http://hdl.handle.net/10023/878 2013-05-21T15:26:23Z http://hdl.handle.net/10023/3541 2010-09-01T00:00:00Z Riccobono, Rossella Maria http://hdl.handle.net/10023/3540 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. 2012-11-21T00:00:00Z Bentley, Bernard Pierre Emile 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. http://hdl.handle.net/10023/3539 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. 2013-06-01T00:00:00Z Tran, Chuong Van Yu, Xinwei Blackbourn, Luke Austen Kazimierz 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. http://hdl.handle.net/10023/3538 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. 2013-07-01T00:00:00Z Tran, Chuong Van Yu, Xinwei Zhai, Zhichun 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. http://hdl.handle.net/10023/3537 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? 2013-01-01T00:00:00Z Roscoe, Philip John Chillas, Shiona Allison 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? http://hdl.handle.net/10023/3536 2013-09-01T00:00:00Z Meyer, Karen Alison Mackay, Duncan Hendry van Ballegooijen, Aad Parnell, Clare Elizabeth http://hdl.handle.net/10023/3535 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. 2010-01-27T00:00:00Z Baily, Charles Finkelstein, Noah D. 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. http://hdl.handle.net/10023/3534 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. 2010-09-16T00:00:00Z Baily, Charles Finkelstein, Noah D. 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. http://hdl.handle.net/10023/3533 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. 2013-05-09T00:00:00Z Kosmeier, Sebastian De Luca, Anna Chiara Zolotovskaya, Svetlana Di Falco, Andrea Dholakia, Kishan Mazilu, Michael 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. http://hdl.handle.net/10023/3530 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. 2013-01-01T00:00:00Z Baily, Charles Dubson, Michael Pollock, Steven J. 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. http://hdl.handle.net/10023/3529 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. 2009-03-23T00:00:00Z Baily, Charles Finkelstein, Noah D. 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. http://hdl.handle.net/10023/3527 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. 2012-02-01T00:00:00Z Baily, Charles Finkelstein, Noah D. 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. http://hdl.handle.net/10023/3526 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. 2010-01-01T00:00:00Z Baily, Charles Finkelstein, Noah D. 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. http://hdl.handle.net/10023/3525 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. 2008-01-01T00:00:00Z Baily, Charles Finkelstein, Noah D. 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. http://hdl.handle.net/10023/3524 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. 2009-01-01T00:00:00Z Baily, Charles Finkelstein, Noah D. 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. http://hdl.handle.net/10023/3523 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. 2009-07-01T00:00:00Z Fowler, William 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. http://hdl.handle.net/10023/3522 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. 2012-11-26T00:00:00Z Ferguson, Ronnie 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. http://hdl.handle.net/10023/3521 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. 2011-01-01T00:00:00Z Duncan, Derek Egerton 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. http://hdl.handle.net/10023/3520 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. 2009-01-01T00:00:00Z Culpin, David John 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. http://hdl.handle.net/10023/3519 2011-11-01T00:00:00Z Bowd, Gavin Philip http://hdl.handle.net/10023/3518 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. 2013-02-01T00:00:00Z Nutley, Sandra Margaret Powell, Alison Elizabeth Davies, Huw Talfryn Oakley 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. http://hdl.handle.net/10023/3517 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. 2012-06-01T00:00:00Z Bentley, Michael John 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. http://hdl.handle.net/10023/3516 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. 2013-06-01T00:00:00Z Roscoe, Philip John 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. http://hdl.handle.net/10023/3510 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. 2013-01-23T00:00:00Z Moynie, Lucile Leckie, Stuart M. McMahon, Stephen A. Duthie, Fraser G. Koehnke, Alessa Taylor, James W. Alphey, Magnus S. Brenk, Ruth Smith, Andrew D. Naismith, James H. 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. http://hdl.handle.net/10023/3509 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. 2013-01-01T00:00:00Z Collett, Christopher J. Massey, Richard S. Maguire, Oliver R. Batsanov, Andrei S. O'Donoghue, AnnMarie C. Smith, Andrew D. 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. http://hdl.handle.net/10023/3508 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. 2013-01-01T00:00:00Z Hua, Guoxiong Slawin, Alexandra M. Z. Randall, Rebecca A. M. Cordes, David B. Crawford, Luke Buehl, Michael Woollins, J. Derek 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. http://hdl.handle.net/10023/3507 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. 2012-09-01T00:00:00Z Partzsch, Henriette Anna Margarete 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. http://hdl.handle.net/10023/3506 2007-10-01T00:00:00Z Andrews, Frances http://hdl.handle.net/10023/3505 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. 2010-12-01T00:00:00Z Andrews, Frances 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. http://hdl.handle.net/10023/3504 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. 2013-01-01T00:00:00Z Lim, Ji-Hyun Iggo, Richard D Barker, Daniel 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. http://hdl.handle.net/10023/3503 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. 2013-01-01T00:00:00Z Nightingale, Peter Gent, Ian Philip Jefferson, Christopher Anthony Miguel, Ian James 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. http://hdl.handle.net/10023/3502 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. 2012-11-01T00:00:00Z Okumura, Yuko Schneider, David Deser, Clara Wilson, Rob 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. http://hdl.handle.net/10023/3501 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. 