Research@StAndrews:FullText

Some aspects of visual discomfort

O'Hare, Louise — 2013-06-25T00:00:00Z

Abstract: Visual discomfort is the adverse sensations, such as headaches and eyestrain, encountered on viewing certain stimuli. These sensations can arise under certain viewing conditions, such as stereoscopic viewing and prolonged reading of text patterns. Also, discomfort can occur as a result of viewing stimuli with certain spatial properties, including stripes and filtered noise patterns of particular spatial frequency. This thesis is an exploration of the stimulus properties causing discomfort, within the framework of two theoretical explanations. Both of the explanations relate to the stimuli being difficult for the visual system to process. The first is concerned with discomfort being the result of inefficient neural processing. Neural activity requires energy to process information, and stimuli that demand a lot of energy to be processed might be uncomfortable. The second explanation revolves around uncomfortable stimuli not being effective in driving the accommodative (focussing) response. Accommodation relies on the stimulus as a cue to drive the response effectively - an uninformative cue might result in discomfort from an uncertain accommodative response. The following research investigates both these possibilities using a combination of psychophysical experimentation, questionnaire-based surveys on non-clinical populations, and computational modelling. The implications of the work for clinical populations are also discussed.

Structure of the archaeal Cascade subunit Csa5 : Relating the small subunits of CRISPR effector complexes

Reeks, Judith Anne — 2013-05-01T00:00:00Z

Abstract: The Cascade complex for CRISPR-mediated antiviral immunity uses CRISPR RNA (crRNA) to target invading DNA species from mobile elements such as viruses, leading to their destruction. The core of the Cascade effector complex consists of the Cas5 and Cas7 subunits, which are widely conserved in prokaryotes. Cas7 binds crRNA and forms the helical backbone of Cascade. Many archaea encode a version of the Cascade complex (denoted Type I-A) that includes a Csa5 (or small) subunit, which interacts weakly with the core proteins. Here, we report the crystal structure of the Csa5 protein from Sulfolobus solfataricus. Csa5 comprises a conserved α-helical domain with a small insertion consisting of a weakly conserved β-strand domain. In the crystal, the Csa5 monomers have multimerized into infinite helical threads. At each interface is a strictly conserved intersubunit salt bridge, deletion of which disrupts multimerization. Structural analysis indicates a shared evolutionary history among the small subunits of the CRISPR effector complexes. The same α-helical domain is found in the C-terminal domain of Cse2 (from Type I-E Cascade), while the N-terminal domain of Cse2 is found in Cmr5 of the CMR (Type III-B) effector complex. As Cmr5 shares no match with Csa5, two possibilities present themselves: selective domain loss from an ancestral Cse2 to create two new subfamilies or domain fusion of two separate families to create a new Cse2 family. A definitive answer awaits structural studies of further small subunits from other CRISPR effector complexes. Description: This work was funded by a grant from the Biotechnology and Biological Sciences Research Council (BBSRC) (REF: BB/G011400/1) to M.F.W. and J.H.N. and a BBSRC-funded studentship to J.R.

The effects of conflict strength and ageing on cognitive control

Strozyk, Jessica Vanessa — 2013-06-01T00:00:00Z

Abstract: In this thesis, I investigated effects of conflict strength and ageing on cognitive control. Conflict strength was manipulated in the Eriksen flanker task using two different approaches: 1. independent variation of flanker and target contrast; 2. manipulation of stimulus onset asynchrony (SOA). Reducing flanker contrast relative to target contrast decreased conflict strength, as shown by a reduction in compatibility effects, when contrast conditions were presented in a randomized fashion but not when they were presented block-wise. An SOA of 100 ms did lead to increased compatibility effects compared to SOAs of 0 ms and 200 ms. Effects of conflict appear to be reflected in the N2 component of the ERP. Although priming played a crucial role in the emergence of the sequential adjustment effect, conflict strength also influenced this effect to a certain degree, supporting the claim that sequential adjustments represent an adaptation of cognitive control. Post-error slowing and error-related ERP components, on the other hand, were not affected by the conflict manipulations, suggesting that errors cannot be explained in terms of conflict processing. Effects of ageing on cognitive control were investigated in a group of middle-aged participants. Although physiological indicators of conflict and error processing were compromised in this age group and overall response times were increased, compatibility, sequential adjustment, and post-error slowing effects were of comparable size as in young adults. These findings suggest that participants could successfully compensate for age-related physiological changes at this early stage of ageing. In conclusion, the research presented in this thesis provided important information to extend our knowledge of factors influencing cognitive control processes.

Equilibrium and stability properties of collisionless current sheet models

Wilson, Fiona — 2013-06-28T00:00:00Z

Abstract: The work in this thesis focuses primarily on equilibrium and stability properties of collisionless current sheet models, in particular of the force-free Harris sheet model. A detailed investigation is carried out into the properties of the distribution function found by Harrison and Neukirch (Physical Review Letters 102, 135003, 2009) for the force-free Harris sheet, which is so far the only known nonlinear force-free Vlasov-Maxwell equilibrium. Exact conditions on the parameters of the distribution function are found, which show when it can be single or multi-peaked in two of the velocity space directions. This is important because it may have implications for the stability of the equilibrium. One major aim of this thesis is to find new force-free equilibrium distribution functions. By using a new method which is different from that of Harrison and Neukirch, it is possible to find a complete family of distribution functions for the force-free Harris sheet, which includes the Harrison and Neukirch distribution function (Physical Review Letters 102, 135003, 2009). Each member of this family has a different dependence on the particle energy, although the dependence on the canonical momenta remains the same. Three detailed analytical examples are presented. Other possibilities for finding further collisionless force-free equilibrium distribution functions have been explored, but were unsuccessful. The first linear stability analysis of the Harrison and Neukirch equilibrium distribution function is then carried out, concentrating on macroscopic instabilities, and considering two-dimensional perturbations only. The analysis is based on the technique of integration over unperturbed orbits. Similarly to the Harris sheet case (Nuovo Cimento, 23:115, 1962), this is only possible by using approximations to the exact orbits, which are unknown. Furthermore, the approximations for the Harris sheet case cannot be used for the force-free Harris sheet, and so new techniques have to be developed in order to make analytical progress. Full analytical expressions for the perturbed current density are derived but, for the sake of simplicity, only the long wavelength limit is investigated. The dependence of the stability on various equilibrium parameters is investigated.

The concept of happiness in Kant's moral, legal and political philosophy

Pinheiro Walla, Alice — 2012-11-30T00:00:00Z

Abstract: This doctoral thesis analyzes the systematic role of Kant’s conception of happiness in his moral, legal and political theory. Although many of his conclusions and arguments are directly or indirectly influenced by his conception of human happiness, Kant’s underlying assumptions are rarely overtly discussed or given much detail in his works. Kant also provides different and apparently incompatible definitions of happiness. This research explores the domains of Kant’s practical philosophy in which his conception of happiness plays a systematic role: the relation between the natural need of human beings to pursue happiness and the ends-oriented structure of the human will; Kant’s anti-eudaimonism in ethical theory; Kant’s claim that we have an indirect duty to promote our own happiness and the problem that under certain circumstances, the indeterminacy of happiness makes it not irrational to choose short term satisfaction at the costs of one’s overall, long term happiness, given Kant’s conception of non-moral choice as expectation of pleasure; Kant’s justification of the duty to adopt the happiness of others as our ends (the duty of beneficence) and the latitude and eventual demandingness of this duty; finally, since Kant also subsumes subsistence needs and welfare under the concept of happiness of individuals, I also engage with the question of state provision for the poor in the Kantian Rechtsstaat and explore Kant’s conception of equity or fairness (Billigkeit) as an alternative to the traditional minimalist and the welfare interpretations of the Kantian state.

Progress towards the synthesis of perophoramidine : formation of the contiguous quaternary centres

Johnston, Craig A. — 2013-06-01T00:00:00Z

Abstract: Perophoramidine 1 is a halogenated natural product which contains two contiguous quaternary centres within its structure. In this thesis, approaches towards the synthesis of perophoramidine are described. In particular, the synthesis of the tetracyclic core structure and the formation of the quaternary centres have been examined. In Chapter 1, the natural product perophoramidine 1 is introduced and its isolation, structure and biological activity is discussed. The structurally related communesin family of natural products are also introduced before the literature published on both the biosynthesis and laboratory synthesis of perophoramidine 1, is reviewed. Finally the Westwood group’s approach towards the synthesis of perophoramidine 1 is introduced with a summary of non-halogenated model system investigations previously carried out within the group being provided. Chapter 2 describes studies towards the synthesis of an appropriately halogenated indolo[2,3-b]quinoline core structure of perophoramidine 1. This then allowed methodology previously developed within the group on model system substrates to be applied to the formation of the first of the two quaternary centres required for the synthesis of perophoramidine 1. Chapter 3 describes the attempted formation of the second quaternary centre using an ester alkylation approach. After initial studies failed to generate the desired quaternary centre, non-halogenated model system studies were carried out in an attempt to develop an alternative approach. In Chapter 4, model system studies were continued with cyclic ether compounds investigated as potential intermediates towards the synthesis of perophoramidine 1. The results obtained in this chapter provided a novel route to the formation of the second quaternary centre and led to a redesigned approach towards perophoramidine 1 being developed. In Chapter 5, this redesigned approach was applied to the halogenated intermediates synthesised in Chapter 1. This led to the formation of the first halogenated intermediate synthesised within the group which contained the two contiguous quaternary centres required for the synthesis of perophoramidine 1.

The subversion of everyday life : an anthropological study of radical political practices : the Greek revolt of December 2008

Kallianos, Ioannis — 2012-11-30T00:00:00Z

Abstract: Based on eighteen months of fieldwork amongst anarchist and anti-authoritarian groups in Athens this thesis focuses on the December 2008 Greek revolt. It is an ethnographic exploration of collective self-organised practices in the public spaces of Athens and the occupied buildings of that period. It posits that these sets of processes were developed in the revolt as politics of subversion of the everyday life which in the thesis is considered both the site of alienation and emancipation. Based on Bourdieu, this study suggests that the everyday practices of subversion in radical politics are habitual dispositions of action that have been developed, based on past events which go as far back as the Greek civil war (1946-49), to establish a political living in the present, a process that is explored based on what Friedman calls ‘mythologisation’ . Drawing on De Certeau, Lefebvre and Vaneigem it is argued that these collective dispositions are the productive factors of tactics of the subversion which emerge in the context of everyday situations defined by the particularities of public space, imagination and public memory.This suggests that the revolt was not an organised process to create a counter-hegemony but rather, a multitude of micro-processes which used everyday situations as sites of subversion. This argument is explored based on the notion of the social imaginary as defined by Taylor and Castoriadis. In this thesis imagination is considered to be constitutive of the politics of subversion. Fuelled by past events and habitual dispositions of actions radical political practices in the revolt were formative of an ontological process which imagines and explains the political as personal and the private as public. According to that interpretation the event of the death of Alexandros Grigoropoulos generated sites where official power could be challenged, escaped and confronted by tactics of subversion.

Appealing to intuitions

Langkau, Julia — 2013-06-27T00:00:00Z

Abstract: This thesis is concerned with the ontology, epistemology, and methodology of intuitions in philosophy. It consists of an introduction, Chapter 1, and three main parts. In the first part, Chapter 2, I defend an account of intuitions as appearance states according to which intuitions cannot be reduced to beliefs or belief-like states. I argue that an account of intuitions as appearance states can explain some crucial phenomena with respect to intuitions better than popular accounts in the current debate over the ontology of intuitions. The second part, Chapters 3 to 5, is a reply to Timothy Williamson’s (2004, 2007) view on the epistemology and methodology of intuitions. The practice of appealing to the fact that we have an intuition as evidence from thought experiments has recently been criticised by experimental philosophers. Williamson argues that since thought experiments reliably lead to knowledge of the content of our intuition, we can avoid this criticism and the resulting sceptical threat by appealing to the content of the intuition. I agree that thought experiments usually lead to knowledge of the content of our intuition. However, I show that appealing to the fact that we have an intuition is a common and useful practice. I defend the view that for methodological reasons, we ought to appeal to the fact that we have an intuition as initial evidence from thought experiments. The third part, Chapter 6, is devoted to a paradigm method involving intuitions: the method of reflective equilibrium. Some philosophers have recently claimed that it is trivial and could even accommodate scepticism about the reliability of intuitions. I argue that reflective equilibrium is not compatible with such scepticism. While it is compatible with the view I defend in the second part of the thesis, more specific methodological claims have to be made.

Rudyard Kipling and Victorian Buddhism

Louttit, Erin — 2013-06-01T00:00:00Z

Abstract: The thesis recontextualises the fiction of the nineteenth- and twentieth-century writer Rudyard Kipling by exploring aspects of Victorian Buddhism in a selection of his published work. It demonstrates his engagement with a variety of Buddhist histories and cultures, showing a serious artistic and imaginative response to and interpretation of Buddhism. Focusing primarily on the novel Kim, the thesis develops existing criticism, examining the character of the lama. Additionally, it studies features of Victorian Buddhism other than textual sources, drawing on work by scholars in fields such as the history of art and the history of religion. As well as considering varied Buddhist elements in Kim, the thesis examines the theme of the survival of the soul, situating short stories from various periods of Kipling’s writing life in the context of scholarly debates about Nirvana and reincarnation. Attention is also given to critically neglected travel writing from the Letters of Marque series written for periodical publication. Kipling’s work is shown to be deeply concerned with and sympathetic to Buddhism and Buddhist cultures.

The genome of the obligate intracellular parasite Trachipleistophora hominis : new insights into microsporidian genome dynamics and reductive evolution

Heinz, Eva — 2012-10-25T00:00:00Z

Abstract: The dynamics of reductive genome evolution for eukaryotes living inside other eukaryotic cells are poorly understood compared to well-studied model systems involving obligate intracellular bacteria. Here we present 8.5 Mb of sequence from the genome of the microsporidian Trachipleistophora hominis, isolated from an HIV/AIDS patient, which is an outgroup to the smaller compacted-genome species that primarily inform ideas of evolutionary mode for these enormously successful obligate intracellular parasites. Our data provide detailed information on the gene content, genome architecture and intergenic regions of a larger microsporidian genome, while comparative analyses allowed us to infer genomic features and metabolism of the common ancestor of the species investigated. Gene length reduction and massive loss of metabolic capacity in the common ancestor was accompanied by the evolution of novel microsporidian-specific protein families, whose conservation among microsporidians, against a background of reductive evolution, suggests they may have important functions in their parasitic lifestyle. The ancestor had already lost many metabolic pathways but retained glycolysis and the pentose phosphate pathway to provide cytosolic ATP and reduced coenzymes, and it had a minimal mitochondrion (mitosome) making Fe-S clusters but not ATP. It possessed bacterial-like nucleotide transport proteins as a key innovation for stealing host-generated ATP, the machinery for RNAi, key elements of the early secretory pathway, canonical eukaryotic as well as microsporidian-specific regulatory elements, a diversity of repetitive and transposable elements, and relatively low average gene density. Microsporidian genome evolution thus appears to have proceeded in at least two major steps: an ancestral remodelling of the proteome upon transition to intracellular parasitism that involved reduction but also selective expansion, followed by a secondary compaction of genome architecture in some, but not all, lineages.

Fantasising the self, fantasising the other : memory and re-visions in Mario Martone's L'amore molesto

Riccobono, Rossella Maria — 2010-09-01T00:00:00Z

“The ‘Ars vivendi’ of Laura Mañà’s Morir en San Hilario/To Die in San Hilario (2005)”

Bentley, Bernard Pierre Emile — 2012-11-21T00:00:00Z

Abstract: Over the past decade Spanish-Language Cinema has established itself beside Spanish and Latin American Cinema, and Morir en San Hilario is a good example of these new flexible collaborations rather than a strict transnational co-production. Billed as a comedy, the film could also be described as a variation on the road film, a circular journey to Utopia, a Spanish village/pueblo film, and a twenty-first-century ‘Ars moriendi’ developing the topos of ‘Homo viator’. This is not a frequent combination to be found on cinema screens and Laura Mañà’s gamble was to integrate these ingredients and create a fable to reflect on life and death. She does this through comedy, exaggerations, parody and a narrative style identified as magic realism. Her originality, however, overlaps with the lasting legacy of the fifteenth-century Castilian soldier-poet, Jorge Manrique (c.1440-1479) and his ‘Stanzas written upon the death of his father’, a landmark of Spanish Literature.

Two-dimensional magnetohydrodynamic turbulence in the limits of infinite and vanishing magnetic Prandtl number

Tran, Chuong Van — 2013-06-01T00:00:00Z

Abstract: We study both theoretically and numerically two-dimensional magnetohydrodynamic turbulence at infinite and zero magnetic Prandtl number $Pm$ (and the limits thereof), with an emphasis on solution regularity. For $Pm=0$, both $\norm{\omega}^2$ and $\norm{j}^2$, where $\omega$ and $j$ are, respectively, the vorticity and current, are uniformly bounded. Furthermore, $\norm{\nabla j}^2$ is integrable over $[0,\infty)$. The uniform boundedness of $\norm{\omega}^2$ implies that in the presence of vanishingly small viscosity $\nu$ (i.e. in the limit $Pm\to0$), the kinetic energy dissipation rate $\nu\norm{\omega}^2$ vanishes for all times $t$, including $t=\infty$. Furthermore, for sufficiently small $Pm$, this rate decreases linearly with $Pm$. This linear behaviour of $\nu\norm{\omega}^2$ is investigated and confirmed by high-resolution simulations with $Pm$ in the range $[1/64,1]$. Several criteria for solution regularity are established and numerically tested. As $Pm$ is decreased from unity, the ratio $\norm{\omega}_\infty/\norm{\omega}$ is observed to increase relatively slowly. This, together with the integrability of $\norm{\nabla j}^2$, suggests global regularity for $Pm=0$. When $Pm=\infty$, global regularity is secured when either $\norm{\nabla\u}_\infty/\norm{\omega}$, where $\u$ is the fluid velocity, or $\norm{j}_\infty/\norm{j}$ is bounded. The former is plausible given the presence of viscous effects for this case. Numerical results over the range $Pm\in[1,64]$ show that $\norm{\nabla\u}_\infty/\norm{\omega}$ varies slightly (with similar behaviour for $\norm{j}_\infty/\norm{j}$), thereby lending strong support for the possibility $\norm{\nabla\u}_\infty/\norm{\omega}<\infty$ in the limit $Pm\to\infty$. The peak of the magnetic energy dissipation rate $\mu\norm{j}^2$ is observed to decrease rapidly as $Pm$ is increased. This result suggests the possibility $\norm{j}^2<\infty$ in the limit $Pm\to\infty$. We discuss further evidence for the boundedness of the ratios $\norm{\omega}_\infty/\norm{\omega}$, $\norm{\nabla\u}_\infty/\norm{\omega}$ and $\norm{j}_\infty/\norm{j}$ in conjunction with observation on the density of filamentary structures in the vorticity, velocity gradient and current fields. Description: LAKB was supported by an EPSRC post-graduate studentship.

Note on solution regularity of the generalized magnetohydrodynamic equations with partial dissipation

Tran, Chuong Van — 2013-07-01T00:00:00Z

Abstract: In this brief note we study the $n$-dimensional magnetohydrodynamic equations with hyper-viscosity and zero resistivity. We prove global regularity of solutions when the hyper-viscosity is sufficiently strong.

The state of affairs : critical performativity and the online dating industry

Roscoe, Philip John — 2013-01-01T00:00:00Z

Abstract: In this paper we pursue a dialogue between Callon’s (1998) ‘performativity thesis’ and Critical Management Studies (CMS). We make use of the performativity thesis to elaborate on the construction of a market and the generation of calculative and rational economic agency in a specific empirical setting: the markets for relationships offered by dating services. We find evidence for ‘effective’ performativity, where technical processes and outcomes are shaped by academic theory. We link the performativity analysis with three critical perspectives: a novel enclosure in the commodification and sale of relationships; the politics of standardisation, classification, expertise and responsibility; and the enactment of instrumentally rational, self-interested social relations through the individualist assumptions of matching systems. We argue that a performativity analysis must begin with a critical politics: what kind of world would we like to see performed?

Solar magnetic carpet III : coronal modelling of synthetic magnetograms

Meyer, Karen Alison — 2013-09-01T00:00:00Z

Teaching and understanding of quantum interpretations in modern physics courses

Baily, Charles — 2010-01-27T00:00:00Z

Abstract: Just as expert physicists vary in their personal stances on interpretation in quantum mechanics, instructors vary on whether and how to teach interpretations of quantum phenomena in introductory modern physics courses. In this paper, we document variations in instructional approaches with respect to interpretation in two similar modern physics courses recently taught at the University of Colorado, and examine associated impacts on student perspectives regarding quantum physics. We find students are more likely to prefer realist interpretations of quantum-mechanical systems when instructors are less explicit in addressing student ontologies. We also observe contextual variations in student beliefs about quantum systems, indicating that instructors who choose to address questions of ontology in quantum mechanics should do so explicitly across a range of topics.

Refined characterization of student perspectives on quantum physics

Baily, Charles — 2010-09-16T00:00:00Z

Abstract: The perspectives of introductory classical physics students can often negatively influence how those students later interpret quantum phenomena when taking an introductory course in modern physics. A detailed exploration of student perspectives on the interpretation of quantum physics is needed, both to characterize student understanding of physics concepts, and to inform how we might teach traditional content. Our previous investigations of student perspectives on quantum physics have indicated they can be highly nuanced, and may vary both within and across contexts. In order to better understand the contextual and often seemingly contradictory stances of students on matters of interpretation, we interviewed 19 students from four introductory modern physics courses taught at the University of Colorado. We find that students have attitudes and opinions that often parallel the stances of expert physicists when arguing for their favored interpretations of quantum mechanics, allowing for more nuanced characterizations of student perspectives in terms of three key interpretive themes. We present a framework for characterizing student perspectives on quantum mechanics, and demonstrate its utility in interpreting the sometimes contradictory nature of student responses to previous surveys. We further find that students most often vacillate in their responses when what makes intuitive sense to them is not in agreement with what they consider to be a correct response, underscoring the need to distinguish between the personal and the public perspectives of introductory modern physics students.

Coherent control of plasmonic nanoantennas using optical eigenmodes

Kosmeier, Sebastian — 2013-05-09T00:00:00Z

Abstract: The last decade has seen subwavelength focusing of the electromagnetic field in the proximity of nanoplasmonic structures with various designs. However, a shared issue is the spatial confinement of the field, which is mostly inflexible and limited to fixed locations determined by the geometry of the nanostructures, which hampers many applications. Here, we coherently address numerically and experimentally single and multiple plasmonic nanostructures chosen from a given array, resorting to the principle of optical eigenmodes. By decomposing the light field into optical eigenmodes, specifically tailored to the nanostructure, we create a subwavelength, selective and dynamic control of the incident light. The coherent control of plasmonic nanoantennas using this approach shows an almost zero crosstalk. This approach is applicable even in the presence of large transmission aberrations, such as present in holographic diffusers and multimode fibres. The method presents a paradigm shift for the addressing of plasmonic nanostructures by light.

Told and retold : the Solomon narratives in the context of Tanak

Cook, Sean E. — 2013-06-25T00:00:00Z

Abstract: This thesis explores the relationship between the books of Kings and Chronicles and considers the value of having two different versions of the same monarchic history within the Tanak. It furthermore explores how these books are read in relation to one another. To be more specific, its concern is how the book of Chronicles is read in relation to the book of Kings as Chronicles is so often considered to be a later rewritten text drawing upon an earlier version of the Masoretic Text of Kings. The predominant scholarly approach to reading the book of Chronicles is to read it in light of how the text was emended (additions, deletions, etc.). This approach has great value and has furthered our understanding of the theology and purpose of Chronicles. While this thesis fully affirms this diachronic approach to reading Chronicles, it also finds it to be lacking. This said, I suggest that this predominant way of reading Chronicles through the lens of its source (Kings) sometimes misses the theological and rhetorical features of the Chronicler’s text. In light of this suggestion, this thesis will answer the following question: “why were two narratives retained in the Tanak and what possible answers to this question might emerge by looking at the similarities and differences in the two narratives’ contents, arguments, and theology?” The method by which this question will be addressed is to read the Solomon narratives in the books of Kings and Chronicles in two ways: first, to read each narrative as a whole and independently of one another, and second, to examine each narrative together in an effort to understand their uniqueness. The result of this analysis will show that these narratives can in fact read as whole narratives independent of one another, and furthermore, that Solomon is in fact less idealized (contra popular scholarly opinion) in the book of Chronicles.

Investigating protein- protein interactions in order to develop novel therapeutics for the treatment of Alzheimer’s disease

Aitken, Laura — 2013-06-26T00:00:00Z

Abstract: Alzheimer’s disease (AD) accounts for around two thirds of all dementia cases and an increase in life expectancy of the population has resulted in a substantial increase in dementia cases and with that a rise in AD. AD is a debilitating and ultimately fatal neurodegenerative disorder of the elderly, and despite being identified over a century ago, the current treatments do not treat the underlying causes behind the disease, instead they help to mask the symptoms of the disease and prolong the brain’s remaining function. It is therefore vital that an effective, disease modifying treatment for this disease is established as soon as possible. Soluble intracellular forms of amyloid β (peptide Aβ), a hallmark of AD have been identified and intracellular targets of Aβ are being investigated as potential drug targets for the disease. Two key intracellular, mitochondrial proteins investigated as potential drug targets: amyloid binding alcohol dehydrogenase (ABAD) and cyclophilin D (CypD) are the focus of the work reported in this thesis. To begin identifying potential inhibitors of the ABAD-Aβ interaction, a two-pronged approach was taken. Firstly, a series of analogues based on a known inhibitor of the interaction were tested using a variety of biophysical assays, for their therapeutic affect on the interaction, and secondly a fragment based screening approach was used to identify new small molecule binding partners of ABAD which could potentially be modified to produced inhibitors of the ABAD-Aβ interaction. Three different CypD constructs have been successfully expressed and purified, and taken into crystal trials. It is hoped that these constructs can be used to significantly aid the progress of identifying any potential inhibitors and binding partners of CypD that may produce therapeutic effects, and in the future could lead to the identification of an effective disease modifying drug in the treatment of AD. The work reported in this thesis has built upon previously reported findings and the groundwork has also been established for several in vitro biophysical assays, these include for example: measuring ABAD enzyme activity, and the novel morphology specific Aβ aggregation assay, which can be used as screening tools to help identify potential inhibitors of these interactions. Both the ABAD-Aβ interaction, and the blockade of CypD are known to be drug targets in the treatment of AD, and by elucidating the molecular mechanisms behind these interactions, through implementing biophysical assays, this will help in the identification and design of potential new therapeutic agents for the treatment of AD.

Research-based course materials and assessments for upper-division electrodynamics (E&M II)

Baily, Charles — 2013-01-01T00:00:00Z

Abstract: Favorable outcomes from ongoing research at the University of Colorado Boulder on student learning in junior-level electrostatics (E&M I) have led us to extend this work to upper-division electrodynamics (E&M II). We describe here our development of a set of research-based instructional materials designed to actively engage students during lecture (including clicker questions and other in-class activities); and an instrument for assessing whether our faculty-consensus learning goals are being met. We also discuss preliminary results from several recent implementations of our transformed curriculum, plans for the dissemination and further refinement of these materials, and offer some insights into student difficulties in advanced undergraduate electromagnetism.

Development of quantum perspectives in modern physics

Baily, Charles — 2009-03-23T00:00:00Z

Abstract: Introductory undergraduate courses in classical physics stress a perspective that can be characterized as realist; from this perspective, all physical properties of a classical system can be simultaneously specified and thus determined at all future times. Such a perspective can be problematic for introductory quantum physics students, who must develop new perspectives in order to properly interpret what it means to have knowledge of quantum systems. We document this evolution in student thinking in part through pre- and post-instruction evaluations using the Colorado Learning Attitudes about Science Survey. We further characterize variations in student epistemic and ontological commitments by examining responses to two essay questions, coupled with responses to supplemental quantum attitude statements. We find that, after instruction in modern physics, many students are still exhibiting a realist perspective in contexts where a quantum-mechanical perspective is needed. We further find that this effect can be significantly influenced by instruction, where we observe variations for courses with differing learning goals. We also note that students generally do not employ either a realist or a quantum perspective in a consistent manner.

