is the moral obligation and inclination of properly constituted human
beings to make new human beings, by intentionally forging their bodies, their
thoughts/emotions and their ‘baskets of knowledge.’ They must do this by
transforming evil substances into proper substances, through work and
through everyday or sporadic rituals.
The matters addressed in this monograph -native theories of sociality,
of self, of livelihood and so on- are of central pertinence to ongoing
discussions in Amazonianist anthropology.
2000-01-01T00:00:00ZLondoño Sulkin, Carlos DavidIn this monograph I interpret a wide-ranging native theory of sociality of
the Muinane, an indigenous group of the Colombian Amazon. This theory
simultaneously addresses their livelihood activities, some aspects of their
phenomenological experience, their bodily form, their group identity, and their
views on the achievement of a uniquely human, morally sociable way of life.
The Muinane understand their thoughts/emotions as well as their bodies to be
material in origin and character. Proper bodies and thoughts/emotions are
made out of ritual substances and foodstuffs, which have divine subjectivities
and agencies of their own, and which ‘sound’ through people, establishing
people's subjectivities and agencies. Such subjectivities and agencies lead to
the communal achievement of `coolness', the state of convivial sociability,
tranquility, abundance and generalised good health that constitutes ideal
community life. Because they share substances, kin are also understood to
share bodily features and thoughts/emotions. Their consubstantiality leads to
mutual love and to an intersubjectivity that enables them to live well together,
without unseemly contestations or differences in ultimate moral purposes.
However, the material character of bodies and thoughts/emotions is
also a source of danger. Animals and other evil beings can sabotage proper
community life by replacing people's moral substances with their own false
ones, causing people to experience mad, envious, angry and even sorcerous
thoughts/emotions, and to suffer from weakening or lethal bodily diseases.
It is the moral obligation and inclination of properly constituted human
beings to make new human beings, by intentionally forging their bodies, their
thoughts/emotions and their ‘baskets of knowledge.’ They must do this by
transforming evil substances into proper substances, through work and
through everyday or sporadic rituals.
The matters addressed in this monograph -native theories of sociality,
of self, of livelihood and so on- are of central pertinence to ongoing
discussions in Amazonianist anthropology.Nahuatl in the Huasteca Hidalguense : a case study in the sociology of languageStiles, Nevillehttps://hdl.handle.net/10023/10092019-04-01T09:29:14Z1982-01-01T00:00:00ZThis thesis examines the vitality of Hidalgo Nahuatl (HN) in the
communities of Jaltocan, Panacaxtlan, Santa Cruz, Santa Teresa
and Zohuala in the Huasteca Hidalguense, Mexico.
The research, conducted in Mexico and St. Andrews University
from 1976-1982, applies an analysis of HN within the framework of
the Sociology of Language and Dependency Theory, thereby using a
multi-disciplinary approach. Through an investigation of the historical,
social, cultural and economic factors related to HN, the
latter is embedded in its reality.
HN is shown to be originally a language of dependency and oppression,
supported by a long mestizo tradition of "caciquismo". It is
demonstrated that an increasing number of Spanish (S) monolinguals,
together with other socio-economic factors, is encouraging Nahuas
to bilingualize and S:: =A. is fast becoming the new language of dependency.
The Hidalgo Nahuas possess practical reasons for the acquisition
of S., these being to solve their daily problems - especially
land tenancy -, to communicate with the mestizo out-group and to
undertake trading with non-HN speakers. However, the Nahuas are
not surrendering their native language as they bilingualize, but
rather, tend to limit its usage to native Nahua contexts and speakers.
HN has become important to the Nahuas in order to demonstrate
their ethnic identity and territoriality.
The introduction of government projects to the communities, such as
the Castellanizacion project or bilingual-bicultural education, are
shown to be theoretically bilingual in approach, but fail to take
into account sufficiently the regional Indian language in the praxis.
The stable maintenance of HN is highlighted by statistical results
from the word-count of recorded texts, documents and publications
and the range of morphological phenomena affecting S. words
in HN is described with examples from the Corpus.
The linguistic interference from S. in HN is located within Dependency
Theory and this author suggests the use of the term dependency
word rather than loan word and dependency language, thus implying
a diachronic sociological process which is reflected in HN.
Extended Texts are offered as evidence of the linguistic standard
of HN and attitudes of Nahuas towards their language are presented.
The final conclusion is that modern HN is a viable, vital and
functional language at the time of undertaking this research and
demonstrates a frequent usage by a large number of speakers. HN
has still not entered into:. -avital process of language death, as
is the case in other Nahuatl-speaking regions of Mexico, and is
still being maintained, particularly at community level, by adults
and children alike.
1982-01-01T00:00:00ZStiles, NevilleThis thesis examines the vitality of Hidalgo Nahuatl (HN) in the
communities of Jaltocan, Panacaxtlan, Santa Cruz, Santa Teresa
and Zohuala in the Huasteca Hidalguense, Mexico.
The research, conducted in Mexico and St. Andrews University
from 1976-1982, applies an analysis of HN within the framework of
the Sociology of Language and Dependency Theory, thereby using a
multi-disciplinary approach. Through an investigation of the historical,
social, cultural and economic factors related to HN, the
latter is embedded in its reality.
HN is shown to be originally a language of dependency and oppression,
supported by a long mestizo tradition of "caciquismo". It is
demonstrated that an increasing number of Spanish (S) monolinguals,
together with other socio-economic factors, is encouraging Nahuas
to bilingualize and S:: =A. is fast becoming the new language of dependency.
The Hidalgo Nahuas possess practical reasons for the acquisition
of S., these being to solve their daily problems - especially
land tenancy -, to communicate with the mestizo out-group and to
undertake trading with non-HN speakers. However, the Nahuas are
not surrendering their native language as they bilingualize, but
rather, tend to limit its usage to native Nahua contexts and speakers.
HN has become important to the Nahuas in order to demonstrate
their ethnic identity and territoriality.
The introduction of government projects to the communities, such as
the Castellanizacion project or bilingual-bicultural education, are
shown to be theoretically bilingual in approach, but fail to take
into account sufficiently the regional Indian language in the praxis.
The stable maintenance of HN is highlighted by statistical results
from the word-count of recorded texts, documents and publications
and the range of morphological phenomena affecting S. words
in HN is described with examples from the Corpus.
The linguistic interference from S. in HN is located within Dependency
Theory and this author suggests the use of the term dependency
word rather than loan word and dependency language, thus implying
a diachronic sociological process which is reflected in HN.
Extended Texts are offered as evidence of the linguistic standard
of HN and attitudes of Nahuas towards their language are presented.
The final conclusion is that modern HN is a viable, vital and
functional language at the time of undertaking this research and
demonstrates a frequent usage by a large number of speakers. HN
has still not entered into:. -avital process of language death, as
is the case in other Nahuatl-speaking regions of Mexico, and is
still being maintained, particularly at community level, by adults
and children alike.The hearer, the hunter and the agouti head : aspects of intercommunication and conviviality among the Pa'ikwené (Palikur) of French GuianaPasses, Alanhttps://hdl.handle.net/10023/10082019-07-01T10:12:40Z1998-01-01T00:00:00ZThe thesis is in the broadest terms an anthropological exploration of
intercommunication; it concerns concepts and practices of speech and
hearing among a Lowland Amazonian people, the Pa'ikwene, concentrating
particularly on the community of Deuxieme Village Esperance in southern
Guyane (French Guiana). A significant aspect of the subject is the
axiological one, i. e., the moral and aesthetic values attaching to proper
dialogic, and consequently social, relations - or what Ingold describes
(1986: 141) as the "conversation that is social life".
Revealing the speech of ordinary people to be as `powerful' in its way as that
of chiefs, the study addresses the instrumentality of speaking and hearing in
the creation and maintenance of sociality. Essentially, I argue that
intersubjective communication does not so much `imply' Pa'ikwene society
(Levi-Strauss 1973: 390) as construct it as a sociable, pleasurable and
egalitarian entity; that it is, in short, one of the fundamental `tools for
conviviality' (Illich 1973).
While the role of language in the process of society has long been
recognised by anthropology, and comprehensively investigated, tht of
listening to it seems, perhaps because of the more `private' nature of the act,
not to have enjoyed the same level of sociological interest. Given this
imbalance, special emphasis is laid on native audition as embodied by the
cultural phenomenon of "Tchimap", "to hear-listen-understand", and its use
in three key spheres, the political, economic and magico-religious.
One central issue deals with the agency and perceived value of "good
hearing" in the generation of good relations between humans, and of
productive ones between humans and non-humans. Another major theme,
of relevance to the ongoing theoretical debate on 'individualismcollectivism',
involves the efficacy of "Tchimap" as a performative means of
personal autonomy, within and as part of, rather than in opposition to, the
group.
1998-01-01T00:00:00ZPasses, AlanThe thesis is in the broadest terms an anthropological exploration of
intercommunication; it concerns concepts and practices of speech and
hearing among a Lowland Amazonian people, the Pa'ikwene, concentrating
particularly on the community of Deuxieme Village Esperance in southern
Guyane (French Guiana). A significant aspect of the subject is the
axiological one, i. e., the moral and aesthetic values attaching to proper
dialogic, and consequently social, relations - or what Ingold describes
(1986: 141) as the "conversation that is social life".
Revealing the speech of ordinary people to be as `powerful' in its way as that
of chiefs, the study addresses the instrumentality of speaking and hearing in
the creation and maintenance of sociality. Essentially, I argue that
intersubjective communication does not so much `imply' Pa'ikwene society
(Levi-Strauss 1973: 390) as construct it as a sociable, pleasurable and
egalitarian entity; that it is, in short, one of the fundamental `tools for
conviviality' (Illich 1973).
While the role of language in the process of society has long been
recognised by anthropology, and comprehensively investigated, tht of
listening to it seems, perhaps because of the more `private' nature of the act,
not to have enjoyed the same level of sociological interest. Given this
imbalance, special emphasis is laid on native audition as embodied by the
cultural phenomenon of "Tchimap", "to hear-listen-understand", and its use
in three key spheres, the political, economic and magico-religious.
One central issue deals with the agency and perceived value of "good
hearing" in the generation of good relations between humans, and of
productive ones between humans and non-humans. Another major theme,
of relevance to the ongoing theoretical debate on 'individualismcollectivism',
involves the efficacy of "Tchimap" as a performative means of
personal autonomy, within and as part of, rather than in opposition to, the
group.Quechua religious terms in the departments of Apurimac and San Martin, PeruMcIntosh, G. Stewarthttps://hdl.handle.net/10023/10072019-04-01T09:29:51Z1976-01-01T00:00:00ZMy thesis "Quechua Religious Terms in the Departments of
Apurimac and San Martin, Peru" deals with the problem
of changing meaning-loads of Quechua religious terms.
I chose the departments (counties) of Apurimac and
San Martin as representative of a montana (jungle)
and sierra (mountain) Quechua culture respectively.
The purpose of the thesis is to show though the analysis
from a corpus of one hundred and thirty-two terms that
Quechua religious terms still carry much of tine nearing
load they had before the Spanish conquest despite more
than four hundred years of religious and other cultural
pressures. This study also highlights the difficulties
and unresearched areas in the fields of dialectology
and folklore of the Quechua culture, a culture that is
still very much the life of some ten million people
in Latin America today.
1976-01-01T00:00:00ZMcIntosh, G. StewartMy thesis "Quechua Religious Terms in the Departments of
Apurimac and San Martin, Peru" deals with the problem
of changing meaning-loads of Quechua religious terms.
I chose the departments (counties) of Apurimac and
San Martin as representative of a montana (jungle)
and sierra (mountain) Quechua culture respectively.
The purpose of the thesis is to show though the analysis
from a corpus of one hundred and thirty-two terms that
Quechua religious terms still carry much of tine nearing
load they had before the Spanish conquest despite more
than four hundred years of religious and other cultural
pressures. This study also highlights the difficulties
and unresearched areas in the fields of dialectology
and folklore of the Quechua culture, a culture that is
still very much the life of some ten million people
in Latin America today.Evangelization in the writings of Latin American liberation theologiansPope-Levison, Priscillahttps://hdl.handle.net/10023/10062019-04-01T09:29:49Z1988-01-01T00:00:00ZThis dissertation investigates evangelization in the writings of
ten Roman Catholic and Protestant theologians who were chosen due to
their interaction with the major themes of Liberation Theology and their
interest in evangelization. The six Roman Catholic theologians include
Leonardo Boff, Segundo Gulilea, Gustavo Gutihrrez, Archbishop Oscar
Romero, Juan Luis Segundo, and Jon Sobrino. The four Protestant
theologians include Mortimer Arias, Emilio Castro, Orlando Costas, and
Jose Miguez Bonino. Along with a chapter on each theologian, two separate
chapters are devoted to a comparison of the Roman Catholics as a
group and the Protestants as a group. The concluding chapter collects
the findings and presents a common view of evangelization in Latin
American Liberation Theology. In addition, this thesis is set in its
historical context with studies of evangelization in four Roman Catholic
Documents – Vatican II, Medellin, Evanglii Nuntiandi, and Puebla, and
WCC documents tram the New Delhi Assembly (1961) to the Vancouver
Assembly (1983).
This study demonstrates that evangelization is a central theme of
Latin American Liberation Theology. Both Roman Catholic and Protestant
liberation theologians devote a great deal of attention to this topic
which serves for them as a bridge between theology and praxis. In the
theological realm, evangelization is founded on the concept of the reign
of God. III the arena of praxis, evangelization is centered on proclamation and action.
In addition, evangelization stands as a theme around
which Roman Catholic and Protestant liberation theologians unite; the
similarities between them are significant and numerous.
These theologians present a view of evangelization which has the
potential to alter traditional understandings and existing structures of
evangelization. Their concept of evangelization pioneers new frontiers
as it interacts with liberation, the poor, denunciation, action, collective conversion,
and a comprehensive view of the reign of God.
1988-01-01T00:00:00ZPope-Levison, PriscillaThis dissertation investigates evangelization in the writings of
ten Roman Catholic and Protestant theologians who were chosen due to
their interaction with the major themes of Liberation Theology and their
interest in evangelization. The six Roman Catholic theologians include
Leonardo Boff, Segundo Gulilea, Gustavo Gutihrrez, Archbishop Oscar
Romero, Juan Luis Segundo, and Jon Sobrino. The four Protestant
theologians include Mortimer Arias, Emilio Castro, Orlando Costas, and
Jose Miguez Bonino. Along with a chapter on each theologian, two separate
chapters are devoted to a comparison of the Roman Catholics as a
group and the Protestants as a group. The concluding chapter collects
the findings and presents a common view of evangelization in Latin
American Liberation Theology. In addition, this thesis is set in its
historical context with studies of evangelization in four Roman Catholic
Documents – Vatican II, Medellin, Evanglii Nuntiandi, and Puebla, and
WCC documents tram the New Delhi Assembly (1961) to the Vancouver
Assembly (1983).
This study demonstrates that evangelization is a central theme of
Latin American Liberation Theology. Both Roman Catholic and Protestant
liberation theologians devote a great deal of attention to this topic
which serves for them as a bridge between theology and praxis. In the
theological realm, evangelization is founded on the concept of the reign
of God. III the arena of praxis, evangelization is centered on proclamation and action.
In addition, evangelization stands as a theme around
which Roman Catholic and Protestant liberation theologians unite; the
similarities between them are significant and numerous.
These theologians present a view of evangelization which has the
potential to alter traditional understandings and existing structures of
evangelization. Their concept of evangelization pioneers new frontiers
as it interacts with liberation, the poor, denunciation, action, collective conversion,
and a comprehensive view of the reign of God.The biblical concept of conversion and its social implications from a Latin American perspectiveMahecha, Guidobertohttps://hdl.handle.net/10023/10052019-04-01T09:32:09Z1991-01-01T00:00:00ZThis work presents a concept of conversion using the
researches of Liberation theologians and the relation of
Jesus to four groups in the Synoptics.
In chapter one, the main concern is the hermeneutical
problem as it defines the kind of emphasis the
interpretation of the Bible will support. Liberation
theology focuses on its context as the key aspect for a
practical interpretation.
In chapter two six Liberation theologians are studied with
a focus on the concept of conversion. All of them criticize
the type of conversion that has produced a Christianity
centered on spiritual features and disregarding the Latin
American situation.
In chapter three the situation of Palestine in Jesus' time
is described and the political, economic, and religious
situation is explored. The aim of this chapter is to show
that Jesus was born and lived under political, economic, and
religious oppression.
In chapter four the relationship of Jesus to four groups
is stated. In relation to the Pharisees, two aspects are
considered: that the table-fellowship of Jesus with the
outcasts produced a confrontation with the Pharisees; and
that, at least one time, Jesus talked about overriding the
Law because of the Kingdom of God. In relation to the
religious authorities, Jesus prophetically rejected the
Temple and Its system. In relation to the Roman authorities,
Jesus established that all things belong to God and that
loyalty to any government must be relative. In relation to
the rich and the poor, Jesus stressed through hard criticism
of riches that the Good News are preferentially to the poor.
In the conclusion, using "the relation of relationship"
model of C. Boff, it is stated that the concept of
conversion of Liberation theologians with social, economic
and political implications, is based on the Scriptures and
it is the best solution for Christianity in an oppressive
situation.
1991-01-01T00:00:00ZMahecha, GuidobertoThis work presents a concept of conversion using the
researches of Liberation theologians and the relation of
Jesus to four groups in the Synoptics.
In chapter one, the main concern is the hermeneutical
problem as it defines the kind of emphasis the
interpretation of the Bible will support. Liberation
theology focuses on its context as the key aspect for a
practical interpretation.
In chapter two six Liberation theologians are studied with
a focus on the concept of conversion. All of them criticize
the type of conversion that has produced a Christianity
centered on spiritual features and disregarding the Latin
American situation.
In chapter three the situation of Palestine in Jesus' time
is described and the political, economic, and religious
situation is explored. The aim of this chapter is to show
that Jesus was born and lived under political, economic, and
religious oppression.
In chapter four the relationship of Jesus to four groups
is stated. In relation to the Pharisees, two aspects are
considered: that the table-fellowship of Jesus with the
outcasts produced a confrontation with the Pharisees; and
that, at least one time, Jesus talked about overriding the
Law because of the Kingdom of God. In relation to the
religious authorities, Jesus prophetically rejected the
Temple and Its system. In relation to the Roman authorities,
Jesus established that all things belong to God and that
loyalty to any government must be relative. In relation to
the rich and the poor, Jesus stressed through hard criticism
of riches that the Good News are preferentially to the poor.
In the conclusion, using "the relation of relationship"
model of C. Boff, it is stated that the concept of
conversion of Liberation theologians with social, economic
and political implications, is based on the Scriptures and
it is the best solution for Christianity in an oppressive
situation.When sadness is beautiful : a study of the place of rationality and emotions within the social life of the Àve de JesusCampos, Roberta Bivar Carneirohttps://hdl.handle.net/10023/10042019-04-01T09:32:16Z2000-01-01T00:00:00ZThe ethnographic object of study of my thesis is a group of penitents, called ‘Ave de
Jesus’, that dwells in the hinterlands of Northeast Brazil. As many other groups and
penitents of this area they have a strong devotion to Padre Cicero -a deceased priest who
founded the city in which they live, Juazeiro do Norte - who they believe to be Jesus
himself. In fact, according to them, all the events of the Bible there in Juazeiro do Norte,
such that they live in a biblical time, the Bible being their actual history which should
culminate in destruction - A final end to the world.
The Ave de Jesus have incorporated into their form of life the ways of being and relating to
the world of those missionaries and religious leaders from the past, such as Padre Ibiapina,
Antonio Conselheiro, Padre Cicero, and many ‘beatos’ who wandered throughout the
‘Sertao’* preaching penance and charity. Although these religious images make a lot of
sense for those who live in such a harsh area as the ‘Sertoes’, there is no doubt that they
are also in conflict with the mainstream system of interpretation of reality.
In my thesis I explore how the biblical images take part in the construction and negotiation
of truth and meaning, and how they work as references for acting, thinking and ‘feeling’.
Because these biblical images are invariably related to moral sentiments - such as
compassion, generosity, mercy, commiseration and a highly moral evaluation of the
experience of suffering - that underlies the way of life of many penitents in Juazeiro, my
thesis focuses on the social role of emotion in building up truth and creating sociability.
The Chapter I provides the Introduction in which is given a bibliographical review on
messianic and millenarian movements and pilgrimage, and points to my own theoretical
choice. It is also in the introduction that I discuss the issue of rationality, ideology and
narratives related to the problem of my research and the methodological approach.
In Chapter III provide an overall ethnography of penance within the surrounds of Juazeiro
do Norte in the past and present.
In Chapter III I first introduce a brief ethnography of the Ave de Jesus.
In Chapter IV I explore the situation of conflict between systems of interpretation within
which Master Jose - the leader of the Ave de Jesus - finds himself. The subject of
discussion in this chapter is the role of the affective and beauty in negotiating meaning and
constructing truth.
In Chapter VI dwell upon Emotions. In this chapter I provide a discussion concerning the
importance of emotions in understanding the way of life of many penitents in Juazeiro do
Norte, with special attention to the Ave de Jesus. Another subject of discussion is what an
emotion is about and their relation to action and thought. In my ethnography and
interpretation of emotions I have focused on those emotions which are cognitively stressed
by the Ave de Jesus, such as suffering, compassion, mercy, etc. which underlies their form
of life.
In Chapter VI I provide a discussion on how images of charity are related to an ideal image
of society -a Utopia. By going deeper into the relation between images of suffering,
poverty and mendicancy I explore how the Ave de Jesus creates a sociality based on
generosity, hospitality and sharing whereby they realise a messianic expectation.
In the Conclusion I have tried to answer the main task of my thesis, that is, to provide an
understanding of how sadness is beautiful. Through all the issues elected to for discussion
in each chapter I intend to give support to my interpretation of the role and importance of
emotions within the social life of the Ave de Jesus.
*The semi-arid backlands of Northeast Brazil
2000-01-01T00:00:00ZCampos, Roberta Bivar CarneiroThe ethnographic object of study of my thesis is a group of penitents, called ‘Ave de
Jesus’, that dwells in the hinterlands of Northeast Brazil. As many other groups and
penitents of this area they have a strong devotion to Padre Cicero -a deceased priest who
founded the city in which they live, Juazeiro do Norte - who they believe to be Jesus
himself. In fact, according to them, all the events of the Bible there in Juazeiro do Norte,
such that they live in a biblical time, the Bible being their actual history which should
culminate in destruction - A final end to the world.
The Ave de Jesus have incorporated into their form of life the ways of being and relating to
the world of those missionaries and religious leaders from the past, such as Padre Ibiapina,
Antonio Conselheiro, Padre Cicero, and many ‘beatos’ who wandered throughout the
‘Sertao’* preaching penance and charity. Although these religious images make a lot of
sense for those who live in such a harsh area as the ‘Sertoes’, there is no doubt that they
are also in conflict with the mainstream system of interpretation of reality.
In my thesis I explore how the biblical images take part in the construction and negotiation
of truth and meaning, and how they work as references for acting, thinking and ‘feeling’.
Because these biblical images are invariably related to moral sentiments - such as
compassion, generosity, mercy, commiseration and a highly moral evaluation of the
experience of suffering - that underlies the way of life of many penitents in Juazeiro, my
thesis focuses on the social role of emotion in building up truth and creating sociability.
The Chapter I provides the Introduction in which is given a bibliographical review on
messianic and millenarian movements and pilgrimage, and points to my own theoretical
choice. It is also in the introduction that I discuss the issue of rationality, ideology and
narratives related to the problem of my research and the methodological approach.
In Chapter III provide an overall ethnography of penance within the surrounds of Juazeiro
do Norte in the past and present.
In Chapter III I first introduce a brief ethnography of the Ave de Jesus.
In Chapter IV I explore the situation of conflict between systems of interpretation within
which Master Jose - the leader of the Ave de Jesus - finds himself. The subject of
discussion in this chapter is the role of the affective and beauty in negotiating meaning and
constructing truth.
In Chapter VI dwell upon Emotions. In this chapter I provide a discussion concerning the
importance of emotions in understanding the way of life of many penitents in Juazeiro do
Norte, with special attention to the Ave de Jesus. Another subject of discussion is what an
emotion is about and their relation to action and thought. In my ethnography and
interpretation of emotions I have focused on those emotions which are cognitively stressed
by the Ave de Jesus, such as suffering, compassion, mercy, etc. which underlies their form
of life.
In Chapter VI I provide a discussion on how images of charity are related to an ideal image
of society -a Utopia. By going deeper into the relation between images of suffering,
poverty and mendicancy I explore how the Ave de Jesus creates a sociality based on
generosity, hospitality and sharing whereby they realise a messianic expectation.