2012-05-04T00:00:00Z Valdivia, Nelson Gollety, Claire Migne, Aline Davoult, Dominique Molis, Marcus 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. http://hdl.handle.net/10023/3497 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. 2013-04-01T00:00:00Z La Manna, Manfredi M A 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. http://hdl.handle.net/10023/3496 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 2013-05-01T00:00:00Z Marques, Tiago A. Thomas, Len Martin, Stephen Mellinger, David Ward, Jessica Moretti, David Harris, Danielle Veronica Tyack, Peter Lloyd 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 http://hdl.handle.net/10023/3495 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. 2013-01-01T00:00:00Z Cochet, Hélène Byrne, Richard William 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. http://hdl.handle.net/10023/3494 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). 2013-01-01T00:00:00Z King, Ruth Bird, Sheila Overstall, Antony Hay, Gordon Hutchinson, Sharon 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). http://hdl.handle.net/10023/3493 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. 2013-01-01T00:00:00Z Sheikh, Sana Janoff-Bulman, Ronnie 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. http://hdl.handle.net/10023/3492 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. 2012-07-12T00:00:00Z Girelli, Elisabetta 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. http://hdl.handle.net/10023/3489 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. 2001-01-01T00:00:00Z Giardini, M E Guizzetti, G G Bavera, M Lago, P Corti, A Falcone, C Pastore, F 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. http://hdl.handle.net/10023/3488 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] 2012-07-01T00:00:00Z Krstajic, Nikola Brown, C Tom A Dholakia, Kishan Giardini, Mario Ettore 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] http://hdl.handle.net/10023/3487 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 2010-02-15T00:00:00Z Levell, J. W. Giardini, M. E. Samuel, I. D. W. 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 http://hdl.handle.net/10023/3486 2013-01-01T00:00:00Z Nacenta, Miguel Kamber, Yemliha Qiang, Yizhou Kristensson, Per Ola http://hdl.handle.net/10023/3485 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. 2011-01-01T00:00:00Z Whitehead, Claire Eugenie 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. http://hdl.handle.net/10023/3484 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. 2010-07-01T00:00:00Z Evans, David Elwyn 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. http://hdl.handle.net/10023/3483 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]. 2012-01-01T00:00:00Z Macias Garcia, C. Smith, G. Gonzalez Zuarth, C. Graves, J. A. Ritchie, M. G. 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]. http://hdl.handle.net/10023/3481 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. 2012-04-01T00:00:00Z Kemp, Jonathan A Smith, Richard 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. http://hdl.handle.net/10023/3480 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] 2013-04-09T00:00:00Z G. Kirton, P. D. Armour, A. 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. http://hdl.handle.net/10023/3479 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. 2010-10-01T00:00:00Z Brien, C. J. Bailey, R. A. 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. http://hdl.handle.net/10023/3478 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. 2009-12-01T00:00:00Z Brien, C. J. Bailey, R. A. 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. http://hdl.handle.net/10023/3477 2004-05-20T00:00:00Z Richardson, Louise http://hdl.handle.net/10023/3474 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. 2013-04-08T00:00:00Z Moleirinho, Susana Patrick, Calum Tilston-Lunel, Andrew Martin Higginson, JR Angus, Liselotte Antkowiak, Maciej Barnett, Susan Prystowsky, Michael Reynolds, Paul Andrew Gunn-Moore, Frank J 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. http://hdl.handle.net/10023/3473 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. 2012-06-12T00:00:00Z Burgoyne, Robert James 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. http://hdl.handle.net/10023/3472 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. 2011-01-01T00:00:00Z Guillette, Lauren Bloomfiled, Laurie Batty, Emily Dawson, Michael Sturdy, Chris 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. http://hdl.handle.net/10023/3468 2009-08-01T00:00:00Z Halliwell, Francis Stephen http://hdl.handle.net/10023/3467 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. 2011-09-23T00:00:00Z Girelli, Elisabetta 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. http://hdl.handle.net/10023/3466 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. 2013-01-01T00:00:00Z Sachs, Benjamin Alan 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. http://hdl.handle.net/10023/3460 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. 2011-12-01T00:00:00Z Bernatchez, Louis St-Cyr, Jerome Normandeau, Eric Maes, Gregory Als, Thomas Kalujnaia, Svetlana Cramb, Gordon Castonguay, Martin Hansen, Michael 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. http://hdl.handle.net/10023/3459 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. 2013-01-01T00:00:00Z Wilson, David Ian Greig Langston, Rosamund F. Schlesiger, Magdalene I. Wagner, Monica Watanabe, Sakurako Ainge, James Alexander 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. http://hdl.handle.net/10023/3457 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. 2013-03-01T00:00:00Z Manzini, Paola Mariotti, Marco 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. http://hdl.handle.net/10023/3456 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. 2011-11-09T00:00:00Z Williams, Robert Krkošek, Martin Ashe, Erin Branch, Trevor A Clark, Stephen Hammond, Philip Steven Hoyt, Eric Noren, Dawn P Rosen, David Winship, Arliss 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. http://hdl.handle.net/10023/3454 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. 2009-01-01T00:00:00Z Sharples, RJ MacKenzie, Monique Lea Hammond, Philip Steven 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. http://hdl.handle.net/10023/3445 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. 