A biographical and critical study of the life and writings of Sir David Dalrymple, Lord Hailes

Carnie, Robert Hay — 1954-01-01T00:00:00Z

Abstract: The name of Sir David Dalrymple, Lord Hailes has always been known to students of Scottish history by reason of his "Annals of Scotland", long accepted as a fundamental reference book for that period of Scottish history which it covers. It is safe to say, however that few of his other historical publications are now read. Those familiar with the anti-Gibbon literature also know him as one of Gibbon's most respected critics, while the recent studies of the 18th Century revival of interest in early and medieval literature have revealed his key position in this movement, both as an editor, and as an adviser and helper to others. In the legal profession, he was highly thought of as a lawyer and judge, and the number and importance of his correspondents testify to his wide acquaintance and high reputation amongst men of learning. Despite all this, no full account of the man and his work has previously been made, although there have been several unfinished attempts. [...] An attempt has been made to fit Hailes into the cultural and social background of his times, and to make some estimate of the influence and importance of his published work, with particular reference to the fields of history and literature. Much of the basic research in this thesis was done in compiling Appendices A and B. No reliable list of Hailes's publications has ever been drawn up, and Appendix A is a serious attempt to fill this gap. A complete check-list of Hailes's extant correspondence has not been attempted previously and Appendix B is designed to supply this omission. [Abstract taken from longer Foreword].

Interpretive themes in quantum physics : curriculum development and outcomes

Baily, Charles — 2012-02-01T00:00:00Z

Abstract: A common learning goal for modern physics instructors is for students to recognize a difference between the experimental uncertainty of classical physics and the fundamental uncertainty of quantum mechanics. Our prior work has shown that student perspectives on the physical interpretation of quantum mechanics can be characterized, and are differentially influenced by the myriad ways instructors approach interpretive themes in their introductory courses. We report how a transformed modern physics curriculum (recently implemented at the University of Colorado) has positively impacted student perspectives on quantum physics, by making questions of classical and quantum reality a central theme of the course, but also by making the beliefs of students (and not just those of scientists) an explicit topic of discussion.

Interpretation in quantum physics as hidden curriculum

Baily, Charles — 2010-01-01T00:00:00Z

Abstract: Prior research has demonstrated how the realist perspectives of classical physics students can translate into specific beliefs about quantum phenomena when taking an introductory modern physics course. Student beliefs regarding the interpretation of quantum mechanics often vary by context, and are most often in alignment with instructional goals in topic areas where instructors are explicit in promoting a particular perspective. Moreover, students are more likely to maintain realist perspectives in topic areas where instructors are less explicit in addressing interpretive themes, thereby making such issues part of a hidden curriculum. We discuss various approaches to addressing student perspectives and interpretive themes in a modern physics course, and explore the associated impacts on student thinking.

Student perspectives in quantum physics

Baily, Charles — 2008-01-01T00:00:00Z

Abstract: Introductory courses in classical physics are promoting in students a realist perspective, made up in part by the belief that all physical properties of a system can be simultaneously specified, and thus determined at all future times. Such a perspective can be problematic for introductory quantum physics students, who must develop new framings of epistemic and ontological resources in order to properly interpret what it means to have knowledge of quantum systems. We document this evolution in student thinking in part through pre/post instruction evaluations using the CLASS attitude survey. We further characterize variations in student epistemic and ontological commitments by examining responses to an essay question, coupled with responses to supplemental quantum attitude statements. We find that, after instruction in modern physics, many students are still exhibiting a realist perspective in contexts where a quantum perspective is needed. We also find that this effect can be significantly influenced by instruction, where we observe variations for courses with differing learning goals.

Quantum interpretations in modern physics instruction

Baily, Charles — 2009-01-01T00:00:00Z

Abstract: Just as expert physicists vary in their personal stances on interpretation in quantum mechanics, instructors hold different views on teaching interpretations of quantum phenomena in introductory modern physics courses. There has been relatively little research in the physics education community on the variation in instructional approaches with respect to quantum interpretation, and how instructional choices impact student thinking. We compare two modern physics courses taught at the University of Colorado with similar learning environments, but where the instructors held different views on how to teach students about interpretations of quantum processes. We find significant differences in how students from these two courses responded to a survey on their beliefs about quantum mechanics; findings also suggest that instructors who choose to address student ontologies should do so across a range of topics.

El pronunciamiento mexicano del siglo XIX. Hacia una nueva tipología

Fowler, William — 2009-07-01T00:00:00Z

Abstract: Tras la guerra de Independencia (1810-1821) estallaron más de 1 500 pronunciamientos entre el Plan de Iguala de 1821 y el Plan de Tuxtepec de 1876. En varios casos degeneraron en enfrentamientos de una violencia atroz como el saqueo del Parián en la ciudad de México de 1828. En otros resultaron en guerras civiles brutales (1832, 1854-1855, 1858-1860). En muchos casos, sin embargo, sus demandas fueron atendidas o sofocadas dependiendo de cuántos pronunciamientos de adhesión recibieron. Este artículo busca redefinir la práctica del pronunciamiento en México, haciendo hincapié en el protagonismo que tuvieron grupos e instituciones civiles al adoptar este medio legítimo, aunque no constitucional, para forzar cambios políticos tanto a nivel regional como nacional durante las primeras décadas nacionales.

Primi influssi culturali italo-veneti sull'inglese : la testimonianza dei venezianismi in Florio, Coryate e Jonson

Ferguson, Ronnie — 2012-11-26T00:00:00Z

Abstract: This article demonstates that the earliest body of Italianisms in English, in the sixteenth and early seventeenth centuries, was in large measure of Venetian origin. After establishing and dating the fifty Venetianisms that entered English in this period the study goes on to analyse Venetian lexical influence in John Florio's Italian-English dictionaries (1598 and 1611), in Thomas Coryate's travel book (the "Crudities") (1611) and in Ben Jonson's play "Volpone" (1607) set in Venice.

Double time : Facing the future in migration’s past

Duncan, Derek Egerton — 2011-01-01T00:00:00Z

Abstract: Interpretations of Italian films about migration tend to refer to the historical experience of emigration or of colonialism as the historical coordinates through which these films are best understood. This article looks at four recent films featuring migrants in prominent roles that appear to elide such an interpretive framework. While the past and its intrusive effects do feature strongly in these films, it is difficult to produce a predictable linear and causal narrative that would link past, present, and future in predictable ways. Stylistically, the four films also represent a notable move away from the realist political agenda and aesthetic that has tended to dominate Italian film production on the topic of migration. This article argues that their adoption of the features that recall those of film noir (in its Italian manifestation) suggests a new range of thematic and social concerns that refer as much to possible futures as well as known pasts. There is a particular focus on the topic of bodily reproduction which is no longer limited to the sphere of the sexual. The opportunities offered by technology for the body to reproduce in new ways alters the parameters of how the nation might be imagined.

Perceptions of France : French books in the early libraries of South Australia, 1848-1884

Culpin, David John — 2009-01-01T00:00:00Z

Abstract: In 1848, the South Australian Library and Mechanics’ Institute came into existence. It was the first stable library in South Australia. In 1856 its books passed to the library of the South Australian Institute, whose holdings continued to grow until 1883, when many of the books were transferred to the fledgling Public Library, forerunner of today’s State Library. Between 1848 and 1883 the two early libraries built up a collection of nearly 20,000 works of which a little over 500 were by French authors, and almost half of those books were in French. This paper follows the growth of the collection of French books and examines the nature of the books that were acquired. In doing so it highlights the place which French culture continued to occupy within the intellectual life of early South Australia and illustrates the gradual change of taste as an elite culture was displaced by the demands of a more popular readership.

Scotland for Franco : Charles Saroléa v. The Red Duchess

Bowd, Gavin Philip — 2011-11-01T00:00:00Z

What counts as good evidence

Nutley, Sandra Margaret — 2013-02-01T00:00:00Z

Abstract: Making better use of evidence is essential if public services are to deliver more for less. Central to this challenge is the need for a clearer understanding about standards of evidence that can be applied to the research informing social policy. This paper reviews the extent to which it is possible to reach a workable consensus on ways of identifying and labelling evidence. It does this by exploring the efforts made to date and the debates that have ensued. Throughout, the focus is on evidence that is underpinned by research, rather than other sources of evidence such as expert opinion or stakeholder views.

Henry Hallam revisited

Bentley, Michael John — 2012-06-01T00:00:00Z

Abstract: Although Henry Hallam (1777–1859) is best known for his Constitutional History of England (1827) and as a founder of ‘whig’ history, to situate him primarily as a mere critic of David Hume or as an apprentice to Thomas Babington Macaulay does him a disservice. He wrote four substantial books of which the first, his View of the state of Europe during the middle ages (1818), deserves to be seen as the most important; and his correspondence shows him to have been integrated into the contemporary intelligentsia in ways that imply more than the Whig acolyte customarily portrayed by commentators. This article re-situates Hallam by thinking across both time and space and depicts a significant historian whose filiations reached to Europe and North America. It proposes that Hallam did not originate the whig interpretation of history but rather that he created a sense of the past resting on law and science which would be reasserted in the age of Darwin.

Constructing the retail investor : performativity and power in the market for investment services

Roscoe, Philip John — 2013-06-01T00:00:00Z

Abstract: This paper examines retail investment as a practice performed by marketing knowledge and highlights the power effects of market devices. Using a qualitative study of retail investors in the United Kingdom, it considers the devices and discourses that structure investment behaviour. It draws attention to parallels between the precepts of the market studies programme and the Foucauldian literature of governance technologies in neo-liberal capitalism. Market devices and heterodox ways of understanding the financial market constitute investors as docile consumers of investment services. Self-discipline and confession are normalising technologies that help investors cope with difficulties and losses in the market.

Pavilioned on nothing : nihilism and its counterforces in the works of Oscar Wilde

Cavendish-Jones, Colin — 2013-01-01T00:00:00Z

Abstract: This thesis explores the role of Nihilism in Oscar Wilde's thought and writing, beginning with the depiction of Russian Political Nihilism in Wilde's first play; Vera, or the Nihilists and tracing the engagement with philosophical Nihilism in his fiction, drama and essays, up to and including De Profundis. It is argued that Russian Political Nihilism derives from the same sources and expresses the same concerns as the philosophical Nihilism discussed by Nietzsche in The Will to Power, and that Nietzsche and Wilde, working independently, came to a strikingly similar understanding of Nihilism. Philosophical Nihilism is defined in two ways; as the complete absence of values (Absolute Nihilism) and as a sense that, while absolute values may exist, they are unattainable, unknowable or inexpressible (Relative Nihilism). Wilde uses his writing to express Nihilism while simultaneously seeking aesthetic and ethical counterforces to it, eventually coming to see Art and the life of the Artist as the ultimate forms of resistance to Nihilism. Wilde's philosophical views are examined in the context of his time, and in the light of his exceptionally wide reading. He is compared and contrasted with Nietzsche, the philosopher who has done most to shape our view of what Nihilism means, in his ethical and aesthetic response to Nihilism. The conclusion also considers the reception of Wilde's expression of Nihilism and his employment of Art as the only superior counterforce in the first half of the twentieth century, with particular reference to the works of Gide and Proust. Their engagement with Nihilism is explored both in historical context and as a way of addressing a problem which has become uniquely pervasive and pressing in the modern era.

Face evaluation : perceptual and neurophysiological responses to pro-social attributions

Dzhelyova, Milena P. — 2013-06-25T00:00:00Z

Abstract: The pro-sociality of humans is manifested by the existence of cooperation in levels not common with any other species. Previous studies suggest that snap judgements of individuals are enough to determine if someone is a potential partner for cooperation. In addition to the often studied facial characteristics affecting cooperativeness and trustworthiness attribution (kin resemblance; attractiveness and emotional expression), the experimental work reported here examined the influence of head posture; gaze direction and skin colour on the attribution of trustworthiness and cooperation. A slightly tilted head (less than 3° downward) increased the perception of cooperativeness, especially for male and hostile looking faces. The importance of head tilt increased with decreased self-assessed dominance. Furthermore, even though some evidence that the effect of head posture is independent of gaze direction was found, gaze direction was also a strong indicator of cooperative intentions. Direct gaze and gaze slightly looking down (3°) were perceived as more cooperative than deviations of gaze outside this range (3° up or 6°- 9° down). Skin colour, a putative cue to current health status, was also found to impact on trustworthiness perception with a healthy skin colour increasing trustworthiness ratings. Additionally, as cooperative and trust decisions are vital for survival and social interactions, decisions based on facial appearance are made quickly and automatically as demonstrated by a trustworthiness modulation on an early face related component with 170 ms of exposure. Collectively, these findings suggest that facial characteristics employed to infer trust and cooperativeness help the observer to assess the motives and intentions of the individuals and assist the choice of partners that will lead to increased benefits and reduced costs in collaborative actions. Such considerations fit well with the evolutionary theory of cooperation as reciprocated social exchange. Description: Electronic version excludes embargoed material (Chapters 2-6)

Novel routes to high performance lithium-ion batteries

Drewett, Nicholas E. — 2013-06-26T00:00:00Z

Abstract: This thesis investigates several approaches to the development of high-performance batteries. A general background to the field and an introduction to the experimental methods used are given in Chapters 1 and 2 respectively. Chapter 3 presents a study of ordered and disordered LiNi₀.₅Mn₁.₅O₄ materials produced using an optimised resorcinol-formaldehyde gel (R-F gel) synthetic technique. Both materials exhibited good electrochemical properties and minimal side reaction with the electrolyte. Structural analyses of the materials in various states of discharge and charge were undertaken, and from these the charge / discharge processes were elucidated. In chapter 4 R-F gel synthesised Li(Ni₁/₃Mn₁/₃Co₁/₃)O₂ is studied and found to exhibit a high degree of structural stability on cycling, as well as excellent capacity, cyclability and rate capability. Photoelectron spectroscopy studies revealed that the R-F gel derived particles have highly stable surfaces. A discussion of the results and their significance, with particular regard to the outstanding electrochemical performance observed, is also presented. Chapter 5 sets out an investigation into the nature of R-F gel synthesised 0.5Li₂MnO₃:0.5LiNi₁/₃Mn₁/₃Co₁/₃O₂. The electrochemical data revealed that, after an initial activation stage, the R-F gel derived material exhibited a high capacity, good cyclability and exceptional rate capability. This chapter also considers some initial structural investigations and the electrochemical processes occurring on charge. In chapter 6 the use of ether-based electrolytes, combined with various cathode materials, in lithium-oxygen batteries is examined. The formation of decomposition products was observed, and a scheme suggesting probable reaction pathways is given. It was noted that significant quantities of the desired discharge product, lithium peroxide, were formed on the 1st cycle discharge, implying some electrolyte / cathode combinations do demonstrate a degree of stability. A summary of the results and a discussion of their significance are also included.

Structural basis of Lassa fever nucleoprotein binding pathogen-associated pattern molecule dsRNA

Xue, Jiang — 2012-11-30T00:00:00Z

Abstract: Lassa fever virus (LASV) infects thousands of people and produces more than 5,000 deaths each year in West Africa. This severe virus is a huge threat, as it transmits between human and rodents, and no effective vaccine or drug is available currently. One key of getting control of this disease lies in the nucleoprotein (NP) of LASV, which plays an essential role in viral replication, transcription and immune suppression. The full length NP crystal structure has been solved, showing a novel structural fold and multi-functions with unusual mechanisms in immune suppression and viral RNA transcription. The C-terminal domain of LAVS NP is a 3’-5’ exonuclease, whose activity is essential for viral immune suppression. This domain alone can suppress an immune response and can degrade dsRNAs with specific preference higher than for ssRNAs. However, the detail of the mechanism is unclear. To understand the mechanism while avoiding another domain’s effect (the N-terminal domain), the C-terminal domain of LASV NP was expressed and purified, and pathogen-associated pattern molecular RNAs were synthesized chemically and biologically to carry on crystallization and functional testing. The C-domain crystals in complex with a pathogen-associated pattern molecule, triphosphate 8 nucleotide dsRNA were obtained. The crystal belongs to the space group P3 with unit cell dimension a=b=177.6 Å, c=56.49Å, α =β=90°, γ=120°. This crystal structure showed that the dsRNA binds in the 3’-5’ exonuclease active site with one 3’ end of the dsRNA perfectly sitting for cleavage. We are trying to figure out the detailed mechanism by mutagenesis, fluorescence-labeled RNA gel scan and band shift assays.

Biochemical and functional characterisation of phospholipase C-η2

Popovics, Petra — 2013-06-28T00:00:00Z

Abstract: Phospholipase C enzymes are important cell signalling enzymes that catalyse the cleavage of phosphatidylinositol 4,5-bisphophate PI(4,5)P₂ into two biologically active second messenger molecules. These are the inositol 1,4,5-trisphosphate which initiates Ca²⁺ release from the endoplasmic reticulum and the diacylglycerol that activates protein kinase C. Although this basic function is shared between the different isoforms, the PLC family encompasses a diverse collection of proteins with various domain structures in addition to the PLC-specific domains. The neuron-specific “6th family” of these enzymes, PLCηs have most recently been identified with two members, PLCη1 and PLCη2. The aim of the thesis is to characterise the PLCη2 variant from several aspects. Firstly, it describes that PLCη2 possesses a high sensitivity towards Ca²⁺. Secondly, it investigates how the Ca²⁺-induced enzymatic activity of PLCη2 is controlled by its different domains. Also it provides evidence that the pleckstrin homology domain targets PLCη2 to membranes by recognising PI(3,4,5)P₃. Moreover, the uniquely structured EF-hand is responsible for the Ca²⁺-sensitivity of the enzyme. Finally, it is demonstrated that the C2 domain is important for activity. The initial biochemical characterisation is followed by the description of a physiological role for PLCη2. It is shown using a neuroblast model that PLCη2 is crucial for neuronal differentiation and neurite growth. Further efforts were made to assess how PLCη2 is responsible for this effect. It was revealed that it might be involved in regulating intracellular Ca²⁺ dynamics, transcriptional activity and actin reorganisation in differentiating neurons. As the functions of PLCη2 are just beginning to come to light, more aspects for future research are also suggested in the thesis. Hopefully, this and the data presented within the thesis will stimulate even greater interest in this fascinating new field of research.

Structural insights into the mechanism and inhibition of the beta-Hydroxydecanoyl-Acyl carrier protein dehydratase from pseudomonas aeruginosa

Moynie, Lucile — 2013-01-23T00:00:00Z

Abstract: Fatty acid biosynthesis is an essential component of metabolism in both eukaryotes and prokaryotes. The fatty acid biosynthetic pathway of Gram-negative bacteria is an established therapeutic target. Two homologous enzymes FabA and FabZ catalyze a key step in fatty acid biosynthesis; both dehydrate hydroxyacyl fatty acids that are coupled via a phosphopantetheine to an acyl carrier protein (ACP). The resulting trans-2-enoyl-ACP is further polymerized in a processive manner. FabA, however, carries out a second reaction involving isomerization of trans-2-enoyl fatty acid to cis-3-enoyl fatty acid. We have solved the structure of Pseudomonas aeruginosa FabA with a substrate allowing detailed molecular insight into the interactions of the active site. This has allowed a detailed examination of the factors governing the second catalytic step. We have also determined the structure of FabA in complex with small molecules (so-called fragments). These small molecules occupy distinct regions of the active site and form the basis for a rational inhibitor design program. (C) 2012 Elsevier Ltd. All rights reserved.

Mechanistic insights into the triazolylidene-catalysed Stetter and benzoin reactions : role of the N-aryl substituent

Collett, Christopher J. — 2013-01-01T00:00:00Z

Abstract: The in situ observation, isolation and reversible formation of intermediate 3-(hydroxybenzyl) azolium salts derived from NHC addition to a range of substituted benzaldehydes is probed. Equilibrium constants for the formation of these 3-(hydroxybenzyl) azolium salts, as well as rate constants of hydrogen-deuterium exchange (k(ex)) at C(alpha) of these intermediates for a range of N-aryl triazolinylidenes is reported. These combined studies give insight into the preference of N-pentafluorophenyl NHCs to participate in benzoin and Stetter reaction processes.

An efficient route for the synthesis of phosphorus-selenium macro-heterocycles

Hua, Guoxiong — 2013-01-01T00:00:00Z

Abstract: Four-membered ring [PhP(Se)(mu-Se)](2) (Woollins' reagent, WR) reacts with disodium alkenyl-diols followed by in situ ring-closure reaction with appropriate dibromoalkanes affording a series of unusual nine-to fifteen-membered organoselenophosphorus macrocycles bearing the O-P-Se-C-n-Se-P-O or O-P-Se-C-n-O-P-Se linkage.

Violets and abolition : The discourse on slavery in Faustina Saez de Melgar's magazine La Violeta (1862-1866)

Partzsch, Henriette Anna Margarete — 2012-09-01T00:00:00Z

Abstract: Although the commitment of several nineteenth-century Spanish women writers to abolitionism is a well-established fact, not much is known about the concrete forms their engagement took in a society in which the bourgeois ideology of woman as the angel in the house played a prominent role. The close study of the weekly magazine La Violeta (1862-66), directed by Faustina Sáez de Melgar, shows how the active and public support for this international cause was linked to the development of a model of compassionate intervention by women, most notably formulated by the magazine's regular contributor Rogelia León in response to the very mixed reviews of the foundational meeting of a ladies' abolitionist society. The press coverage of this event clearly demonstrates how political conflict is cast in terms of gender and class and used to threaten middle-class women who step into the political sphere. The analysis of the discourse on slavery reveals an equal importance of both categories in La Violeta, together with the patronising and casual racism of its authors.

The privilege of poverty. Clare of Assisi, Agnes of Prague, and the struggle for a Franciscan rule for women

Andrews, Frances — 2007-10-01T00:00:00Z

Living like the laity? The negotiation of religious status in the cities of late medieval Italy

Andrews, Frances — 2010-12-01T00:00:00Z

Abstract: Framed 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.

Models incorporating chromatin modification data identify functionally important p53 binding sites

Lim, Ji-Hyun — 2013-01-01T00:00:00Z

Abstract: Genome-wide prediction of transcription factor binding sites is notoriously difficult. We have developed and applied a logistic regression approach for prediction of binding sites for the p53 transcription factor that incorporates sequence information and chromatin modification data. We tested this by comparison of predicted sites with known binding sites defined by chromatin immunoprecipitation (ChIP), by the location of predictions relative to genes, by the function of nearby genes and by analysis of gene expression data after p53 activation. We compared the predictions made by our novel model with predictions based only on matches to a sequence position weight matrix (PWM). In whole genome assays, the fraction of known sites identified by the two models was similar, suggesting that there was little to be gained from including chromatin modification data. In contrast, there were highly significant and biologically relevant differences between the two models in the location of the predicted binding sites relative to genes, in the function of nearby genes and in the responsiveness of nearby genes to p53 activation. We propose that these contradictory results can be explained by PWM and ChIP data reflecting primarily biophysical properties of protein–DNA interactions, whereas chromatin modification data capture biologically important functional information.

Short and long supports for constraint propagation

Nightingale, Peter — 2013-01-01T00:00:00Z

Abstract: Special-purpose constraint propagation algorithms frequently make implicit use of short supports -- by examining a subset of the variables, they can infer support (a justification that a variable-value pair may still form part of an assignment that satisfies the constraint) for all other variables and values and save substantial work -- but short supports have not been studied in their own right. The two main contributions of this paper are the identification of short supports as important for constraint propagation, and the introduction of HaggisGAC, an efficient and effective general purpose propagation algorithm for exploiting short supports. Given the complexity of HaggisGAC, we present it as an optimised version of a simpler algorithm ShortGAC. Although experiments demonstrate the efficiency of ShortGAC compared with other general-purpose propagation algorithms where a compact set of short supports is available, we show theoretically and experimentally that HaggisGAC is even better. We also find that HaggisGAC performs better than GAC-Schema on full-length supports. We also introduce a variant algorithm HaggisGAC-Stable, which is adapted to avoid work on backtracking and in some cases can be faster and have significant reductions in memory use. All the proposed algorithms are excellent for propagating disjunctions of constraints. In all experiments with disjunctions we found our algorithms to be faster than Constructive Or and GAC-Schema by at least an order of magnitude, and up to three orders of magnitude.

Decadal-interdecadal climate variability over Antarctica and linkages to the tropics : analysis of ice core, instrumental, and tropical proxy data

Okumura, Yuko — 2012-11-01T00:00:00Z

Abstract: The Antarctic continent contains the majority of the global ice volume and plays an important role in a changing climate. The nature and causes of Antarctic climate variability are, however, poorly understood beyond interannual time scales due to the paucity of long, reliable meteorological observations. This study analyzes decadal-interdecadal climate variability over Antarctica using a network of annually resolved ice core records and various instrumental and tropical proxy data for the 19th and 20th centuries. During the 20th century, Antarctic ice core records indicate strong linkages to sea surface temperature (SST) variations in the tropical Pacific and Atlantic on decadal-interdecadal time scales. Antarctic surface temperature anomalies inferred from the ice cores are consistent with the associated changes in atmospheric circulation and thermal advection. A set of atmospheric general circulation model experiments supports the idea that decadal SST variations in the tropics force atmospheric teleconnections that affect Antarctic surface temperatures. When coral and other proxies for tropical climate are used to extend the analysis back to 1799, a similar Antarctic-tropical Pacific linkage is found, with evidence for a weaker connection during the first half of the 19th century. Over the past 50 years, a change in the phase of Pacific and Atlantic interdecadal variability may have contributed to the rapid warming of the Antarctic Peninsula and West Antarctica.

Stressed but stable : Canopy loss decreased species synchrony and metabolic variability in an intertidal hard-bottom community

Valdivia, Nelson — 2012-05-04T00:00:00Z

Abstract: The temporal stability of aggregate community properties depends on the dynamics of the component species. Since species growth can compensate for the decline of other species, synchronous species dynamics can maintain stability (i.e. invariability) in aggregate properties such as community abundance and metabolism. In field experiments we tested the separate and interactive effects of two stressors associated with storminess–loss of a canopy-forming species and mechanical disturbances–on species synchrony and community respiration of intertidal hard-bottom communities on Helgoland Island, NE Atlantic. Treatments consisted of regular removal of the canopy-forming seaweed Fucus serratus and a mechanical disturbance applied once at the onset of the experiment in March 2006. The level of synchrony in species abundances was assessed from estimates of species percentage cover every three months until September 2007. Experiments at two sites consistently showed that canopy loss significantly reduced species synchrony. Mechanical disturbance had neither separate nor interactive effects on species synchrony. Accordingly, in situ measurements of CO2-fluxes showed that canopy loss, but not mechanical disturbances, significantly reduced net primary productivity and temporal variation in community respiration during emersion periods. Our results support the idea that compensatory dynamics may stabilise aggregate properties. They further suggest that the ecological consequences of the loss of a single structurally important species may be stronger than those derived from smaller-scale mechanical disturbances in natural ecosystems.

A top-level ontology for smart environments

Ye, Juan — 2011-06-01T00:00:00Z

Abstract: Recognising human activities is a problem characteristic of a wider class of systems in which algorithms interpret multi-modal sensor data to extract semantically meaningful classifications. Machine learning techniques have demonstrated progress, but the lack of underlying formal semantics impedes the potential for sharing and re-using classifications across systems. We present a top-level ontology model that facilitates the capture of domain knowledge. This model serves as a conceptual backbone when designing ontologies, linking the meaning implicit in elementary information to higher-level information that is of interest to applications. In this way it provides the common semantics for information at different levels of granularity that supports the communication, re-use and sharing of ontologies between systems.