In the Conclusion I have tried to answer the main task of my thesis, that is, to provide an
understanding of how sadness is beautiful. Through all the issues elected to for discussion
in each chapter I intend to give support to my interpretation of the role and importance of
emotions within the social life of the Ave de Jesus.
*The semi-arid backlands of Northeast BrazilFertile words : aspects of language and sociality among Yanomami people of VenezuelaRubio, Javier Carrerahttps://hdl.handle.net/10023/10032019-04-01T09:32:20Z2004-01-01T00:00:00ZIn the first part of the thesis (Chapters I to 7)1 discuss two Yanomami myths of
origin, namely the myth of the origin of the night, and the myth of the master of
banana plants. While drawing heavily on Lizot's ethnographical and linguistic
work, my analysis of the myth will be embedded within two interconnected
debates of present concern to anthropology: On the one hand, the strong
linkage between the poetics of myth narration and the poetics of the everyday
life. To better explore this relationship I will also drawn on Overing's recent work
on the fundamental importance of understanding the political philosophy that
pervades such linkage. On the other hand there is also the important role that
the world of the felt, the senses and passions play in Yanomami conceptions
and practices of sociality.
In part 2 of the thesis, I deal with the issue of Yanomami warfare by describing
Yanomami people's understanding of warfare. In doing this, I endeavour to
develop a shift from the anthropologist's theories of war among the Yanomami
to the Yanomami's own theories about both peace and its failure. War and
conflict are addressed here from the point of view of the Yanomami aesthetics
of their own convivial relations and sociality, along with its multiple oral
expressions. I demonstrate that Yanomami people have their own (strong)
theories about what is conducive to peace and war and how these theories are
grounded in moral and political values attached to a particular Yanomami
aesthetics of egalitarianism. In doing this, I explore the way Lizot emphasises
the dialectic between Yanomami conceptions of peace and warfare.
Furthermore, through an exploration of the linkage Lizot establishes between
Yanomami warfare and their morality, I wish to shed new light on the political
dimensions of their conflicts and the place of warfare in their culturally specific
aesthetics of egalitarian relationships.
Part 3 of the thesis (chapters 9, 10, 11) deals with the Yanomami elders'
speech, a mode of communication that has been almost neglected in other
previous works. After having discussed various topics (myth and the everyday,
Yanomami warfare) through which various aspects of Yanomami moral and
political philosophy can be grasped, in this last part of the thesis I show the
strong linkage between such philosophy and this type of speech. The elders'
speech is dealt with in various parts of the thesis and also in various ways. First,
and departing from the way a myth of origin explicitly makes references to it, I
illustrate, the way Yanomami people conceive of this type of speech. I do this by
describing, following Hymes' (1981,2003) insights, the way in which the myth
teller "describes" this speech in his narrative. Second, in Chapter 3, I make a
brief description of the speech and in Chapters 9, 10, and 11 I provide
fragments of the speech of an elder that I transcribed and analysed.
2004-01-01T00:00:00ZRubio, Javier CarreraIn the first part of the thesis (Chapters I to 7)1 discuss two Yanomami myths of
origin, namely the myth of the origin of the night, and the myth of the master of
banana plants. While drawing heavily on Lizot's ethnographical and linguistic
work, my analysis of the myth will be embedded within two interconnected
debates of present concern to anthropology: On the one hand, the strong
linkage between the poetics of myth narration and the poetics of the everyday
life. To better explore this relationship I will also drawn on Overing's recent work
on the fundamental importance of understanding the political philosophy that
pervades such linkage. On the other hand there is also the important role that
the world of the felt, the senses and passions play in Yanomami conceptions
and practices of sociality.
In part 2 of the thesis, I deal with the issue of Yanomami warfare by describing
Yanomami people's understanding of warfare. In doing this, I endeavour to
develop a shift from the anthropologist's theories of war among the Yanomami
to the Yanomami's own theories about both peace and its failure. War and
conflict are addressed here from the point of view of the Yanomami aesthetics
of their own convivial relations and sociality, along with its multiple oral
expressions. I demonstrate that Yanomami people have their own (strong)
theories about what is conducive to peace and war and how these theories are
grounded in moral and political values attached to a particular Yanomami
aesthetics of egalitarianism. In doing this, I explore the way Lizot emphasises
the dialectic between Yanomami conceptions of peace and warfare.
Furthermore, through an exploration of the linkage Lizot establishes between
Yanomami warfare and their morality, I wish to shed new light on the political
dimensions of their conflicts and the place of warfare in their culturally specific
aesthetics of egalitarian relationships.
Part 3 of the thesis (chapters 9, 10, 11) deals with the Yanomami elders'
speech, a mode of communication that has been almost neglected in other
previous works. After having discussed various topics (myth and the everyday,
Yanomami warfare) through which various aspects of Yanomami moral and
political philosophy can be grasped, in this last part of the thesis I show the
strong linkage between such philosophy and this type of speech. The elders'
speech is dealt with in various parts of the thesis and also in various ways. First,
and departing from the way a myth of origin explicitly makes references to it, I
illustrate, the way Yanomami people conceive of this type of speech. I do this by
describing, following Hymes' (1981,2003) insights, the way in which the myth
teller "describes" this speech in his narrative. Second, in Chapter 3, I make a
brief description of the speech and in Chapters 9, 10, and 11 I provide
fragments of the speech of an elder that I transcribed and analysed.Genetic characterisation and social structure of the East Scotland population of bottlenose dolphins (Tursiops truncatus)Islas, Valentinahttps://hdl.handle.net/10023/10022019-12-09T14:30:14Z2010-06-23T00:00:00ZThe Eastern Scottish population of bottlenose dolphins (Tursiops truncatus) is
the northernmost population of this species. The resident core of this
population consists of 120 to 150 different individuals. This small size and its
geographical isolation from other populations raises questions about its
viability and whether the population has behavioural patterns that differ
from those common to other populations of the same species. Microsatellite
genetic diversity was low and mitochondrial DNA genetic diversity values
were lowest in East Scotland compared to other populations worldwide and
to neighbouring populations around UK waters. It has been well
documented, from four different field sites worldwide, that male bottlenose
dolphins form alliances with preferred male associates. These alliances can
last for several years and the males involved show association coefficients similar to those of mothers and calves (0.8-1.0). These alliances
appear to be of great importance in obtaining matings for the males. In the
Eastern Scottish population males do not form alliances. No evidence of
strong associations between individuals of either sex was found and there
was no correlation between association and relatedness patterns. I suggest
that the isolation and small size of the population together with reduced
genetic diversity affects the pressure of kin selection for altruistic behaviours.
There is no gain in competing or associating with close relatives for access to
mates and it might be more important to avoid inbreeding by dispersing.
Although evidence of gene flow between East Scotland and its neighbouring
populations was not confirmed with Bayesian clustering analysis, a small set
of individuals from Wales were found to be closely related to individuals
from the East Coast of Scotland. In general the dynamics found in UK water
populations resemble those of the Western North Atlantic with sympatric
populations of coastal as well as pelagic individuals.
2010-06-23T00:00:00ZIslas, ValentinaThe Eastern Scottish population of bottlenose dolphins (Tursiops truncatus) is
the northernmost population of this species. The resident core of this
population consists of 120 to 150 different individuals. This small size and its
geographical isolation from other populations raises questions about its
viability and whether the population has behavioural patterns that differ
from those common to other populations of the same species. Microsatellite
genetic diversity was low and mitochondrial DNA genetic diversity values
were lowest in East Scotland compared to other populations worldwide and
to neighbouring populations around UK waters. It has been well
documented, from four different field sites worldwide, that male bottlenose
dolphins form alliances with preferred male associates. These alliances can
last for several years and the males involved show association coefficients similar to those of mothers and calves (0.8-1.0). These alliances
appear to be of great importance in obtaining matings for the males. In the
Eastern Scottish population males do not form alliances. No evidence of
strong associations between individuals of either sex was found and there
was no correlation between association and relatedness patterns. I suggest
that the isolation and small size of the population together with reduced
genetic diversity affects the pressure of kin selection for altruistic behaviours.
There is no gain in competing or associating with close relatives for access to
mates and it might be more important to avoid inbreeding by dispersing.
Although evidence of gene flow between East Scotland and its neighbouring
populations was not confirmed with Bayesian clustering analysis, a small set
of individuals from Wales were found to be closely related to individuals
from the East Coast of Scotland. In general the dynamics found in UK water
populations resemble those of the Western North Atlantic with sympatric
populations of coastal as well as pelagic individuals.The application of geomatic technologies in an indigenous context : Amazonian Indians and indigenous land rightsMenell, Davidhttps://hdl.handle.net/10023/10002019-07-01T10:12:39Z2003-01-01T00:00:00ZIndigenous people have employed Western analogue techniques (maps, charts, etc) to
support their land rights ever since their traditional territories came under threat.
Although indigenous groups utilise such tools there is still a significant divide between
the epistemological conception of these analogue techniques and the ontology of the
indigenous people. This research looks at one of the latest technologies to be utilised by
indigenous peoples, that of geomatics technologies. It examines their design and
application using the analytical techniques of anthropology juxtaposed with the
geographical methodologies. Using both the literature and three case studies drawing
from fieldwork conducted in the Peruvian Amazonian I argue that although previous
analogue techniques carried a certain epistemological baggage, they were effectively
neutral and did not impact of the ontology of the indigenous peoples. Geomatics
technologies are not neutral and carry more than just baggage, so they are not so simply
appropriated. Indigenous conceptions of landscape are not compatible with the current
design of geomatics technologies but indigenous federations are increasingly employing
them. The indigenous federation along with non-governmental organisations adopt the
geomatics technologies because of their perceived authority in land rights and their
applications in land management and saving cultural heritage. The State recognises this
authority because the design and output of geomatics conforms to its legal system.
However, indigenous peoples have a different agenda and conception of land rights.
Their agenda is based on revitalising their heritage and land rights derived through self-determination.
This research reveals such issues of power, politics and authenticity
behind its application and the ontological and epistemological philosophy of its design.
2003-01-01T00:00:00ZMenell, DavidIndigenous people have employed Western analogue techniques (maps, charts, etc) to
support their land rights ever since their traditional territories came under threat.
Although indigenous groups utilise such tools there is still a significant divide between
the epistemological conception of these analogue techniques and the ontology of the
indigenous people. This research looks at one of the latest technologies to be utilised by
indigenous peoples, that of geomatics technologies. It examines their design and
application using the analytical techniques of anthropology juxtaposed with the
geographical methodologies. Using both the literature and three case studies drawing
from fieldwork conducted in the Peruvian Amazonian I argue that although previous
analogue techniques carried a certain epistemological baggage, they were effectively
neutral and did not impact of the ontology of the indigenous peoples. Geomatics
technologies are not neutral and carry more than just baggage, so they are not so simply
appropriated. Indigenous conceptions of landscape are not compatible with the current
design of geomatics technologies but indigenous federations are increasingly employing
them. The indigenous federation along with non-governmental organisations adopt the
geomatics technologies because of their perceived authority in land rights and their
applications in land management and saving cultural heritage. The State recognises this
authority because the design and output of geomatics conforms to its legal system.
However, indigenous peoples have a different agenda and conception of land rights.
Their agenda is based on revitalising their heritage and land rights derived through self-determination.
This research reveals such issues of power, politics and authenticity
behind its application and the ontological and epistemological philosophy of its design.Caste, class and profession in old regime France: the French army and the Ségur reform of 1781Bien, David D.Smith, Jay M.Blaufarb, R.https://hdl.handle.net/10023/9672019-04-01T11:10:08Z2010-01-01T00:00:00ZFirst published in French in 1974, David D. Bien’s essay on the nature of nobility in old regime France pivoted around the 1781 “Ségur regulation” that required four generations of nobility for most officers entering the army. Once seen as a classic manifestation of the so-called “aristocratic reaction” against commoners, the loi Ségur, in Bien’s deft analysis, instead emerges as a telling sign of tensions within an increasingly divided nobility. While exploding crude myths about class conflict and its causative role in the Revolution, Bien mounts a strong case for viewing eighteenth-century social tensions as the product of professional identity as much as social class. This study is presented here for the first time in English with a short preface by Rafe Blaufarb, and a wide-ranging introduction by Jay M. Smith that places Bien’s work in the wider context of historical thinking over the past half-century on the origins of the French Revolution.
2010-01-01T00:00:00ZBien, David D.Smith, Jay M.Blaufarb, R.First published in French in 1974, David D. Bien’s essay on the nature of nobility in old regime France pivoted around the 1781 “Ségur regulation” that required four generations of nobility for most officers entering the army. Once seen as a classic manifestation of the so-called “aristocratic reaction” against commoners, the loi Ségur, in Bien’s deft analysis, instead emerges as a telling sign of tensions within an increasingly divided nobility. While exploding crude myths about class conflict and its causative role in the Revolution, Bien mounts a strong case for viewing eighteenth-century social tensions as the product of professional identity as much as social class. This study is presented here for the first time in English with a short preface by Rafe Blaufarb, and a wide-ranging introduction by Jay M. Smith that places Bien’s work in the wider context of historical thinking over the past half-century on the origins of the French Revolution.Identification of a novel class of mammalian phosphoinositol-specific phospholipase C enzymes.Stewart, AJMukherjee, JRoberts, SJLester, DFarquharson, Chttps://hdl.handle.net/10023/9562019-04-01T08:50:44Z2005-01-01T00:00:00ZPhosphoinositol (PhoIns)-specific phospholipase C enzymes (PLCs) are central to the inositol lipid signaling pathways and contribute to intracellular Ca2+ release and protein kinase C activation. Five distinct classes of PhoIns-specific PLCs are known to exist in mammals, which are activated by membrane receptor-mediated events. Here we have identified a sixth class of PhoIns-specific PLC with a novel domain structure, which we have termed PLC-eta. Two putative PLC-eta enzymes were identified in humans and in mice. Sequence analysis revealed that residues implicated in substrate binding and catalysis from other PhoIns-specific PLCs are conserved in the novel enzymes. PLC-eta enzymes are most closely related to the PLC-delta class and share a close evolutionary relationship with other PLC isozymes. EST analysis and RT-PCR data suggest that PLC-eta enzymes are expressed in several cell types and, by analogy with other mammalian PhoIns-specific PLCs, are likely to be involved in signal transduction pathways.
2005-01-01T00:00:00ZStewart, AJMukherjee, JRoberts, SJLester, DFarquharson, CPhosphoinositol (PhoIns)-specific phospholipase C enzymes (PLCs) are central to the inositol lipid signaling pathways and contribute to intracellular Ca2+ release and protein kinase C activation. Five distinct classes of PhoIns-specific PLCs are known to exist in mammals, which are activated by membrane receptor-mediated events. Here we have identified a sixth class of PhoIns-specific PLC with a novel domain structure, which we have termed PLC-eta. Two putative PLC-eta enzymes were identified in humans and in mice. Sequence analysis revealed that residues implicated in substrate binding and catalysis from other PhoIns-specific PLCs are conserved in the novel enzymes. PLC-eta enzymes are most closely related to the PLC-delta class and share a close evolutionary relationship with other PLC isozymes. EST analysis and RT-PCR data suggest that PLC-eta enzymes are expressed in several cell types and, by analogy with other mammalian PhoIns-specific PLCs, are likely to be involved in signal transduction pathways.Cellular and molecular studies of postembryonic muscle fibre recruitment in zebrafish (Danio rerio L.)Lee, Hung-Taihttps://hdl.handle.net/10023/9012019-03-29T10:28:31Z2010-06-23T00:00:00ZCellular and molecular mechanisms of postembryonic muscle fibre recruitment were investigated in zebrafish (Danio rerio L.), a standard animal model for developmental and genetic studies.
Distinct cellular mechanisms of postembryonic muscle fibre recruitment in fast and slow myotomal muscles were found. In slow muscle, three overlapping waves of stratified hyperplasia (SH) from distinct germinal zones sequentially contributed to a slow and steady increase in fibre number (FN) through the life span. In fast muscle, SH only contributed to an initial increase of FN in early larvae. Strikingly, mosaic hyperplasia (MH) appeared in late larvae and early juveniles and remained active until early adult stages, accounting for >70% of the final fibre number (FFN).
The molecular regulation of postembryonic muscle fibre recruitment was then studied by characterising myospryn and cee, two strong candidate genes previously identified from a large scale screen for genes differentially expressed during the transition from hyperplastic to hypertrophic muscle phenotypes. Zebrafish myospryn contained very similar functional domains to its mammalian orthologues, which function to bind to other proteins known to regulate muscle dystrophy. Zebrafish myospryn also shared a highly conserved syntenic genomic neighbourhood with other vertebrate orthologues. As in mammals, zebrafish myospryn were specifically expressed in striated muscles. Zebrafish cee was a single-copy gene, highly conserved among metazoans, ubiquitously expressed across tissues, and did not form part of any wider gene family. Its protein encompassed a single conserved domain (DUF410) of unknown function although knock-down of cee in C. elegans and yeast have suggested a role in regulating growth patterns. Both myospyrn and cee transcripts were up-regulated concomitant with the cessation of postembryonic muscle fibre recruitment in zebrafish, indicating a potential role in regulating muscle growth. Furthermore, a genome-wide screen of genes involved in the regulation of postembryonic muscle fibre recruitment was performed using microarray. 85 genes were found to be consistently and differentially expressed between growth stages where muscle hyperplasia was active or inactive, including genes associated with muscle contraction, metabolism, and immunity. Further bioinformatic annotation indicated these genes comprised a complex transcriptional network with molecular functions, including catalytic activity and protein binding as well as pathways associated with metabolism, tight junctions, and human diseases.
Finally, developmental plasticity of postembryonic muscle fibre recruitment to embryonic temperature was characterised. It involved transient effects including the relative timing and contribution of SH and MH, plus the rate and duration of fibre production, as well as a persistent alteration to FFN. Further investigation of FFN of fish over a broader range of embryonic temperature treatments (22, 26, 28, 31, 35°C) indicated that 26°C produced the highest FFN that was approximately 17% greater than at other temperatures. This finding implies the existence of an optimal embryonic temperature range for maximising FFN across a reaction norm. Additionally, a small but significant effect of parental temperature on FFN (up to 6% greater at 24 and 26°C than at 31°C) was evident, suggesting some parental mechanisms can affect muscle fibre recruitment patterns of progeny.
This work provides a comprehensive investigation of mechanisms underlying postembryonic muscle fibre recruitment and demonstrates the power of zebrafish as an ideal teleost model for addressing mechanistic and practical aspects of postembryonic muscle recruitment, especially the presence of all major phases of muscle fibre production in larger commercially important teleost species.
2010-06-23T00:00:00ZLee, Hung-TaiCellular and molecular mechanisms of postembryonic muscle fibre recruitment were investigated in zebrafish (Danio rerio L.), a standard animal model for developmental and genetic studies.
Distinct cellular mechanisms of postembryonic muscle fibre recruitment in fast and slow myotomal muscles were found. In slow muscle, three overlapping waves of stratified hyperplasia (SH) from distinct germinal zones sequentially contributed to a slow and steady increase in fibre number (FN) through the life span. In fast muscle, SH only contributed to an initial increase of FN in early larvae. Strikingly, mosaic hyperplasia (MH) appeared in late larvae and early juveniles and remained active until early adult stages, accounting for >70% of the final fibre number (FFN).
The molecular regulation of postembryonic muscle fibre recruitment was then studied by characterising myospryn and cee, two strong candidate genes previously identified from a large scale screen for genes differentially expressed during the transition from hyperplastic to hypertrophic muscle phenotypes. Zebrafish myospryn contained very similar functional domains to its mammalian orthologues, which function to bind to other proteins known to regulate muscle dystrophy. Zebrafish myospryn also shared a highly conserved syntenic genomic neighbourhood with other vertebrate orthologues. As in mammals, zebrafish myospryn were specifically expressed in striated muscles. Zebrafish cee was a single-copy gene, highly conserved among metazoans, ubiquitously expressed across tissues, and did not form part of any wider gene family. Its protein encompassed a single conserved domain (DUF410) of unknown function although knock-down of cee in C. elegans and yeast have suggested a role in regulating growth patterns. Both myospyrn and cee transcripts were up-regulated concomitant with the cessation of postembryonic muscle fibre recruitment in zebrafish, indicating a potential role in regulating muscle growth. Furthermore, a genome-wide screen of genes involved in the regulation of postembryonic muscle fibre recruitment was performed using microarray. 85 genes were found to be consistently and differentially expressed between growth stages where muscle hyperplasia was active or inactive, including genes associated with muscle contraction, metabolism, and immunity. Further bioinformatic annotation indicated these genes comprised a complex transcriptional network with molecular functions, including catalytic activity and protein binding as well as pathways associated with metabolism, tight junctions, and human diseases.
Finally, developmental plasticity of postembryonic muscle fibre recruitment to embryonic temperature was characterised. It involved transient effects including the relative timing and contribution of SH and MH, plus the rate and duration of fibre production, as well as a persistent alteration to FFN. Further investigation of FFN of fish over a broader range of embryonic temperature treatments (22, 26, 28, 31, 35°C) indicated that 26°C produced the highest FFN that was approximately 17% greater than at other temperatures. This finding implies the existence of an optimal embryonic temperature range for maximising FFN across a reaction norm. Additionally, a small but significant effect of parental temperature on FFN (up to 6% greater at 24 and 26°C than at 31°C) was evident, suggesting some parental mechanisms can affect muscle fibre recruitment patterns of progeny.
This work provides a comprehensive investigation of mechanisms underlying postembryonic muscle fibre recruitment and demonstrates the power of zebrafish as an ideal teleost model for addressing mechanistic and practical aspects of postembryonic muscle recruitment, especially the presence of all major phases of muscle fibre production in larger commercially important teleost species.On the dynamics and selective transport of fatty acids and organochlorines in lactating grey seals (Halichoerus grypus)Arriola Ortiz, Alinehttps://hdl.handle.net/10023/8952019-04-01T11:11:36Z2010-01-01T00:00:00ZThis thesis examines fatty acid (FA) and polychlorinated biphenyl (PCB)
dynamics in a marine top predator, the grey seal (Halichoerus grypus,) and their
transfer during lactation from mother to offspring. It examines regional and annual
variations in FA composition and PCB loads, and also how the physical and chemical
characteristics of these molecules (e.g. their polarity and size) can affect the rates of
accumulation, mobilization and transfer of specific FAs or PCBs. Two UK grey seal
colonies (North Rona (NR) and Isle of May (IOM) were studied during three
consecutive years (1996-1998 and 2004-2006). Lactating grey seals and their pups
were repeatedly captured during the lactation period and sampled for blubber, serum
and milk and analysed for FAs and PCBs.
Overall, the two colonies were clearly distinguished from each other,
suggesting that the main prey species had different FA composition, and possibly
that the seals from these colonies had different diets . These differences are probably
a direct consequence of differences in prey community structure in the two regions
where seals from these two colonies are thought to feed. Within each colony, annual
differences could be detected between some years but not between others. During
1996-98, IOM seals showed a clear change in their FA profiles while NR seals did
not. In contrast, during 2004-2006 NR seals showed a clear change while IOM seals
did not. The changes observed in IOM during 1996-1998 are consistent with the
large-scale regime shift that occurred in the North Sea during the 1990‟s.
The relative proportions of each FA that were mobilized from blubber and
transferred to the milk during lactation were very similar between colonies, and
could be explained to a large degree by their physico-chemical properties. For a given
carbon chain length the mobilization increased with increasing number of double
bonds; and for a given number of double bonds the mobilization decrease with
increasing carbon chain length. However, the mobilization also appeared to be
influenced by the specific nutritional requirements of the growing pups. For instance,
FAs that are considered essential for pup development or efficient energy storage
(e.g. saturated FAs) were more highly mobilised than expected. This selectivity was
also reflected in the FA composition of the different body compartments (maternal blubber and milk, pup blubber) that persisted throughout lactation. These changes
were also similar between the colonies.
Colonies could also be clearly distinguished by their blubber PCB profiles. IOM
seals had higher total concentrations on average than NR seals (1327.9 vs. 680.2
ng/g lipid in 2005 and 1199.7 vs. 819.0 ng/g lipid in 2006). IOM seals also had
higher total amounts in both years (79.2 vs. 38.0 mg in 2005 and 61.7 vs. 53.4 mg in
2006). One of the main differences between colonies was that females from IOM had
higher concentrations of highly chlorinated congeners than NR seals.PCB
concentrations in blubber increased towards the end of lactation. Serum and milk
PCB concentrations also increased rapidly, especially for the highly chlorinated
congeners. These results were consistent with other studies showing the increase in
concentrations as a result of lipid loss. Serum concentrations stayed constant during
the first part of lactation and increased at late lactation. This was also observed in
milk PCB concentrations. The changes in the PCB profiles in the three body
compartments were very similar between colonies. However IOM seals always had
higher total concentrations of PCBs in all of the body compartments. The
concentrations of individual congeners relative to PCB-153 showed that blubber
contained higher proportions of the highly chlorinated PCBs relative to other tissues.