2010-03-01T00:00:00Z Lacey, Claire Leaper, Russell Moscrop, Anna Gillespie, Douglas Michael McLanaghan, Richard Brown, Steve 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. http://hdl.handle.net/10023/3444 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. 2009-07-27T00:00:00Z Nasomjai, Pitak O'Hagan, David Slawin, Alexandra M. Z. 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. http://hdl.handle.net/10023/3443 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. 2009-11-05T00:00:00Z Brunet, Vincent A. Slawin, Alexandra M. Z. O'Hagan, David 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. http://hdl.handle.net/10023/3442 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 2012-02-01T00:00:00Z Lagatsky, A. A. Koopmann, P. Fuhrberg, P. Huber, G. Brown, C. T. A. Sibbett, W. 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 http://hdl.handle.net/10023/3441 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 2012-03-26T00:00:00Z Metzger, N. K. Olle, V. F. Wonfor, A. Penty, R. V. White, I. H. Mazilu, M. Brown, C. T. A. Sibbett, W. 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 http://hdl.handle.net/10023/3440 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. 2013-01-01T00:00:00Z Driessen, Rosalie P. C. Meng, He Suresh, Gorle Shahapure, Rajesh Lanzani, Giovanni Priyakumar, U. Deva White, Malcolm F. Schiessel, Helmut van Noort, John Dame, Remus Th 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. http://hdl.handle.net/10023/3439 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. 2011-05-01T00:00:00Z Richard, Derek J. Cubeddu, Liza Urquhart, Aaron J. Bain, Amanda Bolderson, Emma Menon, Dinoop White, Malcolm F. Khanna, Kum Kum 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. http://hdl.handle.net/10023/3438 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). 2011-03-01T00:00:00Z Richard, Derek J. Savage, Kienan Bolderson, Emma Cubeddu, Liza So, Sairei Ghita, Mihaela Chen, David J. White, Malcolm F. Richard, Kerry Prise, Kevin M. Schettino, Giuseppe Khanna, Kum Kum 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). http://hdl.handle.net/10023/3437 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. 2006-11-01T00:00:00Z McMahon, Stephen Walsh, MA Ching, RTY Carter, Lester Dorward, M Johnson, Kenneth Alan Liu, Huanting Oke, Muse Block Jr, C Kennedy, MW Latiff, AA Cooper, A Taylor, Garry Lindsay White, Malcolm Frederick Naismith, James Henderson 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. http://hdl.handle.net/10023/3434 2009-10-01T00:00:00Z Sachs, Benjamin http://hdl.handle.net/10023/3433 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. 2010-09-01T00:00:00Z Sachs, Benjamin 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. http://hdl.handle.net/10023/3432 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. 2009-12-01T00:00:00Z Stephen, Ian David Law Smith, Miriam Jane Stirrat, Michael Robert Perrett, David Ian 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. http://hdl.handle.net/10023/3431 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. 2009-04-01T00:00:00Z Stephen, Ian David Coetzee, Vinet Law Smith, Miriam Jane Perrett, David Ian 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. http://hdl.handle.net/10023/3430 2013-01-01T00:00:00Z Hawley, Katherine Jane http://hdl.handle.net/10023/3429 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. 2012-09-01T00:00:00Z Bailey, Nathan William Moore, Allen J. 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. http://hdl.handle.net/10023/3428 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. 2012-03-07T00:00:00Z Whitehead, Ross Re, Daniel Xiao, Dengke Ozakinci, Gozde Perrett, David Ian 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. http://hdl.handle.net/10023/3427 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. 2013-01-01T00:00:00Z Dalgarno, Paul Allan Bordello, J Morris, Rhodri St-Pierre, P Dubé, A Samuel, Ifor David William Lafontaine, Daniel Penedo-Esteiro, Juan Carlos 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. http://hdl.handle.net/10023/3426 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 2013-03-21T00:00:00Z Patabendige, Chami Nilasha Kahakachchi Azad, Abul Kalam Connor, Paul Alexander Rolle, Aurélie Irvine, John Thomas Sirr 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. http://hdl.handle.net/10023/3425 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. 2013-01-29T00:00:00Z Lan, Rong Irvine, John T. S. Tao, Shanwen 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. http://hdl.handle.net/10023/3424 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. 2013-01-01T00:00:00Z Buehl, Michael Knight, Fergus Ross Kristkova, Anezka Ondik, Irina Malkina, Olga Randall, Rebecca Amy Michele Slawin, Alexandra Martha Zoya Woollins, J Derek 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. http://hdl.handle.net/10023/3423 2012-10-01T00:00:00Z Surgenor, Brian A. Buehl, Michael Slawin, Alexandra M. Z. Woollins, J. Derek Kilian, Petr http://hdl.handle.net/10023/3422 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. 2013-01-01T00:00:00Z Konrad, Tina Maria Durrani, Jamie Cobley, Christopher J. Clarke, Matt 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. http://hdl.handle.net/10023/3420 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) 2009-11-01T00:00:00Z Makiyi, Edward F. Frade, Raquel F. M. Lebl, Tomas Jaffray, Ellis G. Cobb, Susan E. Harvey, Alan L. Slawin, Alexandra M. Z. Hay, Ronald T. Westwood, Nicholas J. 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) http://hdl.handle.net/10023/3418 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. 2013-01-01T00:00:00Z Senay, Ozge Sutherland, Alan 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. http://hdl.handle.net/10023/3417 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. 2009-02-01T00:00:00Z Roscoe, Philip Howorth, Carole 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. http://hdl.handle.net/10023/3415 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. 2010-01-01T00:00:00Z Sachs, Benjamin Alan 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. http://hdl.handle.net/10023/3408 Description: Responce to Helena Watson, Aid, aid everywhere but still not a drop in the sink. BMJ 2009; 338: a3136 2009-01-26T00:00:00Z O'Hare, Bernadette Ann-Marie http://hdl.handle.net/10023/3406 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. 2013-03-01T00:00:00Z Davies, Huw Talfryn Oakley Mannion, Russell 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. http://hdl.handle.net/10023/3402 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. 