Multi-task research and research joint ventures

La Manna, Manfredi M A — 2013-04-01T00:00:00Z

Abstract: The paper shows that, whenever the completion of a research project requires the overcoming of more than one research obstacle, then Research Joint Ventures enjoy an intrinsic advantage relative to independent firms. This advantage, which has hitherto escaped attention in the RJV literature, relates to the RJV’s ability to organize research more efficiently than independent firms. The fact that RJVs can be both more profitable and yield higher expected net welfare than independent firms is surprising because it is derived from a model in which RJVs do not optimize over R&D investment. The paper exploits a basic result in systems reliability theory to establish the organizational superiority of RJVs.

Estimating animal population density using passive acoustics

Marques, Tiago A. — 2013-05-01T00:00:00Z

Abstract: Reliable estimation of the size or density of wild animal populations is very important for effective wildlife management, conservation and ecology. Currently, the most widely used methods for obtaining such estimates involve either sighting animals from transect lines or some form of capture-recapture on marked or uniquely identifiable individuals. However, many species are difficult to sight, and cannot be easily marked or recaptured. Some of these species produce readily identifiable sounds, providing an opportunity to use passive acoustic data to estimate animal density. In addition, even for species for which other visually based methods are feasible, passive acoustic methods offer the potential for greater detection ranges in some environments (e.g. underwater or in dense forest), and hence potentially better precision. Automated data collection means that surveys can take place at times and in places where it would be too expensive or dangerous to send human observers. Here, we present an overview of animal density estimation using passive acoustic data, a relatively new and fast-developing field. We review the types of data and methodological approaches currently available to researchers and we provide a framework for acoustics-based density estimation, illustrated with examples from real-world case studies. We mention moving sensor platforms (e.g. towed acoustics), but then focus on methods involving sensors at fixed locations, particularly hydrophones to survey marine mammals, as acoustic-based density estimation research to date has been concentrated in this area. Primary among these are methods based on distance sampling and spatially explicit capture-recapture. The methods are also applicable to other aquatic and terrestrial sound-producing taxa. We conclude that, despite being in its infancy, density estimation based on passive acoustic data likely will become an important method for surveying a number of diverse taxa, such as sea mammals, fish, birds, amphibians, and insects, especially in situations where inferences are required over long periods of time. There is considerable work ahead, with several potentially fruitful research areas, including the development of (i) hardware and software for data acquisition, (ii) efficient, calibrated, automated detection and classification systems, and (iii) statistical approaches optimized for this application. Further, survey design will need to be developed, and research is needed on the acoustic behaviour of target species. Fundamental research on vocalization rates and group sizes, and the relation between these and other factors such as season or behaviour state, is critical. Evaluation of the methods under known density scenarios will be important for empirically validating the approaches presented here

Evolutionary origins of human handedness : evaluating contrasting hypotheses

Cochet, Hélène — 2013-01-01T00:00:00Z

Abstract: Variation in methods and measures, resulting in past dispute over the existence of population handedness in nonhuman great apes, has impeded progress into the origins of human right-handedness and how it relates to the human hallmark of language. Pooling evidence from behavioral studies, neuroimaging and neuroanatomy, we evaluate data on manual and cerebral laterality in humans and other apes engaged in a range of manipulative tasks and in gestural communication. A simplistic human/animal partition is no longer tenable, and we review four (nonexclusive) possible drivers for the origin of population-level right-handedness: skilled manipulative activity, as in tool use; communicative gestures; organizational complexity of action, in particular hierarchical structure; and the role of intentionality in goal-directed action. Fully testing these hypotheses will require developmental and evolutionary evidence as well as modern neuroimaging data.

Estimating prevalence of injecting drug users and associated heroin-related death rates in England by using regional data and incorporating prior information

King, Ruth — 2013-01-01T00:00:00Z

Abstract: Injecting drug users (IDUs) have a direct social and economic effect yet can typically be regarded as a hidden population within a community. We estimate the size of the IDU population across the nine different Government Office regions of England in 2005–2006 by using capture–recapture methods with age (ranging from 15 to 64 years) and gender as covariate information. We consider a Bayesian model averaging approach using log-linear models, where we can include explicit prior information within the analysis in relation to the total IDU population (elicited from the number of drug-related deaths and injectors’ drug-related death rates). Estimation at the regional level allows for regional heterogeneity with these regional estimates aggregated to obtain a posterior mean estimate for the number of England's IDUs of 195840 with 95% credible interval (181700, 210480). There is significant variation in the estimated regional prevalence of current IDUs per million of population aged 15–64 years, and in injecting drug-related death rates across the gender × age cross-classifications. The propensity of an IDU to be seen by at least one source also exhibits strong regional variability with London having the lowest propensity of being observed (posterior mean probability 0.21) and the South West the highest propensity (posterior mean 0.46).

Paradoxical consequences of prohibitions

Sheikh, Sana — 2013-01-01T00:00:00Z

Abstract: Explanations based in attribution theory claim that strong external controls such as parental restrictiveness and punishment undermine moral internalization. In contrast, three studies provide evidence that parental punishment does socialize morality, but of a particular sort: a morality focused on prohibitions (i.e., proscriptive orientation), rather than positive obligations (i.e., prescriptive orientation). Study 1 found young adults’ accounts of parental restrictiveness and punishment activated their sensitivity to prohibitions and predicted a proscriptive orientation. Consistent with the greater potency of temptations for proscriptively-oriented children, as well as past research linking shame to proscriptive morality, Study 2 found that restrictive parenting was also associated with greater suppression of temptations. Finally, Studies 3a and 3b found that suppressing these immoral thoughts is paradoxically harder for those with strong proscriptive orientations; more specifically, priming a proscriptive (versus prescriptive) orientation and inducing mental suppression of “immoral” thoughts led to the most ego depletion for those with restrictive parents. Overall, individuals who had restrictive parents had the lowest self-regulatory ability to resist their “immoral” temptations after prohibitions were activated. In contrast to common attributional explanations, these studies suggest that harsh external control by parents does not undercut moral socialization, but rather undermines individuals’ ability to resist temptation.

The traitor as patriot : Guy Burgess, Englishness and camp in Another Country and An Englishman Abroad

Girelli, Elisabetta — 2012-07-12T00:00:00Z

Abstract: This article focuses on the representation of the spy Guy Burgess, one of the famous Cambridge ring, in two very successful British heritage films, An Englishman Abroad (John Schlesinger, UK, 1983) and Another Country (Marek Kanievska, UK, 1984). The article argues that the films rely on popular notions of Englishness as politically safe and non-extremist, thus fabricating a view of the past that misrepresents Burgess in the effort to normalize him. Similarly, stereotypical views of gay men as frivolous and non-ideological are amply exploited in the films' portrayal of their protagonist. Burgess's upper-class English roots are used to package him as part of the heritage experience, while his homosexuality is not only presented as the reason for spying, but it is also constructed as a camp performance, effectively defusing the threat of ideological commitment and political betrayal. The radical, lethal and devoutly Marxist Burgess is thus stripped of his ideology and turned into a safe national icon.

Low threshold organic semiconductor lasers and their application as explosive sensors

Wang, Yue — 2012-11-30T00:00:00Z

Abstract: This thesis presents studies of organic semiconductor lasers, including their operation when pumped by a light-emitting diode (LED), and their application as explosive sensors. The photophysics and amplified spontaneous emission (ASE) of star-shaped oligofluorene truxene molecules were investigated. These materials exhibit high gain and low optical loss in thin-film waveguides. Low ASE thresholds were achieved with the truxene T3 and T4. Second-order distributed feedback (DFB) lasers were fabricated, with pump threshold intensities below 0.5 kW/cm² and broad tunability of the emission. DFB lasers were demonstrated with a novel polymer BBEHP-PPV, pumped by a pulsed commercial InGaN LED. The laser emission occurred at 533 nm for peak drive current above 15 A. The output beams and pulse-dynamics of the lasers were investigated for the first time, along with a 'double-threshold' phenomenon that was observed in this long-pulse pumping regime. BBEHP-PPV lasers based on various types of diffractive resonators were also fabricated by UV nanoimprint-lithography (NIL). By optimising the resonator design and the fabrication, and the pump-beam geometry, polymer laser thresholds of ~60 W/cm², the lowest recorded for NIL lasers, were demonstrated, enabling them to be pumped by pulsed commercial LEDs and custom micro-LED arrays. One promising application of organic lasers is in explosive sensing. A polymer of intrinsic microporosity (PIM-1) was used to detect nitroaromatic vapours. Rapid detection of dinitrobenzene (DNB) of low vapour pressure was achieved by monitoring the photoluminescence and laser emission during exposure. In addition, a CMOS time-resolved fluorescence lifetime microsystem with a commercial green-emitting copolymer was used as a novel, portable sensor to detect DNB vapour. An InGaN LED pumped BBEHP-PPV laser was also used as a miniature sensor to detect 10 ppb of DNB. These highly sensitive hybrid sensors could be used in humanitarian demining, complementing existing technologies leading to improvement in the detection of hazardous objects.

Furnishing Britain : Gothic as a national aesthetic, 1740–1840

Lindfield, Peter Nelson — 2012-09-01T00:00:00Z

Abstract: Furniture history is often considered a niche subject removed from the main discipline of art history, and one that has little to do with the output of painters, sculptors and architects. This thesis, however, connects the key intellectual, artistic and architectural debates surfacing in ‘the arts’ between 1740 and 1840 with the design of British furniture. Despite the expanding corpus of scholarly monographs and articles dealing with individual cabinet-makers, furniture making in geographic areas and periods of time, little attention has been paid to exploring Gothic furniture made between 1740 and 1840. Indeed, no body of research on ‘mainstream’ Gothic furniture made at this time has been published. No sustained attempt has been made to trace its stylistic evolution, establish stylistic phases, or to place this development within the context of contemporary architectural practice and historiography — except for the study of A.W.N. Pugin’s ‘Reformed Gothic’. Neither have furniture historians been willing to explore the aesthetic’s connection with the intellectual and sentimental position of ‘the Gothic’ in the period. This thesis addresses these shortcomings and is the first to bridge the historiographic, cultural and architectural concerns of the time with the stylistic, constructional and material characteristics of Gothic furniture. It argues that it, like architecture, was charged with social and political meanings that included national identity in the eighteenth century — around a century before Charles Barry and A.W.N. Pugin designed the Palace of Westminster and prominently associated the Gothic legacy with Britishness. Description: Electronic version excludes material for which permission has not been granted by the rights holder

Near-infrared spectroscopy study of tourniquet-induced forearm ischaemia in patients with coronary artery disease

Giardini, M E — 2001-01-01T00:00:00Z

Abstract: Near-Infrared Spectroscopy (NIR) can be employed to monitor local changes in haemodynamics and oxygenation of human tissues. A preliminary study has been performed in order to evaluate the NIRS transmittance response to induced forearm ischaemia in patients with coronary artery disease (CAD). The population consists in 40 patients with cardiovascular risk factors and angiographically documented CAD, compared to a group of 13 normal subjects. By inflating and subsequently deflating a cuff placed around the patient arm, an ischaemia has been induced and released, and the patients have been observed until recovery of the basal conditions. A custom LAIRS spectrometer (IRIS) has been used to collect the backscattered light intensities from the patient forearm throughout the ischaemic and the recovery phase. The time dependence of the near-infrared transmittance on the control group is consistent with the available literature. On the contrary, the magnitude and dynamics of the NIRS signal on the CAD patients show deviations from the documented normal behavior, which can be tentatively attributed to abnormal vessel stiffness. These preliminary results, while validating the performance of the IRIS spectrometer, are strongly conducive towards the applicability of the NIRS technique to ischaemia analysis and to endothelial dysfunction characterization in CAD patients with cardiovascular risk factors.

Tissue surface as the reference arm in Fourier domain optical coherence tomography

Krstajic, Nikola — 2012-07-01T00:00:00Z

Abstract: We present a simple method applicable to common-path Fourier domain optical coherence tomography (OCT) in which the tissue surface is used as the reference arm. We propose using aluminium hydroxide powder as a potential tissue surface diffuser to allow wider application of this method. This technique allows one to avoid placing a reference arm reflective element, such as glass plate, on tissue, and intrinsically avoids both coherent and complex conjugate mirror artifacts associated with glass plates. Aluminium hydroxide can be sprayed onto tissue using spray nozzles commonly found in endoscopes. The sensitivity of the tissue reference arm common-path OCT image is 94 dB for a 50-mu s charge-coupled device integration time, and 97.5 dB for a 200-mu s CCD integration time. (C) 2012 Society of Photo-Optical Instrumentation Engineers (SPIE). [DOL 10.1117/1.JBO.17.7.071305]

A hybrid organic semiconductor/silicon photodiode for efficient ultraviolet photodetection

Levell, J. W. — 2010-02-15T00:00:00Z

Abstract: A method employing conjugated polymer thin film blends is shown to provide a simple and convenient way of greatly enhancing the ultraviolet response of silicon photodetectors. Hybrid organic semiconductor/silicon photodetectors are demonstrated using fluorene copolymers and give a quantum efficiency of 60% at 200 nm. The quantum efficiency is greater than 34% over the entire 200-620 nm range. These devices show promise for use in high sensitivity, low cost UV-visible photodetection and imaging applications. (C) 2007 Optical Society of America

Memorability of pre-designed and user-defined gesture sets

Nacenta, Miguel — 2013-01-01T00:00:00Z

The Letter of the law : literacy and orality in S. A. Panov's Murder in Medveditsa Village

Whitehead, Claire Eugenie — 2011-01-01T00:00:00Z

Abstract: This article takes as its subject a nineteenth-century detective story: S.A. Panov’s Murder in Medveditsa Village (1872). Panov’s work is remarkable amongst its contemporaries for the way in which it interrogates the relative authority of the written and the spoken word in the criminal investigation and, in so doing, foregrounds the role and status that detective fiction assigns to language. The aim of the present article is to discuss the ambiguously nuanced illustration Panov provides of the relative power of written, spoken and non-verbal language in the particular context of the functioning of the law and the pursuit of the ‘truth’, two cornerstones of detective fiction. Language, and especially the written word, is thus shown to play the decisive role in structuring the various networks of authority operating in and around the fictional world.

Paul Valéry and the search for poetic rhythm

Evans, David Elwyn — 2010-07-01T00:00:00Z

Abstract: Throughout his theoretical writings, Valéry insists on two fundamental principles: poetic rhythm is undefinable and yet it is central to poetry. Although his verse practice evolves from irregularity to regularity, Valéry insists that predictable metrical forms are no guarantee of poeticity, and rejects the Romantic model of rhythmic mimesis based on the cosmos, nature or the human body. It is not by confirming the meaningfulness of regular patterns, therefore, that poetic rhythm signifies; rather, the complex overlapping of multiple, elusive and unanalysable rhythms provides a source of questions to which the answer is constantly deferred; and that, for Valéry, is the definition of poetry.

Variation in sexual dimorphism and assortative mating do not predict genetic divergence in the sexually dimorphic Goodeid fish Girardinichthys multiradiatus

Macias Garcia, C. — 2012-01-01T00:00:00Z

Abstract: Sexual dimorphism is often used as a proxy for the intensity of sexual selection in comparative studies of sexual selection and diversification. The Mexican Goodeinae are a group of livebearing freshwater fishes with large variation between species in sexual dimorphism in body shape. Previously we found an association between variation in morphological sexual dimorphism between species and the amount of gene flow within populations in the Goodeinae. Here we have examined if morphological differentiation within a single dimorphic species is related to assortative mating or gene flow between populations. In the Amarillo fish Girardinichthys multiradiatus studies have shown that exaggerated male fins are targets of female preferences. We find that populations of the species differ in the level of sexual dimorphism displayed due to faster evolution of differences in male than female morphology. However, this does not predict variation in assortative mating tests in the laboratory; in fact differences in male morphology are negatively correlated with assortative mating. Microsatellite markers reveal significant genetic differences between populations. However, gene flow is not predicted by either morphological differences or assortative mating. Rather, it demonstrates a pattern of isolation by distance with greater differentiation between watersheds. We discuss the caveats of predicting behavioural and genetic divergence from so-called proxies of sexual selection [Current Zoology 58 (3): 440-452, 2012].

A phonological description of Modern Standard Arabic

Sitrak, Sami J. — 1981-01-01T00:00:00Z

Abstract: The present work is concerned with some aspects of the phonology of Modern Standard Arabic. The thesis is divided into two parts: Part I, dealing with the theoretical background, consists of three chapters, and each chapter sub-branches into a number of smaller units. Chapter I is concerned with the Axiomatic Functionalism principle of maintaining a strict distinction between the linguistic theory, linguistic descriptions, and the speech-phenomena; it also deals with the 'hypothetico-deductive method' which sets out to explain the philosophical principles underlying the 'Axiomatic Functionalist' approach. This chapter is divided into three sections, the first deals with the 'structure of the theory', the second concerns 'linguistic description and the speech-phenomena', followed by the 'criterion for evaluating the linguistic description and theory'. Chapter II treats the classification of semiotic systems in Axiomatic Functionalism as well as explaining the definition of 'Language' as "a semiotic system with a double articulation" (Mulder 1968, 'b'). Though this is a type of definition found in most functionalist approaches (Martinet 1962 1nd 1964), in Axiomatic Functionalism it has a unique interpretation. Chapter III, which deals with a brief explanation of the phonological system as a whole, comprises two sections, the first of which discusses 'phonematics and phonotactics', and the second introduces some of the main theoretical notions of the phonological theory, such as the notions "phoneme", "distinctive feature", "archi-phoneme", "position", "distributional unit", "archi-position", which is relevant for the phonological description of Modern Standard Arabic. This introduction to the phonological sub-component of the theory is important because description cannot take place without the knowledge of a theory, since a description is "the application of a particular linguistic theory to a selected field of linguistic-phenomena" (Mulder 1980, b). Part II, dealing with the phonological description, consists of five chapters (Chaps. IV-VIII). Chapter IV treats the distributional unit(s) and archi-position of Modern Standard Arabic. Chapter V deals with the consonantal phonemes, their identities and distinctive functions, as well as their realisations. Chapter VI explains the types of neutralisation and the consonantal archi-phonemes. Chapter VII deals with the vowel and semi-vowel phonemes, their identities and distinctive function as well as their realisations. Chapter VIII deals with the neutralisation and vocalic archi-phonemes.

Measuring the effect of the reflection of sound from the lips in brass musical instruments

Kemp, Jonathan A — 2012-04-01T00:00:00Z

Abstract: The lips of the player are often assumed to perfectly reflect sounds that strike them. Experimental and theoretical calculations of input impedance demonstrate the pressure that would build up if a flat, perfectly reflecting volume velocity source were used to excite the air into vibration. In reality the lips should project slightly into the instrument mouthpiece and absorb a small amount of the energy that strikes them and this study will quantify this effect using wave separation/impedance apparatus. For closed lips it is expected that the strength of resonances will be reduced, but that the correction will be small. The condition for reflection from lips that are not fully closed will differ more significantly from perfect reflection and it is anticipated that this data will be useful for integration into physical models of brass instruments.

Non-linear dynamics of a driven nanomechanical single electron transistor

G. Kirton, P. — 2013-04-09T00:00:00Z

Abstract: We analyze the response of a nanomechanical resonator to an external drive when it is also coupled to a single-electron transistor (SET). The interaction between the SET electrons and the mechanical resonator depends on the amplitude of the mechanical motion leading to a strongly non-linear response to the drive which is similar to that of a Duffing oscillator. We show that the average dynamics of the resonator is well-described by a simple effective model which incorporates damping and frequency renormalization terms which are amplitude dependent. We also find that for a certain range of parameters the system displays interesting bistable dynamics in which noise arising from charge fluctuations causes the resonator to switch slowly between different dynamical states. Description: This work was supported by EPSRC [Grant number EP/I017818/1]

Decomposition tables for experiments. II. Two–one randomizations

Brien, C. J. — 2010-10-01T00:00:00Z

Abstract: We investigate structure for pairs of randomizations that do not follow each other in a chain. These are unrandomized-inclusive, independent, coincident or double randomizations. This involves taking several structures that satisfy particular relations and combining them to form the appropriate orthogonal decomposition of the data space for the experiment. We show how to establish the decomposition table giving the sources of variation, their relationships and their degrees of freedom, so that competing designs can be evaluated. This leads to recommendations for when the different types of multiple randomization should be used.

Decomposition tables for experiments I. A chain of randomizations

Brien, C. J. — 2009-12-01T00:00:00Z

Abstract: One aspect of evaluating the design for an experiment is the discovery of the relationships between subspaces of the data space. Initially we establish the notation and methods for evaluating an experiment with a single randomization. Starting with two structures, or orthogonal decompositions of the data space, we describe how to combine them to form the overall decomposition for a single-randomization experiment that is "structure balanced." The relationships between the two structures are characterized using efficiency factors. The decomposition is encapsulated in a decomposition table. Then, for experiments that involve multiple randomizations forming a chain, we take several structures that pairwise are structure balanced and combine them to establish the form of the orthogonal decomposition for the experiment. In particular, it is proven that the properties of the design for Such an experiment are derived in a straightforward manner from those of the individual designs. We show how to formulate an extended decomposition table giving the sources of variation, their relationships and their degrees of freedom, so that competing designs can be evaluated.

Buying biosafety - is the price right?

Richardson, Louise — 2004-05-20T00:00:00Z

Residential mobility desires and behaviour over the life course : linking lives through time

Coulter, Rory — 2013-06-01T00:00:00Z

Abstract: As residential mobility recursively links individual life courses and the characteristics of places, it is unsurprising that geographers have long sought to understand how people make moving decisions. However, much of our knowledge of residential mobility processes derives from cross-sectional analyses of either mobility decision-making or moving events. Comparatively few studies have linked these separate literatures by analysing how residential (im)mobility decisions unfold over time within particular biographical, household and spatio-temporal contexts. This is problematic, as life course theories suggest that people frequently do not act in accordance with their underlying moving desires. To evaluate the extent to which residential (im)mobility is volitional or the product of constraints therefore requires a longitudinal approach linking moving desires to subsequent moving behaviour. This thesis develops this longitudinal perspective through four linked empirical studies, which each use British Household Panel Survey data to analyse how the life course context affects the expression and realisation of moving desires. The first study investigates how people make moving decisions in different ways in response to different motivations, triggers and life events. The second study harnesses the concept of ‘linked lives’, exploring the extent to which the likelihood of realising a desire to move is dependent upon the desires of a person’s partner. The third study analyses the biographical dimension of mobility decision-making, investigating how the long-term trajectories of life course careers are associated with particular mobility biographies. The final empirical chapter develops these insights, exploring the duration and abandonment of moving desires. Taken together, these studies test and extend conceptual models of mobility decision-making by empirically engaging with neglected facets of life course theories. Fundamentally, the thesis uncovers how aggregate mobility patterns are produced by the interactions between individual choices and multi-scalar constraints.

Concepts of folly in English Renaissance literature : with particular reference to Shakespeare and Jonson

Bulman, Helen Lois — 1991-01-01T00:00:00Z

Abstract: Chapter 1 considers Barclay's 'Ship of Fools' in relation to other folly literature in English, particularly Lydgate's 'Order of Fools', Skelton's 'Bowge of Courte', and 'Cocke Lorrel's Bote'. Motifs, allegories and the woodcuts of the text are discussed and some are included in an Illustrations section. Chapter 2 discusses Erasmian folly looking back to the Neoplatonic writings of Nicholas of Cusa, and to the debt Erasmian exegeses owe to Origen. Erasmus' own philosophical and theological views are examined, particularly as they are found in his 'Enchiridion', and in the influence of Thomas à Kempis' 'Imitation of Christ'. A close textual analysis of the 'Moriae Encomium' is undertaken in this light. Chapter 3 defines the lateral boundaries of folly, where it blends into madness. In the context of Renaissance psychology sixteenth century medical works are analysed, including Boorde's 'Breviary of Healthe', Barrough's 'Method of Physicke' and Elyot's 'Castel of Helth'. Blurring between madness and sin, the negative judgments on the mad as demon-possessed, and the biblical models from which such judgments largely arose give alternative perspectives on madness and its relation to folly. Chapters 4-6 look at three Shakespearean comedies showing the development of a primarily Erasmian view of folly. This moves from overt references in 'Love's Labour's Lost' to natural folly, the folly of love and theological folly, through carnivalesque aspects of folly and madness in 'Twelfth Night', to an embedded notion of folly which influences and affects the darker comedy of 'Measure for Measure'. Chapter 7 considers satires of Hall, Marston and Guilpin, and looks at Jonson's Humour plays in this context. 'Volpone' and 'Epicoene', and 'The Alchemist' and 'Bartholomew Fair' are discussed in pairs, showing the softening of Jonson's attitude to folly, and his increasing representation of Erasmian folly reaching its full expression in 'Bartholomew Fair'.

Willin, an upstream component of the Hippo signaling pathway, orchestrates mammalian peripheral nerve fibroblasts

Moleirinho, Susana — 2013-04-08T00:00:00Z

Abstract: Willin/FRMD6 was first identified in the rat sciatic nerve, which is composed of neurons, Schwann cells, and fibroblasts. Willin is an upstream component of the Hippo signaling pathway, which results in the inactivation of the transcriptional coactivator YAP through Ser127 phosphorylation. This in turn suppresses the expression of genes involved in cell growth, proliferation and cancer development ensuring the control of organ size, cell contact inhibition and apoptosis. Here we show that in the mammalian sciatic nerve, Willin is predominantly expressed in fibroblasts and that Willin expression activates the Hippo signaling cascade and induces YAP translocation from the nucleus to the cytoplasm. In addition within these cells, although it inhibits cellular proliferation, Willin expression induces a quicker directional migration towards scratch closure and an increased expression of factors linked to nerve regeneration. These results show that Willin modulates sciatic nerve fibroblast activity indicating that Willin may have a potential role in the regeneration of the peripheral nervous system.

Embodiment in the war film : Paradise Now and The Hurt Locker

Burgoyne, Robert James — 2012-06-12T00:00:00Z

Abstract: In this article I compare two recent films that foreground the body at risk in the new wars of the twenty-first century. Paradise Now (Abu-Assad, 2005) and The Hurt Locker (Bigelow, 2008) convey the subject of the body in war from what would seem to be opposing perspectives, the first representing the experience of a resistance fighter, a suicide bomber in present-day Palestine, and the latter rendering the perceptions of a US soldier, the leader of a bomb disposal squad in Iraq. Seeming opposites, antitheses of each other, the two protagonists and the two films can be set face to face in a way that brings the changing nature of modern war into frame. No longer defined by the ideology of total war that shaped the grand narratives of twentieth-century combat, the new imagery of war and resistance, of insurgency and counter-insurgency, is crystallized here in a new symbolic iteration of the body at risk.

Development of a contact call in black-capped chickadees (Poecile atricapillus) hand-reared in different acoustic environments

Guillette, Lauren — 2011-01-01T00:00:00Z

Abstract: The 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.