There were no clear changes in these proportions in blubber during lactation, but the
relative proportions of highly chlorinated PCB In serum and milk increased
throughout lactation while the less chlorinated PCBs stayed constant. The highly
chlorinated PCBs were found in lower concentration in the milk compared to the less
chlorinated compounds suggesting a selective release from blubber to blood and a
selective transfer of PCBs to the milk.
2010-01-01T00:00:00ZArriola Ortiz, AlineThis thesis examines fatty acid (FA) and polychlorinated biphenyl (PCB)
dynamics in a marine top predator, the grey seal (Halichoerus grypus,) and their
transfer during lactation from mother to offspring. It examines regional and annual
variations in FA composition and PCB loads, and also how the physical and chemical
characteristics of these molecules (e.g. their polarity and size) can affect the rates of
accumulation, mobilization and transfer of specific FAs or PCBs. Two UK grey seal
colonies (North Rona (NR) and Isle of May (IOM) were studied during three
consecutive years (1996-1998 and 2004-2006). Lactating grey seals and their pups
were repeatedly captured during the lactation period and sampled for blubber, serum
and milk and analysed for FAs and PCBs.
Overall, the two colonies were clearly distinguished from each other,
suggesting that the main prey species had different FA composition, and possibly
that the seals from these colonies had different diets . These differences are probably
a direct consequence of differences in prey community structure in the two regions
where seals from these two colonies are thought to feed. Within each colony, annual
differences could be detected between some years but not between others. During
1996-98, IOM seals showed a clear change in their FA profiles while NR seals did
not. In contrast, during 2004-2006 NR seals showed a clear change while IOM seals
did not. The changes observed in IOM during 1996-1998 are consistent with the
large-scale regime shift that occurred in the North Sea during the 1990‟s.
The relative proportions of each FA that were mobilized from blubber and
transferred to the milk during lactation were very similar between colonies, and
could be explained to a large degree by their physico-chemical properties. For a given
carbon chain length the mobilization increased with increasing number of double
bonds; and for a given number of double bonds the mobilization decrease with
increasing carbon chain length. However, the mobilization also appeared to be
influenced by the specific nutritional requirements of the growing pups. For instance,
FAs that are considered essential for pup development or efficient energy storage
(e.g. saturated FAs) were more highly mobilised than expected. This selectivity was
also reflected in the FA composition of the different body compartments (maternal blubber and milk, pup blubber) that persisted throughout lactation. These changes
were also similar between the colonies.
Colonies could also be clearly distinguished by their blubber PCB profiles. IOM
seals had higher total concentrations on average than NR seals (1327.9 vs. 680.2
ng/g lipid in 2005 and 1199.7 vs. 819.0 ng/g lipid in 2006). IOM seals also had
higher total amounts in both years (79.2 vs. 38.0 mg in 2005 and 61.7 vs. 53.4 mg in
2006). One of the main differences between colonies was that females from IOM had
higher concentrations of highly chlorinated congeners than NR seals.PCB
concentrations in blubber increased towards the end of lactation. Serum and milk
PCB concentrations also increased rapidly, especially for the highly chlorinated
congeners. These results were consistent with other studies showing the increase in
concentrations as a result of lipid loss. Serum concentrations stayed constant during
the first part of lactation and increased at late lactation. This was also observed in
milk PCB concentrations. The changes in the PCB profiles in the three body
compartments were very similar between colonies. However IOM seals always had
higher total concentrations of PCBs in all of the body compartments. The
concentrations of individual congeners relative to PCB-153 showed that blubber
contained higher proportions of the highly chlorinated PCBs relative to other tissues.
There were no clear changes in these proportions in blubber during lactation, but the
relative proportions of highly chlorinated PCB In serum and milk increased
throughout lactation while the less chlorinated PCBs stayed constant. The highly
chlorinated PCBs were found in lower concentration in the milk compared to the less
chlorinated compounds suggesting a selective release from blubber to blood and a
selective transfer of PCBs to the milk.Kinship and the saturation of life among the Kuna of PanamáMargiotti, Margheritahttps://hdl.handle.net/10023/8912019-04-01T09:32:14Z2010-05-01T00:00:00ZThis thesis is an ethnographic analysis of kinship among the Kuna of the San Blas Archipelago of eastern Panamá, which focuses on the creation of bodies and persons. San Blas island villages are characterized by a compact layout and a burgeoning demographic concentration in relation to space. Despite land is available on surrounding mainland areas, the Kuna continue living in nucleated villages, emphasizing kinship as the value of a life in spatial and social concentration. By describing quotidian life in one Kuna community, this thesis considers what it means to live in concentration from a Kuna perspective, and how wellbeing is created through daily practices and rituals aimed at contrasting the social disengagement, that people consider an effect of domestic splitting, the ramification of collateral ties, and illnesses inflicted by invisible pathogenic beings.
My analysis focuses on two main lines of enquiry: 1) the progression of social relations from close to distant. Beginning from the house, where the bodies of co-residents are made consubstantial through commensality, the thesis analyses marriageability as the management of social distance, and the celebration of communal drinking festivals as the re-patterning of relations with different types of non-kin (e.g. non co-resident kin, the dead, and pathogenic spirits) for the regeneration of fertility and wellbeing. 2) It focuses on the person and discusses how adults make sense of babies and processes of body and kinship making in relation to non-human beings.
By describing how ritual and micro-quotidian practices operate according to patterns of density and repetition, this thesis demonstrates that concentration and saturation are the core notions of sociality and personhood for the Kuna. The thesis argues that saturation is interior to the ongoing creation of kinship.
2010-05-01T00:00:00ZMargiotti, MargheritaThis thesis is an ethnographic analysis of kinship among the Kuna of the San Blas Archipelago of eastern Panamá, which focuses on the creation of bodies and persons. San Blas island villages are characterized by a compact layout and a burgeoning demographic concentration in relation to space. Despite land is available on surrounding mainland areas, the Kuna continue living in nucleated villages, emphasizing kinship as the value of a life in spatial and social concentration. By describing quotidian life in one Kuna community, this thesis considers what it means to live in concentration from a Kuna perspective, and how wellbeing is created through daily practices and rituals aimed at contrasting the social disengagement, that people consider an effect of domestic splitting, the ramification of collateral ties, and illnesses inflicted by invisible pathogenic beings.
My analysis focuses on two main lines of enquiry: 1) the progression of social relations from close to distant. Beginning from the house, where the bodies of co-residents are made consubstantial through commensality, the thesis analyses marriageability as the management of social distance, and the celebration of communal drinking festivals as the re-patterning of relations with different types of non-kin (e.g. non co-resident kin, the dead, and pathogenic spirits) for the regeneration of fertility and wellbeing. 2) It focuses on the person and discusses how adults make sense of babies and processes of body and kinship making in relation to non-human beings.
By describing how ritual and micro-quotidian practices operate according to patterns of density and repetition, this thesis demonstrates that concentration and saturation are the core notions of sociality and personhood for the Kuna. The thesis argues that saturation is interior to the ongoing creation of kinship.Effects of cationic antimicrobial peptides on Candida and Saccharomyces speciesHarris, Mark R.https://hdl.handle.net/10023/8812019-07-01T10:12:46Z2010-06-23T00:00:00ZAntimicrobial peptides (AMPs) are found throughout the animal kingdom and act as a natural defence against a broad spectrum of pathogens. These peptides are toxic to invading organisms without acting on host cells, so are of interest for their potential to act as potent new drugs against pathogenic organisms. AMPs traverse the cell wall and predominantly target the plasma membrane, resulting in destabilisation, leakage of intracellular components and cell death. In this thesis the mode of action of several AMPs was investigated. The role of the cell wall was studied and found to mediate peptide binding, the inhibition of certain cell wall components also increased peptide action, subsequent internalisation events were observed with varying localisation patterns and the effect of several genes that alter cell susceptibility to AMP were examined.
Several Candida albicans mutants, each deficient in cell wall protein mannosylation, were tested in relation to their susceptibility to AMPs. It was discovered that cells lacking or deficient in the phosphomannan fraction, with a concomitant reduction in surface negative charge, correlated with reduced susceptibility to AMP action. To ascertain whether peptide binds to negatively charged phosphate, the effect of exogenous glucosamine 6-phosphate (but not glucosamine hydrochloride) was studied demonstrating that peptide efficacy was reduced due to the presence of exogenous phosphate. More specifically, sequestration of the truncated cationic AMP dermaseptin S3 (DsS3(1-16)) was reduced in these phosphomannan deficient mutants. Microscopy analysis of fluorescein tagged DsS3(1-16) also revealed the differential localisation patterns of this AMP: transiently binding to the plasma membrane, localisation to the vacuole or diffuse distribution throughout the cytoplasm. It is proposed that for these cationic AMPs to exert their full antifungal action they must first bind to the negatively charged phosphate.
The echinocandins are a relatively new class of antifungal that function by inhibiting 1,3-β glucan synthase resulting in reduced 1,3-β glucan in the cell wall. As AMPs have to traverse the cell wall it was postulated that cells lacking this fraction would display increased AMP binding to the membrane. Clinical isolate strains of Candida and Cryptococcus spp. were acquired to test their susceptibility to AMP and echinocandin combinations. Comparing the fractional inhibitory concentration index (FICI) (supported by viable cell counts and on a solid surface using disc diffusion assays) synergy was observed between caspofungin, anidulafungin and several AMPs in vitro. In vitro toxicity assays revealed no increase in haemolytic or cytotoxic action on combination. These synergistic combinations could provide a novel treatment against fungal pathogens.
The final area of study was based upon work that identified genes whose expression altered cell susceptibility to AMPs. Three genes were selected for investigation that upon deletion increased the action of DsS3(1-16) or magainin 2 on S. cerevisiae. Results from growth analysis, peptide sequestration and cell viability counts confirmed that deletion of HAL5, LDB7 or IMP2’ did increase susceptibility. Additionally, deletion of HAL5 increased the probability of cell depolarisation upon peptide exposure. Expression of GFP-tagged Imp2’ also increased when cells were exposed to DsS3(1-16). It was concluded that deletion of HAL5 increases depolarisation due to insufficient potassium efflux, leading to ion leakage and cell death facilitated by AMP action. Double strand break repair and DNA protection are probably compromised upon deletion of LDB7 and IMP2’, increasing the inhibitory action of DsS3(1-16) that has previously been shown to bind to DNA.
Electronic version does not contain associated previously published material
2010-06-23T00:00:00ZHarris, Mark R.Antimicrobial peptides (AMPs) are found throughout the animal kingdom and act as a natural defence against a broad spectrum of pathogens. These peptides are toxic to invading organisms without acting on host cells, so are of interest for their potential to act as potent new drugs against pathogenic organisms. AMPs traverse the cell wall and predominantly target the plasma membrane, resulting in destabilisation, leakage of intracellular components and cell death. In this thesis the mode of action of several AMPs was investigated. The role of the cell wall was studied and found to mediate peptide binding, the inhibition of certain cell wall components also increased peptide action, subsequent internalisation events were observed with varying localisation patterns and the effect of several genes that alter cell susceptibility to AMP were examined.
Several Candida albicans mutants, each deficient in cell wall protein mannosylation, were tested in relation to their susceptibility to AMPs. It was discovered that cells lacking or deficient in the phosphomannan fraction, with a concomitant reduction in surface negative charge, correlated with reduced susceptibility to AMP action. To ascertain whether peptide binds to negatively charged phosphate, the effect of exogenous glucosamine 6-phosphate (but not glucosamine hydrochloride) was studied demonstrating that peptide efficacy was reduced due to the presence of exogenous phosphate. More specifically, sequestration of the truncated cationic AMP dermaseptin S3 (DsS3(1-16)) was reduced in these phosphomannan deficient mutants. Microscopy analysis of fluorescein tagged DsS3(1-16) also revealed the differential localisation patterns of this AMP: transiently binding to the plasma membrane, localisation to the vacuole or diffuse distribution throughout the cytoplasm. It is proposed that for these cationic AMPs to exert their full antifungal action they must first bind to the negatively charged phosphate.
The echinocandins are a relatively new class of antifungal that function by inhibiting 1,3-β glucan synthase resulting in reduced 1,3-β glucan in the cell wall. As AMPs have to traverse the cell wall it was postulated that cells lacking this fraction would display increased AMP binding to the membrane. Clinical isolate strains of Candida and Cryptococcus spp. were acquired to test their susceptibility to AMP and echinocandin combinations. Comparing the fractional inhibitory concentration index (FICI) (supported by viable cell counts and on a solid surface using disc diffusion assays) synergy was observed between caspofungin, anidulafungin and several AMPs in vitro. In vitro toxicity assays revealed no increase in haemolytic or cytotoxic action on combination. These synergistic combinations could provide a novel treatment against fungal pathogens.
The final area of study was based upon work that identified genes whose expression altered cell susceptibility to AMPs. Three genes were selected for investigation that upon deletion increased the action of DsS3(1-16) or magainin 2 on S. cerevisiae. Results from growth analysis, peptide sequestration and cell viability counts confirmed that deletion of HAL5, LDB7 or IMP2’ did increase susceptibility. Additionally, deletion of HAL5 increased the probability of cell depolarisation upon peptide exposure. Expression of GFP-tagged Imp2’ also increased when cells were exposed to DsS3(1-16). It was concluded that deletion of HAL5 increases depolarisation due to insufficient potassium efflux, leading to ion leakage and cell death facilitated by AMP action. Double strand break repair and DNA protection are probably compromised upon deletion of LDB7 and IMP2’, increasing the inhibitory action of DsS3(1-16) that has previously been shown to bind to DNA.Aversiveness of sound in marine mammals : psycho-physiological basis, behavioural correlates and potential applicationsGötz, Thomashttps://hdl.handle.net/10023/8482019-07-01T10:15:16Z2008-01-01T00:00:00ZUnderstanding what psycho-physiological and behavioural factors influence
aversiveness of sound in marine mammals is important for conservation and practical
applications. The aim of this study was to determine predictors for impact of
anthropogenic noise and to develop a target-specific predator deterrence system for
use on fish farms. Three classes of stimuli were tested: 1.) grey seal underwater
communication calls expected to be used in territorial defence, 2.) high duty-cycle
moderately loud artificial sounds (some of which were based on models of
unpleasantness for humans), 3.) brief, intense pulses designed to elicit the acoustic
startle reflex.
Communication calls had no deterrence effect but instead caused attraction
responses. Tests with high duty-cycle artificial sounds showed that food-motivated
animals habituate quickly, although sound exposure caused subtle changes in diving
patterns over a longer time. Field trials using the same stimuli were used to
determine avoidance thresholds but also indicated that sound features like
‘roughness’ play a role. The startle eliciting stimuli, however, had the most dramatic
effects. To this stimulus most seals exhibited rapid flight responses, hauled out,
sensitised and showed signs of fear conditioning. Startle thresholds were found to be
80-85 dB above the assumed hearing threshold. The data showed that startle
thresholds are a crucial predictor for the occurrence of strong avoidance behaviour
and suggests that the startle response evolved to increase an animal’s propensity for
flight. Finally, a prototype predator deterrence system based on the startle sounds
was developed to repel seals whilst not affecting toothed whales. In fish farm trials,
seals were deterred at close ranges but local abundance of cetaceans did not
change showing that it is possible to cause differential responses between species
based on differences in their audiograms.
The results are used to develop noise exposure criteria and to elucidate acoustic
parameters that can be used to predict responses to anthropogenic noise.
2008-01-01T00:00:00ZGötz, ThomasUnderstanding what psycho-physiological and behavioural factors influence
aversiveness of sound in marine mammals is important for conservation and practical
applications. The aim of this study was to determine predictors for impact of
anthropogenic noise and to develop a target-specific predator deterrence system for
use on fish farms. Three classes of stimuli were tested: 1.) grey seal underwater
communication calls expected to be used in territorial defence, 2.) high duty-cycle
moderately loud artificial sounds (some of which were based on models of
unpleasantness for humans), 3.) brief, intense pulses designed to elicit the acoustic
startle reflex.
Communication calls had no deterrence effect but instead caused attraction
responses. Tests with high duty-cycle artificial sounds showed that food-motivated
animals habituate quickly, although sound exposure caused subtle changes in diving
patterns over a longer time. Field trials using the same stimuli were used to
determine avoidance thresholds but also indicated that sound features like
‘roughness’ play a role. The startle eliciting stimuli, however, had the most dramatic
effects. To this stimulus most seals exhibited rapid flight responses, hauled out,
sensitised and showed signs of fear conditioning. Startle thresholds were found to be
80-85 dB above the assumed hearing threshold. The data showed that startle
thresholds are a crucial predictor for the occurrence of strong avoidance behaviour
and suggests that the startle response evolved to increase an animal’s propensity for
flight. Finally, a prototype predator deterrence system based on the startle sounds
was developed to repel seals whilst not affecting toothed whales. In fish farm trials,
seals were deterred at close ranges but local abundance of cetaceans did not
change showing that it is possible to cause differential responses between species
based on differences in their audiograms.
The results are used to develop noise exposure criteria and to elucidate acoustic
parameters that can be used to predict responses to anthropogenic noise.The new enfant du siècle: Joseph de Maistre as a writerhttps://hdl.handle.net/10023/8472019-04-01T11:10:09Z2010-01-01T00:00:00ZJoseph de Maistre's reputation as a writer is legendary. His style, unique and alive, moulded the French language anew. It sabotaged his attempts at anonymous publication and earned him, through the centuries, the praises of enemies and admirers. Yet the relationship between Maistre's thought and writing remains ill-known. This collection is the first to examine how Maistre's ideas – including his denunciation of the written word – intersected with his writing practices and personas. The essays disclose an author formed by duty and affectionate relationships, by the conventions of public combat, by an intense sense of history, and by the imperatives of Revolution.
The essays contained within this volume were first presented at Reappraisals/Reconsidérations, the Fifth International Colloquium on Joseph de Maistre, held at Jesus College, Cambridge on 4 and 5 December 2008.; Series editor-in-chief: Guy Rowlands, University of St Andrews
2010-01-01T00:00:00ZJoseph de Maistre's reputation as a writer is legendary. His style, unique and alive, moulded the French language anew. It sabotaged his attempts at anonymous publication and earned him, through the centuries, the praises of enemies and admirers. Yet the relationship between Maistre's thought and writing remains ill-known. This collection is the first to examine how Maistre's ideas – including his denunciation of the written word – intersected with his writing practices and personas. The essays disclose an author formed by duty and affectionate relationships, by the conventions of public combat, by an intense sense of history, and by the imperatives of Revolution.Distance software: design and analysis of distance sampling surveys for estimating population sizeThomas, LenBuckland, Stephen TerrenceRexstad, EricLaake, J LStrindberg, SHedley, S LBishop, J R BMarques, Tiago A.https://hdl.handle.net/10023/8172019-04-01T08:35:29Z2010-01-01T00:00:00Z1. Distance sampling is a widely used technique for estimating the size or density of biological populations. Many distance sampling designs and most analyses use the software Distance. 2. We briefly review distance sampling and its assumptions, outline the history, structure and capabilities of Distance, and provide hints on its use. 3. Good survey design is a crucial pre-requisite for obtaining reliable results. Distance has a survey design engine, with a built-in geographic information system, that allows properties of different proposed designs to be examined via simulation, and survey plans to be generated. 4. A first step in analysis of distance sampling data is modelling the probability of detection. Distance contains three increasingly sophisticated analysis engines for this: CDS (conventional distance sampling), which models detection probability as a function of distance from the transect and assumes all objects at zero distance are detected; MCDS (multiple covariate distance sampling), which allows covariates in addition to distance; and MRDS (mark-recapture distance sampling), which relaxes the assumption of certain detection at zero distance. 5. All three engines allow estimation of density or abundance, stratified if required, with associated measures of precision calculated either analytically or via the bootstrap. 6. Advanced analysis topics covered include the use of multipliers to allow analysis of indirect surveys (such as dung or nest surveys), the DSM (density surface modelling) analysis engine for spatial and habitat modelling, and information about accessing the analysis engines directly from other software. 7. Synthesis and applications. Distance sampling is a key method for producing abundance and density estimates in challenging field conditions. The theory underlying the methods continues to expand to cope with realistic estimation situations. In step with theoretical developments, state-of-the-art software that implements these methods is described that makes the methods accessible to practicing ecologists.
2010-01-01T00:00:00ZThomas, LenBuckland, Stephen TerrenceRexstad, EricLaake, J LStrindberg, SHedley, S LBishop, J R BMarques, Tiago A.1. Distance sampling is a widely used technique for estimating the size or density of biological populations. Many distance sampling designs and most analyses use the software Distance. 2. We briefly review distance sampling and its assumptions, outline the history, structure and capabilities of Distance, and provide hints on its use. 3. Good survey design is a crucial pre-requisite for obtaining reliable results. Distance has a survey design engine, with a built-in geographic information system, that allows properties of different proposed designs to be examined via simulation, and survey plans to be generated. 4. A first step in analysis of distance sampling data is modelling the probability of detection. Distance contains three increasingly sophisticated analysis engines for this: CDS (conventional distance sampling), which models detection probability as a function of distance from the transect and assumes all objects at zero distance are detected; MCDS (multiple covariate distance sampling), which allows covariates in addition to distance; and MRDS (mark-recapture distance sampling), which relaxes the assumption of certain detection at zero distance. 5. All three engines allow estimation of density or abundance, stratified if required, with associated measures of precision calculated either analytically or via the bootstrap. 6. Advanced analysis topics covered include the use of multipliers to allow analysis of indirect surveys (such as dung or nest surveys), the DSM (density surface modelling) analysis engine for spatial and habitat modelling, and information about accessing the analysis engines directly from other software. 7. Synthesis and applications. Distance sampling is a key method for producing abundance and density estimates in challenging field conditions. The theory underlying the methods continues to expand to cope with realistic estimation situations. In step with theoretical developments, state-of-the-art software that implements these methods is described that makes the methods accessible to practicing ecologists.Comparison of aerial survey methods for estimating abundance of common scotersRexstad, EricBuckland, Stephen T.https://hdl.handle.net/10023/7842019-04-01T11:10:18Z2009-01-01T00:00:00ZDuring the month of March, four survey methods were applied to the SPA at Camarthen Bay. WWT staff carried out visual aerial surveys using distance sampling methodology (Camphuysen et al. 2004). Visual shore-based counts were also conducted. Distance measures were not consistently taken by these observers, nor was survey effort equal among the four surveys. Because they are intended to be complete counts without replication within a day, it is not possible to estimate precision of these counts, or assess bias, making comparison with other survey results difficult. Digital still data were collected and processed by APEM Ltd. Digital video imagery were captured and processed by HiDef. This report revision includes 29 March survey data from HiDef not available at the time of the release of our 17 July report.
2009-01-01T00:00:00ZRexstad, EricBuckland, Stephen T.During the month of March, four survey methods were applied to the SPA at Camarthen Bay. WWT staff carried out visual aerial surveys using distance sampling methodology (Camphuysen et al. 2004). Visual shore-based counts were also conducted. Distance measures were not consistently taken by these observers, nor was survey effort equal among the four surveys. Because they are intended to be complete counts without replication within a day, it is not possible to estimate precision of these counts, or assess bias, making comparison with other survey results difficult. Digital still data were collected and processed by APEM Ltd. Digital video imagery were captured and processed by HiDef. This report revision includes 29 March survey data from HiDef not available at the time of the release of our 17 July report.Foraging strategies in grey seals (Halichoerus grypus) : foraging effort and prey selectionGallon, Susan Louisehttps://hdl.handle.net/10023/7042019-04-01T11:10:42Z2008-01-01T00:00:00ZSwimming speeds and prey selection of temporally captive, wild grey seals
(Halichoerus grypus) were investigated in relation to prey characteristics in an
experimental set-up at the Sea Mammal Research Unit (St Andrews, UK). For breath-
hold divers, such as seals, the cost of swimming is a key variable in the management
of oxygen stores. Thus it is likely that they modulate their swim speeds in order to
maximise time spent feeding at a prey patch. We observed a strong relationship
between swimming speed and stroke and glide pattern. Seals decreased their swim
speeds by increasing their gliding period and as a result they decreased their oxygen
consumption. Results indicated that mean swim speed decreased significantly with
increasing distance to the patch, consistent with optimality model predictions. In
addition, seals modified their swim speeds in response to changes in the speed and
density of their prey. Seals decreased their swim speed as the speed of the prey
increased. On the other hand, seals increased their swim speed as the density of the
prey increased. Concurrently, bottom durations significantly increased suggesting that
seals’ foraging strategies allowed them to most efficiently exploit their environment.
Prey selection experiments investigated dietary preferences and the factors affecting
their choice to select between different types of food. In the present study, seals
maximised some aspects of their energy intake but also displayed some individual
prey preferences.