2012-01-01T00:00:00Z Graham, Elspeth Jordan, Lucy Yeoh, Brenda Lam, Theodora Asis, Maruja kamdi, Su 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. http://hdl.handle.net/10023/3401 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. 2013-05-15T00:00:00Z Tran, Chuong Van Yu, Xinwei Zhai, Zhichun 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. http://hdl.handle.net/10023/3400 Abstract: Review of 'Unmasking the Entrepreneur' by Campbell Jones and Andre Spicer, Edward Elgar, 2009 2011-08-01T00:00:00Z Roscoe, Philip John Review of 'Unmasking the Entrepreneur' by Campbell Jones and Andre Spicer, Edward Elgar, 2009 http://hdl.handle.net/10023/3399 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. 2010-01-08T00:00:00Z Hill, Antony A. Carr, Magda 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. http://hdl.handle.net/10023/3398 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. 2010-09-01T00:00:00Z Hill, A A Carr, Magda 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. http://hdl.handle.net/10023/3397 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. 2012-01-01T00:00:00Z Carr, Magda King, Stuart Edward Dritschel, David Gerard 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. http://hdl.handle.net/10023/3396 2009-02-01T00:00:00Z Fructus, D Carr, Magda Grue, J Jensen, A Davies, P A http://hdl.handle.net/10023/3395 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. 2008-12-01T00:00:00Z Carr, Magda Fructus, D Grue, J Jensen, A Davies, P A 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. http://hdl.handle.net/10023/3394 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. 2013-01-01T00:00:00Z Dawson, Steve Northridge, Simon Patrick Waples, Danielle Read, Andrew 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. http://hdl.handle.net/10023/3393 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. 2013-05-01T00:00:00Z Sheikh, Sana Botindari, Lucia White, Emma 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. http://hdl.handle.net/10023/3392 2007-08-01T00:00:00Z Halliwell, Francis Stephen http://hdl.handle.net/10023/3391 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. 2013-02-01T00:00:00Z Bailey, Nathan William Veltsos, Paris Tan, Yew-Foon Millar, A. Harvey Ritchie, Michael Gordon Simmons, Leigh W. 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. http://hdl.handle.net/10023/3385 2013-01-01T00:00:00Z Kamusella, Tomasz Dominik http://hdl.handle.net/10023/3384 2012-01-01T00:00:00Z Halliwell, Francis Stephen http://hdl.handle.net/10023/3383 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. 2010-09-01T00:00:00Z Mitchell, James David Morayne, Michal Peresse, Yann Hamon Quick, Martyn 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. http://hdl.handle.net/10023/3382 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. 2010-09-01T00:00:00Z Campbell, Martin 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. http://hdl.handle.net/10023/3381 Description: Special Issue: Safeguarding adults at risk of harm in Scotland. 2012-01-01T00:00:00Z Campbell, Martin Penhale, Bridget http://hdl.handle.net/10023/3380 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. 2010-03-01T00:00:00Z Campbell, Martin Martin, M 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. http://hdl.handle.net/10023/3379 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. 2012-01-01T00:00:00Z Campbell, Martin McCue, Michael 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. http://hdl.handle.net/10023/3378 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. 2012-08-06T00:00:00Z Campbell, Martin Chamberlin, Dionne 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. http://hdl.handle.net/10023/3377 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. 2011-10-01T00:00:00Z Tran, Chuong V. Blackbourn, Luke A. K. Scott, Richard K. 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. http://hdl.handle.net/10023/3376 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. 2008-04-19T00:00:00Z Finch, Adrian A. Allison, Nicola 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. http://hdl.handle.net/10023/3375 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. 2007-06-01T00:00:00Z Campbell, Martin 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. http://hdl.handle.net/10023/3374 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. 2010-04-01T00:00:00Z Jelinska, Clare Petrovic-Stojanovska, Biljana Ingledew, W John White, Malcolm F. 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. http://hdl.handle.net/10023/3373 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. 2013-02-01T00:00:00Z Bareford, Michael Hood, Alan Browning, Philippa 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. http://hdl.handle.net/10023/3370 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. 2012-09-01T00:00:00Z Arthun, Marius Nicholls, Keith Makinson, Keith Fedak, Mike Boehme, Lars 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. http://hdl.handle.net/10023/3366 2006-01-01T00:00:00Z San Roman, Gustavo Francisco http://hdl.handle.net/10023/3364 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. 2013-01-01T00:00:00Z Illian, Janine Baerbel Martino, Sara Sørbye, Sigrunn H. Gallego-Fernández, Juan B. Zunzunegui, Maria Esquivias, M. Paz Travis, Justin M. 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. http://hdl.handle.net/10023/3363 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. 2012-04-01T00:00:00Z Morrissey, Michael Blair Walling, Craig Wilson, Alastair Pemberton, Josephine Clutton-Brock, Tim Kruuk, Loeske 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. http://hdl.handle.net/10023/3361 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. 2013-04-22T00:00:00Z King, Stephanie Laura Sayigh, Laela Wells, Randall Fellner, Wendi Janik, Vincent M. 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. http://hdl.handle.net/10023/3359 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. 2013-02-14T00:00:00Z Zhou, Linna Stewart, Gavin Rideau, Emeline Westwood, Nicholas James Smith, Terry K 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. http://hdl.handle.net/10023/3357 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. 2013-01-09T00:00:00Z Moult, Peter Robert Cottrell, Glen Alfred Li, Wenchang 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. http://hdl.handle.net/10023/3355 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. 