Development of novel active site and allosteric inhibitors of enzymes associated with cancer, neurodegenerative diseases and bacterial infections

Pirrie, Lisa — 2013-06-01T00:00:00Z

Abstract: The sirtuins are a family of NAD⁺-dependent deacetylase enzymes which are implicated in various illnesses including cancer and neurodegenerative diseases. Part I of this thesis describes the synthesis and biological evaluation of inhibitors of the SIRT1 and SIRT2 isoforms of this important family of enzymes. Chapter 1 gives an overview of sirtuin biology and the physiological roles of these enzymes. In particular the link between SIRT1 and cancer and SIRT2 and its role in the onset of neurodegenerative diseases is discussed. A review of the most potent and selective inhibitors of SIRT1 and SIRT2 is given including an introduction to the tenovin and cambinol classes of inhibitor. Chapter 2 describes various issues relating to the structure of the important chemical tool tenovin-6. The synthesis of analogues to improve the solubility, determine the preferred conformation and verify the products of metabolism of tenovin-6 is presented including their evaluation by in vitro and in cell methods. Part II of this chapter reports the design and use of a ¹H NMR method used to monitor the sirtuin-mediated deacetylation reaction. This was particularly relevant due to concerns raised about the possibility of false positive results obtained with the commercially available assay kit commonly used by the sirtuin community. This new ¹H NMR method was used to validate the inhibition of SIRT2 by tenovin-6. Chapter 3 describes the parallel synthesis and evaluation of tenovin analogues as inhibitors of SIRT1 and SIRT2. This study identified that replacement of the t-butyl substituent of tenovin-6 with the 3,5-dihalogen-4-alkoxy substitution pattern led to a variety of analogues having SIRT2 selectivity. As well as the collection of valuable SAR data, in cell data is also presented for the analogues. Chapter 4 provides attempts to rationalise the SAR data collected in Chapters 2 and 3 through a computational study. The molecular docking software GOLD was used to predict the binding site of the tenovin scaffold and hence rationalise the observed potencies of various analogues. Chapter 5 reports the synthesis and biological evaluation of triazole and cambinol analogues as SIRT1 and SIRT2 inhibitors. Part I details the synthesis and in vitro testing of a series of ring constrained tenovin analogues based on the 1,4-disubstituted triazole using click chemistry. A series of 1,5-disubstituted analogues were also synthesised. Part II describes the synthesis of S-alkylated cambinol analogues and the effect of N3-methylation upon activity and selectivity towards SIRT1. Part II of this thesis details the synthesis and biological testing of novel potent allosteric inhibitors of RmlA. RmlA is the first enzyme in the L-rhamnose biosynthetic pathway in bacteria. L-rhamnose is an important component of the bacterial cell wall and as such RmlA is therefore an important target in the discovery of novel anti-bacterial compounds. Chapter 7 provides an overview of the RmlA enzyme including its role in L-rhamnose biosynthesis and why it is an attractive target for anti-bacterial drug discovery. No small molecule inhibitors of RmlA have been reported previously. Chapter 8 describes the design and synthesis of pyrimidine-2,4-dione analogues as novel allosteric inhibitors of RmlA. SAR data is generated and rationalised by X-ray crystallographic techniques to study the structures of complexes of RmlA with various analogues. Analogues were also tested for their ability to inhibit the growth of the important human pathogen Mycobacterium tuberculosis.

Carbon monoxide hydrogenation using ruthenium catalysts

Blank, Jan Hendrik — 2012-11-30T00:00:00Z

Class, consumption and currency : commercial photography in mid-Victorian Scotland

Laurence-Allen, Antonia — 2012-11-30T00:00:00Z

Abstract: This thesis examines a thirty year span in the history of Scottish photography, focusing on the rise of the commercial studio from 1851 to assess how images were produced and consumed by the middle class in the mid-Victorian period. Using extensive archival material and a range of theoretical approaches, the research explores how photography was displayed, circulated, exploited and discussed in Scotland during its nascent years as a commodity. In doing so, it is unlike previous studies on Scottish photography that have not attended to the history of the medium as it is seen through exhibitions or the national journals, but instead have concentrated on explicating how an individual photographer or singular set of images are evidence of excellence in the field. While this thesis pays close attention to individual projects and studios, it does so to illuminate how photography functioned as a material object that equally shaped and was shaped by ideological constructs peculiar to mid-Victorian life in Scotland. It does not highlight particular photographers or works in order to elevate their standing in the history of photography but, rather, to show how they can be used as examples of a class phenomenon and provide an analytical frame for elucidating the cultural impact of commercial photography. Therefore, while the first two chapters provide a panoramic view of how photography was introduced to the Scottish middle class and how commercial photographers initially visualized Scotland, the second section is comprised of three ‘case studies’ that show how the subject of the city, the landscape and the portrait were turned into objects of cultural consumption. This allows for a re-appraisal of photographs produced in Scotland during this era to suggest the impact of photography’s products and processes was as vital as its visual content.

The theory and practice of narrative in Plato

Halliwell, Francis Stephen — 2009-08-01T00:00:00Z

Man and boy : Montgomery Clift as a queer star in Wild River

Girelli, Elisabetta — 2011-09-23T00:00:00Z

Abstract: Montgomery Clift has been underexplored by film scholars, who have mostly focused on his early career. This article uses queer theory to examine Clift's later work, focusing on Wild River (dir. Elia Kazan, 1960); it argues that in this film Clift's narrative role, performance, and star persona radically challenge normative masculinity and heterosexuality.

Why coercion is wrong when it’s wrong

Sachs, Benjamin Alan — 2013-01-01T00:00:00Z

Abstract: It is usually thought that wrongful acts of threat-involving coercion are wrong because they involve a violation of the freedom or autonomy of the targets of those acts. I argue here that this cannot possibly be right, and that in fact the wrongness of wrongful coercion has nothing at all to do with the effect such actions have on their targets. This negative thesis is supported by pointing out that what we say about the ethics of threatening (and thus the ethics of coercion) constrains what we can say about the ethics of warning and offering. Importantly, our favoured explanation of the wrongness of certain kinds of threatening should not commit us to condemning as wrong parallel cases of warning and offering. My positive project is to show how this can be done. I defend the claim that wrongful coercion is nothing more than the issuing of a conditional threat to do wrong, and that an agent's issuing of a conditional threat to do wrong is wrong because it constitutes motivation for that agent to adopt the announced intention to do wrong. The idea of explaining the wrongness of wrongful coercion in this way has gone unnoticed because we have thus far been mistaken about what a threat is. In this essay I present my moral analysis of coercion only after presenting a careful descriptive analysis of threats. On my view, it is essential to a threat that the announced intention is one that the agent does not possess before announcing it. This analysis makes it possible to elucidate the descriptive differences between threats, warnings and offers, which sets up the later project of elucidating the moral differences between them.

Epistemic theories of democracy, constitutionalism and the procedural legitimacy of fundamental rights

Allard-Tremblay, Yann — 2012-11-30T00:00:00Z

Abstract: The overall aim of this thesis is to assess the legitimacy of constitutional laws and bills of rights within the framework of procedural epistemic democracy. The thesis is divided into three sections. In the first section, I discuss the relevance of an epistemic argument for democracy under the circumstances of politics: I provide an account of reasonable disagreement and explain how usual approaches to the authority of decision-making procedures fail to take it seriously. In the second part of the thesis, I provide an account of the epistemic features of democracy and of the requirements of democratic legitimacy. I develop a revised pragmatist argument for democracy which relies on three presumptive aims of decision-making: justice, sustainability and concord. In the third and last section, I first argue for the desirability of constitutionalism. I then explain why constitutionalism, as it is usually understood, is incompatible with my procedural epistemic account of democratic legitimacy. In the last chapter, I offer a two-pronged solution to the apparent incompatibility of constitutionalism and epistemic democracy. I first argue for the appropriateness of political constitutionalism, as opposed to legal constitutionalism, in understanding the relationship between rights and democracy. I then provide an account of rights protection and judicial review compatible with epistemic democratic legitimacy. Finally, I use the notion of pragmatic encroachment to explain how constitutional laws can achieve normative supremacy through the increased epistemic credentials of the procedure.

The study of exosomes and microvesicles secreted from breast cancer cell lines

Zheng, Ying — 2012-11-30T00:00:00Z

Abstract: Exosomes are small secreted vesicles of endocytic origin with a size range of 50-150 nm. They are secreted by many cell types and display multiple biological functions including immune-activation, immune-suppression, antigen presentation, and the shuttling of mRNA and miRNA, as well as other cargo. We have characterised the exosomes secreted from two breast cancer cell lines, MDA-MB-231 and MCF7. Exosomes secreted from both cell lines display typical markers including ALIX, Tsg101, CD9 and CD63, and were capable of inducing apoptosis of the Jurkat T cell line, indicating the potential immune-suppressive function of such tumour-derived exosomes. To further investigate the biological potential of exosomes, we loaded purified exosomes with gene specific siRNAs using electroporation, and observed the targeted inhibition of both a known component of the exosome pathway, Rab27a, and also the arthritis associated gene ERAP1, demonstrating the potential novel use of exosomes as therapeutic gene delivery vectors. We have also shown that exosomes derived from MDA-MB-231 cells and the parental cells have different lipid composition, as analysed by lipidomics study. Nanoparticle tracking analysis (NTA), which allows the rapid detection of size and concentration of nanoparticles within the size range 10 nm-1000 nm was tested for its ability to accurately measure size and concentration of exosomes and microvesicles under different conditions. NTA was capable of detecting apoptotic vesicles induced by Taxol and Curcumin treatment. Immunodepletion was used to determine the percentage of CD9 and CD63 positive vesicles. Our data suggest that NTA is a useful technique for measuring size and concentration of exosomes and microvesicles. We hypothesized that NTA could assist in the screening of agents that interfere or promote exosome release. NTA was therefore used to detect increases in exosomes secretion induced by Tamoxifen and Thimerosal treatment, and to monitor the inhibition of exosome secretion from MDA-MB-231 breast cancer cells expressing inhibitory RNA targeted for Rab27a, a component of the exosome pathway. Increases in exosome release induced by Tamoxifen and Thimerosal was detected by NTA and a significant reduction in the release of exosomes by inhibition of Rab27a expression was also observed. Treatment with the known exosomal pathway inhibitor DMA also reduced exosome release, establishing the principle of NTA as a screening technique. We further compared the siRNA targeted cells for their ability to migrate, invade and form anchorage-independent colonies, which were all significantly reduced. Supplementation with MDA-MB-231 derived exosomes restored the ability to form colonies, suggesting exosomes may contribute to metastatic lesion formation. These data suggest that the exosomal pathway is a valid target to disrupt the behaviour of tumour cells and NTA can be used to monitor its activity.

Estimating whale abundance using sparse hydrophone arrays

Harris, Danielle V. — 2012-06-20T00:00:00Z

Abstract: Passive 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 context

Onofri, Andrea — 2013-01-01T00:00:00Z

Abstract: My thesis discusses two related problems that have taken center stage in the recent literature on concepts: 1) What are the individuation conditions of concepts? Under what conditions is a concept C₁ the same concept as a concept C₂? 2) What are the possession conditions of concepts? What conditions must be satisfied for a thinker to have a concept C? The thesis defends a novel account of concepts, which I call “pluralist-contextualist”: 1) Pluralism: Different concepts have different kinds of individuation and possession conditions: some concepts are individuated more “coarsely”, have less demanding possession conditions and are widely shared, while other concepts are individuated more “finely” and not shared. 2) Contextualism: When a speaker ascribes a propositional attitude to a subject S, or uses his ascription to explain/predict S’s behavior, the speaker’s intentions in the relevant context determine the correct individuation conditions for the concepts involved in his report. In chapters 1-3 I defend a contextualist, non-Millian theory of propositional attitude ascriptions. Then, I show how contextualism can be used to offer a novel perspective on the problem of concept individuation/possession. More specifically, I employ contextualism to provide a new, more effective argument for Fodor’s “publicity principle”: if contextualism is true, then certain specific concepts must be shared in order for interpersonally applicable psychological generalizations to be possible. In chapters 4-5 I raise a tension between publicity and another widely endorsed principle, the “Fregean constraint” (FC): subjects who are unaware of certain identity facts and find themselves in so-called “Frege cases” must have distinct concepts for the relevant object x. For instance: the ancient astronomers had distinct concepts (HESPERUS/PHOSPHORUS) for the same object (the planet Venus). First, I examine some leading theories of concepts and argue that they cannot meet both of our constraints at the same time. Then, I offer principled reasons to think that no theory can satisfy (FC) while also respecting publicity. (FC) appears to require a form of holism, on which a concept is individuated by its global inferential role in a subject S and can thus only be shared by someone who has exactly the same inferential dispositions as S. This explains the tension between publicity and (FC), since holism is clearly incompatible with concept shareability. To solve the tension, I suggest adopting my pluralist-contextualist proposal: concepts involved in Frege cases are holistically individuated and not public, while other concepts are more coarsely individuated and widely shared; given this “plurality” of concepts, we will then need contextual factors (speakers’ intentions) to “select” the specific concepts to be employed in our intentional generalizations in the relevant contexts. In chapter 6 I develop the view further by contrasting it with some rival accounts. First, I examine a very different kind of pluralism about concepts, which has been recently defended by Daniel Weiskopf, and argue that it is insufficiently radical. Then, I consider the inferentialist accounts defended by authors like Peacocke, Rey and Jackson. Such views, I argue, are committed to an implausible picture of reference determination, on which our inferential dispositions fix the reference of our concepts: this leads to wrong predictions in all those cases of scientific disagreement where two parties have very different inferential dispositions and yet seem to refer to the same natural kind.

'New-found methods and . . . compounds strange' : reading the 1640 Poems: Written by Wil. Shake-speare. Gent.

Acker, Faith D. — 2012-11-30T00:00:00Z

Abstract: The second edition of Shakespeare’s sonnets, titled Poems: Written by Wil. Shake-Speare, Gent, and published by stationer John Benson in 1640, was a text typical of its time. In an effort to update the old-fashioned sonnet sequence in which its contents had first reached print, the compiler or editor of the Bensonian version rearranged the poems from the earlier quarto text, adding titles and other texts thought to have been written by or about the sonnets’ author. The immediate reception of the 1640 Poems was a quiet one, but the volume’s contents and structure served as the foundation for more than half of the editions of Shakespeare’s sonnets produced in the eighteenth century. In part due to the textual instability created by the presence of two disparate arrangements of the collection, Shakespeare’s sonnets served only as supplements to the preferred Shakespearean canon from 1709 to 1790. When, at the end of the century, the sonnets finally entered the canon in Edmond Malone’s groundbreaking edition of the plays and poems together, Benson’s version was quickly overshadowed by the earlier text, which was preferred as both more authorial and, due to Malone’s careful critical readings, autobiographical. In contrast to the many scholars since Malone who have overlooked or denigrated the Poems of 1640, this thesis studies the second edition of Shakespeare’s sonnets within the framework of the early modern culture that produced it, arguing that Benson’s edition provides valuable evidence about the editorial habits and literary preferences of the individuals and culture for which it was originally intended.

Differential timing of gene expression regulation between leptocephali of the two Anguilla eel species in the Sargasso Sea

Bernatchez, Louis — 2011-12-01T00:00:00Z

Abstract: The unique life-history characteristics of North Atlantic catadromous eels have long intrigued evolutionary biologists, especially with respect to mechanisms that could explain their persistence as two ecologically very similar but reproductively and geographically distinct species. Differential developmental schedules during young larval stages have commonly been hypothesized to represent such a key mechanism. We performed a comparative analysis of gene expression by means of microarray experiments with American and European eel leptocephali collected in the Sargasso Sea in order to test the alternative hypotheses of (1) differential timing of gene expression regulation during early development versus (2) species-specific differences in expression of particular genes. Our results provide much stronger support for the former hypothesis since no gene showed consistent significant differences in expression levels between the two species. In contrast, 146 genes showed differential timings of expression between species, although the observed expression level differences between the species were generally small. Consequently, species-specific gene expression regulation seems to play a minor role in species differentiation. Overall, these results show that the basis of the early developmental divergence between the American and European eel is probably influenced by differences in the timing of gene expression regulation for genes involved in a large array of biological functions.

Lateral entorhinal cortex is critical for novel object-context recognition

Wilson, David Ian Greig — 2013-01-01T00:00:00Z

Abstract: Episodic memory incorporates information about specific events or occasions including spatial locations and the contextual features of the environment in which the event took place. It has been modeled in rats using spontaneous exploration of novel configurations of objects, their locations, and the contexts in which they are presented. While we have a detailed understanding of how spatial location is processed in the brain relatively little is known about where the nonspatial contextual components of episodic memory are processed. Initial experiments measured c-fos expression during an object-context recognition (OCR) task to examine which networks within the brain process contextual features of an event. Increased c-fos expression was found in the lateral entorhinal cortex (LEC; a major hippocampal afferent) during OCR relative to control conditions. In a subsequent experiment it was demonstrated that rats with lesions of LEC were unable to recognize object-context associations yet showed normal object recognition and normal context recognition. These data suggest that contextual features of the environment are integrated with object identity in LEC and demonstrate that recognition of such object-context associations requires the LEC. This is consistent with the suggestion that contextual features of an event are processed in LEC and that this information is combined with spatial information from medial entorhinal cortex to form episodic memory in the hippocampus. © 2013 Wiley Periodicals, Inc.

"Making room" for one's own : Virginia Woolf and technology of place

Sriratana, Verita — 2013-01-01T00:00:00Z

Abstract: This thesis offers an analysis of selected works by Virginia Woolf through the theoretical framework of technology of place. The term “technology”, meaning both a finished product and an ongoing production process, a mode of concealment and unconcealment in Martin Heidegger’s sense, is used as part of this thesis’s argument that place can be understood through constant negotiations of concrete place perceived through the senses, a concept based on the Heideggerian notion of “earth”, and abstract place perceived in the imagination, a concept based on the Heideggerian notion of “world”. The term “technology of place”, coined by Irvin C. Schick in The Erotic Margin: Sexuality and Spatiality in Alteritist Discourse (1999), is appropriated and re-interpreted as part of this thesis’s adoption and adaptation of Woolf’s notion of ideal biographical writing as an amalgamation of “granite” biographical facts and “rainbow” internal life. Woolf’s granite and rainbow dichotomy is used as a foreground to this thesis’s proposed theoretical framework, through which questions of space/place can be examined. My analysis of Flush (1933) demonstrates that place is a technology which can be taken at face value and, at the same time, appropriated to challenge the ideology of its construction. My analysis of Orlando (1928) demonstrates that Woolf’s idea of utopia exemplifies the technological “coming together”, in Heidegger’s term, of concrete social reality and abstract artistic fantasy. My analysis of The Years (1937) demonstrates that sense of place as well as sense of identity is ambivalent and constantly changing like the weather, reflecting place’s Janus-faced function as both concealment and unconcealment. Lastly, my analysis of Woolf’s selected essays and marginalia illustrates that writing can serve as a revolutionary “place-making” technology through which one can mentally “make room” for (re-)imagining the lives of “the obscure”, often placed in oblivion throughout the course of history.

Stochastic choice and consideration sets

Manzini, Paola — 2013-03-01T00:00:00Z

Abstract: We model a boundedly rational agent who su¤ers from limited attention. The agent considers each feasible alternative with a given (unobservable) probability, the attention parameter, and then chooses the alternative that maximises a prefer- ence relation within the set of considered alternatives. We show that this random choice rule is the only one for which the impact of removing an alternative on the choice probability of any other alternative is asymmetric and menu independent. Both the preference relation and the attention parameters are identi…ed uniquely by stochastic choice data.

Competing conservation objectives for predators and prey : estimating killer whale prey requirements for Chinook salmon

Williams, Robert — 2011-11-09T00:00:00Z

Abstract: Ecosystem-based management (EBM) of marine resources attempts to conserve interacting species. In contrast to single-species fisheries management, EBM aims to identify and resolve conflicting objectives for different species. Such a conflict may be emerging in the northeastern Pacific for southern resident killer whales (Orcinus orca) and their primary prey, Chinook salmon (Oncorhynchus tshawytscha). Both species have at-risk conservation status and transboundary (Canada–US) ranges. We modeled individual killer whale prey requirements from feeding and growth records of captive killer whales and morphometric data from historic live-capture fishery and whaling records worldwide. The models, combined with caloric value of salmon, and demographic and diet data for wild killer whales, allow us to predict salmon quantities needed to maintain and recover this killer whale population, which numbered 87 individuals in 2009. Our analyses provide new information on cost of lactation and new parameter estimates for other killer whale populations globally. Prey requirements of southern resident killer whales are difficult to reconcile with fisheries and conservation objectives for Chinook salmon, because the number of fish required is large relative to annual returns and fishery catches. For instance, a U.S. recovery goal (2.3% annual population growth of killer whales over 28 years) implies a 75% increase in energetic requirements. Reducing salmon fisheries may serve as a temporary mitigation measure to allow time for management actions to improve salmon productivity to take effect. As ecosystem-based fishery management becomes more prevalent, trade-offs between conservation objectives for predators and prey will become increasingly necessary. Our approach offers scenarios to compare relative influence of various sources of uncertainty on the resulting consumption estimates to prioritise future research efforts, and a general approach for assessing the extent of conflict between conservation objectives for threatened or protected wildlife where the interaction between affected species can be quantified.

In and around Beijing with Mr Yang and others : space, modernisation and social interaction

Yang, Qingqing — 2013-06-01T00:00:00Z

Abstract: The aim of my PhD project has been to understand how Hutong residents’ ideas about living space have been different from those living in the high-rise compound and how their concept of living space has been changed by both internal and external factors, meaning additional affiliated functions and governmental city-planning. I conducted my fieldwork in Beijing between July 2009 and September 2012: fourteen months in total, interspersed with trips to St. Andrews. I spent ten months from July 2009 to May 2010 living in a Hutong called Xingfu Street (the word translates as ‘happiness’). Then I moved into a high-rise apartment outside the inner city, called Suojiafen Compound, for a further four months. This study concerns space in the contemporary city of Beijing: how space is humanly built and transformed, classified and differentiated, and most importantly how space is perceived and experienced. In the end I have developed the concept “overlapped” space as a way to detect the “personality” of space in both Hutong and high-rise apartment: how they differentiated from each other and how they have been transformed in different way by the residents inside.

Estimating seasonal abundance of a central place forager using counts and telemetry data

Sharples, RJ — 2009-01-01T00:00:00Z

Abstract: Obtaining population estimates of species that are not easily observed directly can be problematic. However, central place foragers can often be observed some of the time, e.g. when seals are hauled out. In these instances, population estimates can be derived from counts, combined with information on the proportion of time that animals can be observed. We present a modelling framework to estimate seasonal absolute abundance using counts and information from satellite telemetry data. The method was tested on a harbour seal population in an area of southeast Scotland. Counts were made monthly, between November 2001 and June 2003, when seals were hauled out on land and were corrected for the proportion of time the seals were at sea using satellite telemetry. Harbour seals (n=25) were tagged with satellite relay data loggers between November 2001 and March 2003. To estimate the proportion of time spent hauled out, time at sea on foraging trips was modelled separately from haul-out behaviour close to haul-out sites because of the different factors affecting these processes. A generalised linear mixed model framework was developed to capture the longitudinal nature of the data and the repeated measures across individuals. Despite seasonal variability in the number of seals counted at haul-out sites, the model generated estimates of abundance, with an overall mean of 846 (95% CI: 767 to 979). The methodology shows the value of using count and telemetry data collected concurrently for estimating absolute abundance, information that is essential to assess interactions between predators, fish stocks and fisheries. Description: R.J.S. was supported by a Natural Environment Research Council studentship.

Synergism between N-heterocyclic carbene and phosphorus-based ligands in ruthenium and palladium catalytic systems

Schmid, Thibault E. — 2012-12-18T00:00:00Z

Abstract: N-heterocyclic carbenes (NHCs) have become a very popular class of ligands, which has found uses in numerous catalytic applications. The use of such compounds in combination with phosphorus-based ligands within metal complexes has enabled the design of very active yet robust catalytic systems. The following chapters will describe the design of novel well-defined palladium- and ruthenium-based pre-catalysts featuring a NHC and a phosphorus-based ligand, referred at as mixed ligand systems. Such species were employed in catalysis where their properties appeared highly beneficial, uses at low catalysts loading and under harsh conditions were then envisioned. The preparation of a series of well-defined palladium mixed NHC/phosphine species is presented in chapter 2. Their catalytic activity in the aqueous Suzuki-Miyaura reaction of aryl chlorides and boronic acids, using low catalyst loadings, is described. The observation of catalytic activity of the latter systems in the hydration of nitriles prompted us to further investigate this reactivity. This reaction appeared to be operative in the absence of palladium species and could be performed under base-catalysed conditions, which was studied in detail and depicted in chapter 3. The combination of a NHC and a phosphite ligand in ruthenium olefin metathesis pre-catalysts has been underexplored. Preliminary results showed that such species could be readily prepared and presented an unusual geometry and a high catalytic activity. Variations in phosphite-containing ruthenium olefin metathesis pre-catalysts are presented. Chapter 4 describes the investigation of various Schrock carbene moieties in such architectures, as well as their implications in structure and catalysis. Chapter 5 depicts attempts to design olefin metathesis Z-selective pre-catalysts by inserting a chelating NHC moiety within phosphite-containing ruthenium species. This dissertation concludes on the potential of such mixed species in catalysis, and armed with the new knowledge provided by this work, proposes potential developments of such chemistry in the design of always more robust and active catalytic systems.

The search for allosteric inhibitors

Brear, Paul — 2013-06-26T00:00:00Z

Abstract: This thesis describes the development of chemical tools that inhibit the sialidases NanA and NanB from Streptococcus pneumonia. The primary focus was on the discovery of allosteric inhibitors of NanA and NanB, however, promising inhibitors that act by binding at the active site of these enzymes were also investigated. Chapter 1 gives an overview of the use of chemical tools in the field of chemical biology. It focuses in particular on chemical tools that function by the allosteric regulation of their target proteins. The uses, advantages and methods of discovery of allosteric tools are discussed. Finally this chapter introduces the use of serendipitous binders for the discovery of allosteric sites. In particular, the use of CHES to identify novel allosteric sites on the sialidase NanB is proposed. Chapter 2 describes how the ‘hits’ from a series of high throughput screens were reanalysed using a wide range of secondary assays to eliminate any false positives that were contaminating the results. This process removed eight of the eleven ‘hits’. Two of the remaining three compounds were then analysed further in an attempt to characterise their binding mode to NanA and/or NanB using modelling and X-ray crystallographic studies. Whilst, it was not possible to confirm the binding mode by X-ray crystallography modelling studies using the modelling software GOLD generated possible binding modes for these inhibitors. A structure activity relationship study was conducted for both compounds in an attempt to generate more potent inhibitors. Chapter 3 moves from the use of high throughput screens to identify hits against NanA and NanB to the use of the serendipitous binding of N-cyclohexyl-2-aminoethanesulfonic acid in the active site of NanB for the development of selective NanB inhibitors. First taurine was identified as the minimum unit of N-cyclohexyl-2-aminoethanesulfonic acid required to bind to the active site of NanB. Taurine was then used as the basis of an optimisation study. This chapter concludes with the identification of 2-(benzylammonio)ethanesulfonate as the next key intermediate in the development of N-cyclohexyl-2-aminoethanesulfonic acid based active site inhibitors of NanB. Chapter 4 follows on from Chapter 3 with the optimisation of 2-(benzylammonio)ethanesulfonate describing the design and synthesis of a wide range of analogues. From these compounds 2-[(3-chlorobenzyl)ammonio]ethanesulfonate was identified as the most potent and selective inhibitor. Detailed analysis of the binding of 2-[(3-chlorobenzyl)ammonio]ethanesulfonate to NanB gave a rationale for its improved inhibitory activity. The increase in inhibition occurred because on binding of 2-[(3-chlorobenzyl)ammonio]ethanesulfonate to the active site of NanB a well coordinated water molecule was displaced. The displacement of this water caused an increase in the flexibility of the enzyme’s 352 loop. A detailed study of the flexibility of this loop in response to various N-cyclohexyl-2-aminoethanesulfonic acid based chemical tools was then conducted. The research in chapters 2 and 3 has recently been published. In Chapter 5 a molecule of N-cyclohexyl-2-aminoethanesulfonic acid that binds serendipitously in a previously unmentioned secondary site is elaborated into a ligand, known as Optactin, that binds strongly and selectively at this secondary site. It was then shown that Optactin inhibited NanB by binding at this secondary site. It was therefore concluded that this secondary site was in fact an allosteric site that could be used for the regulation of NanB. Chapter 6 describes the development of a rationalisation for the inhibition of NanB by Optactin. This study included the X-ray crystallographic analysis of the apo-NanB structure and the NanB-Optactin complex under a range of conditions. This was followed by mechanistic studies that identified the point in the catalytic cycle at which Optactin was inhibiting NanB. This chapter concludes with a hypothesis for the mechanism of inhibition of NanB by Optactin.