These findings indicate the importance of fine-scale observations of foraging
behaviour and the value of experimental protocols in developing our understanding of
marine mammal foraging behaviour.
2008-01-01T00:00:00ZGallon, Susan LouiseSwimming speeds and prey selection of temporally captive, wild grey seals
(Halichoerus grypus) were investigated in relation to prey characteristics in an
experimental set-up at the Sea Mammal Research Unit (St Andrews, UK). For breath-
hold divers, such as seals, the cost of swimming is a key variable in the management
of oxygen stores. Thus it is likely that they modulate their swim speeds in order to
maximise time spent feeding at a prey patch. We observed a strong relationship
between swimming speed and stroke and glide pattern. Seals decreased their swim
speeds by increasing their gliding period and as a result they decreased their oxygen
consumption. Results indicated that mean swim speed decreased significantly with
increasing distance to the patch, consistent with optimality model predictions. In
addition, seals modified their swim speeds in response to changes in the speed and
density of their prey. Seals decreased their swim speed as the speed of the prey
increased. On the other hand, seals increased their swim speed as the density of the
prey increased. Concurrently, bottom durations significantly increased suggesting that
seals’ foraging strategies allowed them to most efficiently exploit their environment.
Prey selection experiments investigated dietary preferences and the factors affecting
their choice to select between different types of food. In the present study, seals
maximised some aspects of their energy intake but also displayed some individual
prey preferences.
These findings indicate the importance of fine-scale observations of foraging
behaviour and the value of experimental protocols in developing our understanding of
marine mammal foraging behaviour.The frontal system of the Antarctic Circumpolar Current : marine mammals as ocean explorersBoehme, Larshttps://hdl.handle.net/10023/6872019-07-01T10:15:58Z2008-11-27T00:00:00ZIn this thesis, I describe large-scale and small-scale features of the Antarctic Circumpolar Current (ACC) by merging conductivity-temperature-depth (CTD) data
obtained by novel animal-borne sensors with data obtained by more conventional
means. Twenty-one CTD-Satellite Relay Data Loggers (CTD-SRDLs) were attached
to Southern elephant seals (Mirounga leonina) on South Georgia in 2004 and 2005.
This was part of a larger international study (Southern Elephant Seals as Oceanographic Samplers; SEaOS), in which I played a major role in developing the oceanographic approach used to integrate physical data from a range of sources, and the means to link biological findings to oceanographic parameters.
The development of animal-borne oceanographic sensors and their potential place within an ocean observing system is reviewed initially. Then, I describe the Series 9000 CTD-SRDL in detail, discussing its performance in the lab and during two field experiences with Southern elephant seals and Weddell seals (Leptonychotes weddellii ).
Following this, a detailed study of the ACC frontal system in the South Atlantic is
presented that uses merged Argo float data and CTD-SRDL data. The structure of
the frontal field revealed by this unique dataset is examined, and unprecedented insight into its variability is obtained. Amongst the important findings is that, contrary to most climate models, our in situ data suggest a northward shift of the ACC east of 40W in 2004 and 2005 compared to previous work. Next, two CTD-SRDL sections
are presented to identify the locations of the ACC fronts across Drake Passage,
and an empirical relationship between upper ocean temperature and baroclinic mass
transport is used to determine the transport through Drake Passage at the times of
the sections. This technique is a powerful complement to more conventional means
of data collection in this region, especially given the ability of the seals to conduct "sections" at times when ship-based fieldwork is logistically most challenging, i.e. in the winter time.
The CTD-SRDLs do not only record hydrographic data, but simultaneously record
seal movements and diving behavior. This enables insight to be obtained on the behavioral and physiological responses of Southern elephant seals to spatial environmental variability throughout their circumpolar range. The resulting energetic consequences of these variations could help explain recently observed spatially varying population trends. With a stable population at South Georgia and declining populations at
Kerguelen and Macquarie Island. This study also highlights the benefits to the sensorcarrying animals themselves by showing the usefulness of this approach in examining
the sensitivity of top predators to global and regional-scale climate variability. More
importantly, I conclude that, by implementing animal-borne sensors into ocean observing strategies, we not only gain information about global ocean circulation and enhance our understanding of climate and the corresponding heat and salt transports,
but at the same time we increase our knowledge about ocean’s top predators, their
life history and their sensitivity to climate change.
2008-11-27T00:00:00ZBoehme, LarsIn this thesis, I describe large-scale and small-scale features of the Antarctic Circumpolar Current (ACC) by merging conductivity-temperature-depth (CTD) data
obtained by novel animal-borne sensors with data obtained by more conventional
means. Twenty-one CTD-Satellite Relay Data Loggers (CTD-SRDLs) were attached
to Southern elephant seals (Mirounga leonina) on South Georgia in 2004 and 2005.
This was part of a larger international study (Southern Elephant Seals as Oceanographic Samplers; SEaOS), in which I played a major role in developing the oceanographic approach used to integrate physical data from a range of sources, and the means to link biological findings to oceanographic parameters.
The development of animal-borne oceanographic sensors and their potential place within an ocean observing system is reviewed initially. Then, I describe the Series 9000 CTD-SRDL in detail, discussing its performance in the lab and during two field experiences with Southern elephant seals and Weddell seals (Leptonychotes weddellii ).
Following this, a detailed study of the ACC frontal system in the South Atlantic is
presented that uses merged Argo float data and CTD-SRDL data. The structure of
the frontal field revealed by this unique dataset is examined, and unprecedented insight into its variability is obtained. Amongst the important findings is that, contrary to most climate models, our in situ data suggest a northward shift of the ACC east of 40W in 2004 and 2005 compared to previous work. Next, two CTD-SRDL sections
are presented to identify the locations of the ACC fronts across Drake Passage,
and an empirical relationship between upper ocean temperature and baroclinic mass
transport is used to determine the transport through Drake Passage at the times of
the sections. This technique is a powerful complement to more conventional means
of data collection in this region, especially given the ability of the seals to conduct "sections" at times when ship-based fieldwork is logistically most challenging, i.e. in the winter time.
The CTD-SRDLs do not only record hydrographic data, but simultaneously record
seal movements and diving behavior. This enables insight to be obtained on the behavioral and physiological responses of Southern elephant seals to spatial environmental variability throughout their circumpolar range. The resulting energetic consequences of these variations could help explain recently observed spatially varying population trends. With a stable population at South Georgia and declining populations at
Kerguelen and Macquarie Island. This study also highlights the benefits to the sensorcarrying animals themselves by showing the usefulness of this approach in examining
the sensitivity of top predators to global and regional-scale climate variability. More
importantly, I conclude that, by implementing animal-borne sensors into ocean observing strategies, we not only gain information about global ocean circulation and enhance our understanding of climate and the corresponding heat and salt transports,
but at the same time we increase our knowledge about ocean’s top predators, their
life history and their sensitivity to climate change.The importance of analysis method for breeding bird survey population trend estimatesThomas, LenMartin, Kathyhttps://hdl.handle.net/10023/6852019-04-01T08:35:19Z1996-01-01T00:00:00ZPopulation trends from the Breeding Bird Survey are widely used to focus conservation efforts on species thought to be in decline and to test preliminary hypotheses regarding the causes of these declines. A number of statistical methods have been used to estimate population trends, but there is no consensus us to which is the most reliable. We quantified differences in trend estimates or different analysis methods applied to the same subset of Breeding Bird Survey data. We estimated trends for 115 species in British Columbia using three analysis methods: U.S. National Biological Service route regression, Canadian Wildlife Service route regression, and nonparametric rank-trends analysis. Overall, the number of species estimated to be declining was similar among the three methods, but the number of statistically significant declines was not similar (15, 8, and 29 respectively). In addition, many differences existed among methods in the trend estimates assigned to individual species. Comparing the two route regression methods, Canadian Wildlife Service estimates had a greater absolute magnitude on average than those of the U.S. National Biological Service method. U.S. National Biological Service estimates were on average more positive than the Canadian Wildlife Service estimates when the respective agency's data selection criteria were applied separately. These results imply that our ability to detect population declines and to prioritize species of conservation concern depend strongly upon the analysis method used. This highlights the need for further research to determine how best to accurately estimate trends from the data. We suggest a method for evaluating the performance of the analysis methods by using simulated Breeding Bird Survey data.
1996-01-01T00:00:00ZThomas, LenMartin, KathyPopulation trends from the Breeding Bird Survey are widely used to focus conservation efforts on species thought to be in decline and to test preliminary hypotheses regarding the causes of these declines. A number of statistical methods have been used to estimate population trends, but there is no consensus us to which is the most reliable. We quantified differences in trend estimates or different analysis methods applied to the same subset of Breeding Bird Survey data. We estimated trends for 115 species in British Columbia using three analysis methods: U.S. National Biological Service route regression, Canadian Wildlife Service route regression, and nonparametric rank-trends analysis. Overall, the number of species estimated to be declining was similar among the three methods, but the number of statistically significant declines was not similar (15, 8, and 29 respectively). In addition, many differences existed among methods in the trend estimates assigned to individual species. Comparing the two route regression methods, Canadian Wildlife Service estimates had a greater absolute magnitude on average than those of the U.S. National Biological Service method. U.S. National Biological Service estimates were on average more positive than the Canadian Wildlife Service estimates when the respective agency's data selection criteria were applied separately. These results imply that our ability to detect population declines and to prioritize species of conservation concern depend strongly upon the analysis method used. This highlights the need for further research to determine how best to accurately estimate trends from the data. We suggest a method for evaluating the performance of the analysis methods by using simulated Breeding Bird Survey data.Retrospective power analysisThomas, Lenhttps://hdl.handle.net/10023/6792019-04-01T08:35:18Z1997-01-01T00:00:00ZMany papers have appeared in the recent biological literature encouraging us to incorporate statistical power analysis into our hypothesis testing protocol (Peterman 1990; Fairweather 1991; Muller & Benignus 1992; Taylor & Gerrodette 1993; Searcy-Bernal 1994; Thomas & Juanes 1996). The importance of doing a power analysis before beginning a study (prospective power analysis) is universally accepted: such analyses help us to decide how many samples are required to have a good chance of getting unambiguous results. In contrast, the role of power analysis after the data are collected and analyzed (retrospective power analysis) is controversial, as is evidenced by the papers of Reed and Blaustein (1995) and Hayes and Steidl (1997). The controversy is over the use of information from the sample data in retrospective power calculations. As I will show, the type of information used has fundamental implications for the value of such analyses. I compare the approaches to calculating retrospective power, noting the strengths and weaknesses of each, and make general recommendations as to how and when retrospective power analyses should be conducted.
The pdf contains the article; the ASCII file contains SAS code to calculate power and confidence limits for simple linear regression, as detailed in the article appendix.
1997-01-01T00:00:00ZThomas, LenMany papers have appeared in the recent biological literature encouraging us to incorporate statistical power analysis into our hypothesis testing protocol (Peterman 1990; Fairweather 1991; Muller & Benignus 1992; Taylor & Gerrodette 1993; Searcy-Bernal 1994; Thomas & Juanes 1996). The importance of doing a power analysis before beginning a study (prospective power analysis) is universally accepted: such analyses help us to decide how many samples are required to have a good chance of getting unambiguous results. In contrast, the role of power analysis after the data are collected and analyzed (retrospective power analysis) is controversial, as is evidenced by the papers of Reed and Blaustein (1995) and Hayes and Steidl (1997). The controversy is over the use of information from the sample data in retrospective power calculations. As I will show, the type of information used has fundamental implications for the value of such analyses. I compare the approaches to calculating retrospective power, noting the strengths and weaknesses of each, and make general recommendations as to how and when retrospective power analyses should be conducted.A unified framework for modelling wildlife population dynamicsThomas, LenBuckland, Stephen T.Newman, KBHarwood, Johnhttps://hdl.handle.net/10023/6782019-04-01T08:35:17Z2005-01-01T00:00:00ZThis paper proposes a unified framework for defining and fitting stochastic, discrete-time, discrete-stage population dynamics models. The biological system is described by a state–space model, where the true but unknown state of the population is modelled by a state process, and this is linked to survey data by an observation process. All sources of uncertainty in the inputs, including uncertainty about model specification, are readily incorporated. The paper shows how the state process can be represented as a generalization of the standard Leslie or Lefkovitch matrix. By dividing the state process into subprocesses, complex models can be constructed from manageable building blocks. The paper illustrates the approach with a model of the British Grey Seal metapopulation, using sequential importance sampling with kernel smoothing to fit the model.
The pdf document contains the full article text; program code (in S-PLUS 6.1) for the example analysis is in the three text files; data is available from the Sea Mammal Research Unit (http://www.smru.st-and.ac.uk)
2005-01-01T00:00:00ZThomas, LenBuckland, Stephen T.Newman, KBHarwood, JohnThis paper proposes a unified framework for defining and fitting stochastic, discrete-time, discrete-stage population dynamics models. The biological system is described by a state–space model, where the true but unknown state of the population is modelled by a state process, and this is linked to survey data by an observation process. All sources of uncertainty in the inputs, including uncertainty about model specification, are readily incorporated. The paper shows how the state process can be represented as a generalization of the standard Leslie or Lefkovitch matrix. By dividing the state process into subprocesses, complex models can be constructed from manageable building blocks. The paper illustrates the approach with a model of the British Grey Seal metapopulation, using sequential importance sampling with kernel smoothing to fit the model.WinBUGS for population ecologists: Bayesian modeling using Markov Chain Monte Carlo methods.Giminez, OBonner, S JKing, RuthParker, R ABrooks, S PJamieson, L EGrosbois, VMorgan, B J TThomas, Lenhttps://hdl.handle.net/10023/6772019-04-01T08:35:53Z2008-01-01T00:00:00ZThe computer package WinBUGS is introduced. We first give a brief introduction to Bayesian theory and its implementation using Markov chain Monte Carlo (MCMC) algorithms. We then present three case studies showing how WinBUGS can be used when classical theory is difficult to implement. The first example uses data on white storks from Baden Württemberg, Germany, to demonstrate the use of mark-recapture models to estimate survival, and also how to cope with unexplained variance through random effects. Recent advances in methodology and also the WinBUGS software allow us to introduce (i) a flexible way of incorporating covariates using spline smoothing and (ii) a method to deal with missing values in covariates. The second example shows how to estimate population density while accounting for detectability, using distance sampling methods applied to a test dataset collected on a known population of wooden stakes. Finally, the third case study involves the use of state-space models of wildlife population dynamics to make inferences about density dependence in a North American duck species. Reversible Jump MCMC is used to calculate the probability of various candidate models. For all examples, data and WinBUGS code are provided.
This paper was presented at the EURING 2007 Technical Meeting, January 14-21, Dunedin, New Zealand. It has been submitted for publication in the conference proceedings, which will appear as a special issue of Environmental and Ecological Statistics.; The zip file contains accompanying code in WinBUGS
2008-01-01T00:00:00ZGiminez, OBonner, S JKing, RuthParker, R ABrooks, S PJamieson, L EGrosbois, VMorgan, B J TThomas, LenThe computer package WinBUGS is introduced. We first give a brief introduction to Bayesian theory and its implementation using Markov chain Monte Carlo (MCMC) algorithms. We then present three case studies showing how WinBUGS can be used when classical theory is difficult to implement. The first example uses data on white storks from Baden Württemberg, Germany, to demonstrate the use of mark-recapture models to estimate survival, and also how to cope with unexplained variance through random effects. Recent advances in methodology and also the WinBUGS software allow us to introduce (i) a flexible way of incorporating covariates using spline smoothing and (ii) a method to deal with missing values in covariates. The second example shows how to estimate population density while accounting for detectability, using distance sampling methods applied to a test dataset collected on a known population of wooden stakes. Finally, the third case study involves the use of state-space models of wildlife population dynamics to make inferences about density dependence in a North American duck species. Reversible Jump MCMC is used to calculate the probability of various candidate models. For all examples, data and WinBUGS code are provided.Designing a shipboard line transect survey to estimate cetacean abundance off the Azores Archipelago, PortugalFaustino, Cláudia Estevinho Santoshttps://hdl.handle.net/10023/6672019-03-29T10:16:20Z2008-01-01T00:00:00ZManagement schemes dedicated to the conservation of wildlife populations rely on the effective monitoring of population size, and this requires the accurate and precise estimation of abundance. The accuracy and precision of estimates are determined to a large extent by the survey design. Line transect surveys are commonly applied to wildlife population assessments in which the primary purpose of a survey design is to ensure that the critical distance sampling assumptions are met.
Little information is available regarding cetacean abundance in the Archipelago of the Azores (Portugal). This study aims to design a line transect shipboard survey that allows the collection of data required to provide abundance estimates for such species. Several aspects must be taken into consideration when designing a survey to estimate cetacean abundance. This is an iterative process, and there is a constant trade off between the logistic constraints and the desired statistical robustness. Information on this process is provided to aid policy makers and environmental managers, such as the criteria used for the choices made when defining the elements of a survey design.
Three survey effort scenarios are provided to illustrate the range of possibilities between statistical robustness and logistic/ management restrictions. A survey is designed for the more economical scenario (L=5000Km), although the second scenario is the one recommended to be implemented (L=17,600Km) given it provides robust estimates of
abundance (CV<=0.2).
Revised version November 2008. MRes in Marine Mammal Science
2008-01-01T00:00:00ZFaustino, Cláudia Estevinho SantosManagement schemes dedicated to the conservation of wildlife populations rely on the effective monitoring of population size, and this requires the accurate and precise estimation of abundance. The accuracy and precision of estimates are determined to a large extent by the survey design. Line transect surveys are commonly applied to wildlife population assessments in which the primary purpose of a survey design is to ensure that the critical distance sampling assumptions are met.
Little information is available regarding cetacean abundance in the Archipelago of the Azores (Portugal). This study aims to design a line transect shipboard survey that allows the collection of data required to provide abundance estimates for such species. Several aspects must be taken into consideration when designing a survey to estimate cetacean abundance. This is an iterative process, and there is a constant trade off between the logistic constraints and the desired statistical robustness. Information on this process is provided to aid policy makers and environmental managers, such as the criteria used for the choices made when defining the elements of a survey design.
Three survey effort scenarios are provided to illustrate the range of possibilities between statistical robustness and logistic/ management restrictions. A survey is designed for the more economical scenario (L=5000Km), although the second scenario is the one recommended to be implemented (L=17,600Km) given it provides robust estimates of
abundance (CV<=0.2).Behavioural changes of a long-ranging diver in response to oceanographic conditionsPhotopoulos, Theonihttps://hdl.handle.net/10023/6652019-03-29T10:16:22Z2007-01-01T00:00:00ZThe development of an animal-borne instrument that can record oceanographic measurements (CTD-SRDL) has enabled the collection of oceanographic data at a scale relevant to the counterpart behavioural data, both in time and 3-dimensional space. This has advanced the potential for studies of the behaviour of deep-diving marine animals and the way in which they respond to their environment, yet the nature of the data delivered by CTD-SRDLs presents substantial analytical challenges and places constraints on its biological interpretation. Behavioural and environmental data, collected using CTD-SRDLs deployed on southern elephant seals (Mirounga leonina) from the South Georgia subpopulation in 2004 and 2005, are analysed for 13 females and 4 males (21,015 dives). Compressed dive profiles are used to classify individual dives into six distinct types based on their 2-dimensional time-depth characteristics using random forest classification. The relationship between dive type and environmental variables, derived from oceanographic data recorded on board the animals, is investigated in the context of regression analysis, employing a multinomial model, as well as independently fitted Generalized Linear Models (GLM) and Generalized Additive Models (GAM) for each dive type. Regression is not found to be an appropriate method for analysing abstracted behavioural dive data, and other methods are suggested. We show that functional specializations can be manifested within a dive type, using square bottom dives (SQ) as an example. The usefulness of dive classification is discussed in the context of behavioural interpretation, and validity of the ecological functions attached to each class. Preliminary analyses are important drivers of further research into improving the interpretability of abstracted behavioural data, and developing efficient, standardized methods for widespread application to this type of data, which is obtained in abundance via satellite telemetry.
BL 5019 Research project. MRes Environmental Biology
2007-01-01T00:00:00ZPhotopoulos, TheoniThe development of an animal-borne instrument that can record oceanographic measurements (CTD-SRDL) has enabled the collection of oceanographic data at a scale relevant to the counterpart behavioural data, both in time and 3-dimensional space. This has advanced the potential for studies of the behaviour of deep-diving marine animals and the way in which they respond to their environment, yet the nature of the data delivered by CTD-SRDLs presents substantial analytical challenges and places constraints on its biological interpretation. Behavioural and environmental data, collected using CTD-SRDLs deployed on southern elephant seals (Mirounga leonina) from the South Georgia subpopulation in 2004 and 2005, are analysed for 13 females and 4 males (21,015 dives). Compressed dive profiles are used to classify individual dives into six distinct types based on their 2-dimensional time-depth characteristics using random forest classification. The relationship between dive type and environmental variables, derived from oceanographic data recorded on board the animals, is investigated in the context of regression analysis, employing a multinomial model, as well as independently fitted Generalized Linear Models (GLM) and Generalized Additive Models (GAM) for each dive type. Regression is not found to be an appropriate method for analysing abstracted behavioural dive data, and other methods are suggested. We show that functional specializations can be manifested within a dive type, using square bottom dives (SQ) as an example. The usefulness of dive classification is discussed in the context of behavioural interpretation, and validity of the ecological functions attached to each class. Preliminary analyses are important drivers of further research into improving the interpretability of abstracted behavioural data, and developing efficient, standardized methods for widespread application to this type of data, which is obtained in abundance via satellite telemetry.Why Don’t the French Do Think Tanks?: France Faces up to the Anglo-Saxon Superpowers, 1918-1921Williams, Ahttps://hdl.handle.net/10023/6432019-04-01T08:17:23Z2008-01-01T00:00:00ZAbstract. This article asks the question: ‘Why have the French not developed ‘‘think tanks’’?’ by looking at the period when such institutions were being set up in The UK and the United States, during the preparation for the Paris Peace Conference and its aftermath. It is suggested that the reasons were a mixture of French bureaucratic and intellectual disposition but also in a growing revulsion in Paris at what was seen as duplicity and conspiracy by its Allies to ignore the legitimate concerns and needs of the French people. The central source material used is the papers of the ‘Commission Bourgeois’ whose deliberations are often rather air brushed out of academic literature on the period and work done within the French Foreign Ministry.
Copyright of Cambridge University Press
2008-01-01T00:00:00ZWilliams, AAbstract. This article asks the question: ‘Why have the French not developed ‘‘think tanks’’?’ by looking at the period when such institutions were being set up in The UK and the United States, during the preparation for the Paris Peace Conference and its aftermath. It is suggested that the reasons were a mixture of French bureaucratic and intellectual disposition but also in a growing revulsion in Paris at what was seen as duplicity and conspiracy by its Allies to ignore the legitimate concerns and needs of the French people. The central source material used is the papers of the ‘Commission Bourgeois’ whose deliberations are often rather air brushed out of academic literature on the period and work done within the French Foreign Ministry.The Reformation in Fife, 1560-1640McCallum, Johnhttps://hdl.handle.net/10023/6382019-07-01T10:16:33Z2008-11-27T00:00:00ZThis thesis traces the establishment and development of a functioning reformed
church in the parishes of Fife after the official Reformation of 1560. Based
principally on archival sources, especially the records of the kirk sessions which
governed the church at parish level, it examines how ecclesiastical institutions
developed and interacted with laypeople, and evaluates the progress made in the
challenging task of inculcating Protestant values and identity in Fife’s parishioners.
The first section examines the development of the reformed church in three chapters
on the parish ministry, church discipline, and reformed worship respectively. The
progress made in providing parish ministers and establishing kirk sessions was
hesitant, and it took several decades before the church’s institutions were functioning
healthily across Fife. This gradual process of reformation was not what the original
reformers wanted, but it may have in fact eased the transition to the more firmly
Protestant parish culture that emerged around the turn of the century.
The second section looks more thematically at three key aspects of the church,
focusing mainly on this latter period. The fourth chapter analyses the ministry as a
profession, while the fifth chapter goes on to discuss the efforts made to instruct the
laity in more detailed Protestant understandings from the 1590s onwards. The sixth
and final chapter returns to the subject of discipline, describing the main targets of the
disciplinary regime and evaluating the effectiveness of discipline. The church that
emerged in the seventeenth century was relatively healthy, staffed by a stable and
well-educated ministry, and was starting to make much stronger efforts to educate and
discipline the laypeople of Fife.
The thesis concludes that while the Scottish Reformation still emerges as an
ultimately successful transformation, the path to religious change was more
complicated than has been appreciated by historians.
2008-11-27T00:00:00ZMcCallum, JohnThis thesis traces the establishment and development of a functioning reformed
church in the parishes of Fife after the official Reformation of 1560. Based
principally on archival sources, especially the records of the kirk sessions which
governed the church at parish level, it examines how ecclesiastical institutions
developed and interacted with laypeople, and evaluates the progress made in the
challenging task of inculcating Protestant values and identity in Fife’s parishioners.