2012-05-01T00:00:00Z Ross, Laura Shuker, David M. Normark, Benjamin B. Pen, Ido 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. http://hdl.handle.net/10023/3354 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. 2012-12-10T00:00:00Z Oyola, Samuel O. Evans, Krystal J. Smith, Terry K. Smith, Barbara A. Hilley, James D. Mottram, Jeremy C. Kaye, Paul M. Smith, Deborah F. 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. http://hdl.handle.net/10023/3353 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. 2012-12-10T00:00:00Z Fuentes García, José Antonio Phillips, Scott D. Clarke, Matthew L. 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. http://hdl.handle.net/10023/3352 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. 2013-01-01T00:00:00Z Moynie, Lucile Schnell, Robert McMahon, Stephen A. Sandalova, Tatyana Abdelli Boulkeroua, Wassila Schmidberger, Jason W. Alphey, Magnus Cukier, Cyprian Duthie, Fraser Kopec, Jolanta Liu, Huanting Jacewicz, Agata Hunter, William N. Naismith, James H. Schneider, Gunter 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. http://hdl.handle.net/10023/3351 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. 2010-01-15T00:00:00Z Heaslip, Aoife T. Leung, Jacqueline M. Carey, Kimberly L. Catti, Federica Warshaw, David M. Westwood, Nicholas J. Ballif, Bryan A. Ward, Gary E. 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. http://hdl.handle.net/10023/3350 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. 2012-12-01T00:00:00Z Rajala, T Illian, Janine Baerbel 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. http://hdl.handle.net/10023/3346 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. 2012-01-01T00:00:00Z Kamusella, Tomasz Dominik 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. http://hdl.handle.net/10023/3345 Abstract: Atlantic minke whales are important predators in the Barents Sea ecosystem; capelin Mallotus villosus, krill Thysanoessa sp. and Meganyctephanes norvegica and herring Clupea harengus are their major prey. Their consumption of commercial species may present an economic problem for the local fishery. In order to estimate this consumption and understand the potential consequences for prey dynamics, it is essential to determine the multispecies functional response of the whales. The parameterisation of a functional response requires measurements of consumption rates and prey availability. In this localised study, undigested stomach contents were used to assess the amount of each prey that had been consumed immediately prior to capture. To determine the availability of prey to the whales, standard acoustic surveys were run in the same area within 2 d of the capture of the whales. The spatial distribution of prey was modelled using generalised additive models (GAMs). In order to generate a measure of prey availability and the uncertainty in this value, a simple model was assumed for whale movement, and prey abundance was sampled over space according to a Gaussian kernel. A multispecies functional response (MSFR) model was then fitted to the consumption and prey availability data using Bayesian methods. Simple simulations, based on the fitted MSFR, indicate that minke whales may deplete local capelin aggregations at small spatial scales. This is the first time that a multispecies functional response has been fitted for a cetacean predator, and the methods outlined here may prove useful for modelling marine mammal-fish interactions in other systems. 2007-07-01T00:00:00Z Smout, Sophie Caroline Lindstrom, Ulf Atlantic minke whales are important predators in the Barents Sea ecosystem; capelin Mallotus villosus, krill Thysanoessa sp. and Meganyctephanes norvegica and herring Clupea harengus are their major prey. Their consumption of commercial species may present an economic problem for the local fishery. In order to estimate this consumption and understand the potential consequences for prey dynamics, it is essential to determine the multispecies functional response of the whales. The parameterisation of a functional response requires measurements of consumption rates and prey availability. In this localised study, undigested stomach contents were used to assess the amount of each prey that had been consumed immediately prior to capture. To determine the availability of prey to the whales, standard acoustic surveys were run in the same area within 2 d of the capture of the whales. The spatial distribution of prey was modelled using generalised additive models (GAMs). In order to generate a measure of prey availability and the uncertainty in this value, a simple model was assumed for whale movement, and prey abundance was sampled over space according to a Gaussian kernel. A multispecies functional response (MSFR) model was then fitted to the consumption and prey availability data using Bayesian methods. Simple simulations, based on the fitted MSFR, indicate that minke whales may deplete local capelin aggregations at small spatial scales. This is the first time that a multispecies functional response has been fitted for a cetacean predator, and the methods outlined here may prove useful for modelling marine mammal-fish interactions in other systems. http://hdl.handle.net/10023/3344 Abstract: In mark-recapture studies, various techniques can be used to uniquely identify individual animals, such as ringing, tagging or photo-identification using natural markings. In some long-term studies more than one type of marking procedure may be implemented during the study period. In these circumstances, ignoring the different mark types can produce biased survival estimates since the assumption that the different mark types are equally catchable (homogeneous capture probability across mark types) may be incorrect.We implement an integrated approach where we simultaneously analyse data obtained using three different marking techniques, assuming that animals can be cross-classified across the different mark types. We discriminate between competing models using the AIC statistic. This technique also allows us to estimate both relative mark-loss probabilities and relative recapture efficiency rates for the different marking methods.We initially perform a simulation study to explore the different biases that can be introduced if we assume a homogeneous recapture probability over mark type, before applying the method to a real dataset. We make use of data obtained from an intensive long-term observational study of UK female grey seals (Halichoerus grypus) at a single breeding colony, where three different methods are used to identify individuals within a single study: branding, tagging and photo-identification based on seal coat pattern or pelage. 