Synthesis of porous metal phosphonate frameworks for applications in gas separation and storage

Wharmby, Michael T. — 2012-05-22T00:00:00Z

Abstract: Porous metal phosphonate framework materials were synthesised by solvothermal reaction of bis(α-aminomethylenephosphonic acid) ligands with divalent and trivalent metal cations. The syntheses and characterisation by NMR and, where possible, single crystal X-ray diffraction of seven bisphosphonic acid ligands, including N,N′-piperazinebis(methylenephosphonic acid) (H₄L), its racemic and enantiopure (R) 2-methyl (H₄L′ and R-H₄L′) and 2,5-dimethyl (H₄L′′) derivatives, and N,N′-4,4′-bipiperidinebis(methylenephosphonic acid) (H₄LL) are reported. Syntheses of the known phase Y₂(LH₂)₃·5H₂O and the new phases, STA-13(Y) (St Andrews microporous material No. 13) and Y₂(R-L′H₂)₃·4H₂O, from reactions of Y(AcO)₃ with H₄L, H₄L′ and R-H₄L′ respectively are reported. The as-prepared and dehydrated structures of each phase have been determined from either laboratory or synchrotron powder X-ray diffraction data. Reaction of Y(AcO)₃ and H₄L′′ is shown to form a phase with a different structure. The features determining which structure crystallises are discussed. Syntheses of other rare-earth forms of STA-13 (Sc³⁺, Gd³⁺–Yb³⁺) and the porosity of each phase to N₂ are reported. STA-13(Y) is the most porous form with loadings of ∼3 mmol g⁻¹ and ∼4 mmol g⁻¹ for N₂ and CO₂ respectively. MIL-91(Fe) was synthesised for the first time from reactions of Fe³⁺ cations with H₄L. Its structure was confirmed by Rietveld refinement, but it was not porous. The first syntheses of [Fe₄L₁.₅(AcO)₁.₅(OH,H₂O)₃]·0.5NH₄5.5H₂O (L= L or L′) are reported, from reactions of H₄L or H₄L′ in the presence of an excess of Fe³⁺ cations. The phase is related to a previously reported Co phase. The synthesis of divalent metal bisphosphonate STA-12(Mg) (Mg₂(H₂O)₂L·5.6H₂O) was reported for the first time and its structure determined from single crystal X-ray diffraction. The dehydration behaviour of this material was compared with the known forms of STA-12. STA-12(Mg) is porous to both N₂ (∼5.5 mmol g⁻¹) and CO₂ (~ 8.5 mmol g⁻¹). Reaction of H₄LL with Co²⁺ and Ni²⁺ gave two materials isoreticular with STA-12, labelled STA-16(Co) and STA-16(Ni). The structures of both materials were solved from synchrotron powder X-ray diffraction data. On dehydration, STA-16(Co) undergoes a reversible structural transition to an unknown structure. By contrast, STA-16(Ni) retains the same symmetry in the dehydrated form and its structure was determined from synchrotron powder X-ray diffraction data. Both materials are porous to N₂, with an uptake of up to 22.2 mmol g⁻¹, and CO₂ with maximum loading of 21.7 mmol g⁻¹. NLDFT analysis of N₂ adsorption data confirm the crystallographically determined pore radii. Syntheses of other frameworks with divalent cations and initial reactions of H₄LL with trivalent cations are also reported.

The English provincial book trade : bookseller stock-lists, c.1520-1640

Winters, Jennifer — 2012-11-30T00:00:00Z

Abstract: The book world of sixteenth-century England was heavily focused on London. London’s publishers wholly dominated the production of books, and with Oxford and Cambridge the booksellers of the capital also played the largest role in the supplying and distribution of books imported from Continental Europe. Nevertheless, by the end of the sixteenth century a considerable network of booksellers had been established in England’s provincial towns. This dissertation uses scattered surviving evidence from book lists and inventories to investigate the development and character of provincial bookselling in the period between 1520 and 1640. It draws on information from most of England’s larger cities, including York, Norwich and Exeter, as well as much smaller places, such as Kirkby Lonsdale and Ormskirk. It demonstrates that, despite the competition from the metropolis, local booksellers played an important role in supplying customers with a considerable range and variety of books, and that these bookshops became larger and more ambitious in their services to customers through this period. The result should be a significant contribution to understanding the book world of early modern England. The dissertation is accompanied by an appendix, listing and identifying the books documented in nine separate lists, each of which, where possible, has been matched to surviving editions.

Nyungar wiring boodja : Aboriginality in urban Australia

Hemmers, Carina — 2012-11-30T00:00:00Z

Abstract: The present thesis examines the themes of ‘shared history,’ ‘place-making,’ and ‘reconciliation’ to assess how these come together in the establishment of an Aboriginal identity in Perth, Western Australia. Focusing on individuals who do not represent the common stereotypes associated with Aboriginal Australians, it will be demonstrated that these individuals are forced into an in-between place where they have to continually negotiate what Aboriginality means in the twenty-first century. Taking on this responsibility they become mediators, stressing a ‘shared history’ in order to create a place for themselves in the non-Aboriginal landscape and to advance reconciliation between Aboriginal and non-Aboriginal Australia by fighting the dominant discourse from within. Beginning with the State and Government’s Native Title appeal premiss that Nyungar never existed, this thesis will examine this claim by first presenting an account of the history of southwest Western Australia to establish the place Aboriginal people have been forced into by the colonists during early settlement, and the processes of which extend into the present day. From there on in the focus will be on individual Aboriginal people and their careers and businesses, examining how they attempt to redefine what is perceived and accepted as Aboriginality through different interaction and mediation ‘tactics’ with non-Aboriginal Australians. Finally, this thesis will take a closer look at the reconciliation movement in Australia and the people involved in it. It will determine different approaches to reconciliation and assess their possibility and meaning for the construction of a twenty-first century Aboriginal identity. The thesis will conclude that although Nyungar are forced into the dominant discourse, their resistance from within credits a new kind of Aboriginality that is just as valid as the ‘traditional’ and ‘authentic’ Aboriginality imagined by non-Aboriginal Australia.

Male mating tactics in the rose bitterling (Rhodeus ocellatus) and European bitterling (Rhodeus amarus)

Casalini, Mara — 2013-06-26T00:00:00Z

Abstract: The 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.

Cognitive and brain function in adults with Type 1 diabetes mellitus : is there evidence of accelerated ageing?

Johnston, Harriet N. — 2013-06-25T00:00:00Z

Abstract: The physical complications of Type 1 diabetes mellitus (T1DM) have been understood as an accelerated ageing process (Morley, 2008). Do people with T1DM also experience accelerated cognitive and brain ageing? Using findings from research of the normal cognitive and brain ageing process and conceptualized in theories of the functional brain changes in cognitive ageing, a combination of cognitive testing and functional magnetic resonance imaging (fMRI) techniques were used to evaluate evidence of accelerated cognitive and brain ageing in middle-aged adults with T1DM. The first part of this thesis comprises a cognitive study of 94 adults (≥ 45 years of age) with long duration (≥ 10 years) of T1DM. Participants completed cognitive assessment and questionnaires on general mood and feelings about living with diabetes. Findings highlighted the importance of microvascular disease (specifically retinopathy) as an independent predictor of cognitive function. The incidence and predictors of mild cognitive impairment (MCI) were then explored. Results indicate a higher percentage of the group met criteria for MCI than expected based on incidence rates in the general population, providing initial evidence of accelerated cognitive ageing. Psychological factors were explored next. The relationship between the measures of well-being, diabetes health, and cognitive function highlighted the need for attention to patient’s psychological well-being in diabetes care. Finally, a subgroup of 30 participants between the ages of 45 and 65 who differed on severity of retinopathy were selected to take part in an fMRI study. Blood oxygen level dependent (BOLD) activity was evaluated while participants were engaged in cognitive tasks and during rest. The findings provided evidence that the pattern of BOLD activation and functional connectivity for those with high severity of retinopathy are similar to patterns found in adults over the age of 65. In line with the theories of cognitive ageing, functional brain changes appear to maintain a level of cognitive function. Evidence of accelerated brain ageing in this primarily middle-aged group, emphasizes the importance of treatments and regimens to prevent or minimize microvascular complications.

Photo-grammetric measurements of swimming speed and body length of basking sharks observed around the Hebrides, Scotland

Lacey, Claire — 2010-03-01T00:00:00Z

Abstract: Photo-grammetric techniques developed for measuring body length and small scale movement patterns of cetaceans were applied to surface swimming basking sharks off the west coast of Scotland. These methods removed the need for close approaches, reducing the likelihood of disturbing the focal animal. Average swimming speed was calculated from the total path length between shark locations measured at approximately one minute intervals. These average speeds varied from 0.49 to 0.73 ms−1 for tracks of between 30 and 170 minutes' duration. Body length measurements ranged between 2.35 and 6.43 m. For ten sharks where body length and swimming speed were measured there was a significant correlation between body length (L) and swimming speed (V) expressed as V = 0.36L033.

Synthesis of phosphonate and phostone analogues of ribose-1-phosphates

Nasomjai, Pitak — 2009-07-27T00:00:00Z

Abstract: The synthesis of phosphonate analogues of ribose-1-phosphate and 5-fluoro-5-deoxyribose-1-phosphate is described. Preparations of both the alpha- and beta-phosphonate anomers are reported for the ribose and 5-fluoro-5-deoxyribose series and a synthesis of the corresponding cyclic phostones of each alpha-ribose is also reported. These compounds have been prepared as tools to probe the details of fluorometabolism in S. cattleya.

Three step synthesis of single diastereoisomers of the vicinal trifluoro motif

Brunet, Vincent A. — 2009-11-05T00:00:00Z

Abstract: A three step route to single diastereoisomers of the vicinal trifluoromethyl motif is described. The route starts from either syn- or anti-alpha,beta-epoxy alcohols and takes a direct approach in that each of the three steps introduces a fluorine atom in a regio- and stereospecific manner. Starting from either the syn- or the anti-alpha,beta-epoxy alcohol, stereospecific reactions generate two separate diastereoisomeric series of this motif. The route is a significant improvement on an earlier six step strategy.

Passively mode locked femtosecond Tm:Sc2O3 laser at 2.1 mu m

Lagatsky, A. A. — 2012-02-01T00:00:00Z

Abstract: We report on the passive mode locking of a Tm3+:Sc2O3 laser at 2.1 mu m using a semiconductor saturable absorber mirror based on InGaAsSb quantum wells. Transform-limited 218 fs pulses are generated with an average power of 210 mW. A maximum output power of 325 mW is produced during mode locking with the corresponding pulse duration of 246 fs at a pulse repetition frequency of 124.3 MHz. A Ti:sapphire laser is used as the pump source operating at 796 nm. (C) 2012 Optical Society of America Description: This work was supported by EPSRC

Algorithm-based continuous pulse duration tuning and performance control of a mode-locked laser diode

Metzger, N. K. — 2012-03-26T00:00:00Z

Abstract: A control algorithm is presented that addresses the stability issues inherent to the operation of monolithic mode-locked laser diodes. It enables a continuous pulse duration tuning without any onset of Q-switching instabilities. A demonstration of the algorithm performance is presented for two radically different laser diode geometries and continuous pulse duration tuning between 0.5 ps to 2.2 ps and 1.2 ps to 10.2 ps is achieved. With practical applications in mind, this algorithm also facilitates control over performance parameters such as output power and wavelength during pulse duration tuning. The developed algorithm enables the user to harness the operational flexibility from such a laser with 'push-button' simplicity. (C) 2012 Optical Society of America

Crenarchaeal chromatin proteins Cren7 and Sul7 compact DNA by inducing rigid bends

Driessen, Rosalie P. C. — 2013-01-01T00:00:00Z

Abstract: Archaeal chromatin proteins share molecular and functional similarities with both bacterial and eukaryotic chromatin proteins. These proteins play an important role in functionally organizing the genomic DNA into a compact nucleoid. Cren7 and Sul7 are two crenarchaeal nucleoid-associated proteins, which are structurally homologous, but not conserved at the sequence level. Co-crystal structures have shown that these two proteins induce a sharp bend on binding to DNA. In this study, we have investigated the architectural properties of these proteins using atomic force microscopy, molecular dynamics simulations and magnetic tweezers. We demonstrate that Cren7 and Sul7 both compact DNA molecules to a similar extent. Using a theoretical model, we quantify the number of individual proteins bound to the DNA as a function of protein concentration and show that forces up to 3.5 pN do not affect this binding. Moreover, we investigate the flexibility of the bending angle induced by Cren7 and Sul7 and show that the protein-DNA complexes differ in flexibility from analogous bacterial and eukaryotic DNA-bending proteins.

hSSB1 interacts directly with the MRN complex stimulating its recruitment to DNA double-strand breaks and its endo-nuclease activity

Richard, Derek J. — 2011-05-01T00:00:00Z

Abstract: hSSB1 is a recently discovered single-stranded DNA binding protein that is essential for efficient repair of DNA double-strand breaks (DSBs) by the homologous recombination pathway. hSSB1 is required for the efficient recruitment of the MRN complex to sites of DSBs and for the efficient initiation of ATM dependent signalling. Here we explore the interplay between hSSB1 and MRN. We demonstrate that hSSB1 binds directly to NBS1, a component of the MRN complex, in a DNA damage independent manner. Consistent with the direct interaction, we observe that hSSB1 greatly stimulates the endo-nuclease activity of the MRN complex, a process that requires the C-terminal tail of hSSB1. Interestingly, analysis of two point mutations in NBS1, associated with Nijmegen breakage syndrome, revealed weaker binding to hSSB1, suggesting a possible disease mechanism.

hSSB1 rapidly binds at the sites of DNA double-strand breaks and is required for the efficient recruitment of the MRN complex

Richard, Derek J. — 2011-03-01T00:00:00Z

Abstract: hSSB1 is a newly discovered single-stranded DNA (ssDNA)-binding protein that is essential for efficient DNA double-strand break signalling through ATM. However, the mechanism by which hSSB1 functions to allow efficient signalling is unknown. Here, we show that hSSB1 is recruited rapidly to sites of double-strand DNA breaks (DSBs) in all interphase cells (G1, S and G2) independently of, CtIP, MDC1 and the MRN complex (Rad50, Mre11, NBS1). However expansion of hSSB1 from the DSB site requires the function of MRN. Strikingly, silencing of hSSB1 prevents foci formation as well as recruitment of MRN to sites of DSBs and leads to a subsequent defect in resection of DSBs as evident by defective RPA and ssDNA generation. Our data suggests that hSSB1 functions upstream of MRN to promote its recruitment at DSBs and is required for efficient resection of DSBs. These findings, together with previous work establish essential roles of hSSB1 in controlling ATM activation and activity, and subsequent DSB resection and homologous recombination (HR).

Crystallization of Ranasmurfin, a blue coloured protein from Polypedates leucomystax

McMahon, Stephen — 2006-11-01T00:00:00Z

Abstract: Ranasmurfin, a previously uncharacterized similar to 13 kDa blue protein found in the nests of the frog Polypedates leucomystax, has been purified and crystallized. The crystals are an intense blue colour and diffract to 1.51 angstrom with P2(1) symmetry and unit-cell parameters a = 40.9, b = 59.9, c = 45.0 angstrom, beta = 93.3 degrees. Self-rotation function analysis indicates the presence of a dimer in the asymmetric unit. Biochemical data suggest that the blue colour of the protein is related to dimer formation. Sequence data for the protein are incomplete, but thus far have identified no model for molecular replacement. A fluorescence scan shows a peak at 9.676 keV, indicating that the protein binds zinc and suggesting a route for structure solution.

Research information meets research data management

Clements, Anna — 2013-03-18T00:00:00Z

Annual report 2011-2012

University of St Andrews. Library — 2013-02-01T00:00:00Z

Abstract: The Library's annual report for 2011-2012 highlights the redevelopment of the Main Library and changes to Library services. The report also covers notable new print and electronic acquisitions, events and staff activities over the past year. Description: Foreword by John A. MacColl, University Librarian & Director of Library Services

Extortion and the ethics of "topping up"

Sachs, Benjamin — 2009-10-01T00:00:00Z

Consequentialism's double-edged aword

Sachs, Benjamin — 2010-09-01T00:00:00Z

Abstract: Recent work on consequentialism has revealed it to be more flexible than previously thought. Consequentialists have shown how their theory can accommodate certain features with which it has long been considered incompatible, such as agent-centered constraints. This flexibility is usually thought to work in consequentialism's favor. I want to cast doubt on this assumption. I begin by putting forward the strongest statement of consequentialism's flexibility: the claim that, whatever set of intuitions the best non-consequentialist theory accommodates, we can construct a consequentialist theory that can do the same while still retaining whatever is compelling about consequentialism. I argue that if this is true then most likely the non-consequentialist theory with which we started will turn out to have that same compelling feature. So while this extreme flexibility, if indeed consequentialism has it (a question I leave to the side), makes consequentialism more appealing, it makes non-consequentialism more appealing too.

Facial skin coloration affects perceived health of human faces

Stephen, Ian David — 2009-12-01T00:00:00Z

Abstract: Numerous researchers have examined the effects of skin condition, including texture and color, on the perception of health, age, and attractiveness in human faces. They have focused on facial color distribution, homogeneity of pigmentation, or skin quality. We here investigate the role of overall skin color in determining perceptions of health from faces by allowing participants to manipulate the skin portions of color-calibrated Caucasian face photographs along CIELab color axes. To enhance healthy appearance, participants increased skin redness (a*), providing additional support for previous findings that skin blood color enhances the healthy appearance of faces. Participants also increased skin yellowness (b*) and lightness (L*), suggesting a role for high carotenoid and low melanin coloration in the healthy appearance of faces. The color preferences described here resemble the red and yellow color cues to health displayed by many species of nonhuman animals. Description: I stephen was funded by a BBSRC Studentship. M Stirrat was funded by an EPSRC Studentship.

Skin blood perfusion and oxygenation colour affect affect perceived human health

Stephen, Ian David — 2009-04-01T00:00:00Z

Abstract: Skin blood perfusion and oxygenation depends upon cardiovascular, hormonal and circulatory health in humans and provides socio-sexual signals of underlying physiology, dominance and reproductive status in some primates. We allowed participants to manipulate colour calibrated facial photographs along empirically-measured oxygenated and deoxygenated blood colour axes both separately and simultaneously, to optimise healthy appearance. Participants increased skin blood colour, particularly oxygenated, above basal levels to optimise healthy appearance. We show, therefore, that skin blood perfusion and oxygenation influence perceived health in a way that may be important to mate choice. Description: I Stephen was funded by a BBSRC Studentship.

Trust, distrust and commitment

Hawley, Katherine Jane — 2013-01-01T00:00:00Z

Runaway sexual selection without genetic correlations : social environments and flexible mate choice initiate and enhance the Fisher process

Bailey, Nathan William — 2012-09-01T00:00:00Z

Abstract: Female mating preferences are often flexible, reflecting the social environment in which they are expressed. Associated indirect genetic effects (IGEs) can affect the rate and direction of evolutionary change, but sexual selection models do not capture these dynamics. We incorporate IGEs into quantitative genetic models to explore how variation in social environments and mate choice flexibility influence Fisherian sexual selection. The importance of IGEs is that runaway sexual selection can occur in the absence of a genetic correlation between male traits and female preferences. Social influences can facilitate the initiation of the runaway process and increase the rate of trait elaboration. Incorporating costs to choice do not alter the main findings. Our model provides testable predictions: (1) genetic covariances between male traits and female preferences may not exist, (2) social flexibility in female choice will be common in populations experiencing strong sexual selection, (3) variation in social environments should be associated with rapid sexual trait divergence, and (4) secondary sexual traits will be more elaborate than previously predicted. Allowing feedback from the social environment resolves discrepancies between theoretical predictions and empirical data, such as why indirect selection on female preferences, theoretically weak, might be sufficient for preferences to become elaborated.

You are what you eat : Within-subject increases in fruit and vegetable consumption confer beneficial skin-color changes

Whitehead, Ross — 2012-03-07T00:00:00Z

Abstract: Background: Fruit and vegetable consumption and ingestion of carotenoids have been found to be associated with human skin-color (yellowness) in a recent cross-sectional study. This carotenoid-based coloration contributes beneficially to the appearance of health in humans and is held to be a sexually selected cue of condition in other species. Methodology and Principal Findings: Here we investigate the effects of fruit and vegetable consumption on skin-color longitudinally to determine the magnitude and duration of diet change required to change skin-color perceptibly. Diet and skin-color were recorded at baseline and after three and six weeks, in a group of 35 individuals who were without makeup, self-tanning agents and/or recent intensive UV exposure. Six-week changes in fruit and vegetable consumption were significantly correlated with changes in skin redness and yellowness over this period, and diet-linked skin reflectance changes were significantly associated with the spectral absorption of carotenoids and not melanin. We also used psychophysical methods to investigate the minimum color change required to confer perceptibly healthier and more attractive skin-coloration. Modest dietary changes are required to enhance apparent health (2.91 portions per day) and attractiveness (3.30 portions). Conclusions: Increased fruit and vegetable consumption confers measurable and perceptibly beneficial effects on Caucasian skin appearance within six weeks. This effect could potentially be used as a motivational tool in dietary intervention. Description: R Whitehead was funded by an ESRC Studentship.

Single-molecule chemical denaturation of riboswitches

Dalgarno, Paul Allan — 2013-01-01T00:00:00Z

Abstract: To date, single-molecule RNA science has been developed almost exclusively around the effect of metal ions as folding promoters and stabilizers of the RNA structure. Here, we introduce a novel strategy that combines single-molecule Förster resonance energy transfer (FRET) and chemical denaturation to observe and manipulate RNA dynamics. We demonstrate that the competing interplay between metal ions and denaturant agents provides a platform to extract information that otherwise will remain hidden with current methods. Using the adenine-sensing riboswitch aptamer as a model, we provide strong evidence for a rate-limiting folding step of the aptamer domain being modulated through ligand binding, a feature that is important for regulation of the controlled gene. In the absence of ligand, the rate-determining step is dominated by the formation of long-range key tertiary contacts between peripheral stem-loop elements. In contrast, when the adenine ligand interacts with partially folded messenger RNAs, the aptamer requires specifically bound Mg2+ ions, as those observed in the crystal structure, to progress further towards the native form. Moreover, despite that the ligand-free and ligand-bound states are indistinguishable by FRET, their different stability against urea-induced denaturation allowed us to discriminate them, even when they coexist within a single FRET trajectory; a feature not accessible by existing methods.

Remarkable transition from rocksalt/perovskite layered structure to fluorite/rocksalt layered structure in rapidly cooled Ln2CuO4

Patabendige, Chami Nilasha Kahakachchi — 2013-03-21T00:00:00Z

Abstract: Lanthanide cuprates of formula Ln2CuO4 exist in two principal forms, T and T′ which are renowned for their exhibition at low temperatures of hole and electronic types of superconductivity, respectively. These structures differ primarily in the arrangement of oxygen between the perovskite layers and also in nature of the copper oxygen planes. The Cu-O distance in the T structure (~1.90 Å) is much shorter than the T′ (1.97Å), reflecting a transition between partial Cu+ and partial Cu3+ character. In seeking to find compositions that bridge these two structure/electron carrier types, we observed the transition from a T structure to a T′ type structure, resulting in the metastable form T″ with slightly larger volume but similar character to T′. This transition from T to T″ is associated with 5% increase in a and a 5% decrease in c parameters of the tetragonal unit cells, which results in disintegration of ceramic bodies. Description: This work was supported by EPSRC

Synthesis of ammonia directly from air and water at ambient temperature and pressure

Lan, Rong — 2013-01-29T00:00:00Z

Abstract: The N equivalent to Nbond (225 kcal mol(-1)) in dinitrogen is one of the strongest bonds in chemistry therefore artificial synthesis of ammonia under mild conditions is a significant challenge. Based on current knowledge, only bacteria and some plants can synthesise ammonia from air and water at ambient temperature and pressure. Here, for the first time, we report artificial ammonia synthesis bypassing N-2 separation and H-2 production stages. A maximum ammonia production rate of 1.14 x 10(-5) mol m(-2) s(-1) has been achieved when a voltage of 1.6 V was applied. Potentially this can provide an alternative route for the mass production of the basic chemical ammonia under mild conditions. Considering climate change and the depletion of fossil fuels used for synthesis of ammonia by conventional methods, this is a renewable and sustainable chemical synthesis process for future.

Weak Te,Te interactions through the looking glass of NMR spin-spin coupling

Buehl, Michael — 2013-01-01T00:00:00Z

Abstract: Across the bay: J(125Te,125Te) spin–spin coupling is a highly sensitive probe into the electronic and geometric structure of 1,8-peri-substituted naphthalene tellurium derivatives. The coupling is related to the onset of multicenter bonding in these systems.

Isolable phosphanylidene phosphorane with a sterically accessible two-coordinate phosphorus atom

Surgenor, Brian A. — 2012-10-01T00:00:00Z

Simultaneous control of regioselectivity and enantioselectivity in the hydroxycarbonylation and methoxycarbonylation of vinyl arenes

Konrad, Tina Maria — 2013-01-01T00:00:00Z

Abstract: Using a family of novel mononuclear and dinuclear palladium complexes of phanephos ligands, the simultaneous control of regioselectivity and enantioselectivity in the hydroxycarbonylation and alkoxycarbonylation of styrene derivatives has been realised for the first time.

Hasse Ekman : a question of authorship in a national context

Gustafsson, Fredrik — 2013-06-27T00:00:00Z

Abstract: This thesis takes a historical approach to its subject and focuses on Swedish cinema of the 1940s and 1950s. The thesis argues that Swedish cinema experienced a renaissance in the 1940s, lasting approximately from 1940 to 1953. It further suggests that one of the most important filmmakers in this renaissance was Hasse Ekman. By focussing upon Ekman and this renaissance, a much-needed contextualisation of Ingmar Bergman will be achieved. Ingmar Bergman is one of the most well-known and well-researched filmmakers of all time, but there are still gaps in the material surrounding him, and one such gap concerns his cinematic origins. Bergman was a part of the 1940s renaissance, during which Bergman worked with, and was influenced by, other filmmakers and in particular Ekman. The thesis is divided into three parts. The first part introduces the relevant literature and discusses ideas of authorship and national cinema. It also provides a historic overview of Swedish society and cinema during the 1940s and 1950s, providing the context needed to better understand the films of Ekman, and Bergman too. This part also looks at the 1930s to illustrate what came before this renaissance, and how the films of the 1940s differed from what had gone before. The second part is a chronological overview of Ekman's career from the late-1930s to his move to Spain in 1964. The last part is a discussion of Ekman's relation to Swedish society and his view of the world, based on close textual readings of his films. The aim of the thesis is to present, for the first time, a coherent and extensive overview of Ekman's career and body of work, while also situating it in the specific context in which it emerged, thereby shedding new light on an important, though neglected, episode in cinema history.