The first section examines the development of the reformed church in three chapters
on the parish ministry, church discipline, and reformed worship respectively. The
progress made in providing parish ministers and establishing kirk sessions was
hesitant, and it took several decades before the church’s institutions were functioning
healthily across Fife. This gradual process of reformation was not what the original
reformers wanted, but it may have in fact eased the transition to the more firmly
Protestant parish culture that emerged around the turn of the century.
The second section looks more thematically at three key aspects of the church,
focusing mainly on this latter period. The fourth chapter analyses the ministry as a
profession, while the fifth chapter goes on to discuss the efforts made to instruct the
laity in more detailed Protestant understandings from the 1590s onwards. The sixth
and final chapter returns to the subject of discipline, describing the main targets of the
disciplinary regime and evaluating the effectiveness of discipline. The church that
emerged in the seventeenth century was relatively healthy, staffed by a stable and
well-educated ministry, and was starting to make much stronger efforts to educate and
discipline the laypeople of Fife.
The thesis concludes that while the Scottish Reformation still emerges as an
ultimately successful transformation, the path to religious change was more
complicated than has been appreciated by historians.Estimating the distribution of demersal fishing effort from VMS data using hidden Markov models.Borchers, David L.Reid, David G.https://hdl.handle.net/10023/6362019-04-01T11:10:17Z2008-01-01T00:00:00ZPreviously in the University eprints HAIRST pilot service at http://eprints.st-andrews.ac.uk/archive/00000461/
2008-01-01T00:00:00ZBorchers, David L.Reid, David G.Incorporating Model Uncertainty into the Sequential Importance Sampling Framework using a Model Averaging Approach, or Trans-Dimensional Sequential Importance Sampling.Lynam, ChristopherKing, RuthThomas, LenBuckland, Stephen T.https://hdl.handle.net/10023/6352019-04-01T11:10:17Z2007-01-01T00:00:00ZA sequential Bayesian Monte Carlo approach is proposed in which model space can be explored during the Sequential Importance Sampling (SIS, a.k.a. Particle Filtering) fitting process. The algorithm allows model space to be explored while filtering forwards through time and takes a similar approach to Reversible Jump Markov Chain Monte Carlo (RJMCMC) strategies, whereby parameters jump into and out of the model structure. Possible efficiency gains of the new Trans-Dimensional SIS routine are discussed and the approach is considered most beneficial when the exploration of large model space in the SIS framework is desired.
Previously in the University eprints HAIRST pilot service at http://eprints.st-andrews.ac.uk/archive/00000463/
2007-01-01T00:00:00ZLynam, ChristopherKing, RuthThomas, LenBuckland, Stephen T.A sequential Bayesian Monte Carlo approach is proposed in which model space can be explored during the Sequential Importance Sampling (SIS, a.k.a. Particle Filtering) fitting process. The algorithm allows model space to be explored while filtering forwards through time and takes a similar approach to Reversible Jump Markov Chain Monte Carlo (RJMCMC) strategies, whereby parameters jump into and out of the model structure. Possible efficiency gains of the new Trans-Dimensional SIS routine are discussed and the approach is considered most beneficial when the exploration of large model space in the SIS framework is desired.Accommodating availability bias on line transect surveys using hidden Markov models.Borchers, David L.Samara, Filipa I. P.https://hdl.handle.net/10023/6332019-04-01T11:10:17Z2007-01-01T00:00:00ZMaximum likelihood methods are developed which accommodate intermittent animal availability of animals on line transect surveys. Existing 'availability bias' correction methods are shown to be inadequate in general. The new method is applied to an aerial survey of whales, using a hidden Markov model to characterise the availability process.
Previously in the University eprints HAIRST pilot service at http://eprints.st-andrews.ac.uk/archive/00000458/
2007-01-01T00:00:00ZBorchers, David L.Samara, Filipa I. P.Maximum likelihood methods are developed which accommodate intermittent animal availability of animals on line transect surveys. Existing 'availability bias' correction methods are shown to be inadequate in general. The new method is applied to an aerial survey of whales, using a hidden Markov model to characterise the availability process.Investigation of towed hydrophone monitoring power for harbour porpoise on the SCANS II survey.Borchers, David L.Burt, M. Louise.https://hdl.handle.net/10023/6322019-04-01T11:10:17Z2007-01-01T00:00:00ZWe investigate the power of harbour porpoise monitoring programmes which use an index of relative abundance to detect change. Power depends on the variability in the constant of proportionality relating the index to absolute abundance, as well as on the variability in the index given this constant. We estimate both from the SCANS II data and from European Seabirds at Sea (ESAS) data. Estimates of the coefficient of variation of the constant of proportionality are large and this results in very low power. Because these estimates may be unrealistically large for well-designed monitoring programs, we feel it is inappropriate to draw strong conclusions about the power of future monitoring programmes based on them.
ESAS surveys are found to be more efficient in terms of effort required to achieve given power, than the SCANS II passive acoustic surveys. However, the comparison may not be a fair one, for the following reason. The estimated CV of the constant of proportionality is obtained from the ratio of the index of density and the corresponding SCANS II absolute density estimate; the ESAS index is likely to be more highly correlated with the SCANS II estimate than the acoustic index, because like the SCANS II estimate, it is based on visual detections. In addition, standardization of the passive acoustic survey methods could yield substantially higher efficiency.
We provide a table giving power as a function of the CV of the constant of proportionality and the CV of the index, given this constant - this can be used to compare methods if reliable estimates of these CVs are available.
Previously in the University eprints HAIRST pilot service at http://eprints.st-andrews.ac.uk/archive/00000457/
2007-01-01T00:00:00ZBorchers, David L.Burt, M. Louise.We investigate the power of harbour porpoise monitoring programmes which use an index of relative abundance to detect change. Power depends on the variability in the constant of proportionality relating the index to absolute abundance, as well as on the variability in the index given this constant. We estimate both from the SCANS II data and from European Seabirds at Sea (ESAS) data. Estimates of the coefficient of variation of the constant of proportionality are large and this results in very low power. Because these estimates may be unrealistically large for well-designed monitoring programs, we feel it is inappropriate to draw strong conclusions about the power of future monitoring programmes based on them.
ESAS surveys are found to be more efficient in terms of effort required to achieve given power, than the SCANS II passive acoustic surveys. However, the comparison may not be a fair one, for the following reason. The estimated CV of the constant of proportionality is obtained from the ratio of the index of density and the corresponding SCANS II absolute density estimate; the ESAS index is likely to be more highly correlated with the SCANS II estimate than the acoustic index, because like the SCANS II estimate, it is based on visual detections. In addition, standardization of the passive acoustic survey methods could yield substantially higher efficiency.
We provide a table giving power as a function of the CV of the constant of proportionality and the CV of the index, given this constant - this can be used to compare methods if reliable estimates of these CVs are available.Methods for estimating sperm whale abundance from passive acoustic line transect surveys.Borchers, David L.Brewer, CiaraMatthews, Justinhttps://hdl.handle.net/10023/6312019-04-01T11:10:18Z2007-01-01T00:00:00ZPreviously in the University eprints HAIRST pilot service at http://eprints.st-andrews.ac.uk/archive/00000456/
2007-01-01T00:00:00ZBorchers, David L.Brewer, CiaraMatthews, JustinPoint and interval estimates of abundance using multiple covariate distance sampling: an example using great bustards.Rexstad, Erichttps://hdl.handle.net/10023/6292019-04-01T11:10:16Z2007-01-01T00:00:00ZDescription of computations to produce sex-specific estimates of density from a multiple-covariate distance sampling analysis. Program Distance 5.0 has limited capacity to bootstrap certain types of analytical situations (e.g., cluster size as a covariate). Herein I describe steps and code to perform an analysis of this sort. Possible ways to adapt this code for similar analyses are described.
Previously in the University eprints HAIRST pilot service at http://eprints.st-andrews.ac.uk/archive/00000447/; The pdf file contains the tech report, the ASCII (.R) file contains the accompanying R code.
2007-01-01T00:00:00ZRexstad, EricDescription of computations to produce sex-specific estimates of density from a multiple-covariate distance sampling analysis. Program Distance 5.0 has limited capacity to bootstrap certain types of analytical situations (e.g., cluster size as a covariate). Herein I describe steps and code to perform an analysis of this sort. Possible ways to adapt this code for similar analyses are described.Non-uniform coverage estimators for distance sampling.Rexstad, Erichttps://hdl.handle.net/10023/6282019-04-01T11:10:16Z2007-01-01T00:00:00ZAllocation of sampling effort in the context of distance sampling is considered.
Specifically, allocation of effort in proportion to portions of the survey region that likely
contain high concentrations of animals are explored. The probability of a portion of the
survey region being included in the sample is proportional to the estimated number of
animals in that portion. These estimated numbers of animals may be derived from a
density surface model. This results in unequal coverage probability, and a Horvitz-
Thompson like estimator can be used to estimate population abundance. The properties
of this estimator is explored here via simulation. The benefits, measured in terms of
increased precision over traditional equal coverage probability estimators, are meagre,
and largely manifested when the underlying population distribution is a smooth gradient.
Previously in the University eprints HAIRST pilot service at http://eprints.st-andrews.ac.uk/archive/00000445/
2007-01-01T00:00:00ZRexstad, EricAllocation of sampling effort in the context of distance sampling is considered.
Specifically, allocation of effort in proportion to portions of the survey region that likely
contain high concentrations of animals are explored. The probability of a portion of the
survey region being included in the sample is proportional to the estimated number of
animals in that portion. These estimated numbers of animals may be derived from a
density surface model. This results in unequal coverage probability, and a Horvitz-
Thompson like estimator can be used to estimate population abundance. The properties
of this estimator is explored here via simulation. The benefits, measured in terms of
increased precision over traditional equal coverage probability estimators, are meagre,
and largely manifested when the underlying population distribution is a smooth gradient.Acoustic and ecological investigations into predator-prey interactions between Antarctic krill (Euphausia superba) and seal and bird predatorsCox, Martin Jameshttps://hdl.handle.net/10023/5792019-07-01T10:14:26Z2008-11-27T00:00:00Z1. Antarctic krill (Euphausia superba) form aggregations known as swarms that vary greatly in size and density. Six acoustic surveys were conducted as part of multidisciplinary studies at two study sites, the western and eastern core boxes (WCB and ECB), during the 1997, 1998 and 1999 austral summers, at South Georgia. A quantitative, automated, image processing algorithm was used to identify swarms, and calculate swarm descriptors, or metrics. In contrast to acoustic surveys of aggregations of other pelagic species, a strong correlation (r = 0.88, p = 0.02, 95% C.I.= 0.24 to 0.99) between the number of krill swarms and the mean areal krill density [rho.hat] was found. Multivariate analysis was used to partition swarms into three types, based on contrasting morphological and internal krill density parameters. Swarm types were distributed differently between inter-surveys and between on and off-shelf regions.
This swarm type variation has implications for krill predators, by causing spatial heterogeneity in swarm detectability, suggesting that for optimal foraging to occur, predators must engage in some sort of adaptive foraging strategy.
2. Krill predator-prey interactions were found to occur at multiple spatial and temporal scales, in a nested, or hierarchical structure. At the largest inter-survey scale, an index of variability, I, was developed to compare variation in survey-scale predator sightings, sea temperature and [rho.hat]. Using I and a two-way ANOVA, core box, rather than year, was found to be a more important factor in determining species distribution. The absence of Blue-petrels (Halobaena caerulea) and the elevated number of Antarctic fur seals (Arctocephalus gazella) suggest that 1998 was a characterised by colder than average water surrounding South Georgia, and a high [rho.hat] in the ECB. At the smaller, intra-survey scales (<80 km, <5 day), the characteristic scale (distances in which
predator group size, or krill density were similar, L_s) were determined. For krill and predators L_s varied by survey and the L_s of krill also varied by depth within a survey. Overlap in L_s were stronger between predator species than between a predator species and krill, indicating predators were taking foraging cues from the activity of predators, rather than from the underlying krill distribution. No relationship was found between swarm characteristics and predator activity, suggesting either there is no relationship between krill swarms and predators, or that the predator and acoustic observation techniques may not be appropriate to detect such a relationship.
3. To overcome the 2-D sampling limitations of conventional echosounders, a multibeam echosounder (MBE) observed entire swarms in three-dimensions. Swarms found in the nearshore environment of Livingston Island situated in the South Shetland Islands, exhibited only a narrow range of surface area to volume ratios or roughnesses (R = 3.3, CV = 0.23), suggesting that krill adopt a consistent group behaviour to maintain swarm shape. Generalized additive models (GAM) suggested that the presence of air-breathing predators influenced the shape of a krill swarm (R decreased in the presence of predators: the swarm became more spherical). A 2D distance sampling framework was used to estimate the abundance, N, and associated variance of krill swarms. This technique took into account angular and range detectability (half-normal, [sigma_r.hat] = 365.00 m, CV = 0.16) and determined the vertical distribution of krill swarms to be best approximated by a beta-distribution ([alpha.hat] = 2.62, [CV.hat] = 0.19; [beta.hat] = 2.41, [CV.hat] = 0.15), giving the abundance of swarms in survey region as [N.hat] = 5,062 ([CV.hat] = 0.35). This research represents a substantial contribution to developing estimation of pelagic biomass using MBEs.
4. When using a single- or split-beam missing pings occur when the transmit or receive cycles are interrupted, often by aeration of the water column, under the echosounder transducer during rough weather. A thin-plate regression spline based approach was used to model the missing krill data, with knots chosen using a branch and bound algorithm. This method performs well for acoustic observations of krill swarms where data are tightly clustered and change rapidly. For these data the technique outperformed the standard MGCV GAM, and the technique is applicable for estimating acoustically derived biomass from line transect surveys.
2008-11-27T00:00:00ZCox, Martin James1. Antarctic krill (Euphausia superba) form aggregations known as swarms that vary greatly in size and density. Six acoustic surveys were conducted as part of multidisciplinary studies at two study sites, the western and eastern core boxes (WCB and ECB), during the 1997, 1998 and 1999 austral summers, at South Georgia. A quantitative, automated, image processing algorithm was used to identify swarms, and calculate swarm descriptors, or metrics. In contrast to acoustic surveys of aggregations of other pelagic species, a strong correlation (r = 0.88, p = 0.02, 95% C.I.= 0.24 to 0.99) between the number of krill swarms and the mean areal krill density [rho.hat] was found. Multivariate analysis was used to partition swarms into three types, based on contrasting morphological and internal krill density parameters. Swarm types were distributed differently between inter-surveys and between on and off-shelf regions.
This swarm type variation has implications for krill predators, by causing spatial heterogeneity in swarm detectability, suggesting that for optimal foraging to occur, predators must engage in some sort of adaptive foraging strategy.
2. Krill predator-prey interactions were found to occur at multiple spatial and temporal scales, in a nested, or hierarchical structure. At the largest inter-survey scale, an index of variability, I, was developed to compare variation in survey-scale predator sightings, sea temperature and [rho.hat]. Using I and a two-way ANOVA, core box, rather than year, was found to be a more important factor in determining species distribution. The absence of Blue-petrels (Halobaena caerulea) and the elevated number of Antarctic fur seals (Arctocephalus gazella) suggest that 1998 was a characterised by colder than average water surrounding South Georgia, and a high [rho.hat] in the ECB. At the smaller, intra-survey scales (<80 km, <5 day), the characteristic scale (distances in which
predator group size, or krill density were similar, L_s) were determined. For krill and predators L_s varied by survey and the L_s of krill also varied by depth within a survey. Overlap in L_s were stronger between predator species than between a predator species and krill, indicating predators were taking foraging cues from the activity of predators, rather than from the underlying krill distribution. No relationship was found between swarm characteristics and predator activity, suggesting either there is no relationship between krill swarms and predators, or that the predator and acoustic observation techniques may not be appropriate to detect such a relationship.
3. To overcome the 2-D sampling limitations of conventional echosounders, a multibeam echosounder (MBE) observed entire swarms in three-dimensions. Swarms found in the nearshore environment of Livingston Island situated in the South Shetland Islands, exhibited only a narrow range of surface area to volume ratios or roughnesses (R = 3.3, CV = 0.23), suggesting that krill adopt a consistent group behaviour to maintain swarm shape. Generalized additive models (GAM) suggested that the presence of air-breathing predators influenced the shape of a krill swarm (R decreased in the presence of predators: the swarm became more spherical). A 2D distance sampling framework was used to estimate the abundance, N, and associated variance of krill swarms. This technique took into account angular and range detectability (half-normal, [sigma_r.hat] = 365.00 m, CV = 0.16) and determined the vertical distribution of krill swarms to be best approximated by a beta-distribution ([alpha.hat] = 2.62, [CV.hat] = 0.19; [beta.hat] = 2.41, [CV.hat] = 0.15), giving the abundance of swarms in survey region as [N.hat] = 5,062 ([CV.hat] = 0.35). This research represents a substantial contribution to developing estimation of pelagic biomass using MBEs.
4. When using a single- or split-beam missing pings occur when the transmit or receive cycles are interrupted, often by aeration of the water column, under the echosounder transducer during rough weather. A thin-plate regression spline based approach was used to model the missing krill data, with knots chosen using a branch and bound algorithm. This method performs well for acoustic observations of krill swarms where data are tightly clustered and change rapidly. For these data the technique outperformed the standard MGCV GAM, and the technique is applicable for estimating acoustically derived biomass from line transect surveys.The synthesis of 5-substituted hydantoinsMurray, Ross Georgehttps://hdl.handle.net/10023/5712019-07-01T10:18:00Z2008-06-25T00:00:00ZThe Bucherer-Bergs reaction is a classical multi-component reaction that yields hydantoins, which can be hydrolysed to afford α-amino acids. Hydantoins have many uses in modern organic synthesis, and this moiety has been included in a number of therapeutic agents, which have a wide range of biological activities. Herein, we report a mild synthesis of 5- and 5,5-substituted hydantoins from α-aminonitriles using Hünig’s base and carbon dioxide. This reaction can be performed in excellent yields, using a variety of organic solvents and is applicable to a range of substrates. In an extension to the above methodology, a one-pot Lewis acid-catalysed synthesis of hydantoins from ketones has also been developed and optimised in organic media. This reaction can be performed in excellent yields and is suitable for the synthesis of 5- and 5,5-substituted hydantoins.
2008-06-25T00:00:00ZMurray, Ross GeorgeThe Bucherer-Bergs reaction is a classical multi-component reaction that yields hydantoins, which can be hydrolysed to afford α-amino acids. Hydantoins have many uses in modern organic synthesis, and this moiety has been included in a number of therapeutic agents, which have a wide range of biological activities. Herein, we report a mild synthesis of 5- and 5,5-substituted hydantoins from α-aminonitriles using Hünig’s base and carbon dioxide. This reaction can be performed in excellent yields, using a variety of organic solvents and is applicable to a range of substrates. In an extension to the above methodology, a one-pot Lewis acid-catalysed synthesis of hydantoins from ketones has also been developed and optimised in organic media. This reaction can be performed in excellent yields and is suitable for the synthesis of 5- and 5,5-substituted hydantoins.Functional analysis of the orthobunyavirus nucleocapsid (N) proteinEifan, Saleh A.https://hdl.handle.net/10023/5422019-07-01T10:16:27Z2008-01-01T00:00:00ZBunyamwera virus (BUNV) is the prototype of the family Bunyaviridae. It has a
tripartite genome consisting of negative sense RNA segments called large (L),
medium (M) and small (S). The S segment encodes the nucleocapsid protein (N) of
233 amino acids. The N protein encapsidates all three segments to form
transcriptionally active ribonucleoproteins (RNPs). The aim of this project was to
determine the domain map of BUNV N protein.
To investigate residues in BUNV N crucial for its functionality, random and site-
specific mutagenesis were performed on a cDNA clone encoding the BUNV N
protein. In total, 102 single amino acid substitutions were generated in the BUNV N
protein sequence.
All mutant N proteins were used in a BUNV minigenome system to compare their
activity to wt BUNV N. The mutant proteins displayed a wide-range of activity, from
parental-like to essentially inactive. The most disruptive mutations were R94A,
I118N, W134A, Y141C, L177A, K179I and W193A.
Sixty-four clones carrying single substitutions in the BUNV N protein were used in the
BUNV rescue system in an attempt to recover viable mutant viruses. Fifty
recombinant mutant viruses were rescued and 14 N genes were nonrescuable.
The 50 mutant viruses were characterized by: titration, protein labelling, western
blotting, temperature sensitivity and host-restriction. Mutant viruses displayed a wide range of titers between 10³
-10⁸ pfu/ml, and three different plaque sizes large,
medium and small. Protein labelling and western blotting showed that mutations in
the N gene did not affect expression of the other viral genes as much as affecting N
protein expression. It was demonstrated that single amino acid substitutions could
alter N protein electrophoretic mobility in SDS- PAGE (e.g. P19Q and L53F).
Temperature sensitivity tests showed that recombinant viruses N74S, S96S, K228T
and G230R were ts, growing at 33˚C but not at 37˚C or 38˚C, while the parental virus grew at all temperatures. Using the northern blotting technique, mutant viruses N74S
and S96G were shown to have a ts defect in genome-synthesis (late replication
step), while mutant viruses K228T and G230R had a ts defect in antigenome-
synthesis (early replication step).
Host-restriction experiments were performed using 5 different cell lines (Vero-E6,
BHK-21, 2FTGH-V, A549-V and 293-V). Overall, the parental virus grew similarly in
all cell lines. Likewise, the majority of mutant viruses follow this pattern except mutant
virus Y23A. It showed a 100-fold reduction in titer in 2FTGH-V cells. Comparing the
ratios of intracellular and extracellular particles revealed that only 15% of the total
virus particles of mutant Y23A was released as extracellular particles compared to
30% of the parental virus.
Fourteen N genes were nonrescuable. They were characterized by (i) their activity in
the BUNV minigenome system, (ii) their activity in BUNV packaging assay, (iii) their
ability to form multimers, (iv) their ability to interact with L protein, and (v) their impact
on RNA synthesis.
In summary, BUNV N protein was shown to be multi-functional and involved in the
regulation of virus transcription and replication, RNA synthesis and assembly, via
interactions with the viral L polymerase, RNA backbone, itself or the viral
glycoproteins.
2008-01-01T00:00:00ZEifan, Saleh A.Bunyamwera virus (BUNV) is the prototype of the family Bunyaviridae. It has a
tripartite genome consisting of negative sense RNA segments called large (L),
medium (M) and small (S). The S segment encodes the nucleocapsid protein (N) of
233 amino acids. The N protein encapsidates all three segments to form
transcriptionally active ribonucleoproteins (RNPs). The aim of this project was to
determine the domain map of BUNV N protein.
To investigate residues in BUNV N crucial for its functionality, random and site-
specific mutagenesis were performed on a cDNA clone encoding the BUNV N
protein. In total, 102 single amino acid substitutions were generated in the BUNV N
protein sequence.
All mutant N proteins were used in a BUNV minigenome system to compare their
activity to wt BUNV N. The mutant proteins displayed a wide-range of activity, from
parental-like to essentially inactive. The most disruptive mutations were R94A,
I118N, W134A, Y141C, L177A, K179I and W193A.
Sixty-four clones carrying single substitutions in the BUNV N protein were used in the
BUNV rescue system in an attempt to recover viable mutant viruses. Fifty
recombinant mutant viruses were rescued and 14 N genes were nonrescuable.
The 50 mutant viruses were characterized by: titration, protein labelling, western
blotting, temperature sensitivity and host-restriction. Mutant viruses displayed a wide range of titers between 10³
-10⁸ pfu/ml, and three different plaque sizes large,
medium and small. Protein labelling and western blotting showed that mutations in
the N gene did not affect expression of the other viral genes as much as affecting N
protein expression. It was demonstrated that single amino acid substitutions could
alter N protein electrophoretic mobility in SDS- PAGE (e.g. P19Q and L53F).
Temperature sensitivity tests showed that recombinant viruses N74S, S96S, K228T
and G230R were ts, growing at 33˚C but not at 37˚C or 38˚C, while the parental virus grew at all temperatures. Using the northern blotting technique, mutant viruses N74S
and S96G were shown to have a ts defect in genome-synthesis (late replication
step), while mutant viruses K228T and G230R had a ts defect in antigenome-
synthesis (early replication step).
Host-restriction experiments were performed using 5 different cell lines (Vero-E6,
BHK-21, 2FTGH-V, A549-V and 293-V). Overall, the parental virus grew similarly in
all cell lines. Likewise, the majority of mutant viruses follow this pattern except mutant
virus Y23A. It showed a 100-fold reduction in titer in 2FTGH-V cells. Comparing the
ratios of intracellular and extracellular particles revealed that only 15% of the total
virus particles of mutant Y23A was released as extracellular particles compared to
30% of the parental virus.