2011-06-01T00:00:00Z Smout, Sophie Caroline King, Ruth Pomeroy, Patrick In mark-recapture studies, various techniques can be used to uniquely identify individual animals, such as ringing, tagging or photo-identification using natural markings. In some long-term studies more than one type of marking procedure may be implemented during the study period. In these circumstances, ignoring the different mark types can produce biased survival estimates since the assumption that the different mark types are equally catchable (homogeneous capture probability across mark types) may be incorrect.We implement an integrated approach where we simultaneously analyse data obtained using three different marking techniques, assuming that animals can be cross-classified across the different mark types. We discriminate between competing models using the AIC statistic. This technique also allows us to estimate both relative mark-loss probabilities and relative recapture efficiency rates for the different marking methods.We initially perform a simulation study to explore the different biases that can be introduced if we assume a homogeneous recapture probability over mark type, before applying the method to a real dataset. We make use of data obtained from an intensive long-term observational study of UK female grey seals (Halichoerus grypus) at a single breeding colony, where three different methods are used to identify individuals within a single study: branding, tagging and photo-identification based on seal coat pattern or pelage. http://hdl.handle.net/10023/3343 Abstract: Whole genome duplication (WGD) was experienced twice by the vertebrate ancestor (2 rounds; 2R), again by the teleost fish ancestor (3R) and most recently in certain teleost lineages (4R). Consequently, vertebrate gene families are often expanded in 3R and 4R genomes. Arguably, many types of ‘functional divergence’ present across 2R gene families will exceed that between 3R/4R paralogues of genes comprising 2R families. Accordingly, 4R offers a form of replication of 2R. Examining if this concept has implications for molecular evolutionary research, we studied insulin-like growth factor (IGF) binding proteins (IGFBPs), whose six 2R family members carry IGF hormones and regulate interactions between IGFs and IGF1-receptors (IGF1Rs). Using phylogenomic approaches, we resolved the complete IGFBP repertoire of 4R-derived salmonid fishes (nineteen genes; thirteen more than human) and established evolutionary relationships/nomenclature with respect to WGDs. Traits central to IGFBP action were determined for all genes, including atomic interactions in IGFBP-IGF1/IGF2 complexes regulating IGF-IGF1R binding. Using statistical methods, we demonstrate that attributes of these protein interfaces are overwhelming a product of 2R IGFBP family membership, explain 49-68% of variation in IGFBP mRNA concentration in several different tissues and strongly predict the strength and direction of IGFBP transcriptional regulation under differing nutritional-states. The results support a model where vertebrate IGFBP family members evolved divergent structural attributes to provide distinct competition for IGFs with IGF1Rs, pre-disposing different functions in the regulation of IGF-signaling. Evolution of gene expression acted to ensure the appropriate physiological production of IGFBPs according to their structural specializations, leading to optimal IGF-signaling according to nutritional-status and the endocrine/local mode of action. This study demonstrates that relatively recent gene family expansion can facilitate inference of functional evolution within ancient genetic systems. Description: This work was supported by the Marine Alliance for Science and Technology for Scotland pooling initiative, funded by the Scottish Funding Council (grant number HR09011) and contributing institutions. 2013-01-01T00:00:00Z MacQueen, Daniel John Garcia de la Serrana Castillo, Daniel Johnston, Ian Alistair Whole genome duplication (WGD) was experienced twice by the vertebrate ancestor (2 rounds; 2R), again by the teleost fish ancestor (3R) and most recently in certain teleost lineages (4R). Consequently, vertebrate gene families are often expanded in 3R and 4R genomes. Arguably, many types of ‘functional divergence’ present across 2R gene families will exceed that between 3R/4R paralogues of genes comprising 2R families. Accordingly, 4R offers a form of replication of 2R. Examining if this concept has implications for molecular evolutionary research, we studied insulin-like growth factor (IGF) binding proteins (IGFBPs), whose six 2R family members carry IGF hormones and regulate interactions between IGFs and IGF1-receptors (IGF1Rs). Using phylogenomic approaches, we resolved the complete IGFBP repertoire of 4R-derived salmonid fishes (nineteen genes; thirteen more than human) and established evolutionary relationships/nomenclature with respect to WGDs. Traits central to IGFBP action were determined for all genes, including atomic interactions in IGFBP-IGF1/IGF2 complexes regulating IGF-IGF1R binding. Using statistical methods, we demonstrate that attributes of these protein interfaces are overwhelming a product of 2R IGFBP family membership, explain 49-68% of variation in IGFBP mRNA concentration in several different tissues and strongly predict the strength and direction of IGFBP transcriptional regulation under differing nutritional-states. The results support a model where vertebrate IGFBP family members evolved divergent structural attributes to provide distinct competition for IGFs with IGF1Rs, pre-disposing different functions in the regulation of IGF-signaling. Evolution of gene expression acted to ensure the appropriate physiological production of IGFBPs according to their structural specializations, leading to optimal IGF-signaling according to nutritional-status and the endocrine/local mode of action. This study demonstrates that relatively recent gene family expansion can facilitate inference of functional evolution within ancient genetic systems. http://hdl.handle.net/10023/3342 Abstract: Given an arbitrary group G we construct a semigroup of idempotents (band) BG with the property that the free idempotent generated semigroup over BG has a maximal subgroup isomorphic to G. If G is finitely presented then BG is finite. This answers several questions from recent papers in the area. 2013-01-01T00:00:00Z Dolinka, I Ruskuc, Nik Given an arbitrary group G we construct a semigroup of idempotents (band) BG with the property that the free idempotent generated semigroup over BG has a maximal subgroup isomorphic to G. If G is finitely presented then BG is finite. This answers several questions from recent papers in the area. http://hdl.handle.net/10023/3341 Abstract: Every semigroup which is a finite disjoint union of copies of the free monogenic semigroup (natural numbers under addition) is finitely presented and residually finite. 