Iso-seco-tanapartholides : isolation, synthesis and biological evaluation

Makiyi, Edward F. — 2009-11-01T00:00:00Z

Abstract: The isolation, identification and total synthesis of two plant-derived inhibitors of the NF-kappa B signaling pathway from the iso-seco-tanapartholide family of natural products is described. A key step in the efficient reaction sequence is a late-stage oxidative cleavage reaction that was carried out in the absence of protecting groups to give the natural products directly. A detailed comparison of the synthetic material with samples of the natural products proved informative. Biological studies on synthetic material confirmed that these compounds act late in the NF-kappa B signaling pathway. ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)

Transient observations : the textualizing of St Helena through five hundred years of colonial discourse

Schulenburg, Alexander Hugo — 1999-01-01T00:00:00Z

Abstract: This thesis explores the textualizing of the South Atlantic island of St Helena (a British Overseas Territory) through an analysis of the relationship between colonizing practices and the changing representations of the island and its inhabitants in a range of colonial 'texts', including historiography, travel writing, government papers, creative writing, and the fine arts. Part I situates this thesis within a critical engagement with post-colonial theory and colonial discourse analysis primarily, as well as with the recent 'linguistic turn' in anthropology and history. In place of post-colonialism's rather monolithic approach to colonial experiences, I argue for a localised approach to colonisation, which takes greater account of colonial praxis and of the continuous re-negotiation and re-constitution of particular colonial situations. Part II focuses on a number of literary issues by reviewing St Helena's historiography and literature, and by investigating the range of narrative tropes employed (largely by travellers) in the textualizing of St Helena, in particular with respect to recurrent imaginings of the island in terms of an earthly Eden. Part III examines the nature of colonial 'possession' by tracing the island's gradual appropriation by the Portuguese, Dutch and English in the sixteenth and early seventeenth century and the settlement policies pursued by the English East India Company in the late seventeenth and early eighteenth century. Part IV provides an account of the changing perceptions, by visitors and colonial officials alike, of the character of the island's inhabitants (from the late eighteenth to the early twentieth century) and assesses the influence that these perceptions have had on the administration of the island and the political status of its inhabitants (in the mid- to late twentieth century). Part V, the conclusion, reviews the principal arguments of my thesis by addressing the political implications of post-colonial theory and of my own research, while also indicating avenues for further research. A localised and detailed exploration of colonial discourse over a period of nearly five hundred years, and a close analysis of a consequently wide range of colonial 'texts', has confirmed that although colonising practices and representations are far from monolithic, in the case of St Helena their continuities are of as much significance as their discontinuities.

The timing of asset trade and optimal policy in dynamic open economies

Senay, Ozge — 2013-01-01T00:00:00Z

Abstract: Using a standard open economy DSGE model, it is shown that the timing of asset trade relative to policy decisions has a potentially important impact on the welfare evaluation of monetary policy at the individual country level. If asset trade in the initial period takes place before the announcement of policy, a national policymaker can choose a policy rule which reduces the work effort of households in the policymaker’s country in the knowledge that consumption is fully insured by optimally chosen international portfolio positions. But if asset trade takes place after the policy announcement, this insurance is absent and households in the policymaker’s country bear the full consumption consequences of the chosen policy rule. The welfare incentives faced by national policymakers are very different between the two cases. Numerical examples confirm that asset market timing has a significant impact on the optimal policy rule.

Identification through technical analysis : A study of charting and UK non-professional investors

Roscoe, Philip — 2009-02-01T00:00:00Z

Abstract: The usefulness of technical analysis, or charting, has been questioned because it flies in the face of the 'random walk' and tests present conflicting results. We examine chartists' decision-making techniques and derive a taxonomy of charting strategies based on investors' market ontologies and calculative strategies. This distinguishes between trend-seekers and pattern-seekers, and trading as a system or an art. We argue that interpretative activity plays a more important role than previously thought and suggest that charting's main appeal for users lies in its power as a heuristic device regardless of its effectiveness at generating returns.

Radicals and reactionaries : the polarisation of community and government in the name of public safety and security

Weeks, Douglas M. — 2013-06-25T00:00:00Z

Abstract: The contemporary threat of terrorism has changed the ways in which government and the public view the world. Unlike the existential threat from nation states in previous centuries, today, government and the public spend much of their effort looking for the inward threat. Brought about by high profile events such as 9/11, 7/7, and 3/11, and exacerbated by globalisation, hyper-connected social spheres, and the media, the threats from within are reinforced daily. In the UK, government has taken bold steps to foment public safety and public security but has also been criticised by some who argue that government actions have labelled Muslims as the ‘suspect other’. This thesis explores the counter-terrorism environment in London at the community/government interface, how the Metropolitan Police Service and London Fire Brigade deliver counter-terrorism policy, and how individuals and groups are reacting. It specifically explores the realities of the lived experience of those who make up London’s ‘suspect community’ and whether or not counter-terrorism policy can be linked to further marginalisation, radicalism, and extremism. By engaging with those that range from London’s Metropolitan Police Service’s Counterterrorism Command (SO15) to those that make up the radical fringe, an ethnographic portrait is developed. Through that ethnographic portrait the ‘ground truth’ and complexities of the lived experience are made clear and add significant contrast to the aseptic policy environment.

Morality, adapted

Sachs, Benjamin Alan — 2010-01-01T00:00:00Z

Abstract: Over the last few decades, scientists have been busy debunking the myth that nonhuman animals relate to each other in a primarily competitive, aggressive way. What they have found is that many species of animal, including many of those most closely related to humans, display a remarkable range of cooperative, "prosocial" behavior. In fact, it appears that some animal societies adhere to a moral code. What is preventing us, then, from saying that the members of these societies are moral beings? Nothing important, according to a recent book. Probing further into this question, I suggest that in fact quite a lot is at risk in making this move. To integrate nonhuman animals fully into the moral domain, we may have to adapt our conception of morality in some very troublesome ways.

Quantifying biodiversity trends in time and space

Studeny, Angelika C. — 2012-11-30T00:00:00Z

Abstract: 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.

Pierre Reverdy : lyrisme de la réalité. Poétique du visuel

Brogly, Marie-Noëlle — 2013-06-01T00:00:00Z

Abstract: This thesis aims to provide the first complete study of the poetics of Pierre Reverdy, who, although famous and influential during his lifetime, has not been widely published or researched. This thesis hopes to change this, as his complete works are just now being republished. The first chapter lays the basis for his conception of reality as something in which man is trapped, and which calls for a distance that, in Reverdy’s eyes, only poetry can offer. His association of the image and lyricism, is presented and analysed. The second chapter aims to provide a linguistic understanding of the poetic image called for and devises the new concept of “illumination”, to give an account of the phenomenon at work in his verse. The third chapter focuses on lyricism, as Reverdy tries to reinvent it for the twentieth century: independent of the self, dealing only with expressing the affective tonalities of the poet and acting as a catalyst for the image. The last chapter defines the visual qualities of Reverdy’s poetry by first re-examining the title of cubist poet that had been attached to him, before focussing on the many forms that the image takes in his work (imagery, but also typography, mental imagery), and finally providing the first analysis of the relationship between paintings and poems in the famous Livres d’artistes that the poet created, in collaboration with Picasso, Matisse, Juan Gris and others. It establishes that while the poems can indeed be read without the illustrations with which they were conceived, these editions deprive the reader of the opportunity to remind himself that poetry is an experience rather than a quest for meaning and also of an introduction to the unique visual qualities of Reverdy’s poetry.

Supporting system deployment decisions in public clouds

Khajeh-Hosseini, Ali — 2013-06-26T00:00:00Z

Abstract: Decisions to deploy IT systems on public Infrastructure-as-a-Service clouds can be complicated as evaluating the benefits, risks and costs of using such clouds is not straightforward. The aim of this project was to investigate the challenges that enterprises face when making system deployment decisions in public clouds, and to develop vendor-neutral tools to inform decision makers during this process. Three tools were developed to support decision makers: 1. Cloud Suitability Checklist: a simple list of questions to provide a rapid assessment of the suitability of public IaaS clouds for a specific IT system. 2. Benefits and Risks Assessment tool: a spreadsheet that includes the general benefits and risks of using public clouds; this provides a starting point for risk assessment and helps organisations start discussions about cloud adoption. 3. Elastic Cost Modelling: a tool that enables decision makers to model their system deployment options in public clouds and forecast their costs. These three tools collectively enable decision makers to investigate the benefits, risks and costs of using public clouds, and effectively support them in making system deployment decisions. Data was collected from five case studies and hundreds of users to evaluate the effectiveness of the tools. This data showed that the cost effectiveness of using public clouds is situation dependent rather than universally less expensive than traditional forms of IT provisioning. Running systems on the cloud using a traditional 'always on' approach can be less cost effective than on-premise servers, and the elastic nature of the cloud has to be considered if costs are to be reduced. Decision makers have to model the variations in resource usage and their systems' deployment options to obtain accurate cost estimates. Performing upfront cost modelling is beneficial as there can be significant cost differences between different cloud providers, and different deployment options within a single cloud. During such modelling exercises, the variations in a system's load (over time) must be taken into account to produce more accurate cost estimates, and the notion of elasticity patterns that is presented in this thesis provides one simple way to do this.

Polymer electrolytes : synthesis and characterisation

Maranski, Krzysztof Jerzy — 2013-06-26T00:00:00Z

Abstract: Crystalline polymer/salt complexes can conduct, in contrast to the view held for 30 years. The alpha-phase of the crystalline poly(ethylene oxide)₆:LiPF₆ is composed of tunnels formed from pairs of (CH₂-CH₂-O)ₓ chains, within which the Li⁺ ions reside and along which the latter migrate.¹ When a polydispersed polymer is used, the tunnels are composed of 2 strands, each built from a string of PEO chains of varying length. It has been suggested that the number and the arrangement of the chain ends within the tunnels affects the ionic conductivity.² Using polymers with uniform chain length is important if we are to understand the conduction mechanism since monodispersity results in the chain ends occurring at regular distances along the tunnels and imposes a coincidence of the chain ends between the two strands.² Since each Li⁺ is coordinated by 6 ether oxygens (3 oxygens from each of the two polymeric strands forming a tunnel), monodispersed PEOs with the number of ether oxygen being a multiple of 3 (NO = 3n) can form either “all-ideal” or “all-broken” coordination environments at the end of each tunnel, while for both NO = 3n-1 and NO = 3n+1 complexes, both “ideal” and “broken” coordinations must occur throughout the structure. A synthetic procedure has been developed and a series of 6 consecutive (increment of EO unit) monodispersed molecular weight PEOs have been synthesised. The synthesis involves one end protection of a high purity glycol, functionalisation of the other end, ether coupling reaction (Williamson’s type ether synthesis³), deprotection and reiteration of ether coupling. The parameters of the process and purification methods have been strictly controlled to ensure unprecedented level of monodispersity for all synthesised samples. Thus obtained high purity polymers have been used to study the influence of the individual chain length on the structure and conductivity of the crystalline complexes with LiPF₆. The results support the previously suggested model of the chain-ends arrangement in the crystalline complexes prepared with monodispersed PEO² over a range of consecutive chain lengths. The synthesised complexes constitute a series of test samples for establishing detailed mechanism of ionic conductivity. Such series of monodispersed crystalline complexes have been studied and characterised here (PXRD, DSC, AC impedance) for the first time. References: 1. G. S. MacGlashan, Y. G. Andreev, P. G. Bruce, Structure of the polymer electrolyte poly(ethylene oxide)₆:LiAsF₆. Nature, 1999, 398(6730): p. 792-794. 2. E. Staunton, Y. G. Andreev, P. G. Bruce, Factors influencing the conductivity of crystalline polymer electrolytes. Faraday Discussions, 2007, 134: p. 143-156. 3. A. Williamson, Theory of Aetherification. Philosophical Magazine, 1850, 37: p. 350-356.

The deglaciation of the northwest sector of the last British-Irish ice sheet : integrating onshore and offshore data relating to chronology and behaviour

Small, David — 2013-06-15T00:00:00Z

Abstract: It is now accepted that the last British-Irish Ice Sheet (BIIS) was highly dynamic and drained by numerous fast flowing ice streams. This dynamic nature combined with its maritime location made the BIIS sensitive to the rapid climate change that characterised the Last Glacial Interglacial Transition. Gaining an understanding of the behaviour of the BIIS at this time is important to explore the nature of forcing between ice sheets and climate. This thesis presents new chronological data relating to the deglaciation of the northwest sector of the BIIS (NW-BIIS) from onshore dating of moraines using cosmogenic exposure dating. This improved chronological framework is supported by offshore data in the form of a newly constructed Ice Rafted Detritus (IRD) record from the offshore sediment core MD95-2007. These data suggest that deglaciation commenced sometime after 18 ka and that the NW-BIIS was located close to the present day shoreline by 16 ka. Further provenance analysis of the IRD using U-Pb dating of detrital minerals demonstrates that during the Last Glacial-Interglacial Transition MD95-2007 was being supplied distal IRD from a source(s) to the west. The absence of diagnostic Scottish material suggests that after retreat to the coastline at 16 ka calving margins were not re-established during Greenland Interstadial 1. By combining these results with existing data relating to the deglaciation of the NW-BIIS it is possible to summarise the deglaciation history of the NW-BIIS from the continental shelf to mountainous source regions and compare this to numerical models of BIIS behaviour during this time. With a better understanding of the chronology of NW-BIIS retreat it is possible to relate the timing of initial deglaciation to possible forcing factors and gain a better understanding of the response of a marine based sector of an ice sheet to rapid climate change.

The opportunity costs of aid

O'Hare, Bernadette Ann-Marie — 2009-01-26T00:00:00Z

Description: Responce to Helena Watson, Aid, aid everywhere but still not a drop in the sink. BMJ 2009; 338: a3136

Chemical biology studies on 5-nitrofurans and sirtuin inhibitors

Zhou, Linna — 2012-12-01T00:00:00Z

Abstract: Part I: Target identification studies are one of the most difficult but rewarding challenges in chemical biology. Part I of this thesis describes target identification studies for 5-nitrofuran containing hits. The 5-nitrofurans used in this study were identified in a phenotypic screen for compounds that induced melanocyte cells death in zebrafish. Chapter 1 provides brief overviews on three related areas of the project: 1) the use of zebrafish as a model organism in drug discovery; 2) phenotypic screening using zebrafish and 3) the strategies used in target identification studies. Chapter 2 describes the synthesis of and SAR studies on two series of 5-nitrofuran containing analogues. The design and preparation of biotinylated chemical probes based on the SAR data is also described. These chemical tools are then used in affinity chromatography studies and genetic validation of a potential target (zebrafish Aldh2) of the 5-nitrofuran compounds is reported. Chapter 3 provides a review of the biological and chemical processes that human ALDHs are known to mediate. In addition, small molecules that modulate ALDH2 activity are reviewed. A detailed study of the interaction between 5-nitrofurans and human ALDH2 including in vitro enzymatic assays is described leading to the conclusion that the 5- nitrofurans under study are substrates of human ALDH2. Further mechanism of action investigations using model reactions are also presented. Chapter 4 introduces the use of 5-nitrofuran containing drugs in the clinic and highlights the reported side-effects. Further investigation of the interaction between ALDH2 and 5- nitrofurans in zebrafish and yeast using ALDH2 inhibitors is described. Based on these results, a combination therapy strategy is proposed. Finally, the trypanocidal activity of the newly synthesised 5-nitrofurans is discussed. Experimental details and future work for Part I are presented in Chapters 5 and 6 respectively. Part II: Human sirtuins are associated with various biological functions and diseases, including cancer and neurodegeneration. Previous work from the Westwood Lab has led to the discovery of the tenovins that act as inhibitors of SIRT1 and SIRT2. Part II of the thesis reports the development of potent fixed ring tenovin analogues with high SIRT2 selectivity. Chapter 7 provides a brief review of the biology of human SIRT2 and the reported SIRT2 inhibitors available to date. This is followed by a short summary of the previous work on the tenovins in the Westwood Lab and the design of the fixed ring tenovin analogues. Chapter 8 describes the synthesis of three series of fixed ring tenovin analogues. SAR data is generated based on in vitro enzymatic assays against both SIRT1 and SIRT2 and the prepared analogues showed relatively high potency and selectivity against SIRT2. Further cell-based deacetylation assay are also discussed. All the experimental details are reported in Chapter 9 and Chapter 10 provides with conclusions and proposed future work.

Will prescriptions for cultural change improve the NHS?

Davies, Huw Talfryn Oakley — 2013-03-01T00:00:00Z

Abstract: The recent Francis report diagnoses serious cultural deficiencies in the NHS and recommends fundamental cultural change. Huw Davies and Russell Mannion examine what research tells us about the likelihood of success.

Slotted photonic crystal biosensors

Scullion, Mark Gerard — 2013-06-26T00:00:00Z

Abstract: Optical biosensors are increasingly being considered for lab-on-a-chip applications due to their benefits such as small size, biocompatibility, passive behaviour and lack of the need for fluorescent labels. The light guiding mechanisms used by many of them result in poor overlap of the optical field with the target molecules, reducing the maximum sensitivity achievable. This thesis presents a new platform for optical biosensors, namely slotted photonic crystals, which engender higher sensitivities due to their ability to confine, spatially and temporally, the peak of optical mode within the analyte itself. Loss measurements showed values comparable to standard photonic crystals, confirming their ability to be used in real devices. A novel resonant coupler was designed, simulated, and experimentally tested, and was found to perform better than other solutions within the literature. Combining with cavities, microfluidics and biological functionalization allowed proof-of-principle demonstrations of protein binding to be carried out. High sensitivities were observed in smaller structures than most competing devices in the literature. Initial tests with cellular material for real applications was also performed, and shown to be of promise. In addition, groundwork to make an integrated device that includes the spectrometer function was also carried out showing that slotted photonic crystals themselves can be used for on-chip wavelength specific filtering and spectroscopy, whilst gas-free microvalves for automation were also developed. This body of work presents slotted photonic crystals as a realistic platform for complete on-chip biosensing; addressing key design, performance and application issues, whilst also opening up exciting new ideas for future study.

Locations of envy : an ethnography of Aguabuena potters

Castellanos Montes, Daniela — 2012-12-04T00:00:00Z

Abstract: This 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.

The effect of interferon on the transcription pattern of parainfluenza virus 5

Norsted, Hanna — 2013-06-26T00:00:00Z

Abstract: Interferon (IFN) is activated in response to virus infections and upregulates interferon-stimulated genes (ISGs) resulting in the expression of hundreds of proteins, many of which have direct or indirect antiviral activity. Parainfluenza virus 5 (PIV5) of the Paramyxoviridae family is a non-segmented negative sense single-stranded RNA virus with seven genes encoding eight proteins. Here we present that IFN induces alterations in the pattern of both virus transcription and translation and that ISG56 is primarily responsible for these effects. We report that when cells were treated with IFN post-infection, virus protein synthesis was inhibited while virus transcription levels were increased. These results suggest that ISG56 selectively inhibits the translation of viral mRNAs. In addition, the relationship of various PIV5 isolates was analysed by next generation sequencing. Four areas with a high degree of single nucleotide polymorphisms (SNPs) were identified and mapped to the intergenic regions of NP-V/P, M-F and HN-L, as well as the entire SH gene. Three of the isolates, the porcine strain SER and the canine strains CPI+ and CPI-, did not express an SH protein due to the lack of a start codon. A low degree of variation was found in the amino acid sequence of the HN glycoprotein suggesting that PIV5 may be less pressured to evolve in order to evade immune responses, such as neutralising antibodies.

Transnational families and the family nexus : perspectives of Indonesian and Filipino children left behind by migrant parent(s)

Graham, Elspeth — 2012-01-01T00:00:00Z

Abstract: As a significant supplier of labour migrants, Southeast Asia presents itself as an important site for the study of children in transnational families who are growing up separated from at least one migrant parent and sometimes cared for by ‘other mothers’. Through the often-neglected voices of left-behind children, this paper investigates the impact of parental migration and the resulting reconfiguration of care arrangements on the subjective well-being of migrants’ children in two Southeast Asian countries, Indonesia and the Philippines. We theorise the child’s position in the transnational family nexus through the framework of the ‘care triangle’, representing interactions between three subject groups – ‘left-behind’ children, non-migrant parents/other carers, and migrant parent/s. Using both quantitative (from 1,010 households) and qualitative (from 32 children) data from a study of Child Health and Migrant Parents in South-East Asia (CHAMPSEA), we examine relationships within the caring spaces of both home and transnational spaces. The interrogation of different dimensions of care reveals the importance of contact with parents (both migrant and non-migrant) to subjective child well-being, and the diversity of experiences and intimacies among children in the two study countries.

On global regularity of 2D generalized magnetohydrodynamic equations

Tran, Chuong Van — 2013-05-15T00:00:00Z

Abstract: In this article we study the global regularity of 2D generalized magnetohydrodynamic equations (2D GMHD), in which the dissipation terms are $- \nu \left( - \triangle \right)^{\alpha} u$ and $- \kappa \left( - \triangle \right)^{\beta} b$. We show that smooth solutions are global in the following three cases: $\alpha \geqslant 1 / 2, \beta \geqslant 1$; $0 \leqslant \alpha < 1 / 2, 2 \alpha + \beta > 2$; $\alpha \geqslant 2, \beta = 0$. We also show that in the inviscid case $\nu = 0$, if $\beta > 1$, then smooth solutions are global as long as the direction of the magnetic field remains smooth enough.

The unbearable emptiness of entrepreneurship

Roscoe, Philip John — 2011-08-01T00:00:00Z

Abstract: Review of 'Unmasking the Entrepreneur' by Campbell Jones and Andre Spicer, Edward Elgar, 2009

Sharp global nonlinear stability for a fluid overlying a highly porous material

Hill, Antony A. — 2010-01-08T00:00:00Z

Abstract: The stability of convection in a two-layer system in which a layer of fluid with a temperature-dependent viscosity overlies and saturates a highly porous material is studied. Owing to the difficulties associated with incorporating the nonlinear advection term in the Navier-Stokes equations into a stability analysis, previous literature on fluid/porous thermal convection has modelled the fluid using the linear Stokes equations. This paper derives global stability for the full nonlinear system, by utilizing a model proposed by Ladyzhenskaya. The nonlinear stability boundaries are shown to be sharp when compared with the linear instability thresholds.

Nonlinear stability of the one-domain approach to modelling convection in superposed fluid and porous layers

Hill, A A — 2010-09-01T00:00:00Z

Abstract: Studies of the nonlinear stability of fluid/porous systems have been developed very recently. A two-domain modelling approach has been adopted in previous works, but was restricted to specific configurations. The extension to the more general case of a Navier–Stokes modelled fluid over a porous material was not achieved for the two-domain approach owing to the difficulties associated with handling the interfacial boundary conditions. This paper addresses this issue by adopting a one-domain approach, where the governing equations for both regions are combined into a unique set of equations that are valid for the entire domain. It is shown that the nonlinear stability bound, in the one-domain approach, is very sharp and hence excludes the possibility of subcritical instabilities. Moreover, the one-domain approach is compared with an equivalent two-domain approach, and excellent agreement is found between the two.

Instability in internal solitary waves with trapped cores

Carr, Magda — 2012-01-01T00:00:00Z

Abstract: A 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.

Shear induced breaking of large amplitude internal solitary waves

Fructus, D — 2009-02-01T00:00:00Z

Convectively induced shear instability in large amplitude internal solitary waves

Carr, Magda — 2008-12-01T00:00:00Z

Abstract: Laboratory study has been carried out to investigate the instability of an internal solitary wave of depression in a shallow stratified fluid system. The experimental campaign has been supported by theoretical computations and has focused on a two layered stratification consisting of a homogeneous dense layer below a linearly stratified top layer. The initial background stratification has been varied and it is found that the onset and intensity of breaking are affected dramatically by changes in the background stratification. Manifestations of a combination of shear and convective instability are seen on the leading face of the wave. It is shown that there is an interplay between the two instability types and convective instability induces shear by enhancing isopycnal compression. Variation in the upper boundary condition is also found to have an effect on stability. In particular, the implications for convective instability are shown to be profound and a dramatic increase in wave amplitude is seen for a fixed (as opposed to free) upper boundary condition.

To ping or not to ping : the use of active acoustic devices in mitigating interactions between small cetaceans and gillnet fisheries

Dawson, Steve — 2013-01-01T00:00:00Z

Abstract: Active sound emitters (‘pingers’) are used in several gillnet fisheries to reduce bycatch of small cetaceans, and/or to reduce depredation by dolphins. Here, we review studies conducted to determine how effective these devices may be as management tools. Significant reductions in bycatch of harbour porpoise Phocoena phocoena, franciscana Pontoporia blainvillei, common Delphinus delphis and striped dolphin Stenella coeruleoalba, and beaked whales as a group have been demonstrated. For harbour porpoise this result has been replicated in 14 controlled experiments in North America and Europe, and appears to be due to porpoises avoiding the area ensonified by pingers. Two gillnet fisheries (California-Oregon driftnet fishery for swordfish; New England groundfish fishery) with mandatory pinger use have been studied for over a decade. Bycatch rates of dolphins/porpoises have fallen by 50 to 60%, and there is no evidence of bycatch increasing over time due to habituation. In both fisheries, bycatch rates were significantly higher in nets sparsely equipped with pingers or in which pingers had failed, than in nets without any pingers at all. Studies of pinger use to reduce depredation by bottlenose dolphins Tursiops truncatus generally show small and inconsistent improvements in fish catches and somewhat reduced net damage. Dolphin bycatch in these fisheries is rare, but still occurs in nets with pingers. Taken together, these studies suggest that the most promising candidates for bycatch reduction via pinger use will be gillnet fisheries in developed countries in which the bycaught cetaceans are generally neophobic species with large home ranges. We offer a set of lessons learned from the last decade of bycatch management.

Embodied metaphors and emotions in the moralization of restrained eating practices

Sheikh, Sana — 2013-05-01T00:00:00Z

Abstract: Moralization is the process whereby preferences are converted to values (Rozin, 1999). Two studies used an embodied metaphor approach, in which moral metaphors are grounded in one’s sense of physical cleanliness, to investigate whether restrained eating practices are moralized among women. Specifically, we predicted that the regulation of food intake by women is embodied in their feelings of physical cleanliness. Study 1 found that failures of restrained eating (i.e., overeating) increased accessibility of physical cleanliness-related words for women, but not men. Study 2 found that increased negative moral emotions fully mediated the effect of overeating on a desire for physical cleanliness. Overall, the studies argue for the importance of morality in restrained eating and in the central role of emotions in the embodiment of cognitive metaphors.

The Life-and-Death Journey of the Soul : Interpreting the Myth of Er

Halliwell, Francis Stephen — 2007-08-01T00:00:00Z

Tissue-specific transcriptomics in the field cricket Teleogryllus oceanicus

Bailey, Nathan William — 2013-02-01T00:00:00Z

Abstract: Field crickets (family Gryllidae) frequently are used in studies of behavioral genetics, sexual selection, and sexual conflict, but there have been no studies of transcriptomic differences among different tissue types. We evaluated transcriptome variation among testis, accessory gland, and the remaining whole-body preparations from males of the field cricket, Teleogryllus oceanicus. Non-normalized cDNA libraries from each tissue were sequenced on the Roche 454 platform, and a master assembly was constructed using testis, accessory gland, and whole-body preparations. A total of 940,200 reads were assembled into 41,962 contigs, to which 36,856 singletons (reads not assembled into a contig) were added to provide a total of 78,818 sequences used in annotation analysis. A total of 59,072 sequences (75%) were unique to one of the three tissues. Testis tissue had the greatest proportion of tissue-specific sequences (62.6%), followed by general body (56.43%) and accessory gland tissue (44.16%). We tested the hypothesis that tissues expressing gene products expected to evolve rapidly as a result of sexual selection—testis and accessory gland—would yield a smaller proportion of BLASTx matches to homologous genes in the model organism Drosophila melanogaster compared with whole-body tissue. Uniquely expressed sequences in both testis and accessory gland showed a significantly lower rate of matching to annotated D. melanogaster genes compared with those from general body tissue. These results correspond with empirical evidence that genes expressed in testis and accessory gland tissue are rapidly evolving targets of selection. Description: This work was supported by a Natural Environment Research Council Junior Postdoctoral Fellowship (NE/G014906/1) and Pacific Rim Foundation funding (08-T-PRRP-05-0029) to N.W.B.