Fourteen N genes were nonrescuable. They were characterized by (i) their activity in
the BUNV minigenome system, (ii) their activity in BUNV packaging assay, (iii) their
ability to form multimers, (iv) their ability to interact with L protein, and (v) their impact
on RNA synthesis.
In summary, BUNV N protein was shown to be multi-functional and involved in the
regulation of virus transcription and replication, RNA synthesis and assembly, via
interactions with the viral L polymerase, RNA backbone, itself or the viral
glycoproteins.Coastal zone management in Dubai with reference to ecological characterization along Dubai CreekAl Zahed, Khalidhttps://hdl.handle.net/10023/5412019-07-01T10:14:58Z2008-01-01T00:00:00ZIntegrated Coastal Zone Management (ICZM) is a dynamic process in which a coordinated
strategy is developed and implemented for the allocation of environmental, socio-cultural, and
institutional resources to achieve the conservation and sustainable multiple use of the coastal
zone.
The present study titled “Coastal Zone Management in Dubai with reference to ecological
characterization” is an effort to consider critical water quality and ecological issues in the
current and future coastal zone of Dubai Creek. The work included water quality, ecology and
numerical modeling for predicting future conditions. This study is utmost significant due to
management of critical coastal environmental issues (fish mortality, bad odour, unaesthetic
view, algal bloom etc.) in Dubai Creek besides protection of internationally recognized bird
sanctuary (Ras Al Khor Wildlife Sanctuary) and sustainable multibillion dollar of property
developments as an extension of Dubai Creek. Comprehensive attempt made to collect
primary data on water quality and ecology during 2005 and 2006 from specific monitoring
stations spreading along Dubai Creek.
The pragmatic results in Dubai Creek are alarming; the upper region is susceptible to high
organic pollution which exhibits 3-122 folds high nutrients levels while biodiversity in the
same region at the seabed is almost died and non-existing. The current assessment suggests a
policy for the ICZM and an “Immediate Action Plan” for the beneficial and sustainable
development of Dubai Creek.
The study recommends the following mitigation as a tool for the management strategies of
Dubai Creek lagoon:
Dredging in the lagoon of Dubai Creek. --
Tertiary treatment of wastewater from Awir STP prior to discharge into the Creek or
divert the discharge from the lagoon of Dubai Creek. --
A new Government Decree for the water quality thresholds in Dubai Creek.
2008-01-01T00:00:00ZAl Zahed, KhalidIntegrated Coastal Zone Management (ICZM) is a dynamic process in which a coordinated
strategy is developed and implemented for the allocation of environmental, socio-cultural, and
institutional resources to achieve the conservation and sustainable multiple use of the coastal
zone.
The present study titled “Coastal Zone Management in Dubai with reference to ecological
characterization” is an effort to consider critical water quality and ecological issues in the
current and future coastal zone of Dubai Creek. The work included water quality, ecology and
numerical modeling for predicting future conditions. This study is utmost significant due to
management of critical coastal environmental issues (fish mortality, bad odour, unaesthetic
view, algal bloom etc.) in Dubai Creek besides protection of internationally recognized bird
sanctuary (Ras Al Khor Wildlife Sanctuary) and sustainable multibillion dollar of property
developments as an extension of Dubai Creek. Comprehensive attempt made to collect
primary data on water quality and ecology during 2005 and 2006 from specific monitoring
stations spreading along Dubai Creek.
The pragmatic results in Dubai Creek are alarming; the upper region is susceptible to high
organic pollution which exhibits 3-122 folds high nutrients levels while biodiversity in the
same region at the seabed is almost died and non-existing. The current assessment suggests a
policy for the ICZM and an “Immediate Action Plan” for the beneficial and sustainable
development of Dubai Creek.
The study recommends the following mitigation as a tool for the management strategies of
Dubai Creek lagoon:
Dredging in the lagoon of Dubai Creek. --
Tertiary treatment of wastewater from Awir STP prior to discharge into the Creek or
divert the discharge from the lagoon of Dubai Creek. --
A new Government Decree for the water quality thresholds in Dubai Creek.Syntactic relations in San Martin QuechuaHowkins, Angelahttps://hdl.handle.net/10023/5292019-07-01T10:16:00Z1977-01-01T00:00:00ZLinguistic description has been described as "the application of a particular linguistic theory to a selected field of linguistic phenomena". The thesis presented here offers a partial application of Axiomatic Functionalism, (partial because its concern is with syntax only), to data collected on the San Martín dialect of Quechua.
Proportionate to the whole body of Quechua studies, there has been little produced on the syntax of any Quechua dialect. Most syntactic studies, as do the large majority of phonological and morphological studies, use American methodology, be it based on Bloomfieldian linguistics, or be it based on those of Chomsky. The present methodology stands diametrically opposed to both schools of American linguistics cited above, and as a result introduces a fresh approach to the study of the syntactic aspect of Quechua. With Axiomatic functionalism, a new way of looking at Quechua grammar is presented and thus much of what is accepted "fact" reappraised. For this reason, while the concern of the thesis is with producing a description of syntactic relations in San Martín Quechua under the terms of Axiomatic Functionalism, reference is made to descriptions of other Quechua dialects, most notably where the application of Axiomatic Functionalism produces statements containing certain phenomena which are quite different from statements made on equivalent phenomena in other dialects using a different linguistic theory. Moreover, Axiomatic Fundamentalism is a deductive theory, and so statements regarding the data contained in the description are not statements of "fact", but are hypotheses which may stand as valid hypotheses regarding the data unless they can be refuted.
Given that the theoretical base on which the description rests is different from that used in other descriptions of Quechua dialects, and so that the hypotheses made regarding syntactic relations in San Martín Quechua may be tested, Part I of the thesis is given over to the theoretical side of the work: to explaining the relation between theory and description in Chapter I, to giving brief explications of those notions in the theory which have particular relevance for a syntactic description in Chapter II, and in noting some of the limits set to the selection of the data for description in Chapter III./ The axioms and definitions of the theory are given in Appendix A. Part II of the thesis, which is in six chapters, deals with the description proper. Structures which may stand as sentences are established and analysed into their constituent structures, the relations between each constituent being ascertained. Analysis is carried through to the stage where there are no constituents analysable in syntactic terms left.
1977-01-01T00:00:00ZHowkins, AngelaLinguistic description has been described as "the application of a particular linguistic theory to a selected field of linguistic phenomena". The thesis presented here offers a partial application of Axiomatic Functionalism, (partial because its concern is with syntax only), to data collected on the San Martín dialect of Quechua.
Proportionate to the whole body of Quechua studies, there has been little produced on the syntax of any Quechua dialect. Most syntactic studies, as do the large majority of phonological and morphological studies, use American methodology, be it based on Bloomfieldian linguistics, or be it based on those of Chomsky. The present methodology stands diametrically opposed to both schools of American linguistics cited above, and as a result introduces a fresh approach to the study of the syntactic aspect of Quechua. With Axiomatic functionalism, a new way of looking at Quechua grammar is presented and thus much of what is accepted "fact" reappraised. For this reason, while the concern of the thesis is with producing a description of syntactic relations in San Martín Quechua under the terms of Axiomatic Functionalism, reference is made to descriptions of other Quechua dialects, most notably where the application of Axiomatic Functionalism produces statements containing certain phenomena which are quite different from statements made on equivalent phenomena in other dialects using a different linguistic theory. Moreover, Axiomatic Fundamentalism is a deductive theory, and so statements regarding the data contained in the description are not statements of "fact", but are hypotheses which may stand as valid hypotheses regarding the data unless they can be refuted.
Given that the theoretical base on which the description rests is different from that used in other descriptions of Quechua dialects, and so that the hypotheses made regarding syntactic relations in San Martín Quechua may be tested, Part I of the thesis is given over to the theoretical side of the work: to explaining the relation between theory and description in Chapter I, to giving brief explications of those notions in the theory which have particular relevance for a syntactic description in Chapter II, and in noting some of the limits set to the selection of the data for description in Chapter III./ The axioms and definitions of the theory are given in Appendix A. Part II of the thesis, which is in six chapters, deals with the description proper. Structures which may stand as sentences are established and analysed into their constituent structures, the relations between each constituent being ascertained. Analysis is carried through to the stage where there are no constituents analysable in syntactic terms left.Carving wood and creating shamans : an ethnographic account of visual capacity among the Kuna of PanamáFortis, Paolohttps://hdl.handle.net/10023/5232019-07-01T10:05:39Z2008-06-25T00:00:00ZThis thesis is an ethnographic account of the carving of wooden ritual statues and of the shamanic figure of the seer among the Kuna of the San Blas archipelago of Panamá. Through a study of the production of wooden ritual statues and of the birth and initiation of seers, I show that the distinction between the visible and the invisible, and between designs and images, is a crucial aspect of Kuna ways of thinking and experiencing their world. On one hand, the Kuna theory of design shows the importance of the development of social skills in the creation of person and sociality. On the other hand, the Kuna concept of image points to the relation between human and ancestral beings and to the transformative capacities of both. Through the constant interplay of the two categories, people interact with cosmic forces and create social life.
The ethnography explores three aspects of the problem. First, the relationship between the islands inhabited by Kuna people and the mainland forest is described, focusing on the distance and separation of the two domains. The forest is perceived as a space populated by ancestral animal and tree entities, as well as demons and souls of the dead.
Second, the carving of the ritual statues and the skill of Kuna carvers are described in relation to human and supernatural fertility. The birth of seers, different from that of other babies, provides evidence of the importance of natal design as the potential skills of each person.
Third, relationships between human and supernatural beings are described considering Kuna myth and ritual action, in comparison with other indigenous American societies. This thesis concludes that it is through carving wooden statues and developing the capacity to see, Kuna people seek security in social life and protection from a predatory cosmos.
2008-06-25T00:00:00ZFortis, PaoloThis thesis is an ethnographic account of the carving of wooden ritual statues and of the shamanic figure of the seer among the Kuna of the San Blas archipelago of Panamá. Through a study of the production of wooden ritual statues and of the birth and initiation of seers, I show that the distinction between the visible and the invisible, and between designs and images, is a crucial aspect of Kuna ways of thinking and experiencing their world. On one hand, the Kuna theory of design shows the importance of the development of social skills in the creation of person and sociality. On the other hand, the Kuna concept of image points to the relation between human and ancestral beings and to the transformative capacities of both. Through the constant interplay of the two categories, people interact with cosmic forces and create social life.
The ethnography explores three aspects of the problem. First, the relationship between the islands inhabited by Kuna people and the mainland forest is described, focusing on the distance and separation of the two domains. The forest is perceived as a space populated by ancestral animal and tree entities, as well as demons and souls of the dead.
Second, the carving of the ritual statues and the skill of Kuna carvers are described in relation to human and supernatural fertility. The birth of seers, different from that of other babies, provides evidence of the importance of natal design as the potential skills of each person.
Third, relationships between human and supernatural beings are described considering Kuna myth and ritual action, in comparison with other indigenous American societies. This thesis concludes that it is through carving wooden statues and developing the capacity to see, Kuna people seek security in social life and protection from a predatory cosmos.Investigations into the use of quantified Bayesian Maximum Entropy methods to generate improved distribution maps and biomass estimates from fisheries acoustic survey dataHeywood, Ben G.https://hdl.handle.net/10023/5122019-04-01T11:10:45Z2008-06-01T00:00:00ZThis thesis describes elements of the assessment and application of Bayesian Maximum Entropy (MaxEnt) image reconstruction techniques for the analysis of fisheries acoustic survey data. The objective is to investigate the utility of this approach in mapping density distributions and estimating biomass. The MaxEnt image reconstruction method derives originally from the field of astrophysics, and this thesis represents an attempt to apply the principles of MaxEnt to the field of ocean ecology. Essentially, what is required is to generate maps of the density distribution of pelagic species (species living in the water column) from extremely limited and sometimes skewed line-transect acoustic survey data. Techniques used presently are largely unsatisfactory for a variety of reasons, and are often inapplicable for data from surveys that do not follow a particular design strategy. This thesis investigates the usefulness of the MaxEnt technique in overcoming some of the difficulties of acoustic survey analysis. A study is made into the possibility of objectively testing whether these techniques offer improvements in accuracy over existing techniques, by attempting to reconstruct simulated data from a virtual survey. I find that plausible reconstructions are possible, and that statistical comparisons indicate these reconstructions are accurate. The technique is also applied quantitatively to
real-world survey data, offering new insights into the abundance of Antarctic krill (Euphausia superba) in the Scotia Sea - raising abundance estimates from 109 million tonnes to 208 million tonnes - and into the relative abundance of fish and jellyfish in the Namibian Benguela, where it is shown that the biomass of jellyfish (12.2 million tonnes) now exceeds that of fish (3.6 million tonnes).
2008-06-01T00:00:00ZHeywood, Ben G.This thesis describes elements of the assessment and application of Bayesian Maximum Entropy (MaxEnt) image reconstruction techniques for the analysis of fisheries acoustic survey data. The objective is to investigate the utility of this approach in mapping density distributions and estimating biomass. The MaxEnt image reconstruction method derives originally from the field of astrophysics, and this thesis represents an attempt to apply the principles of MaxEnt to the field of ocean ecology. Essentially, what is required is to generate maps of the density distribution of pelagic species (species living in the water column) from extremely limited and sometimes skewed line-transect acoustic survey data. Techniques used presently are largely unsatisfactory for a variety of reasons, and are often inapplicable for data from surveys that do not follow a particular design strategy. This thesis investigates the usefulness of the MaxEnt technique in overcoming some of the difficulties of acoustic survey analysis. A study is made into the possibility of objectively testing whether these techniques offer improvements in accuracy over existing techniques, by attempting to reconstruct simulated data from a virtual survey. I find that plausible reconstructions are possible, and that statistical comparisons indicate these reconstructions are accurate. The technique is also applied quantitatively to
real-world survey data, offering new insights into the abundance of Antarctic krill (Euphausia superba) in the Scotia Sea - raising abundance estimates from 109 million tonnes to 208 million tonnes - and into the relative abundance of fish and jellyfish in the Namibian Benguela, where it is shown that the biomass of jellyfish (12.2 million tonnes) now exceeds that of fish (3.6 million tonnes).Sparse codingFoldiak, PEndres, D Mhttps://hdl.handle.net/10023/4942019-04-01T10:39:23Z2008-01-01T00:00:00ZMammalian brains consist of billions of neurons, each capable of independent electrical activity. Information in the brain is represented by the pattern of activation of this large neural population, forming a neural code. The neural code defines what pattern of neural activity corresponds to each represented information item. In the sensory system, such items may indicate the presence of a stimulus object or the value of some stimulus parameter, assuming that each time this item is represented the neural activity pattern will be the same or at least similar. One important and relatively simple property of this code is the fraction of neurons that are strongly active at any one time. For a set of N binary neurons (which can either be 'active' or 'inactive'), the average (i.e., expected value) of this fraction across all information items is the sparseness of the code. This average fraction can vary from close to 0 to about 1/2. Average fractions above 1/2 can always be decreased below 1/2 without loss of information by replacing each active neuron with an inactive one, and vice versa. Sparse coding is the representation of items by the strong activation of a relatively small set of neurons. For each stimulus, this is a different subset of all available neurons.
The(frequently updated) original version is avalable at http://www.scholarpedia.org/article/Sparse_coding
2008-01-01T00:00:00ZFoldiak, PEndres, D MMammalian brains consist of billions of neurons, each capable of independent electrical activity. Information in the brain is represented by the pattern of activation of this large neural population, forming a neural code. The neural code defines what pattern of neural activity corresponds to each represented information item. In the sensory system, such items may indicate the presence of a stimulus object or the value of some stimulus parameter, assuming that each time this item is represented the neural activity pattern will be the same or at least similar. One important and relatively simple property of this code is the fraction of neurons that are strongly active at any one time. For a set of N binary neurons (which can either be 'active' or 'inactive'), the average (i.e., expected value) of this fraction across all information items is the sparseness of the code. This average fraction can vary from close to 0 to about 1/2. Average fractions above 1/2 can always be decreased below 1/2 without loss of information by replacing each active neuron with an inactive one, and vice versa. Sparse coding is the representation of items by the strong activation of a relatively small set of neurons. For each stimulus, this is a different subset of all available neurons.Investigation into a prominent 38 kHz scattering layer in the North SeaMair, Angus MacDonaldhttps://hdl.handle.net/10023/4902019-07-01T10:07:46Z2008-07-01T00:00:00ZThe aim of this study was to investigate the composition of an acoustic scattering layer in the North Sea that is particularly strong at 38 kHz. A full definition of the biological composition of the layer, along with its acoustic properties, would allow for it to be confidently removed from data collected during acoustic fish surveys, where it presents a potential source of bias. The layer, traditionally and informally referred to as consisting of zooplankton, appears similar to others observed internationally. The methodology utilised in this study consisted of biological and acoustic sampling, followed by application of forward and inverse acoustic modelling techniques. Acoustic data was collected at 38, 120 and 200 kHz in July 2003, with the addition of 18 kHz in July 2004. Net samples were collected in layers of relatively strong 38 kHz acoustic scattering using a U-tow vehicle (2003) and a MIKT net (2004). Acoustic data were scrutinised to determine actual backscattering, expressed as mean volume backscattering strength (MVBS) (dB). This observed MVBS (MVBSobs) was compared with backscattering predicted by applying the forward problem solution (MVBSpred) to sampled animal densities in order to determine whether those animals were responsible for the enhanced 38 kHz scattering. In most instances, MVBSobs > MVBSpred, more pronounced at 38 kHz. It was found that MVBSpred approached MVBSobs more closely with MIKT than with U-tow samples, but that the 38 kHz mismatch was present in both. Inversion of candidate acoustic models predicted gas-bearing scatterers, which are strong at 38 kHz, as most likely to be responsible for this. Potential sources of inconsistencies between MVBSpred and MVBSobs were identified. The presented forward and inverse solutions infer that although the layer often contains large numbers of common zooplankton types, such as copepods and euphausiids, these are not the dominant acoustic scatterer at 38 kHz. Rather, there remains an unidentified, probably gas-bearing scatterer that contributes significantly to observed scattering levels at this frequency. This study identifies and considerably narrows the list of candidates that are most likely to be responsible for enhanced 38 kHz scattering in the North Sea layer, and recommendations are made for potential future studies.
2008-07-01T00:00:00ZMair, Angus MacDonaldThe aim of this study was to investigate the composition of an acoustic scattering layer in the North Sea that is particularly strong at 38 kHz. A full definition of the biological composition of the layer, along with its acoustic properties, would allow for it to be confidently removed from data collected during acoustic fish surveys, where it presents a potential source of bias. The layer, traditionally and informally referred to as consisting of zooplankton, appears similar to others observed internationally. The methodology utilised in this study consisted of biological and acoustic sampling, followed by application of forward and inverse acoustic modelling techniques. Acoustic data was collected at 38, 120 and 200 kHz in July 2003, with the addition of 18 kHz in July 2004. Net samples were collected in layers of relatively strong 38 kHz acoustic scattering using a U-tow vehicle (2003) and a MIKT net (2004). Acoustic data were scrutinised to determine actual backscattering, expressed as mean volume backscattering strength (MVBS) (dB). This observed MVBS (MVBSobs) was compared with backscattering predicted by applying the forward problem solution (MVBSpred) to sampled animal densities in order to determine whether those animals were responsible for the enhanced 38 kHz scattering. In most instances, MVBSobs > MVBSpred, more pronounced at 38 kHz. It was found that MVBSpred approached MVBSobs more closely with MIKT than with U-tow samples, but that the 38 kHz mismatch was present in both. Inversion of candidate acoustic models predicted gas-bearing scatterers, which are strong at 38 kHz, as most likely to be responsible for this. Potential sources of inconsistencies between MVBSpred and MVBSobs were identified. The presented forward and inverse solutions infer that although the layer often contains large numbers of common zooplankton types, such as copepods and euphausiids, these are not the dominant acoustic scatterer at 38 kHz. Rather, there remains an unidentified, probably gas-bearing scatterer that contributes significantly to observed scattering levels at this frequency. This study identifies and considerably narrows the list of candidates that are most likely to be responsible for enhanced 38 kHz scattering in the North Sea layer, and recommendations are made for potential future studies.Church & society in eighteenth-century Geneva, 1700-1789Powell McNutt, Jennifer R.https://hdl.handle.net/10023/4772017-04-10T11:52:17Z2008-06-26T00:00:00ZThis doctoral thesis, entitled “Church & Society in Eighteenth-Century Geneva, 1700-1789”, will seek to reappraise the relationship between religion and the Enlightenment through the context of eighteenth-century Geneva. Based on the perspectives of the philosophes, historians have generally understood the Enlightenment as the source of secularization and a period of religious decline. However, more recent work has begun to reassess the developments of religion in the eighteenth century beyond the philosophes, resulting in an increasingly multi-faceted picture of religion in the age of Enlightenment. This thesis will contribute to that revisionist effort.
Eighteenth-century Geneva offers an intriguing example because it allows one to observe the encounter of the Reformation and the Enlightenment in the figurative meeting between Calvin and Voltaire. With that in mind, this work will re-examine the legacy of Calvin from 1700 to 1789 through a socio-historical and theological approach in order to analyze the functioning of religious life in Genevan society, the theological content and development of preaching and worship, and the clerical responses to incidents of conflict in relation to the government and the philosophes. The near totality of this research has stemmed from the study of manuscript sources within the Genevan archives, such as sermons, church and government records, and official and personal correspondence. Through the perspective of Geneva’s church and clergy, a far more complex picture of the dynamic between religion and the Enlightenment will emerge supporting the understanding that the Enlightenment occurred differently in different contexts and challenging the widespread attribution of the secularization theory and the decline of religion thesis to the eighteenth century.
2008-06-26T00:00:00ZPowell McNutt, Jennifer R.This doctoral thesis, entitled “Church & Society in Eighteenth-Century Geneva, 1700-1789”, will seek to reappraise the relationship between religion and the Enlightenment through the context of eighteenth-century Geneva. Based on the perspectives of the philosophes, historians have generally understood the Enlightenment as the source of secularization and a period of religious decline. However, more recent work has begun to reassess the developments of religion in the eighteenth century beyond the philosophes, resulting in an increasingly multi-faceted picture of religion in the age of Enlightenment. This thesis will contribute to that revisionist effort.
Eighteenth-century Geneva offers an intriguing example because it allows one to observe the encounter of the Reformation and the Enlightenment in the figurative meeting between Calvin and Voltaire. With that in mind, this work will re-examine the legacy of Calvin from 1700 to 1789 through a socio-historical and theological approach in order to analyze the functioning of religious life in Genevan society, the theological content and development of preaching and worship, and the clerical responses to incidents of conflict in relation to the government and the philosophes. The near totality of this research has stemmed from the study of manuscript sources within the Genevan archives, such as sermons, church and government records, and official and personal correspondence. Through the perspective of Geneva’s church and clergy, a far more complex picture of the dynamic between religion and the Enlightenment will emerge supporting the understanding that the Enlightenment occurred differently in different contexts and challenging the widespread attribution of the secularization theory and the decline of religion thesis to the eighteenth century.Bayesian binning beats approximate alternatives: estimating peri-stimulus time histogramsEndres, D MOram, M WSchindelin, J.E.Foldiak, Phttps://hdl.handle.net/10023/4732019-04-01T10:36:27Z2008-01-01T00:00:00ZThe peristimulus time histogram (PSTH) and its more continuous cousin, the spike density function (SDF) are staples in the analytic toolkit of neurophysiologists. The former is usually obtained by binning spike trains, whereas the standard method for the latter is smoothing with a Gaussian kernel. Selection of a bin width or a kernel size is often done in an relatively arbitrary fashion, even though there have been recent attempts to remedy this situation. We develop an exact Bayesian, generative model approach to estimating PSTHs and demonstate its superiority to competing methods. Further advantages of our scheme include automatic complexity control and error bars on its predictions.
2008-01-01T00:00:00ZEndres, D MOram, M WSchindelin, J.E.Foldiak, PThe peristimulus time histogram (PSTH) and its more continuous cousin, the spike density function (SDF) are staples in the analytic toolkit of neurophysiologists. The former is usually obtained by binning spike trains, whereas the standard method for the latter is smoothing with a Gaussian kernel. Selection of a bin width or a kernel size is often done in an relatively arbitrary fashion, even though there have been recent attempts to remedy this situation. We develop an exact Bayesian, generative model approach to estimating PSTHs and demonstate its superiority to competing methods. Further advantages of our scheme include automatic complexity control and error bars on its predictions.Characterisation of Sulfolobus solfataricus Ard1, a promiscuous N-acetyltransferaseMackay, Dale Tarahttps://hdl.handle.net/10023/4682019-07-01T10:18:35Z2008-06-27T00:00:00ZCompaction of DNA into chromatin is an important feature of every living cell. This compaction phenomenon is brought about and maintained by a variety of DNA binding proteins, which have evolved to suit the specific needs of the different cell types spanning the three kingdoms of life; the eukaryotes, prokaryotes and archaea. Sulfolobus solfataricus, a member of the crenarchaeal subdivision of the archaea, has two prominent DNA binding proteins known as Alba (1&2) and Sso7d. Alba1 is acetylated in vivo at two positions and this modification lowers its’ affinity for binding DNA. Acetylation levels impact many cellular processes and in higher organisms play a critical role in the development of many cancers and other diseases.