2013-01-01T00:00:00Z Abughazalah, Nabilah Ruskuc, Nik Every semigroup which is a finite disjoint union of copies of the free monogenic semigroup (natural numbers under addition) is finitely presented and residually finite. http://hdl.handle.net/10023/3340 Abstract: Aims. To investigate the spatial damping of propagating kink waves in an inhomogeneous plasma. In the limit of a thin tube surrounded by a thin transition layer, an analytical formulation for kink waves driven in from the bottom boundary of the corona is presented. Methods. The spatial form for the damping of the kink mode was investigated using various analytical approximations. When the density ratio between the internal density and the external density is not too large, a simple di.erential-integral equation was used. Approximate analytical solutions to this equation are presented. Results. For the first time, the form of the spatial damping of the kink mode is shown analytically to be Gaussian in nature near the driven boundary. For several wavelengths, the amplitude of the kink mode is proportional to (1 + exp(-z2 /L2 g))/2, where L2g = 16/ǫκ2 k2 . Although the actual value of 16 in Lg depends on the particular form of the driver, this form is very general and its dependence on the other parameters does not change. For large distances, the damping profile appears to be roughly linear exponential decay. This is shown analytically by a series expansion when the inhomogeneous layer width is small enough. 2013-01-01T00:00:00Z Hood, Alan William Ruderman, Michael Pascoe, David James De Moortel, Ineke Terradas, Jaume Wright, Andrew Nicholas Aims. To investigate the spatial damping of propagating kink waves in an inhomogeneous plasma. In the limit of a thin tube surrounded by a thin transition layer, an analytical formulation for kink waves driven in from the bottom boundary of the corona is presented. Methods. The spatial form for the damping of the kink mode was investigated using various analytical approximations. When the density ratio between the internal density and the external density is not too large, a simple di.erential-integral equation was used. Approximate analytical solutions to this equation are presented. Results. For the first time, the form of the spatial damping of the kink mode is shown analytically to be Gaussian in nature near the driven boundary. For several wavelengths, the amplitude of the kink mode is proportional to (1 + exp(-z2 /L2 g))/2, where L2g = 16/ǫκ2 k2 . Although the actual value of 16 in Lg depends on the particular form of the driver, this form is very general and its dependence on the other parameters does not change. For large distances, the damping profile appears to be roughly linear exponential decay. This is shown analytically by a series expansion when the inhomogeneous layer width is small enough. http://hdl.handle.net/10023/3339 Abstract: A method for the simultaneous calibration of the spring constants of all flexural modes of microcantilevers is presented. It is based on a flow of gas from a microchannel that interacts with the microcantilever. The gas flow causes a measurable shift in the resonance frequencies of thermal noise spectra of the flexural modes. From the magnitude of the frequency shifts of the individual modes the spring constants can be determined with high accuracy and precision. The method is non-invasive and does not risk damage to the cantilever. Experimental data is presented for several V-shaped and rectangular cantilevers with nominal fundamental spring constants in the range of 0.03-1.75 N/m. The spring constants of the fundamental modes compare favorably to those obtained using the Sader method. The higher modes of oscillation are readily calibrated with experimental uncertainties of 5-10%. 2013-02-15T00:00:00Z Parkin, John David Hähner, Georg A method for the simultaneous calibration of the spring constants of all flexural modes of microcantilevers is presented. It is based on a flow of gas from a microchannel that interacts with the microcantilever. The gas flow causes a measurable shift in the resonance frequencies of thermal noise spectra of the flexural modes. From the magnitude of the frequency shifts of the individual modes the spring constants can be determined with high accuracy and precision. The method is non-invasive and does not risk damage to the cantilever. Experimental data is presented for several V-shaped and rectangular cantilevers with nominal fundamental spring constants in the range of 0.03-1.75 N/m. The spring constants of the fundamental modes compare favorably to those obtained using the Sader method. The higher modes of oscillation are readily calibrated with experimental uncertainties of 5-10%. http://hdl.handle.net/10023/3338 Abstract: The linear instability of the gradient zone of a solar pond containing a fluidporous interface is investigated. It is found that the gradient zone can retain the same stability for lower values of the solute Rayleigh number with the introduction of a porous material compared with a purely fluid layer, whilst maintaining the same lower convective zone temperature. Interestingly, it is also shown that for certain parameter values the penetration of a porous medium into the gradient zone can cause the temperature of the lower convective zone to rise. However, for certain parameter ranges, when the fluid-porous interface is towards the top of the gradient zone, the solar pond can become highly unstable. 