The pattern changes changes : gambling value in Highland Papua New Guinea

Pickles, Anthony J. — 2013-06-27T00:00:00Z

Abstract: This thesis explores the part gambling plays in an urban setting in Highland Papua New Guinea. Gambling did not exist in (what is now) Goroka Town before European contact, nor Papua New Guinea more broadly, but when I conducted fieldwork in 2009-2010 it was an inescapable part of everyday life. One card game proliferated into a multitude of games for different situations and participants, and was supplemented with slot machines, sports betting, darts, and bingo and lottery games. One could well imagine gambling becoming popular in societies new to it, especially coming on the back of money, wage-work and towns. Yet the popularity of gambling in the region is surprising to social scientists because the peoples now so enamoured by gambling are famous for their love of competitively giving things away, not competing for them. Gambling spread while gifting remained a central part of the way people did transactions. This thesis resists juxtaposing gifting and selfish acquisition. It shows how their opposition is false; that gambling is instead a new analytic technique for manipulating the value of gifts and acquisitions alike, through the medium of money. Too often gambling takes a familiar form in analyses: as the sharp end of capitalism, or the benign, chance-led redistributor of wealth in egalitarian societies. The thesis builds an ethnographic understanding of gambling, and uses it to interrogate theories of gambling, money, and Melanesian anthropology. In so doing, the thesis speaks to a trend in Melanesian anthropology to debate whether monetisation and urbanisation has brought about a radical split in peoples’ understandings of the world. Dealing with some of the most starkly ‘modern’ material I find a process of inclusive indigenous materialism that consumes the old and the new alike, turning them into a model for action in a dynamic money-led world.

A computational approach to discovering p53 binding sites in the human genome

Lim, Ji-Hyun — 2013-06-01T00:00:00Z

Abstract: The tumour suppressor p53 protein plays a central role in the DNA damage response/checkpoint pathways leading to DNA repair, cell cycle arrest, apoptosis and senescence. The activation of p53-mediated pathways is primarily facilitated by the binding of tetrameric p53 to two 'half-sites', each consisting of a decameric p53 response element (RE). Functional REs are directly adjacent or separated by a small number of 1-13 'spacer' base pairs (bp). The p53 RE is detected by exact or inexact matches to the palindromic sequence represented by the regular expression [AG][AG][AG]C[AT][TA]G[TC][TC][TC] or a position weight matrix (PWM). The use of matrix-based and regular expression pattern-matching techniques, however, leads to an overwhelming number of false positives. A more specific model, which combines multiple factors known to influence p53-dependent transcription, is required for accurate detection of the binding sites. In this thesis, we present a logistic regression based model which integrates sequence information and epigenetic information to predict human p53 binding sites. Sequence information includes the PWM score and the spacer length between the two half-sites of the observed binding site. To integrate epigenetic information, we analyzed the surrounding region of the binding site for the presence of mono- and trimethylation patterns of histone H3 lysine 4 (H3K4). Our model showed a high level of performance on both a high-resolution data set of functional p53 binding sites from the experimental literature (ChIP data) and the whole human genome. Comparing our model with a simpler sequence-only model, we demonstrated that the prediction accuracy of the sequence-only model could be improved by incorporating epigenetic information, such as the two histone modification marks H3K4me1 and H3K4me3.

Supported ionic liquid phase catalysis in continuous supercritical flow

Duque, Ruben — 2013-06-26T00:00:00Z

Abstract: The separation of the expensive catalysts from the solvent and reaction products remains one of the major disadvantages of homogeneous catalytic reactions, which are otherwise advantageous because of their high activity, tuneable selectivity and ease of study. Ideally, the homogeneous reactions would be carried out in continuous flow mode with the catalyst remaining in the reactor at all times, whilst the substrates and products flow over the catalyst. The system we have been studying is one where the catalyst is dissolved in a thin film of an ionic liquid, and this is supported within the pores of a microporous silica. This supported ionic liquid phase (SILP) catalyst is then placed in a tubular flow reactor, similar to that used for heterogeneous reactions. The raw materials are then injected into the rig, pass through the reactor and the products and the raw materials that have not reacted are collected at the other end of the rig. Supercritical CO₂ is used to transport the raw materials and products along the catalyst bed, allowing a continuous flow mode with low leaching for both the catalyst and the ionic liquid. We have applied this procedure first to alkene metathesis catalysed by a ruthenium complex that has been especially designed to dissolve in 1-butyl-3-methyimidazolium triflamide (BMIM NTf₂), which was used as ionic liquid. Activity is observed for the ring closing metathesis of diethyl 2,2-diallylmalonate, but the catalyst is not stable, only allowing about 300 turnovers. This instability is attributed to the formation of Ru=CH₂ moieties, which dimerise to an inactive species. More success is achieved with internal alkenes such as 2-octene and especially methyl oleate. Self metathesis of methyl oleate continues for >10.000 turnovers over 10 h, with only small decreases in activity. The cross metathesis of methyl oleate with dimethyl maleate has also been studied. Cross metathesis dominates in the early stages of the reaction but the cross metathesis products diminish with time. Surprisingly, the catalyst does not deactivate since self metathesis of methyl oleate continues. The phase behaviour of the reaction was monitored and gave us an insight into the reasons for this change in selectivity. Methoxycarbonylation reactions in continuous flow proved to be a much more difficult process than the previous metathesis reactions. Higher catalyst loading was needed to reduce the reaction times. The first continuous flow reactions showed conversion predominantly, if not exclusive, of 1-octene isomerised products. The presence of ionic liquid (IL) in the SILP system was essential, otherwise the catalyst leached out of the reactor very quickly. Batch reactions showed that none of the studied parameters (absence of presence of either BMIM NTf₂, OMIM NTf₂, silica or CO₂) had any influence on the reaction, but when observing the results it was noticed that the reactions that gave the best results were performed in a close range of pressures between 55 and 70 bar, indicating that the reaction might be pressure dependent. Further continuous flow reactions in that range of pressures gave the best conversions to methoxycarbonylation products. Unfortunately, at these pressures and without CO₂ the reaction took place in a liquid phase and thus substantial IL and catalyst leaching was observed, causing a decrease in conversion and making the reaction not feasible under continuous flow conditions. Nevertheless, the catalyst system composed of Pd, 1,2-bis(di-tert-butylphosphinomethyl)benzene (DTBPMB) ligand and acid showed an excellent linear selectivity, usually higher than 90%, both in batch and continuous flow reactions. Hydrogenation reactions of dimethyl itaconate (DMI) and dibutyl itaconate (DBI) using Rh-MeDuPhos showed excellent activity and enantioselestivity in a batch mode. In a continuous flow mode IL leaching caused a decrease of the enantioselectivity. The best results were obtained when CO₂ was not present. On the other hand, the absence of CO₂ implied that the reaction was performed in a liquid phase and therefore abundant IL leaching was observed along with a decrease in the enantioselectivity. A study of the reaction behaviour when using CO₂ in its different phases (liquid, gas and supercritical) was carried out. Under supercritical conditions IL leaching was avoided but conversion was not observed. When using CO₂ in its liquid phase some conversion was observed and full conversion occurred in its gas phase, but abundant IL leaching caused a decrease in the enantioselectivity. Better results were obtained by immobilising a Rh-MeDuPhos catalyst onto alumina via heteropoly acids. The effect of pressure, H₂ flow and substrate flow were studied and the stability of the reaction in the long term was examined under optimal conditions. More than 12,900 TONs were achieved after 4 days of continuous reaction, with conversions higher than 90% during the 3 first days and e.e. higher than 99% during the 2 first days.

The apocalyptic tradition in Scotland, 1588-1688

Drinnon, David A. — 2013-06-01T00:00:00Z

Abstract: Throughout the seventeenth century, numerous Scots became convinced that the major political and religious upheavals of their age signified the fulfillment of, or further unfolding of, the vivid prophecies described in the Book of Revelation which foretell of the final consummation of all things. To date, however, an in-depth analysis of the evolution of Scottish apocalyptic belief during the seventeenth century has never been undertaken. This thesis utilizes a wide variety of source material to demonstrate the existence of a cohesive, persistent, and largely conservative tradition of apocalyptic thought in Scotland that spanned the years 1588 to 1688. Chapter One examines several influential commentaries on the Book of Revelation published by notable Scots during the decades either side of the Union of Crowns. These works reveal many of the principal characteristics that formed the basis of the Scottish apocalyptic tradition. The most important of these traits which became a consistent feature of the tradition was the rejection of millenarianism. In recent years, historians have exaggerated the influence of millenarian ideals in Scotland during the Covenanting movement which began in 1638. Chapter Two argues that Scottish Covenanters consistently denounced millenarianism as a dangerous, subversive doctrine that could lead to the religious radicalism espoused by sixteenth-century German Anabaptists. Chapter Three looks at political and religious factors which led to the general decline of apocalyptic expectancy in Scotland during the Interregnum. It also demonstrates how, despite this decline, Scottish apocalyptic thinkers continued to uphold the primary traits of the apocalyptic tradition which surfaced over the first half of the century. Lastly, Chapter Four explains how state-enforced religious persecution of Scottish Presbyterians during the Restoration period led to the radicalisation of the tradition and inspired the violent actions of Covenanter extremists who believed they had been chosen by God to act as instruments of his divine vengeance in the latter-days.

Migration or immigration? : Ireland’s new and unexpected Polish-language community

Kamusella, Tomasz Dominik — 2013-01-01T00:00:00Z

Amousia : living without the Muses

Halliwell, Francis Stephen — 2012-01-01T00:00:00Z

Generating transformation semigroups using endomorphisms of preorders, graphs, and tolerances

Mitchell, James David — 2010-09-01T00:00:00Z

Abstract: Let ΩΩ be the semigroup of all mappings of a countably infinite set Ω. If U and V are subsemigroups of ΩΩ, then we write U≈V if there exists a finite subset F of ΩΩ such that the subsemigroup generated by U and F equals that generated by V and F. The relative rank of U in ΩΩ is the least cardinality of a subset A of ΩΩ such that the union of U and A generates ΩΩ. In this paper we study the notions of relative rank and the equivalence ≈ for semigroups of endomorphisms of binary relations on Ω. The semigroups of endomorphisms of preorders, bipartite graphs, and tolerances on Ω are shown to lie in two equivalence classes under ≈. Moreover such semigroups have relative rank 0, 1, 2, or d in ΩΩ where d is the minimum cardinality of a dominating family for NN. We give examples of preorders, bipartite graphs, and tolerances on Ω where the relative ranks of their endomorphism semigroups in ΩΩ are 0, 1, 2, and d. We show that the endomorphism semigroups of graphs, in general, fall into at least four classes under ≈ and that there exist graphs where the relative rank of the endomorphism semigroup is 2ℵ0.

Workforce development and challenging behaviour : training staff to treat, to manage or to cope?

Campbell, Martin — 2010-09-01T00:00:00Z

Abstract: Staff working directly with adults challenging behaviours in learning disability services need to be very good at what they do. They also need to want to do the job. A theory-practice gap exists, however, between what is known about effective, evidence-based approaches and whether and how these are used in person-centred, community services. Many front line staff working with people with the most serious challenging behaviours do not have the skills to implement programmes to change behaviour. This discussion paper reviews workforce development in the context of clinical and service guidelines and asks whether the legitimate purview of frontline staff is a balance of treating challenging behaviour, managing it or to simply coping with it on a daily basis, whilst maintaining the best quality of life possible for service users.

Safeguarding adults at risk of harm in Scotland : legislation, policy and practice

Campbell, Martin — 2012-01-01T00:00:00Z

Description: Special Issue: Safeguarding adults at risk of harm in Scotland.

Reducing health inequalities in Scotland : the involvement of people with learning disabilities as national health service reviewers

Campbell, Martin — 2010-03-01T00:00:00Z

Abstract: Reducing health inequalities is a key priority for the Scottish Government. Health authorities are expected to meet quality targets. The involvement of people with learning disabilities in health service review teams has been one of the initiatives used in by NHS Quality Improvement Scotland to empower patients and improve health services. This paper describes this initiative, how it was planned, and an evaluation by health staff, carers and people with learning disabilities. Recommendations are made to ensure the future success of this type of initiative in Scotland and elsewhere. This initiative was evaluated positively and tested traditional assumptions, challenging the power imbalance in patient-provider relationships. The theory and the practice of including people with learning disabilities as “expert patient” reviewers are discussed.

Assessment of interpersonal risk (AIR) in adults with learning disabilities and challenging behaviour – piloting a new risk assessment tool

Campbell, Martin — 2012-01-01T00:00:00Z

Abstract: A new risk assessment tool, Assessment of Interpersonal Risk (AIR), was piloted and evaluated to measure risk factors and compatibility between individuals living in an assessment and treatment unit in one NHS area. The adults with learning disabilities in this unit had severe and enduring mental health problems and/or behaviour that is severely challenging. The aims of this small-scale research project were to estimate the reciprocal risk to and from each individual across five main risk domains and to enhance professional judgement to make defensible decisions about interpersonal risk. Data were recorded on incidents involving five individuals over a period of 6 months. Individual Rating Profiles were incorporated into existing Individual Risk Management Plans, together with interpersonal profiles, recording risk evaluations between named individuals across the five risk domains. Results showed that the AIR tool may be a useful addition to existing effective risk management, to inform assessments and future discharge planning. Description: This article is a report on a research project funded by the Knowledge Transfer Partnership. This research was a joint project with NHS Fife. The accelerated long-stay Learning Disability Hospital closure programme in Scotland throughout the late 1990s and from 2000 onwards, resulted in the movement of residents both within and out-with these Hospitals to either community based housing models or to community based In-patient services. The legacy and impact of this residential service re-provision was that individuals experienced changes in those they lived with, and those who supported them. This process took place against the back-drop and dynamic of associated changes in environmental, procedural, situational and interpersonal risk. It was in recognition of the challenge that this change programme presented to care services in terms of defensible risk assessment and management that the Assessment of Interpersonal Risk tool was developed.

A pilot project : evaluating community nurses' knowledge and understanding of the Adult Support and Protection (Scotland) Act 2007

Campbell, Martin — 2012-08-06T00:00:00Z

Abstract: Purpose: To evaluate understanding and knowledge of the Adult Support and Protection (Scotland) Act 2007 in a sample of community nurses working in learning disability services in Scotland. Design: Ten community nurses who worked in learning disability services in one NHS area were tested at two time points, four months apart using a questionnaire designed for this study by researchers and practitioners. Level of previous national training in the Adult Support and Protection Act, and length of time working with people with learning disabilities were recorded. Three domains of adult protection were included in the questionnaire: Principles of the Act and definitions; Adults at Risk of Harm; Protection, Assessment, Removal and Banning Orders. Findings: Questionnaire scores varied widely overall and across the three domains. There was no correlation between individual scores and training or length of work experience. The level of knowledge was below what might have been expected for this group, given the level of training and experience. Carefully designed verification of the impact of nationally approved Adult Support and Protection training is needed. Originality/Value: There is an absence of research in evaluating the impact of the approved Scottish Government training materials on staff knowledge and understanding of the 2007 Act, with staff attendance being taken as the main measure of training compliance. This was a small scale, pilot study and recommendations are made for the scope and methods of evaluation. Description: This research was funded from a grant from Queens Nursing Institute Scotland. Special Issue: Safeguarding adults at risk of harm in Scotland. Guest editor(s): Martin Campbell, James Hogg and Bridget Penhale.

Number of degrees of freedom and energy spectrum of surface quasi-geostrophic turbulence

Tran, Chuong V. — 2011-10-01T00:00:00Z

Abstract: We study both theoretically and numerically surface quasi-geostrophic turbulence regularized by the usual molecular viscosity, with an emphasis on a number of classical predictions. It is found that the system's number of degrees of freedom N, which is defined in terms of local Lyapunov exponents, scales as Re-3/2, where R e is the Reynolds number expressible in terms of the viscosity, energy dissipation rate and system's integral scale. For general power-law energy spectra k(-alpha), a comparison of N with the number of dynamically active Fourier modes, i.e. the modes within the energy inertial range, yields alpha = 5/3. This comparison further renders the scaling Re-1/2 for the exponential dissipation rate at the dissipation wavenumber. These results have been predicted on the basis of Kolmogorov's theory. Our approach thus recovers these classical predictions and is an analytic alternative to the traditional phenomenological method. The implications of the present findings are discussed in conjunction with related results in the literature. Support for the analytic results is provided through a series of direct numerical simulations. Description: L.A.K.B. was supported by an EPSRC post-graduate studentship.

Mg structural state in coral aragonite and implications for the paleoenvironmental proxy

Finch, Adrian A. — 2008-04-19T00:00:00Z

Abstract: Thermodynamic calculations and inorganic precipitation experiments indicate a relationship between aragonite Mg/Ca and water temperature. This offers a route to reconstruct seawater temperatures from fossil corals. Fundamental to this is the assumption that Mg2+ exchanges for Ca2+ within carbonate. We present X-ray Absorption Fine Structure (XAFS) data to indicate the structural state of Mg in modern Porites coral skeletons. We show Mg is not in aragonite, but hosted by a disordered Mg-bearing material. Mg may be predominantly hosted in organic materials or as a highly disordered inorganic phase, e. g., a nanoparticulate form of Mg carbonate or hydroxide. Reported correlations between seawater temperature and coral Mg/Ca are unlikely to be consistent between corals and hence analysis of Mg/Ca in fossils is unlikely to produce accurate climate reconstructions. We anticipate XAFS will be applied widely to environmental proxies and become an important tool in identifying those that reconstruct accurate climates.

Staff training and challenging behaviour : Who needs it?

Campbell, Martin — 2007-06-01T00:00:00Z

Abstract: Staff working directly with people who have challenging behaviour in learning disability services need to be D good at what they do. These staff are trained by their employers to manage and to treat challenging behaviours and to improve the quality of life of people in their care. While such training is generally well evaluated by care staff, there is limited evidence that training alone changes poor attitudes or improves staff performance. Training has not been linked to quality of outcomes for service users. From research on treating challenging behaviour, achieving maintenance of behavioural gains after treatment has been discontinued is the exception rather than the rule. Can the same be said for maintaining gains achieved through staff training in the area of challenging behaviour? This discussion article reviews the value of training for staff working with people with challenging behaviour.

Dimer-dimer stacking interactions are important for nucleic acid binding by the archaeal chromatin protein Alba

Jelinska, Clare — 2010-04-01T00:00:00Z

Abstract: Archaea use a variety of small basic proteins to package their DNA. One of the most widespread and highly conserved is the Alba (Sso10b) protein. Alba interacts with both DNA and RNA in vitro, and we show in the present study that it binds more tightly to dsDNA (double-stranded DNA) than to either ssDNA (single-stranded DNA) or RNA. The Alba protein is dimeric in solution, and forms distinct ordered complexes with DNA that have been visualized by electron microscopy studies; these studies suggest that, on binding dsDNA, the protein forms extended helical protein fibres. An end-to-end association of consecutive Alba dimers is suggested by the presence of a dimer-dimer interface in crystal structures of Alba from several species, and by the strong conservation of the interface residues, centred on Are and Phe(60). In the present study we map perturbation of the polypeptide backbone of Alba upon binding to DNA and RNA by NMR, and demonstrate the central role of Phe(60) in forming the dimer dimer interface. Site-directed spin labelling and pulsed ESR are used to confirm that an end-to-end, dimer dimer interaction forms in the presence of dsDNA.

Coronal heating by the partial relaxation of twisted loops

Bareford, Michael — 2013-02-01T00:00:00Z

Abstract: Context: Relaxation theory offers a straightforward method for estimating the energy that is released when a magnetic field becomes unstable, as a result of continual convective driving. Aims: We present new results obtained from nonlinear magnetohydrodynamic (MHD) simulations of idealised coronal loops. The purpose of this work is to determine whether or not the simulation results agree with Taylor relaxation, which will require a modified version of relaxation theory applicable to unbounded field configurations. Methods: A three-dimensional (3D) MHD Lagrangian-remap code is used to simulate the evolution of a line-tied cylindrical coronal loop model. This model comprises three concentric layers surrounded by a potential envelope; hence, being twisted locally, each loop configuration is distinguished by a piecewise-constant current profile. Initially, all configurations carry zero-net-current fields and are in ideally unstable equilibrium. The simulation results are compared with the predictions of helicity conserving relaxation theory. Results: For all simulations, the change in helicity is no more than 2% of the initial value; also, the numerical helicities match the analytically-determined values. Magnetic energy dissipation predominantly occurs via shock heating associated with magnetic reconnection in distributed current sheets. The energy release and final field profiles produced by the numerical simulations are in agreement with the predictions given by a new model of partial relaxation theory: the relaxed field is close to a linear force free state; however, the extent of the relaxation region is limited, while the loop undergoes some radial expansion. Conclusions: The results presented here support the use of partial relaxation theory, specifically, when calculating the heating-event distributions produced by ensembles of kink-unstable loops.

Microlensing for extrasolar planets : improving the photometry

Bajek, David J. — 2013-06-01T00:00:00Z

Abstract: Gravitational Microlensing, as a technique for detecting Extrasolar Planets, is recognised for its potential in discovering small-mass planets similar to Earth, at a distance of a few Astronomical Units from their host stars. However, analysing the data from microlensing events (which statistically rarely reveal planets) is complex and requires continued and intensive use of various networks of telescopes working together in order to observe the phenomenon. As such the techniques are constantly being developed and refined; this project outlines some steps of the careful analysis required to model an event and ensure the best quality data is used in the fitting. A quantitative investigation into increasing the quality of the original photometric data available from any microlensing event demonstrates that 'lucky imaging' can lead to a marked improvement in the signal to noise ratio of images over standard imaging techniques, which could result in more accurate models and thus the calculation of more accurate planetary parameters. In addition, a simulation illustrating the effects of atmospheric turbulence on exposures was created, and expanded upon to give an approximation of the lucky imaging technique. This further demonstrated the advantages of lucky images which are shown to potentially approach the quality of those expected from diffraction limited photometry. The simulation may be further developed for potential future use as a 'theoretical lucky imager' in our research group, capable of producing and analysing synthetic exposures through customisable conditions.

Dietary effects on skin colour : appearance-based incentives to improve fruit and vegetable consumption

Whitehead, Ross David — 2013-06-25T00:00:00Z

Abstract: Poor diet precipitates significant social and economic burden, necessitating effective and economical dietary intervention strategies. Current population-level campaigns provide guidelines for living healthily and focus on the impact of lifestyle on chronic disease risk. Behavioural interventions which capitalise on individuals’ existing cognitions are likely to be more effective. A programme of work is presented here which evaluates the feasibility and efficacy of an appearance-based dietary intervention approach. This project aims to improve fruit and vegetable consumption by illustrating the associated benefits to skin appearance. The impact of fruit and vegetable consumption on skin colour is assessed (Chapter 6), corroborating previous between-subjects evidence which finds that dermal yellowness (CIE b*) is positively associated with fruit and vegetable intake. This work also discovers that modest within-subject dietary change is sufficient to perceptibly alter skin colour within six weeks (Chapter 7). Perceptual preferences are examined (Chapters 5 to 9), finding that optimally healthy skin colouration is that associated with increased fruit and vegetable consumption. Two behavioural intervention trials are conducted (Chapters 6 and 9) to evaluate whether visualising the impact of fruit and vegetable consumption on skin colour motivates dietary improvement. Relative to control groups, participants receiving an appearance-based intervention (in which the above effects are illustrated and explained) reported improvements in diet, particularly when illustrations were performed upon images of one’s own face. It may be valuable to disseminate such an intervention at a population level, though a number of further longitudinal studies are necessary to determine the wider effectiveness of this approach.

Seasonal inflow of warm water onto the southern Weddell Sea continental shelf, Antarctica

Arthun, Marius — 2012-09-01T00:00:00Z

Abstract: To capture the austral summer to winter transition in water mass properties over the southern Weddell Sea continental shelf and slope region Weddell seals were tagged with miniaturized conductivity–temperature–depth sensors in February 2011. During the following 8 months the instruments yielded about 9000 temperature–salinity profiles from a previously undersampled area. This allows, for the first time, a description of the seasonality of warm water intrusions onto the shelf. A temperature section across the Filchner Depression and eastern shelf shows a pronounced decrease in warm water inflow from summer to winter, further supported by an almost 3–year long time series from a shelf–break mooring. The seasonal variability is related to the surface wind stress and an associated deepening of the off–shore core of Warm Deep Water.

Optical eigenmodes for illumination & imaging

Kosmeier, Sebastian — 2013-06-26T00:00:00Z

Abstract: This thesis exploits so called “Optical Eigenmodes” (OEi) in the focal plane of an optical system. The concept of OEi is introduced and the OEi operator approach is outlined, for which quadratic measures of the light field are expressed as real eigenvalues of an Hermitian operator. As an example, the latter is employed to locally minimise the width of a focal spot. The limitations of implementing these spots with state of the art spatial beam shaping technique are explored and a selected spot with a by 40 % decreased core width is used to confocally scan an in focus pair of holes, delivering a two-point resolution enhanced by a factor of 1.3. As a second application, OEi are utilised for fullfield imaging. Therefore they are projected onto an object and for each mode a complex coupling coefficient describing the light-sample interaction is determined. The superposition of the OEi weighted with these coefficients delivers an image of the object. Compared to a point-by-point scan of the sample with the same number of probes, i.e. scanning points, the OEi image features higher spatial resolution and localisation of object features, rendering OEi imaging a compressive imaging modality. With respect to a raster scan a compression by a factor four is achieved. Compared to ghost imaging as another fullfield imaging method, 2-3 orders of magnitude less probes are required to obtain similar images. The application of OEi for imaging in transmission as well as for fluorescence and (surface enhanced) Raman spectroscopy is demonstrated. Finally, the applicability of the OEi concept for the coherent control of nanostructures is shown. For this, OEi are generated with respect to elements on a nanostructure, such as nanoantennas or nanopads. The OEi can be superimposed in order to generate an illumination of choice, for example to address one or multiple nanoelements with a defined intensity. It is shown that, compared to addressing such elements just with a focussed beam, the OEi concept reduces illumination crosstalk in addressing individual nanoelements by up to 70 %. Furthermore, a fullfield aberration correction is inherent to experimentally determined OEi, hence enabling addressing of nanoelements through turbid media.

Attention cues in apes and their role in social play behavior of western lowland gorillas (Gorilla gorilla gorilla)

Mayhew, Jessica A. — 2013-06-25T00:00:00Z

Abstract: The research aims of this thesis are to investigate the attention cues available to and used by apes, especially gorillas (Gorilla gorilla), to ascertain the direction of conspecific attention during social interactions with a special reference to social play. Minimal research has been conducted on the role of attention cues - eye gaze, head, and body orientation - to regulate natural social interactions, such as social play, in non-human primates. This thesis begins with an investigation of the "cooperative eye hypothesis", which poses that humans have evolved a unique white sclera adaptation for advertising and detecting gaze direction. Chapter 2 reports the existence of a natural white sclera variation in a proportion of gorilla eyes - contradicting the widely held assumption that white sclera is an exclusively human characteristic - and analyzes the presence of white sclera in relation to other morphological changes in the human eye. The study concludes that the morphological elongation of the eye might be a more important and unique change than the white sclera coloration. Chapter 3 experimentally explores the contribution of white sclera in both great ape and human eye gaze to the perception of gaze direction detection by human observers. This chapter concludes that although white sclera contributes to the accuracy and speed of gaze direction detection (an assumption that this thesis has put to experimental test for the first time), this merely adds to the already efficient gaze cues available in the eye areas of the ape face. Chapter 4 investigates the role of eye gaze, head, and body orientations during gorilla social play behavior, and more specifically, introduces a novel analysis of "vigilance periods" (VPs), in which gorillas may use the interaction between attention cues to gauge the attention and intentions of play partners to successfully navigate play. The final study (Chapter 5) complements Chapter 4 and investigates the role of gorilla postures, behaviors, and movements during changes in attentional cue orientations. This chapter concludes that gorillas often engage in physical rest during VPs but maintain attentional engagement and can assemble and impart socially relevant information based on the behaviors, movements, and attention orientations of their partner. Together, these studies suggest that attention orientation is conveyed and assessed by gorillas through a variety of interacting cues to navigate and modify social play interactions.