This thesis documents the finding and characterisation of the N-terminal acetyltransferase (ssArd1) of SsoAlba1, based on its’ sequence homology to the catalytic subunits Ard1, Nat3 and Mak3 belonging to the larger eukaryal Nat complexes NatA, NatB and NatC, respectively. Mutagenesis studies revealed that ssArd1 preferentially acetylates N-termini bearing a serine or alanine residue at position 1 (after methionine cleavage). It is also capable of acetylating other proteins with very different physical structures. These findings allow classification of ssArd1 as a promiscuous acetyltransferase belonging to the Gcn5-N-acetyltransferase (GNAT) superfamily. The active site of the enzyme was examined through mutagenesis studies, revealing that the mechanism of acetylation is likely to proceed through a direct acetyl transfer involving a tetrahedral intermediate. Structural studies provided some insight into the molecular structure of ssArd1.
2008-06-27T00:00:00ZMackay, Dale TaraCompaction of DNA into chromatin is an important feature of every living cell. This compaction phenomenon is brought about and maintained by a variety of DNA binding proteins, which have evolved to suit the specific needs of the different cell types spanning the three kingdoms of life; the eukaryotes, prokaryotes and archaea. Sulfolobus solfataricus, a member of the crenarchaeal subdivision of the archaea, has two prominent DNA binding proteins known as Alba (1&2) and Sso7d. Alba1 is acetylated in vivo at two positions and this modification lowers its’ affinity for binding DNA. Acetylation levels impact many cellular processes and in higher organisms play a critical role in the development of many cancers and other diseases.
This thesis documents the finding and characterisation of the N-terminal acetyltransferase (ssArd1) of SsoAlba1, based on its’ sequence homology to the catalytic subunits Ard1, Nat3 and Mak3 belonging to the larger eukaryal Nat complexes NatA, NatB and NatC, respectively. Mutagenesis studies revealed that ssArd1 preferentially acetylates N-termini bearing a serine or alanine residue at position 1 (after methionine cleavage). It is also capable of acetylating other proteins with very different physical structures. These findings allow classification of ssArd1 as a promiscuous acetyltransferase belonging to the Gcn5-N-acetyltransferase (GNAT) superfamily. The active site of the enzyme was examined through mutagenesis studies, revealing that the mechanism of acetylation is likely to proceed through a direct acetyl transfer involving a tetrahedral intermediate. Structural studies provided some insight into the molecular structure of ssArd1.Ecological and acoustic investigations of jellyfish (Scyphozoa and Hydrozoa)Lynam, Christopher Philiphttps://hdl.handle.net/10023/4662019-07-01T10:12:56Z2006-04-01T00:00:00ZAs the biomass of jellyfish (medusae of the Scyphozoa and Hydrozoa) has risen in numerous locations worldwide, awareness of their potential to exert a controlling influence on marine ecosystems and hinder the recruitment of fish stocks has increased. Medusae are capable of intensive, size–selective, predation on zooplankton, which may alter the composition of the plankton community. Jellyfish are often found in dense layers, up to hundreds of metres thick, which can extend horizontally for hundreds of kilometres. Such aggregations may benefit specialist feeders, such as turtles, that rely upon jellyfish for food and those fish that are able to find refuge under the jellyfish umbrellas. Nonetheless, the predominance of jellyfish in pelagic ecosystems is not generally viewed as desirable; in fact, this situation has been portrayed as the result of pollution and overexploitation of otherwise productive seas. However, jellyfish are sensitive indicators of environmental change, and their populations appear to respond to climatic fluctuations, so jellyfish warrant study for their intrinsic ecosystem role particularly given present concerns over climate change. With growing acceptance that fishery management should take an holistic ‘ecosystem approach’, knowledge of the interactions between jellyfish, fisheries and climate may be vital in progression towards the goal of ecosystem–based sustainable management of fisheries. Unfortunately, due to their gelatinous nature, medusae are difficult to sample using conventional netting techniques and data on changes in distribution and abundance are consequently sparse. Recent studies have demonstrated that medusae can be detected acoustically and that this technique could provide a rapid and cost–effective estimate of their biomass and distribution. This thesis reports my endeavour to demonstrate the ecosystem role of medusae and to develop acoustic techniques to monitor their biomass. Through regession analyses, I link the abundance of medusae (Aurelia aurita, Cyanea lamarckii, and Cyanea capillata) in regions of the North Sea to climatic fluctuations, as quantified by the North Atlantic Oscillation Index, and show that medusae may be important indicators of regional ecosystem change. The mechanisms linking climatic fluctuations to ecosystem changes are explored via a correlative modelling approach using General Additive Models; I show that the mechanisms are location dependent and explainable in terms of direct, rapidly responding (intra–annual) influences (surface warming, river run–off, and wind–driven mixing and advection) and longer–term (interannual) oceanographic responses (changes in circulation currents i.e. the northward extent of the gulf stream and relative strength of inflow into the North Sea of the North Atlantic current, Continental Shelf Jet and Arctic waters). I present correlative evidence for a detrimental impact by Aurelia aurita on herring 0–group recruitment, once the influence of interannual change in herring spewing stock biomass on recruitment is factored out through modelling with a Ricker stock–recruitment relationship. Similarly, a commensal relationship between whiting and Cyanea spp. medusae is shown to improve North Sea whiting survival to the 1–group. In progress towards the automated acoustic identification of species, I have developed an in situ discrimination tool that can distinguish between echoes from: Aequorea aequorea; Chrysaora hysoscella; clupeid fish (sardine, anchovy and round herring); and horse mackerel/Cape hake. The technique relies upon characteristic differences in echo strength between frequencies, which are determined for each jellyfish species and finfish group using combined multifrequency acoustic and pelagic trawl samples. This method has facilitated the world’s first acoustic–based estimate of jellyfish biomass in the Namibian Benguela Sea. The 12.2 million tonnes of biomass of medusae (Aequorea aequorea and Chrysaora hysoscella) in the Namibian Benguela Sea was found to be greater than the combined biomass, 3.6 million tonnes, of commercially important fish (horse mackerel, Cape hake, sardines, anchovy, and round herring) in the same area. These results suggest that medusae may have an important role in the Benguela ecosystem that has previously been overlooked and that their biomass should be monitored.
2006-04-01T00:00:00ZLynam, Christopher PhilipAs the biomass of jellyfish (medusae of the Scyphozoa and Hydrozoa) has risen in numerous locations worldwide, awareness of their potential to exert a controlling influence on marine ecosystems and hinder the recruitment of fish stocks has increased. Medusae are capable of intensive, size–selective, predation on zooplankton, which may alter the composition of the plankton community. Jellyfish are often found in dense layers, up to hundreds of metres thick, which can extend horizontally for hundreds of kilometres. Such aggregations may benefit specialist feeders, such as turtles, that rely upon jellyfish for food and those fish that are able to find refuge under the jellyfish umbrellas. Nonetheless, the predominance of jellyfish in pelagic ecosystems is not generally viewed as desirable; in fact, this situation has been portrayed as the result of pollution and overexploitation of otherwise productive seas. However, jellyfish are sensitive indicators of environmental change, and their populations appear to respond to climatic fluctuations, so jellyfish warrant study for their intrinsic ecosystem role particularly given present concerns over climate change. With growing acceptance that fishery management should take an holistic ‘ecosystem approach’, knowledge of the interactions between jellyfish, fisheries and climate may be vital in progression towards the goal of ecosystem–based sustainable management of fisheries. Unfortunately, due to their gelatinous nature, medusae are difficult to sample using conventional netting techniques and data on changes in distribution and abundance are consequently sparse. Recent studies have demonstrated that medusae can be detected acoustically and that this technique could provide a rapid and cost–effective estimate of their biomass and distribution. This thesis reports my endeavour to demonstrate the ecosystem role of medusae and to develop acoustic techniques to monitor their biomass. Through regession analyses, I link the abundance of medusae (Aurelia aurita, Cyanea lamarckii, and Cyanea capillata) in regions of the North Sea to climatic fluctuations, as quantified by the North Atlantic Oscillation Index, and show that medusae may be important indicators of regional ecosystem change. The mechanisms linking climatic fluctuations to ecosystem changes are explored via a correlative modelling approach using General Additive Models; I show that the mechanisms are location dependent and explainable in terms of direct, rapidly responding (intra–annual) influences (surface warming, river run–off, and wind–driven mixing and advection) and longer–term (interannual) oceanographic responses (changes in circulation currents i.e. the northward extent of the gulf stream and relative strength of inflow into the North Sea of the North Atlantic current, Continental Shelf Jet and Arctic waters). I present correlative evidence for a detrimental impact by Aurelia aurita on herring 0–group recruitment, once the influence of interannual change in herring spewing stock biomass on recruitment is factored out through modelling with a Ricker stock–recruitment relationship. Similarly, a commensal relationship between whiting and Cyanea spp. medusae is shown to improve North Sea whiting survival to the 1–group. In progress towards the automated acoustic identification of species, I have developed an in situ discrimination tool that can distinguish between echoes from: Aequorea aequorea; Chrysaora hysoscella; clupeid fish (sardine, anchovy and round herring); and horse mackerel/Cape hake. The technique relies upon characteristic differences in echo strength between frequencies, which are determined for each jellyfish species and finfish group using combined multifrequency acoustic and pelagic trawl samples. This method has facilitated the world’s first acoustic–based estimate of jellyfish biomass in the Namibian Benguela Sea. The 12.2 million tonnes of biomass of medusae (Aequorea aequorea and Chrysaora hysoscella) in the Namibian Benguela Sea was found to be greater than the combined biomass, 3.6 million tonnes, of commercially important fish (horse mackerel, Cape hake, sardines, anchovy, and round herring) in the same area. These results suggest that medusae may have an important role in the Benguela ecosystem that has previously been overlooked and that their biomass should be monitored.Gente de isla - island people : an ethnography of Apiao, Chiloé, southern ChileBacchiddu, Giovannahttps://hdl.handle.net/10023/4562019-04-01T09:28:40Z2008-06-24T00:00:00ZThis thesis is based upon fieldwork carried out in the island of Apiao, in the archipelago of Chiloé, southern Chile. It is an ethnographic exploration of the way the small community of Apiao conceive of communication and interaction with both fellow human beings and supernatural creatures. The thesis describes details of every day life, with an emphasis on visiting as the main mode of social interaction. Through reciprocal hospitality the islanders enact balanced reciprocal exchange. Food and drink is offered and received; this is always returned in equal measure with a return visit. Visits between friends or neighbours are articulated according to a formal ritualistic etiquette based on asking. Balance is temporarily interrupted and small debts incurred when favors are asked. These must be reciprocated promptly. Momentary interruption of equilibrium perpetuates relations among people who describe themselves as being 'all the same'.
Marriage equates to forming an independent, productive unit with a focus on inhabitants of households rather than on family in terms of decent or blood ties. Kinship terms are limited to the word mama and this refers to the grandmother, the focal role in raising children. Active memory as expression of love and care is what makes people related to each other. Kin ties must be kept active by constant love and care. Forgetful kin are in turn forgotten and slowly erased from memory.
The thesis shows that religious beliefs are centered on exchange relationships with powerful entities that belong to the supernatural world. The dead and the miraculous San Antonio are powerful and ambivalent: they protect and help the living but can be revengeful and harmful if neglected by the living. Novenas are offered to the dead and the San Antonio in exchange for protection and miracles. Novenas represent a public and powerful ritual display of hospitality, enacting values of memory, solidarity and exchange.
2008-06-24T00:00:00ZBacchiddu, GiovannaThis thesis is based upon fieldwork carried out in the island of Apiao, in the archipelago of Chiloé, southern Chile. It is an ethnographic exploration of the way the small community of Apiao conceive of communication and interaction with both fellow human beings and supernatural creatures. The thesis describes details of every day life, with an emphasis on visiting as the main mode of social interaction. Through reciprocal hospitality the islanders enact balanced reciprocal exchange. Food and drink is offered and received; this is always returned in equal measure with a return visit. Visits between friends or neighbours are articulated according to a formal ritualistic etiquette based on asking. Balance is temporarily interrupted and small debts incurred when favors are asked. These must be reciprocated promptly. Momentary interruption of equilibrium perpetuates relations among people who describe themselves as being 'all the same'.
Marriage equates to forming an independent, productive unit with a focus on inhabitants of households rather than on family in terms of decent or blood ties. Kinship terms are limited to the word mama and this refers to the grandmother, the focal role in raising children. Active memory as expression of love and care is what makes people related to each other. Kin ties must be kept active by constant love and care. Forgetful kin are in turn forgotten and slowly erased from memory.
The thesis shows that religious beliefs are centered on exchange relationships with powerful entities that belong to the supernatural world. The dead and the miraculous San Antonio are powerful and ambivalent: they protect and help the living but can be revengeful and harmful if neglected by the living. Novenas are offered to the dead and the San Antonio in exchange for protection and miracles. Novenas represent a public and powerful ritual display of hospitality, enacting values of memory, solidarity and exchange.Assessing grey seal (Halichoerus grypus) diet in western ScotlandHarris, R.N.https://hdl.handle.net/10023/4322019-04-01T11:11:36Z2007-11-30T00:00:00ZGrey seal diet was last comprehensively studied in western Scotland in 1985. Since then, the grey seal population has increased by approximately 30% and relative abundance of fish stocks in the area has changed markedly. The aim of this study was to provide a current assessment of diet to inform policy issues related to the impact of the still increasing grey seal population on commercial fish populations. During 2002, nine sampling trips totalling 56 days were completed around western Scotland, resulting in the collection of 1,589 grey seal scats. Forty-nine prey species were recorded in these samples revealing that grey seals on the west coast of Scotland remain highly catholic in their diet. Seasonal and regional variation in diet composition was assessed and the annual consumption of commercial fish species estimated. Proportions, by weight, of prey species indicated that gadoids were the main prey. Sandeels were also an important component of the diet. Comparisons between 1985 and 2002 revealed many similarities in diet composition but declines in the importance of sandeels, ling and megrim were balanced by increases in haddock, lemon sole, pelagic species and several benthic species. Changes in the size of fish stocks partially explain some of these changes. One exception is cod, which, despite very low abundance in 2002, formed a significant part of grey seal diet in western Scotland. Results from this study highlight the need for better methods for assessing absolute stock abundances for ‘critical’ fish species west of Scotland. Reducing the uncertainty over estimates of grey seal population size would also improve consumption estimates. The results from this study will be important to conservation and fisheries managers in Scotland.
2007-11-30T00:00:00ZHarris, R.N.Grey seal diet was last comprehensively studied in western Scotland in 1985. Since then, the grey seal population has increased by approximately 30% and relative abundance of fish stocks in the area has changed markedly. The aim of this study was to provide a current assessment of diet to inform policy issues related to the impact of the still increasing grey seal population on commercial fish populations. During 2002, nine sampling trips totalling 56 days were completed around western Scotland, resulting in the collection of 1,589 grey seal scats. Forty-nine prey species were recorded in these samples revealing that grey seals on the west coast of Scotland remain highly catholic in their diet. Seasonal and regional variation in diet composition was assessed and the annual consumption of commercial fish species estimated. Proportions, by weight, of prey species indicated that gadoids were the main prey. Sandeels were also an important component of the diet. Comparisons between 1985 and 2002 revealed many similarities in diet composition but declines in the importance of sandeels, ling and megrim were balanced by increases in haddock, lemon sole, pelagic species and several benthic species. Changes in the size of fish stocks partially explain some of these changes. One exception is cod, which, despite very low abundance in 2002, formed a significant part of grey seal diet in western Scotland. Results from this study highlight the need for better methods for assessing absolute stock abundances for ‘critical’ fish species west of Scotland. Reducing the uncertainty over estimates of grey seal population size would also improve consumption estimates. The results from this study will be important to conservation and fisheries managers in Scotland.Incorporating measurement error and density gradients in distance sampling surveysMarques, Tiago Andre Lamas Oliveirahttps://hdl.handle.net/10023/3912019-07-01T10:15:33Z2007-11-01T00:00:00ZDistance sampling is one of the most commonly used methods for estimating density
and abundance. Conventional methods are based on the distances of detected animals
from the center of point transects or the center line of line transects. These distances
are used to model a detection function: the probability of detecting an animal, given
its distance from the line or point. The probability of detecting an animal in the
covered area is given by the mean value of the detection function with respect to
the available distances to be detected. Given this probability, a Horvitz-Thompson-
like estimator of abundance for the covered area follows, hence using a model-based
framework. Inferences for the wider survey region are justified using the survey design.
Conventional distance sampling methods are based on a set of assumptions. In
this thesis I present results that extend distance sampling on two fronts.
Firstly, estimators are derived for situations in which there is measurement error in
the distances. These estimators use information about the measurement error in two
ways: (1) a biased estimator based on the contaminated distances is multiplied by an
appropriate correction factor, which is a function of the errors (PDF approach), and
(2) cast into a likelihood framework that allows parameter estimation in the presence
of measurement error (likelihood approach).
Secondly, methods are developed that relax the conventional assumption that the
distribution of animals is independent of distance from the lines or points (usually
guaranteed by appropriate survey design). In particular, the new methods deal with
the case where animal density gradients are caused by the use of non-random sampler
allocation, for example transects placed along linear features such as roads or streams.
This is dealt with separately for line and point transects, and at a later stage an
approach for combining the two is presented.
A considerable number of simulations and example analysis illustrate the performance of the proposed methods.
2007-11-01T00:00:00ZMarques, Tiago Andre Lamas OliveiraDistance sampling is one of the most commonly used methods for estimating density
and abundance. Conventional methods are based on the distances of detected animals
from the center of point transects or the center line of line transects. These distances
are used to model a detection function: the probability of detecting an animal, given
its distance from the line or point. The probability of detecting an animal in the
covered area is given by the mean value of the detection function with respect to
the available distances to be detected. Given this probability, a Horvitz-Thompson-
like estimator of abundance for the covered area follows, hence using a model-based
framework. Inferences for the wider survey region are justified using the survey design.
Conventional distance sampling methods are based on a set of assumptions. In
this thesis I present results that extend distance sampling on two fronts.
Firstly, estimators are derived for situations in which there is measurement error in
the distances. These estimators use information about the measurement error in two
ways: (1) a biased estimator based on the contaminated distances is multiplied by an
appropriate correction factor, which is a function of the errors (PDF approach), and
(2) cast into a likelihood framework that allows parameter estimation in the presence
of measurement error (likelihood approach).
Secondly, methods are developed that relax the conventional assumption that the
distribution of animals is independent of distance from the lines or points (usually
guaranteed by appropriate survey design). In particular, the new methods deal with
the case where animal density gradients are caused by the use of non-random sampler
allocation, for example transects placed along linear features such as roads or streams.
This is dealt with separately for line and point transects, and at a later stage an
approach for combining the two is presented.
A considerable number of simulations and example analysis illustrate the performance of the proposed methods.Adapting authoritarianism: institutions and co-optation in Egypt and SyriaStacher, Joshua Ahttps://hdl.handle.net/10023/3542019-07-01T10:16:01Z2007-03-07T00:00:00ZThis PhD thesis compares Egypt and Syria’s authoritarian political systems. While the tendency in social science political research treats Egypt and Syria as similarly authoritarian, this research emphasizes differences between the two systems with special reference to institutions and co-optation. Rather than reducibly understanding Egypt and Syria as sharing similar histories, institutional arrangements, or ascribing to the oft-repeated convention that “Syria is Egypt but 10 years behind,” this thesis focuses on how events and individual histories shaped each states current institutional strengthens and weaknesses. Specifically, it explains the how varying institutional politicization or de-politicization affects each state’s capabilities for co-opting elite and non-elite individuals.
Beginning with a theoretical framework that considers the limited utility of democratization and transition theoretical approaches, the work underscores the persistence and durability of authoritarianism. Chapter two details the politicized institutional divergence between Egypt and Syria that began in the 1970s. Chapter three and four examines how institutional politicization or de-politicization affects elite and non-elite individual co-optation in Egypt and Syria. Chapter five discusses the study’s general conclusions and theoretical implications.
This thesis’s argument is that Egypt and Syria co-opt elites and non-elites differently because of the varying degrees of institutional politicization in each governance system. Rather than view one country as more politically developed than the other, this work argues that Syria’s political institutions are more politicized than their Egyptian counterparts. Syria’s political arena is, thus, described as politicized-patrimonialism. Syria’s politicized-patrimonial arena produces uneven co-optation of elites and non-elites as they are diffused through competing institutions. Conversely, the Egyptian political arena remains highly personalized as weak institutions and individuals are manipulated and molded according to the president’s ruling clique. This is referred to as personalized-patrimonialism. As a consequence, Egypt’s political establishment demonstrates more flexibility in ad hoc altering and adapting its arena depending on the emergence of crises.
This study’s theoretical implications suggest that, contrary to modernization and democratization theory’s adage that institutions lead to a political development, politicized institutions within a patrimonial order actually hinder regime adaptation because consensus is harder to achieve and maintain. It is within this context that Egypt’s de-politicized institutional framework advantages its top political elite. In this reading of Egyptian and Syrian politics, Egypt’s personalized political arena is more adaptable than Syria’s. These conclusions do not indicate that political reform is a process underway in either state.
2007-03-07T00:00:00ZStacher, Joshua AThis PhD thesis compares Egypt and Syria’s authoritarian political systems. While the tendency in social science political research treats Egypt and Syria as similarly authoritarian, this research emphasizes differences between the two systems with special reference to institutions and co-optation. Rather than reducibly understanding Egypt and Syria as sharing similar histories, institutional arrangements, or ascribing to the oft-repeated convention that “Syria is Egypt but 10 years behind,” this thesis focuses on how events and individual histories shaped each states current institutional strengthens and weaknesses. Specifically, it explains the how varying institutional politicization or de-politicization affects each state’s capabilities for co-opting elite and non-elite individuals.
Beginning with a theoretical framework that considers the limited utility of democratization and transition theoretical approaches, the work underscores the persistence and durability of authoritarianism. Chapter two details the politicized institutional divergence between Egypt and Syria that began in the 1970s. Chapter three and four examines how institutional politicization or de-politicization affects elite and non-elite individual co-optation in Egypt and Syria. Chapter five discusses the study’s general conclusions and theoretical implications.
This thesis’s argument is that Egypt and Syria co-opt elites and non-elites differently because of the varying degrees of institutional politicization in each governance system. Rather than view one country as more politically developed than the other, this work argues that Syria’s political institutions are more politicized than their Egyptian counterparts. Syria’s political arena is, thus, described as politicized-patrimonialism. Syria’s politicized-patrimonial arena produces uneven co-optation of elites and non-elites as they are diffused through competing institutions. Conversely, the Egyptian political arena remains highly personalized as weak institutions and individuals are manipulated and molded according to the president’s ruling clique. This is referred to as personalized-patrimonialism. As a consequence, Egypt’s political establishment demonstrates more flexibility in ad hoc altering and adapting its arena depending on the emergence of crises.
This study’s theoretical implications suggest that, contrary to modernization and democratization theory’s adage that institutions lead to a political development, politicized institutions within a patrimonial order actually hinder regime adaptation because consensus is harder to achieve and maintain. It is within this context that Egypt’s de-politicized institutional framework advantages its top political elite. In this reading of Egyptian and Syrian politics, Egypt’s personalized political arena is more adaptable than Syria’s. These conclusions do not indicate that political reform is a process underway in either state.Ecological investigations of euphausiids at high latitudesSaunders, Ryan Alexanderhttps://hdl.handle.net/10023/3472019-07-01T10:15:36Z2007-06-22T00:00:00Z1. Euphausiids are an important component of high latitude pelagic ecosystems, but there is a paucity of information on their distribution, abundance and population processes on within-year time scales. This thesis encompasses new research into the euphausiid-ocean component of two important high latitude ecosystems (South Georgia and the Irminger Sea) on sub-annual time scales.
2. A new method for measuring abundance of Antarctic krill (Euphausia superba) continuously at South Georgia (Southern Ocean) was devised using upward-looking acoustic devices deployed on moorings. These novel platforms provide a new window of observations onto marine systems not open from conventional research vessels. At South Georgia, the moorings provided data at a high temporal resolution giving completely new insight to the function of the coupled biological-physical marine ecosystem. The use of moorings may aid ecosystem-based management at South Georgia and elsewhere.
3. Analysis of mooring data collected between October 2002 and December 2005 indicated a regular annual cycle in krill density: high in summer and low in winter. Mooring estimates of krill density were not statistically different from estimates derived from standard ship-based surveys in adjacent time periods suggesting that the mooring point estimates had relevance in a wider spatial context (c. 100 x 100 km). The results indicated that because of the sharp peaks in the biomass cycle, the exact timing of repeated ship-based acoustic surveys might be critical. Surveys that differ in their timing by only a few weeks might exhibit quite different estimates of biomass because they fall at different points of the cycle. Additionally, within this intra-annual framework, annual ship-based surveys may be able to detect differences between high and low krill years only if they differ by densities of c. 35 g per square m. in summer and c. 20 g per square m. in winter.
4. The mechanisms driving intra-annual variability in Antarctic krill density at South Georgia are likely to be complex. Analysis of mooring data revealed a possible association between high krill density and low water temperatures (at 200 m) at South Georgia. There was evidence that seasonal variation in krill density off-shelf was linked to seasonal variation in current velocity: marked increases in velocity at the end of summer coincided with marked decreases in krill density and abrupt changes in water temperature characteristic of the Sub-Antarctic Current Front (SACCF). Oceanographic data indicated that the SACCF might have impinged in proximity to the moorings during the winter season. However, krill densities were low during these periods and analyses suggest that seasonal variations in krill density were not driven by seasonal oscillations in the position of the SACCF. The data are not consistent with a pattern of seasonal growth, production and mortality of a resident krill population at South Georgia, but are consistent with the notion of large influxes of krill in early summer, and of a predator-driven reduction at between mid- and late-summer.
5. The seasonal distribution, abundance and growth of key euphauiids in the Irminger Sea, North Atlantic was quantified using the first net haul data from the region since the 1930s. Results show a high degree of spatial heterogeneity in the seasonal distribution of euphausiid abundance/biomass during 2001-2002. There was evidence to suggest regional variation in growth and population processes of Meganyctiphanes norvegica and Thysanoessa longicaudata, and this corresponded broadly to distinct physical zones in the Irminger Sea. There were, however, no significant links between growth and temperature and chlorophyll a concentration. This was attributed to high spatial and temporal variability in biological and physical sampling. These data are a prerequisite for understanding ecosystems dynamics in the North Atlantic, and are important for robust ecosystem-based management strategies.
6. Controls on euphausiid spatial heterogeneity at high latitudes are likely to be complex. Important factors include horizontal advection, temperature, resource availability and behavioural mechanisms. Short-term (intra-annual), small-scale (basin-scale) data are fundamental to understanding variability in euphausiid abundance and distribution on broader spatial and temporal scales in these ecosystems.
2007-06-22T00:00:00ZSaunders, Ryan Alexander1. Euphausiids are an important component of high latitude pelagic ecosystems, but there is a paucity of information on their distribution, abundance and population processes on within-year time scales. This thesis encompasses new research into the euphausiid-ocean component of two important high latitude ecosystems (South Georgia and the Irminger Sea) on sub-annual time scales.
2. A new method for measuring abundance of Antarctic krill (Euphausia superba) continuously at South Georgia (Southern Ocean) was devised using upward-looking acoustic devices deployed on moorings. These novel platforms provide a new window of observations onto marine systems not open from conventional research vessels. At South Georgia, the moorings provided data at a high temporal resolution giving completely new insight to the function of the coupled biological-physical marine ecosystem. The use of moorings may aid ecosystem-based management at South Georgia and elsewhere.
3. Analysis of mooring data collected between October 2002 and December 2005 indicated a regular annual cycle in krill density: high in summer and low in winter. Mooring estimates of krill density were not statistically different from estimates derived from standard ship-based surveys in adjacent time periods suggesting that the mooring point estimates had relevance in a wider spatial context (c. 100 x 100 km). The results indicated that because of the sharp peaks in the biomass cycle, the exact timing of repeated ship-based acoustic surveys might be critical. Surveys that differ in their timing by only a few weeks might exhibit quite different estimates of biomass because they fall at different points of the cycle. Additionally, within this intra-annual framework, annual ship-based surveys may be able to detect differences between high and low krill years only if they differ by densities of c. 35 g per square m. in summer and c. 20 g per square m. in winter.
4. The mechanisms driving intra-annual variability in Antarctic krill density at South Georgia are likely to be complex. Analysis of mooring data revealed a possible association between high krill density and low water temperatures (at 200 m) at South Georgia. There was evidence that seasonal variation in krill density off-shelf was linked to seasonal variation in current velocity: marked increases in velocity at the end of summer coincided with marked decreases in krill density and abrupt changes in water temperature characteristic of the Sub-Antarctic Current Front (SACCF). Oceanographic data indicated that the SACCF might have impinged in proximity to the moorings during the winter season. However, krill densities were low during these periods and analyses suggest that seasonal variations in krill density were not driven by seasonal oscillations in the position of the SACCF. The data are not consistent with a pattern of seasonal growth, production and mortality of a resident krill population at South Georgia, but are consistent with the notion of large influxes of krill in early summer, and of a predator-driven reduction at between mid- and late-summer.
5. The seasonal distribution, abundance and growth of key euphauiids in the Irminger Sea, North Atlantic was quantified using the first net haul data from the region since the 1930s. Results show a high degree of spatial heterogeneity in the seasonal distribution of euphausiid abundance/biomass during 2001-2002. There was evidence to suggest regional variation in growth and population processes of Meganyctiphanes norvegica and Thysanoessa longicaudata, and this corresponded broadly to distinct physical zones in the Irminger Sea. There were, however, no significant links between growth and temperature and chlorophyll a concentration. This was attributed to high spatial and temporal variability in biological and physical sampling. These data are a prerequisite for understanding ecosystems dynamics in the North Atlantic, and are important for robust ecosystem-based management strategies.
6. Controls on euphausiid spatial heterogeneity at high latitudes are likely to be complex. Important factors include horizontal advection, temperature, resource availability and behavioural mechanisms. Short-term (intra-annual), small-scale (basin-scale) data are fundamental to understanding variability in euphausiid abundance and distribution on broader spatial and temporal scales in these ecosystems.Seville : between the Atlantic and the Mediterranean, 1248-1492 : pre-Columbus commercial routes from and to SevilleSerradilla Avery, Dan Manuelhttps://hdl.handle.net/10023/3402019-07-01T10:19:50Z2007-06-21T00:00:00ZThe city of Seville and its port have had a prominent place in the history of early modern Europe and America. This city was not only the Gate of the Indies, but also the Gate of Europe for all the exotic goods and people that arrived in Europe via Seville's port. How this city achieved such a prominent place has traditionally been overshadowed by its post-1492 fame. This thesis demonstrates how, during the two hundred or so years before Columbus, different groups were able to shape this city into a commercial port that had made it the axis between the Mediterranean's commercial routes and those of the Atlantic Ocean. Beginning in 1248, with the Christian re-conquest, the monarchs set out to create an independent and powerful municipality, as well as a merchant class with distinctive city quarters and privileges. In turn, this merchant class affected the policies of both monarchy and city-council. Eventually, the policies of both merchants and the city-council led to the creation of an important exchange port that lay nearly between the two bodies of water. The Castilian monarchs, aware of this, also began the construction of the first Royal Ware houses and Dockyards, as well as determining the location of the Castilian Armada. It was those years between 1248 and 1492 that witnessed the birth of one of the most important naval ports of European history.
2007-06-21T00:00:00ZSerradilla Avery, Dan ManuelThe city of Seville and its port have had a prominent place in the history of early modern Europe and America. This city was not only the Gate of the Indies, but also the Gate of Europe for all the exotic goods and people that arrived in Europe via Seville's port. How this city achieved such a prominent place has traditionally been overshadowed by its post-1492 fame. This thesis demonstrates how, during the two hundred or so years before Columbus, different groups were able to shape this city into a commercial port that had made it the axis between the Mediterranean's commercial routes and those of the Atlantic Ocean. Beginning in 1248, with the Christian re-conquest, the monarchs set out to create an independent and powerful municipality, as well as a merchant class with distinctive city quarters and privileges. In turn, this merchant class affected the policies of both monarchy and city-council. Eventually, the policies of both merchants and the city-council led to the creation of an important exchange port that lay nearly between the two bodies of water. The Castilian monarchs, aware of this, also began the construction of the first Royal Ware houses and Dockyards, as well as determining the location of the Castilian Armada. It was those years between 1248 and 1492 that witnessed the birth of one of the most important naval ports of European history.Characterisation of the supply-settlement relationship for Semibalanus balanoides (L.) along a wave swept coast in Fife, East ScotlandPhelan, Patrick J. C.https://hdl.handle.net/10023/3332019-07-01T10:04:02Z2007-01-01T00:00:00ZThis thesis describes the results of a three year study which collected larvae of
the acorn barnacles Semibalanus balanoides on a rocky coastline in Fife, East
Scotland. The nauplii larvae of S. balanoides are released from their parent in
springtime in the United Kingdom and develop in the plankton for approximately one
to two months. During this period they are transported some distance from the parent
population and eventually return to the intertidal shoreline as a cyprid larval stage.
The ‘decision’ to settle is a crucial point in the life history of the organism as most
sessile organisms cannot move once this has occurred. The supply of larvae to
intertidal shorelines was historically neglected until the 1980s. Patterns of settlement
were largely considered irrelevant to distribution patterns of adults relative to postsettlement
processes such as predation and competition.
Despite the resurgence in “supply-side ecology” in the past 20 years there has
been little development towards the measurement of larval supply. Consequently
there has been very little description of fine scale or large spatio-temporal studies
involving larval supply. This study demonstrates the first study directly addressing
larval supply independently from larval settlement at mesoscales (metres to
kilometres; days to years). Improvements were made to the passive larval trap
described by Todd (2003). A conical opening was combined with the spiral trap
design and a number of inlet areas were trialled (0.25cm², 0.5cm², 1cm² and 2cm²).
These were tested across typical wave regimes measured with a new autonomous
pressure sensing wave transducer and the 1cm² inlet was selected as the most
appropriate trap design due to a balance between an increased per unit inlet larval
capture and sufficient absolute larval capture so as to identify daily variation in larval
supply to a site.
Larval settlement has been studied extensively and is often used as a direct
measure of rates of larval supply. It is widely assumed therefore that rates of
settlement are a direct reflection of rates of supply, as long as settlement substrates
and adult conspecific responses remain uniform. This thesis provides a means of
accurately characterising the supply-settlement relationship for S. balanoides
independent of substrate based responses and demonstrates that this is not the case.
The relationship was found to be asymptotic, even at sites where there was low larval
supply. It was concluded that density-dependent larva-larva interactions were present
during the settlement of larvae and were relevant at daily temporal scales, limiting the
rates of larval settlement proportional to larval density. There was no obvious effect
on this relationship due to wave action however differences were observed between
sites and years. Saturation of preferential environments within the tiles was observed
resulting in a settlement preference cascade, with larvae being forced to settle in
increasingly less preferable areas of the tiles with increasing larval density. Larva-larva
interactions are demonstrated as having a considerable effect on the rates of
settlement of S. balanoides.
2007-01-01T00:00:00ZPhelan, Patrick J. C.This thesis describes the results of a three year study which collected larvae of
the acorn barnacles Semibalanus balanoides on a rocky coastline in Fife, East
Scotland. The nauplii larvae of S. balanoides are released from their parent in
springtime in the United Kingdom and develop in the plankton for approximately one
to two months. During this period they are transported some distance from the parent
population and eventually return to the intertidal shoreline as a cyprid larval stage.
The ‘decision’ to settle is a crucial point in the life history of the organism as most
sessile organisms cannot move once this has occurred. The supply of larvae to
intertidal shorelines was historically neglected until the 1980s. Patterns of settlement
were largely considered irrelevant to distribution patterns of adults relative to postsettlement
processes such as predation and competition.
Despite the resurgence in “supply-side ecology” in the past 20 years there has
been little development towards the measurement of larval supply. Consequently
there has been very little description of fine scale or large spatio-temporal studies
involving larval supply. This study demonstrates the first study directly addressing
larval supply independently from larval settlement at mesoscales (metres to
kilometres; days to years). Improvements were made to the passive larval trap
described by Todd (2003). A conical opening was combined with the spiral trap
design and a number of inlet areas were trialled (0.25cm², 0.5cm², 1cm² and 2cm²).
These were tested across typical wave regimes measured with a new autonomous
pressure sensing wave transducer and the 1cm² inlet was selected as the most
appropriate trap design due to a balance between an increased per unit inlet larval
capture and sufficient absolute larval capture so as to identify daily variation in larval
supply to a site.
Larval settlement has been studied extensively and is often used as a direct
measure of rates of larval supply. It is widely assumed therefore that rates of
settlement are a direct reflection of rates of supply, as long as settlement substrates
and adult conspecific responses remain uniform. This thesis provides a means of
accurately characterising the supply-settlement relationship for S. balanoides
independent of substrate based responses and demonstrates that this is not the case.
The relationship was found to be asymptotic, even at sites where there was low larval
supply. It was concluded that density-dependent larva-larva interactions were present
during the settlement of larvae and were relevant at daily temporal scales, limiting the
rates of larval settlement proportional to larval density. There was no obvious effect
on this relationship due to wave action however differences were observed between
sites and years. Saturation of preferential environments within the tiles was observed
resulting in a settlement preference cascade, with larvae being forced to settle in
increasingly less preferable areas of the tiles with increasing larval density. Larva-larva
interactions are demonstrated as having a considerable effect on the rates of
settlement of S. balanoides.Modelling space-use and habitat preference from wildlife telemetry dataAarts, Geerthttps://hdl.handle.net/10023/3272019-11-05T12:45:16Z2007-06-20T00:00:00ZManagement and conservation of populations of animals requires information on where they are, why they are there, and where else they
could be. These objectives are typically approached by collecting data on the
animals’ use of space, relating these to prevailing environmental conditions
and employing these relations to predict usage at other geographical regions.
Technical advances in wildlife telemetry have accomplished manifold
increases in the amount and quality of available data, creating the need for a
statistical framework that can use them to make population-level inferences
for habitat preference and space-use. This has been slow-in-coming because
wildlife telemetry data are, by definition, spatio-temporally autocorrelated,
unbalanced, presence-only observations of behaviorally complex animals,
responding to a multitude of cross-correlated environmental variables.
I review the evolution of techniques for the analysis of space-use and
habitat preference, from simple hypothesis tests to modern modeling
techniques and outline the essential features of a framework that emerges
naturally from these foundations. Within this framework, I discuss eight
challenges, inherent in the spatial analysis of telemetry data and, for each, I
propose solutions that can work in tandem. Specifically, I propose a logistic,
mixed-effects approach that uses generalized additive transformations of the
environmental covariates and is fitted to a response data-set comprising the
telemetry and simulated observations, under a case-control design.
I apply this framework to non-trivial case-studies using data from
satellite-tagged grey seals (Halichoerus grypus) foraging off the east and
west coast of Scotland, and northern gannets (Morus Bassanus) from Bass
Rock. I find that sea bottom depth and sediment type explain little of the
variation in gannet usage, but grey seals from different regions strongly
prefer coarse sediment types, the ideal burrowing habitat of sandeels, their
preferred prey. The results also suggest that prey aggregation within the
water column might be as important as horizontal heterogeneity. More
importantly, I conclude that, despite the complex behavior of the study
species, flexible empirical models can capture the environmental
relationships that shape population distributions.
2007-06-20T00:00:00ZAarts, GeertManagement and conservation of populations of animals requires information on where they are, why they are there, and where else they
could be. These objectives are typically approached by collecting data on the
animals’ use of space, relating these to prevailing environmental conditions
and employing these relations to predict usage at other geographical regions.
Technical advances in wildlife telemetry have accomplished manifold
increases in the amount and quality of available data, creating the need for a
statistical framework that can use them to make population-level inferences
for habitat preference and space-use. This has been slow-in-coming because
wildlife telemetry data are, by definition, spatio-temporally autocorrelated,
unbalanced, presence-only observations of behaviorally complex animals,
responding to a multitude of cross-correlated environmental variables.
I review the evolution of techniques for the analysis of space-use and
habitat preference, from simple hypothesis tests to modern modeling
techniques and outline the essential features of a framework that emerges
naturally from these foundations. Within this framework, I discuss eight
challenges, inherent in the spatial analysis of telemetry data and, for each, I
propose solutions that can work in tandem. Specifically, I propose a logistic,
mixed-effects approach that uses generalized additive transformations of the
environmental covariates and is fitted to a response data-set comprising the
telemetry and simulated observations, under a case-control design.
I apply this framework to non-trivial case-studies using data from
satellite-tagged grey seals (Halichoerus grypus) foraging off the east and
west coast of Scotland, and northern gannets (Morus Bassanus) from Bass
Rock. I find that sea bottom depth and sediment type explain little of the
variation in gannet usage, but grey seals from different regions strongly
prefer coarse sediment types, the ideal burrowing habitat of sandeels, their
preferred prey. The results also suggest that prey aggregation within the
water column might be as important as horizontal heterogeneity. More
importantly, I conclude that, despite the complex behavior of the study
species, flexible empirical models can capture the environmental
relationships that shape population distributions.Investigating monitoring options for harbour seals in Special Areas of Conservation in ScotlandCunningham, Louisehttps://hdl.handle.net/10023/3262019-07-01T10:16:22Z2007-06-22T00:00:00ZManaging a wild population effectively requires knowledge of the abundance and behaviour of the species. Harbour seals (Phoca vitulina) are usually counted when they come ashore at haul-out sites, and so it is important to understand how the number of seals counted at this time relates to total population size. Satellite telemetry studies confirmed that harbour seals on the west coast of Scotland showed a degree of site fidelity and coastal foraging. Most trips taken by tagged animals involved travelling only 10-30 km from haul-outs and lasted less than a day (mean 21.07 hours, SE = 0.54), although some seals travelled over 100 km. Eighteen percent of the time these tagged seals spent hauled out was in the Special Area of Conservation where they were caught.
Individual seals can be recognised from their unique pelage patterns using computer-assisted photo-identification. Capture histories for adult harbour seals at a site in north-west Scotland indicated that the number of seals using the study area between April and October was 3.4 times higher than the number counted during an aerial survey made during the August moult. In the UK, aerial surveys of harbour seals are usually conducted during the first three weeks of August, when seals are moulting. These counts have a coefficient of variation of around 15%. Land-based counts made at study sites on the north-west coast of Scotland indicated that the number of seals hauled out was most consistent during the moult, but highest counts were from the pupping period. Analysis of moult counts indicated that starting surveys one week earlier (on 7th August) and surveying 1½ hours earlier in the tidal cycle would reduce the count variation. There was spatial, seasonal, diurnal and sex-related variation in the proportion of time harbour seals hauled out. Thus the relationship between counts and total population size is likely to vary spatially and temporally. This variation should be included in the estimates of the CV of correction factors.
A 5% annual change in harbour seal population size was predicted to take around 14 years to detect based on annual surveys and a CV = 0.15. This detection period increases when monitoring methods with lower precision are used, or surveys are made less frequently. Trends in seal abundance at pairs of haul-out sites were not synchronous and so it is unlikely that counts from small land-based protected areas, such as Special Areas of Conservation, can be used to monitor overall population status.
2007-06-22T00:00:00ZCunningham, LouiseManaging a wild population effectively requires knowledge of the abundance and behaviour of the species. Harbour seals (Phoca vitulina) are usually counted when they come ashore at haul-out sites, and so it is important to understand how the number of seals counted at this time relates to total population size. Satellite telemetry studies confirmed that harbour seals on the west coast of Scotland showed a degree of site fidelity and coastal foraging. Most trips taken by tagged animals involved travelling only 10-30 km from haul-outs and lasted less than a day (mean 21.07 hours, SE = 0.54), although some seals travelled over 100 km. Eighteen percent of the time these tagged seals spent hauled out was in the Special Area of Conservation where they were caught.
Individual seals can be recognised from their unique pelage patterns using computer-assisted photo-identification. Capture histories for adult harbour seals at a site in north-west Scotland indicated that the number of seals using the study area between April and October was 3.4 times higher than the number counted during an aerial survey made during the August moult. In the UK, aerial surveys of harbour seals are usually conducted during the first three weeks of August, when seals are moulting. These counts have a coefficient of variation of around 15%. Land-based counts made at study sites on the north-west coast of Scotland indicated that the number of seals hauled out was most consistent during the moult, but highest counts were from the pupping period. Analysis of moult counts indicated that starting surveys one week earlier (on 7th August) and surveying 1½ hours earlier in the tidal cycle would reduce the count variation. There was spatial, seasonal, diurnal and sex-related variation in the proportion of time harbour seals hauled out. Thus the relationship between counts and total population size is likely to vary spatially and temporally. This variation should be included in the estimates of the CV of correction factors.
A 5% annual change in harbour seal population size was predicted to take around 14 years to detect based on annual surveys and a CV = 0.15. This detection period increases when monitoring methods with lower precision are used, or surveys are made less frequently. Trends in seal abundance at pairs of haul-out sites were not synchronous and so it is unlikely that counts from small land-based protected areas, such as Special Areas of Conservation, can be used to monitor overall population status.A Bayesian approach to modelling field data on multi-species predator prey-interactionsAsseburg, Christianhttps://hdl.handle.net/10023/1742019-07-01T10:20:00Z2006-01-01T00:00:00ZMulti-species functional response models are required to model the predation of generalist preda-
tors, which consume more than one prey species. In chapter 2, a new model for the multi-species
functional response is presented. This model can describe generalist predators that exhibit func-
tional responses of Holling type II to some of their prey and of type III to other prey. In chapter
3, I review some of the theoretical distinctions between Bayesian and frequentist statistics and
show how Bayesian statistics are particularly well-suited for the fitting of functional response
models because uncertainty can be represented comprehensively. In chapters 4 and 5, the multi-
species functional response model is fitted to field data on two generalist predators: the hen
harrier Circus cyaneus and the harp seal Phoca groenlandica. I am not aware of any previous
Bayesian model of the multi-species functional response that has been fitted to field data.
The hen harrier's functional response fitted in chapter 4 is strongly sigmoidal to the densities
of red grouse Lagopus lagopus scoticus, but no type III shape was detected in the response to
the two main prey species, field vole Microtus agrestis and meadow pipit Anthus pratensis. The
impact of using Bayesian or frequentist models on the resulting functional response is discussed.
In chapter 5, no functional response could be fitted to the data on harp seal predation. Possible
reasons are discussed, including poor data quality or a lack of relevance of the available data for
informing a behavioural functional response model.
I conclude with a comparison of the role that functional responses play in behavioural, population
and community ecology and emphasise the need for further research into unifying these different
approaches to understanding predation with particular reference to predator movement.
In an appendix, I evaluate the possibility of using a functional response for inferring the abun-
dances of prey species from performance indicators of generalist predators feeding on these prey.
I argue that this approach may be futile in general, because a generalist predator's energy intake
does not depend on the density of any single of its prey, so that the possibly unknown densities
of all prey need to be taken into account.
2006-01-01T00:00:00ZAsseburg, ChristianMulti-species functional response models are required to model the predation of generalist preda-
tors, which consume more than one prey species. In chapter 2, a new model for the multi-species
functional response is presented. This model can describe generalist predators that exhibit func-
tional responses of Holling type II to some of their prey and of type III to other prey. In chapter
3, I review some of the theoretical distinctions between Bayesian and frequentist statistics and
show how Bayesian statistics are particularly well-suited for the fitting of functional response
models because uncertainty can be represented comprehensively. In chapters 4 and 5, the multi-
species functional response model is fitted to field data on two generalist predators: the hen
harrier Circus cyaneus and the harp seal Phoca groenlandica. I am not aware of any previous
Bayesian model of the multi-species functional response that has been fitted to field data.
The hen harrier's functional response fitted in chapter 4 is strongly sigmoidal to the densities
of red grouse Lagopus lagopus scoticus, but no type III shape was detected in the response to
the two main prey species, field vole Microtus agrestis and meadow pipit Anthus pratensis. The
impact of using Bayesian or frequentist models on the resulting functional response is discussed.
In chapter 5, no functional response could be fitted to the data on harp seal predation. Possible
reasons are discussed, including poor data quality or a lack of relevance of the available data for
informing a behavioural functional response model.
I conclude with a comparison of the role that functional responses play in behavioural, population
and community ecology and emphasise the need for further research into unifying these different
approaches to understanding predation with particular reference to predator movement.
In an appendix, I evaluate the possibility of using a functional response for inferring the abun-
dances of prey species from performance indicators of generalist predators feeding on these prey.
I argue that this approach may be futile in general, because a generalist predator's energy intake
does not depend on the density of any single of its prey, so that the possibly unknown densities
of all prey need to be taken into account.