Investigation of structure and disorder in inorganic solids using solid-state NMR

Mitchell, Martin R. — 2013-06-26T00:00:00Z

Abstract: The use of solid-state NMR and DFT calculations to study Y₂Sn[subscript(x)]Ti[subscript(2-x)]O₇, Y₂Sn[subscript(x)]Zr[subscript(2-x)]O₇ and Y₂Ti[subscript(x)]Zr[subscript(2-x)]O₇, materials with applications for the safe encapsulation of radioactive actinides is investigated. As a result of cation or anion disorder in these materials, NMR spectra are often complex and difficult to interpret. Therefore, an investigation using a range of NMR active nuclei and measurement of a variety of NMR parameters (isotropic chemical shift, δ[subscript(iso)]; span, Ω and quadrupolar coupling, C[subscript(Q)]) were used to provide a full and detailed picture of each material. The measurement of Ω in these disordered compounds with multiple resonances in the NMR spectra, required the use of 2D CSA-amplified PASS (CAPASS) experiments to enable the separation of each of the spinning sideband manifolds. An experimental assessment of the CAPASS experiment showed that although low ν₁/Ω[subscript(Hz)] ratios (as found in ⁸⁹Y NMR) resulted in distortions in the spectra obtained, a modified fitting procedure could be utilised to compensate for this fact, which allowed the accurate measurement of Ω. Despite the difficulties in acquiring the ⁸⁹Y NMR spectra, they were found to be the most informative of the NMR-active nuclei available. ¹¹⁹Sn NMR spectra, although much easier to acquire than ⁸⁹Y, were more complex and harder to analyse, owing to the overlapping resonances. Therefore, ¹¹⁹Sn NMR could only be used to confirm or support the results obtained using ⁸⁹Y NMR. Although ¹⁷O NMR was found to be useful, a full study could not be implemented due to the lack of ¹⁷O enriched samples; an area where future investigation may prove fruitful. Finally, [superscript(47/49)]Ti and ⁹¹Zr NMR spectra were found to be the most difficult to acquire due to their low receptivities and the quadrupolar broadened lineshapes, and as a result, little additional information was obtained. As a result of this analysis, for the Y₂Sn[subscript(x)]Ti[subscript(2-x)]O₇ pyrochlore solid solution, using primarily ⁸⁹Y δ[subscript(iso)] and Ω, and additionally confirmed with ¹¹⁹Sn δ[subscript(iso)], it was found that the Sn and Ti cations were randomly ordered throughout the B-sites. Additionally, ⁸⁹Y Ω could be used to obtain approximate Y-O[subscript(48f)] and Y-O[subscript(8b)] bond lengths for each type of Y environment. The study of Y₂Sn[subscript(x)]Zr[subscript(2-x)]O₇ using ⁸⁹Y NMR showed that although the end members were single phase, pyrochlore (Y₂Sn₂O₇) or defect fluorite (Y₂Zr₂O₇), the intermediate compositions were mostly two phase mixtures, consisting of an ordered pyrochlore (with an average formula of Y₂Sn₁.₈Zr₀.₂O₇) and a disordered phase, where the proportions of the pyrochlore and disordered phases decreased and increased, respectively, with the Zr content. Additionally, although the coordination states of the Y and Sn cations were easily determined using ⁸⁹Y and ¹¹⁹Sn NMR, respectively, the coordination states of the Zr cations could not be confirmed directly by ⁹¹Zr NMR. However, using indirect analysis from results obtained with ⁸⁹Y and ¹¹⁹Sn NMR, it was determined that 6 coordinate Zr was present in each composition, and it was always present in a greater proportion than 8 coordinate Zr. Finally, although ⁸⁹Y NMR spectra of Y₂Ti[subscript(x)]Zr[subscript(2-x)]O₇ were extremely difficult to analyse, it was tentatively proposed that they could be similar to Y₂Sn[subscript(x)]Zr[subscript(2-x)]O₇ due to some similarities observed between the spectra.

Los hombres-perro de Felisberto Hernández

San Roman, Gustavo Francisco — 2006-01-01T00:00:00Z

Forms of flexibility : associations between executive functions in the rat

Chase, E. Alexander — 2013-06-25T00:00:00Z

Abstract: Executive control is a vital cognitive function that facilitates the focussing and shifting of attention, planning and working towards a goal, ignoring distractions, and flexibly responding to novel situations. Disruptions to executive control are seen in many psychiatric and neurodegenerative disorders, as well as healthy ageing, which can be profoundly detrimental. Despite having many effective and well-validated methodologies for detecting and quantifying these deficits, there are very few treatments — pharmacological or otherwise — for ameliorating executive dysfunction. This lack of progress can partly be blamed on difficulties associated with identifying drugs that enhance cognition in preclinical research. The work in this thesis aimed to expand our understanding of executive dysfunction — as well as the tasks that measure it — in rats. In results presented in chapter three, middle-aged rats demonstrated impaired reversal learning on the standard attentional set-shifting task, but this was treatable with a novel drug targeting the N-methyl-D-aspartate receptor. The age impairments seen in this experiment were similar to those previously found in young rats with orbital prefrontal cortex (OFC) lesions. The results of chapter four expanded on this similarity to show that, along with reversal deficits, young OFC-lesioned rats are impaired at forming attentional sets when tested on a modified task. In chapter five, another modified set-shifting task revealed that middle-aged rats also suffer from impaired set-formation, but their reversal learning impairments only manifest before attentional set has been formed — not after. Finally, in chapter six, the putative cognitive enhancer modafinil was found to exacerbate middle-aged rats’ reversal learning deficit, but it also enhanced their subsequent ability to form attentional set. These experiments reveal that modifying the rat attentional set-shifting task can sometimes make it a more effective tool for testing cognitive enhancers in preclinical settings.

Fitting complex ecological point process models with integrated nested Laplace approximation

Illian, Janine Baerbel — 2013-01-01T00:00:00Z

Abstract: Summary 1. We highlight an emerging statistical method, integrated nested Laplace approximation (INLA), which is ideally suited for fitting complex models to many of the rich spatial data sets that ecologists wish to analyse. 2. INLA is an approximation method that nevertheless provides very exact estimates. In this article, we describe the INLA methodology highlighting where it offers opportunities for drawing inference from (spatial) ecological data that would previously have been too complex to make practical model fitting feasible. 3. We use INLA to fit a complex joint model to the spatial pattern formed by a plant species, Thymus carnosus, as well as to the health status of each individual. 4. The key ecological result revealed by our spatial analysis of these data, relates to the distance-to-water covariate. We find that T. carnosus plants are generally healthier when they are further away from the water. 5. We suggest that this may be the result of a combination of (1) plants having alternative rooting strategies depending on how close to water they grow and (2) the rooting strategy determining how well the plants were able to tolerate an unusually dry summer. 6. We anticipate INLA becoming widely used within spatial ecological analysis over the next decade and suggest that both ecologists and statisticians will benefit greatly from working collaboratively to further develop and apply these emerging statistical methods.

Genetic analysis of life-history constraint and evolution in a wild ungulate population

Morrissey, Michael Blair — 2012-04-01T00:00:00Z

Abstract: Trade-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.

Vocal copying of individually distinctive signature whistles in bottlenose dolphins

King, Stephanie Laura — 2013-04-22T00:00:00Z

Abstract: Vocal learning is relatively common in birds but less so in mammals. Sexual selection and individual or group recognition have been identified as major forces in its evolution. While important in the development of vocal displays, vocal learning also allows signal copying in social interactions. Such copying can function in addressing or labelling selected conspecifics. Most examples of addressing in non-humans come from bird song, where matching occurs in an aggressive context. However, in other animals, addressing with learned signals is very much an affiliative signal. We studied the function of vocal copying in a mammal that shows vocal learning as well as complex cognitive and social behaviour, the bottlenose dolphin (Tursiops truncatus). Copying occurred almost exclusively between close associates such as mother–calf pairs and male alliances during separation and was not followed by aggression. All copies were clearly recognizable as such because copiers consistently modified some acoustic parameters of a signal when copying it. We found no evidence for the use of copying in aggression or deception. This use of vocal copying is similar to its use in human language, where the maintenance of social bonds appears to be more important than the immediate defence of resources.

On the contrary: disagreement, context, and relative truth

Huvenes, Torfinn Thomesen — 2012-11-30T00:00:00Z

A class of 5-nitro-2-furancarboxylamides with potent trypanocidal activity against Trypanosoma brucei in vitro

Zhou, Linna — 2013-02-14T00:00:00Z

Abstract: Recently, the World Health Organization approved the nifurtimox–eflornithine combination therapy for the treatment of human African trypanosomiasis, renewing interest in nitroheterocycle therapies for this and associated diseases. In this study, we have synthesized a series of novel 5-nitro-2-furancarboxylamides that show potent trypanocidal activity, 1000-fold more potent than nifurtimox against in vitro Trypanosoma brucei with very low cytotoxicity against human HeLa cells. More importantly, the most potent analogue showed very limited cross-resistance to nifurtimox-resistant cells and vice versa. This implies that our novel, relatively easy to synthesize and therefore cheap, 5-nitro-2-furancarboxylamides are targeting a different, but still essential, biochemical process to those targeted by nifurtimox or its metabolites in the parasites. The significant increase in potency (smaller dose probably required) has the potential for greatly reducing unwanted side effects and also reducing the likelihood of drug resistance. Collectively, these findings have important implications for the future therapeutic treatment of African sleeping sickness.

Endomorphisms of Fraïssé limits and automorphism groups of algebraically closed relational structures

McPhee, Jillian Dawn — 2012-11-30T00:00:00Z

Abstract: Let Ω be the Fraïssé limit of a class of relational structures. We seek to answer the following semigroup theoretic question about Ω. What are the group H-classes, i.e. the maximal subgroups, of End(Ω)? Fraïssé limits for which we answer this question include the random graph R, the random directed graph D, the random tournament T, the random bipartite graph B, Henson's graphs G[subscript n] (for n greater or equal to 3) and the total order Q. The maximal subgroups of End(Ω) are closely connected to the automorphism groups of the relational structures induced by the images of idempotents from End(Ω). It has been shown that the relational structure induced by the image of an idempotent from End(Ω) is algebraically closed. Accordingly, we investigate which groups can be realised as the automorphism group of an algebraically closed relational structure in order to determine the maximal subgroups of End(Ω) in each case. In particular, we show that if Γ is a countable graph and Ω = R,D,B, then there exist 2[superscript aleph-naught] maximal subgroups of End(Ω) which are isomorphic to Aut(Γ). Additionally, we provide a complete description of the subsets of Q which are the image of an idempotent from End(Q). We call these subsets retracts of Q and show that if Ω is a total order and f is an embedding of Ω into Q such that im f is a retract of Q, then there exist 2[superscript aleph-naught] maximal subgroups of End(Q) isomorphic to Aut(Ω). We also show that any countable maximal subgroup of End(Q) must be isomorphic to Zⁿ for some natural number n. As a consequence of the methods developed, we are also able to show that when Ω = R,D,B,Q there exist 2[superscript aleph-naught] regular D-classes of End(Ω) and when Ω = R,D,B there exist 2[superscript aleph-naught] J-classes of End(Ω). Additionally we show that if Ω = R,D then all regular D-classes contain 2[superscript aleph-naught] group H-classes. On the other hand, we show that when Ω = B,Q there exist regular D-classes which contain countably many group H-classes.

Fast silencing reveals a lost role for reciprocal inhibition in locomotion

Moult, Peter Robert — 2013-01-09T00:00:00Z

Abstract: Summary Alternating contractions of antagonistic muscle groups during locomotion are generated by spinal “half-center” networks coupled in antiphase by reciprocal inhibition. It is widely thought that reciprocal inhibition only coordinates the activity of these muscles. We have devised two methods to rapidly and selectively silence neurons on just one side of Xenopus tadpole spinal cord and hindbrain, which generate swimming rhythms. Silencing activity on one side led to rapid cessation of activity on the other side. Analyses reveal that this resulted from the depression of reciprocal inhibition connecting the two sides. Although critical neurons in intact tadpoles are capable of pacemaker firing individually, an effect that could support motor rhythms without inhibition, the swimming network itself requires ∼23 min to regain rhythmic activity after blocking inhibition pharmacologically, implying some homeostatic changes. We conclude therefore that reciprocal inhibition is critical for the generation of normal locomotor rhythm.

Active slow light in silicon photonic crystals : tunable delay and Raman gain

Rey, Isabella H. — 2012-11-30T00:00:00Z

Abstract: In the past decade, great research effort was inspired by the need to realise active optical functionalities in silicon, in order to develop the full potential of silicon as a photonic platform. In this thesis we explore the possibility of achieving tunable delay and optical gain in silicon, taking advantage of the unique dispersion capabilities of photonic crystals. To achieve tunable optical delay, we adopt a wavelength conversion and group velocity dispersion approach in a miniaturised engineered slow light photonic crystal waveguide. Our scheme is equivalent to a two-step indirect photonic transition, involving an alteration of both the frequency and momentum of an optical pulse, where the former is modiﬁed by the adiabatic tuning possibilities enabled by slow light. We apply this concept in a demonstration of continuous tunability of the delay of pulses, and exploit the ultrafast nature of the tuning process to demonstrate manipulation of a single pulse in a train of two pulses. In order to address the propagation loss intrinsic to slow light structures, with a prospect for improving the performance of the tunable delay device, we also investigate the nonlinear effect of stimulated Raman scattering as a means of introducing optical gain in silicon. We study the influence of slowdown factors and pump-induced losses on the evolution of a signal beam along the waveguide, as well as the role of linear propagation loss and mode profile changes typical of realistic photonic crystal structures. We then describe the work conducted for the experimental demonstration of such effect and its enhancement due to slow light. Finally, as the Raman nonlinearity may become useful also in photonic crystal nanocavities, which confine light in very small volumes, we discuss the design and realisation of structures which satisfy the basic requirements on the resonant modes needed for improving Raman scattering.

The role of endosymbionts in the evolution of haploid-male genetic systems in scale insects (Coccoidea)

Ross, Laura — 2012-05-01T00:00:00Z

Abstract: There is an extraordinary diversity in genetic systems across species, but this variation remains poorly understood. In part, this is because the mechanisms responsible for transitions between systems are often unknown. A recent hypothesis has suggested that conflict between hosts and endosymbiotic microorganisms over transmission could drive the transition from diplodiploidy to systems with male haploidy (haplodiploidy, including arrhenotoky and paternal genome elimination [PGE]). Here, we present the first formal test of this idea with a comparative analysis across scale insects (Hemiptera: Coccoidea). Scale insects are renowned for their large variation in genetic systems, and multiple transitions between diplodiploidy and haplodiploidy have taken place within this group. Additionally, most species rely on endosymbiotic microorganisms to provide them with essential nutrients lacking in their diet. We show that species harboring endosymbionts are indeed more likely to have a genetic system with male haploidy, which supports the hypothesis that endosymbionts might have played a role in the transition to haplodiploidy. We also extend our analysis to consider the relationship between endosymbiont presence and transitions to parthenogenesis. Although in scale insects there is no such overall association, species harboring eukaryote endosymbionts were more likely to be parthenogenetic than those with bacterial symbionts. These results support the idea that intergenomic conflict can drive the evolution of novel genetic systems and affect host reproduction.

Functional analysis of Leishmania cyclopropane fatty acid synthetase

Oyola, Samuel O. — 2012-12-10T00:00:00Z

Abstract: The single gene encoding cyclopropane fatty acid synthetase (CFAS) is present in Leishmania infantum, L. mexicana and L. braziliensis but absent from L. major, a causative agent of cutaneous leishmaniasis. In L. infantum, usually causative agent of visceral leishmaniasis, the CFAS gene is transcribed in both insect (extracellular) and host (intracellular) stages of the parasite life cycle. Tagged CFAS protein is stably detected in intracellular L. infantum but only during the early log phase of extracellular growth, when it shows partial localisation to the endoplasmic reticulum. Lipid analyses of L. infantum wild type, CFAS null and complemented parasites detect a low abundance CFAS-dependent C19 Delta fatty acid, characteristic of a cyclopropanated species, in wild type and add-back cells. Sub-cellular fractionation studies locate the C19 Delta fatty acid to both ER and plasma membrane-enriched fractions. This fatty acid is not detectable in wild type L. major, although expression of the L. infantum CFAS gene in L. major generates cyclopropanated fatty acids, indicating that the substrate for this modification is present in L. major, despite the absence of the modifying enzyme. Loss of the L. infantum CFAS gene does not affect extracellular parasite growth, phagocytosis or early survival in macrophages. However, while endocytosis is also unaffected in the extracellular CFAS nulls, membrane transporter activity is defective and the null parasites are more resistant to oxidative stress. Following infection in vivo, L. infantum CFAS nulls exhibit lower parasite burdens in both the liver and spleen of susceptible hosts but it has not been possible to complement this phenotype, suggesting that loss of C19 Delta fatty acid may lead to irreversible changes in cell physiology that cannot be rescued by re-expression. Aberrant cyclopropanation in L. major decreases parasite virulence but does not influence parasite tissue tropism.

New phosphine-diamine and phosphine-amino-alcohol tridentate ligands for ruthenium catalysed enantioselective hydrogenation of ketones and a concise lactone synthesis enabled by asymmetric reduction of cyano-ketones

Fuentes García, José Antonio — 2012-12-10T00:00:00Z

Abstract: Enantioselective hydrogenation of ketones is a key reaction in organic chemistry. In the past, we have attempted to deal with some unsolved challenges in this arena by introducing chiral tridentate phosphine-diamine/Ru catalysts. New catalysts and new applications are presented here, including the synthesis of phosphine-amino-alcohol P,N,OH ligands derived from (R,S)-1-amino-2-indanol, (S,S)-1-amino-2-indanol and a new chiral P,N,N ligand derived from (R,R)-1,2-diphenylethylenediamine. Ruthenium pre-catalysts of type [RuCl2(L)(DMSO)] were isolated and then examined in the hydrogenation of ketones. While the new P,N,OH ligand based catalysts are poor, the new P,N,N system gives up to 98% e.e. on substrates that do not react at all with most catalysts. A preliminary attempt at realising a new delta lactone synthesis by organocatalytic Michael addition between acetophenone and acrylonitrile, followed by asymmetric hydrogenation of the nitrile functionalised ketone is challenging in part due to the Michael addition chemistry, but also since Noyori pressure hydrogenation catalysts gave massively reduced reactivity relative to their performance for other acetophenone derivatives. The Ru phosphine-diamine system allowed quantitative conversion and around 50% e.e. The product can be converted into a delta lactone by treatment with KOH with complete retention of enantiomeric excess. This approach potentially offers access to this class of chiral molecules in three steps from the extremely cheap building blocks acrylonitrile and methyl-ketones; we encourage researchers to improve on our efforts in this potentially useful but currently flawed process.

The AEROPATH project targeting Pseudomonas aeruginosa : crystallographic studies for assessment of potential targets in early-stage drug discovery

Moynie, Lucile — 2013-01-01T00:00:00Z

Abstract: Bacterial infections are increasingly difficult to treat owing to the spread of antibiotic resistance. A major concern is Gram-negative bacteria, for which the discovery of new antimicrobial drugs has been particularly scarce. In an effort to accelerate early steps in drug discovery, the EU-funded AEROPATH project aims to identify novel targets in the opportunistic pathogen Pseudomonas aeruginosa by applying a multidisciplinary approach encompassing target validation, structural characterization, assay development and hit identification from small-molecule libraries. Here, the strategies used for target selection are described and progress in protein production and structure analysis is reported. Of the 102 selected targets, 84 could be produced in soluble form and the de novo structures of 39 proteins have been determined. The crystal structures of eight of these targets, ranging from hypothetical unknown proteins to metabolic enzymes from different functional classes (PA1645, PA1648, PA2169, PA3770, PA4098, PA4485, PA4992 and PA5259), are reported here. The structural information is expected to provide a firm basis for the improvement of hit compounds identified from fragment-based and high-throughput screening campaigns.

A small-molecule inhibitor of T. gondii motility induces the posttranslational modification of myosin light chain-1 and inhibits myosin motor activity

Heaslip, Aoife T. — 2010-01-15T00:00:00Z

Abstract: Toxoplasma gondii is an obligate intracellular parasite that enters cells by a process of active penetration. Host cell penetration and parasite motility are driven by a myosin motor complex consisting of four known proteins: TgMyoA, an unconventional Class XIV myosin; TgMLC1, a myosin light chain; and two membrane-associated proteins, TgGAP45 and TgGAP50. Little is known about how the activity of the myosin motor complex is regulated. Here, we show that treatment of parasites with a recently identified small-molecule inhibitor of invasion and motility results in a rapid and irreversible change in the electrophoretic mobility of TgMLC1. While the precise nature of the TgMLC1 modification has not yet been established, it was mapped to the peptide Val46-Arg59. To determine if the TgMLC1 modification is responsible for the motility defect observed in parasites after compound treatment, the activity of myosin motor complexes from control and compound-treated parasites was compared in an in vitro motility assay. TgMyoA motor complexes containing the modified TgMLC1 showed significantly decreased motor activity compared to control complexes. This change in motor activity likely accounts for the motility defects seen in the parasites after compound treatment and provides the first evidence, in any species, that the mechanical activity of Class XIV myosins can be modulated by posttranslational modifications to their associated light chains.

A family of spatial biodiversity measures based on graphs

Rajala, T — 2012-12-01T00:00:00Z

Abstract: While much research in ecology has focused on spatially explicit modelling as well as on measures of biodiversity, the concept of spatial (or local) biodiversity has been discussed very little. This paper generalises existing measures of spatial biodiversity and introduces a family of spatial biodiversity measures by flexibly defining the notion of the individuals’ neighbourhood within the framework of graphs associated to a spatial point pattern. We consider two non-independent aspects of spatial biodiversity, scattering, i.e. the spatial arrangement of the individuals in the study area and exposure, the local diversity in an individual’s neighbourhood. A simulation study reveals that measures based on the most commonly used neigh-bourhood defined by the geometric graph do not distinguish well between scattering and exposure. This problem is much less pronounced when other graphs are used. In an analysis of the spatial diversity in a rainforest, the results based on the geometric graph have been shown to spuriously indicate a decrease in spatial biodiversity when no such trend was detected by the other types of neighbourhoods. We also show that the choice neighbourhood markedly impacts on the classification of species according to how strongly and in what way different species spatially structure species diversity. Clearly, in an analysis of spatial or local diversity an appropriate choice of local neighbourhood is crucial in particular in terms of the biological interpretation of the results. Due to its general definition, the approach discussed here offers the necessary flexibility that allows suitable and varying neighbourhood structures to be chosen.

Public information use in ninespine sticklebacks (Pungitius pungitius) : isolating the mechanisms using computer-animated stimuli

Chouinard-Thuly, Laura — 2012-01-01T00:00:00Z

Abstract: Many 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.

The development of free-swimming in Xenopus laevis larvae

Scott, Nicholas W. — 2012-11-30T00:00:00Z

Abstract: In Xenopus laevis frog tadpoles, highly self-motive, free-swimming behaviour emerges at the onset of feeding. This is in contrast to the earlier post-hatched larval form, which is capable of escape swimming when stimulated, but normally lies dormant. This developmental transition in behaviour has been documented here and studied in a semi-intact preparation developed to examine the motor output from larvae at the onset of filter feeding. There is a progressive increase in spontaneous motor activity during this period, where spontaneous fictive swimming occurs in episodes of variable duration but with significantly larger burst durations. This spontaneous activity persists after removal of both the fore- and midbrain, but is absent in spinalised preparations. The spontaneous activity is similar to NMDA (100µM) induced rhythm but shows greater periodic variability in the frequency and occurrence of swimming activity. The activity is not dependent on inhibitory synaptic transmission, but is under the control of central GABAergic restraint, as blocking this inhibition with bicuculine (10µM) increased spontaneous locomotor activity. This is distinct to the role of glycinergic inhibition which influences the character of the ventral root bursts, as strychnine (5µM) caused an initial increase in frequency before bursts were synchronised on both the left and right sides, but not the presence of spontaneous activity. However, activity is abolished by the persistent sodium current blocker riluzole (5µM) and enhanced by veratridine (90nM) which potentiates the current, which may suggest that it originates in neurons with pacemaker-like properties - possibly within the hindbrain. Evidence is also provided which shows that the neuromodulatory gas nitric oxide becomes an excitatory modulator of the Xenopus swimming network at the onset of a free-swimming existence, switching from having a global inhibitory role on locomotion in early larval life. The nitric oxide donor DEA/NO (200µM) increased spontaneous fictive swimming in the semi-intact preparation. In contrast, the nitric oxide synthase inhibitor L-NAME combined with PTIO, which sequesters nitric oxide, decreased spontaneous fictive swimming. It is proposed that the emergence of this rhythmic, spontaneous motor activity parallels the increase in swimming at the onset of feeding, suggesting a direct behavioural role for spontaneous network activity in the developing animal.

Trauma and representation in women's diaries of the Second World War

Richardson, Margaret Ravenel — 2012-11-30T00:00:00Z

Abstract: As a transnational contribution to the study of life-writing and to the understanding of women’s war experiences, ‘Trauma and Representation in Women’s Diaries of the Second World War’ examines women’s war diaries from the point of view of trauma studies. It provides new readings of established texts, such as Frances Partridge’s A Pacifist’s War and Etty Hillesum’s An Interrupted Life, alongside previously unexamined archival diaries and several recently published diaries that have received little critical attention to date. Through close reading, it analyses how traumatic registers, ranging from mild to severe, manifest in both the genesis and subject matter of women’s diaries. The Introduction discusses the post-war cultural imperatives that have worked to repress women’s accounts of the Second World War, particularly those which describe devastation in the domestic sphere. It situates diary writing contextually within the field of autobiographical writing, exploring the characteristics of this contested genre and questioning the possibilities it opens up for the conveyance of traumatic experience. Finally, it provides a brief historiography of trauma studies, focusing on the complicated relationship between trauma and modern warfare and the difficulties traumatic experience poses for testimony. In the ensuing chapters, my analyses demonstrate the various ways war trauma manifests in women’s diaries. Chapter One examines the physiological and psychological costs of repeated exposure to violent situations such as bomb raids and rape through a combination of psychoanalytic and neurobiological discourses on trauma. Chapter Two discusses diaries that were kept at a relative distance from violent conflict, exploring women’s affective responses to the changes in their lives that occurred during wartime through theories of depression and melancholia. Finally, Chapter Three constitutes a final analysis of the relationship between trauma and representation, analysing women’s descriptions of both the physical and societal abjection that proliferated towards the end of the war.

Scripts and politics in modern Central Europe

Kamusella, Tomasz Dominik — 2012-01-01T00:00:00Z

Abstract: At present two scripts are employed in Central Europe, Latin and Cyrillic, or three,if we include Greece in the region. In this article I set out to problematise this oversimplisticpicture drawing at examples from the past and pointing to various politicaland identificational uses of scripts today. Until the mid-20th century, also other scripts(and different types of the Latin and Cyrillic script, for that matter) were used forofficial purposes and in book production, namely Arabic, Armenian, Church Cyrillic,Gothic and Hebrew. In addition, Glagolitic and Runes (both Nordic and Hungarian)were sometimes recalled for ideological reasons. Each of these scripts was used forwriting in numerous languages. Initially, script choices were dictated by religion(Latin letters for Western Christianity, Church Cyrillic for Slavophone OrthodoxChristians, or the Arabic writing system for Muslims), usually connected to a holybook in an ecclesiastical language committed to parchment in a specific script. Whenvernaculars began to make an appearance in writing, especially in the 16th centuryand later, their users stuck to the scripts of their holy books. Two factors, the processof building ethnolinguistically defined nation-states and changing ideas about whatmodernity should be about in the sphere of culture, radically limited the number ofscripts in official and de facto use. Only in Bosnia-Hercegovina, Kosovo, Macedonia,Moldova, Montenegro and Ukraine are two scripts in official use, to varying degrees inthe different countries. The European Union already uses three official scripts, Cyrillic,Greek and Latin; if its actions follow its words and it admits some or all of thesestates to membership, it stands a good chance of reviving the tradition of Europeanmultiscripturality, alongside its legally enshrined commitment to multilingualism.