2013-02-01T00:00:00Z Hill, A. A Carr, Magda The linear instability of the gradient zone of a solar pond containing a fluidporous interface is investigated. It is found that the gradient zone can retain the same stability for lower values of the solute Rayleigh number with the introduction of a porous material compared with a purely fluid layer, whilst maintaining the same lower convective zone temperature. Interestingly, it is also shown that for certain parameter values the penetration of a porous medium into the gradient zone can cause the temperature of the lower convective zone to rise. However, for certain parameter ranges, when the fluid-porous interface is towards the top of the gradient zone, the solar pond can become highly unstable. http://hdl.handle.net/10023/3337 Abstract: Comparing nineteenth-century British and Australian Anglo-Saxonist literature enables a "decentered" exploration of Anglo-Saxonism's intersections with national, imperial, and colonial discourses, challenging assumption that this discourse was an uncritical vehicle of English nationalism and British manifest destiny. Far from reflecting a stable imperial center, evocations of 'ancient Englishness' in British literature were polyvalent and self-contesting, while in Australian literature they offered a response to colonization and emerging knowledge about the vast age of Indigenous Australian cultures. 2013-01-01T00:00:00Z D'Arcens, Louise Jones, Chris Comparing nineteenth-century British and Australian Anglo-Saxonist literature enables a "decentered" exploration of Anglo-Saxonism's intersections with national, imperial, and colonial discourses, challenging assumption that this discourse was an uncritical vehicle of English nationalism and British manifest destiny. Far from reflecting a stable imperial center, evocations of 'ancient Englishness' in British literature were polyvalent and self-contesting, while in Australian literature they offered a response to colonization and emerging knowledge about the vast age of Indigenous Australian cultures. http://hdl.handle.net/10023/3336 Abstract: The article treats the issue of generality. How may one conceive of the relationship between the uniqueness of individuality and the commonality of the human (species and society) without reduction? Can generalization be made moral – es-chewing stereotypes in society – and can it be made authentic – enacting a human science which treats the individual as a thing-in-itself? Simmel’s seminal inter-vention was to see generality as a necessary kind of distortion. In contrast, this article offers rational models of the one and the whole which expect to retain the uniqueness of the one; and it suggests characteristics of human embodiment (ca-pacities, potentialities) that speak to individuality and generality at the same time. The article ends with a reconsideration of distortion as a humane artistic represen-tation, by way of the work of Stanley Spencer. 2012-01-01T00:00:00Z Rapport, Nigel Julian The article treats the issue of generality. How may one conceive of the relationship between the uniqueness of individuality and the commonality of the human (species and society) without reduction? Can generalization be made moral – es-chewing stereotypes in society – and can it be made authentic – enacting a human science which treats the individual as a thing-in-itself? Simmel’s seminal inter-vention was to see generality as a necessary kind of distortion. In contrast, this article offers rational models of the one and the whole which expect to retain the uniqueness of the one; and it suggests characteristics of human embodiment (ca-pacities, potentialities) that speak to individuality and generality at the same time. The article ends with a reconsideration of distortion as a humane artistic represen-tation, by way of the work of Stanley Spencer. http://hdl.handle.net/10023/3335 Abstract: In this paper we consider a number of finiteness conditions for semigroups related to their ideal structure, and ask whether such conditions are preserved by sub- or supersemigroups with finite Rees or Green index. Specific properties under consideration include stability, D=J and minimal conditions on ideals. 2013-01-01T00:00:00Z Gray, Robert Duncan Maltcev, Victor D. Mitchell, J. Ruskuc, N. In this paper we consider a number of finiteness conditions for semigroups related to their ideal structure, and ask whether such conditions are preserved by sub- or supersemigroups with finite Rees or Green index. Specific properties under consideration include stability, D=J and minimal conditions on ideals. http://hdl.handle.net/10023/3334 Abstract: Initially we characterised growth responses to altered nutritional input at the transcriptional and tissue levels in the fast skeletal muscle of juvenile gilthead sea bream. Fish reared at 21–22°C (range) were fed a commercial diet at 3% body mass d−1 (non-satiation feeding, NSF) for 4 weeks, fasted for 4d (F) and then fed to satiation (SF) for 21d. 13 out of 34 genes investigated showed consistent patterns of regulation between nutritional states. Fasting was associated with a 20-fold increase in MAFbx, and a 5-fold increase in Six1 and WASp expression, which returned to NSF levels within 16h of SF. Refeeding to satiation was associated with a rapid (<24 h) 12 to 17-fold increase in UNC45, Hsp70 and Hsp90α transcripts coding for molecular chaperones associated with unfolded protein response pathways. The growth factors FGF6 and IGF1 increased 6.0 and 4.5-fold within 16 h and 24 h of refeeding respectively. The average growth in diameter of fast muscle fibres was checked with fasting and significant fibre hypertrophy was only observed after 13d and 21d SF. To investigate developmental plasticity in growth responses we used the same experimental protocol with fish reared at either 17.5–18.5°C (range) (LT) or 21–22°C (range) (HT) to metamorphosis and then transferred to 21–22°C. There were persistent effects of development temperature on muscle growth patterns with 20% more fibres of lower average diameter in LT than HT group of similar body size. Altering the nutritional input to the muscle to stimulate growth revealed cryptic changes in the expression of UNC45 and Hsp90α with higher transcript abundance in the LT than HT groups, whereas there were no differences in the expression of MAFbx and Six1. It was concluded that myogenesis and gene expression patterns during growth are not fixed, but can be modified by temperature during the early stages of the life cycle. 2012-12-17T00:00:00Z Garcia de la Serrana Castillo, Daniel Vieira-Johnston, Vera Lucia Almeida Andree, Karl B Darias, Maria Estévez, Alicia Gisbert, Enric Johnston, Ian Alistair Initially we characterised growth responses to altered nutritional input at the transcriptional and tissue levels in the fast skeletal muscle of juvenile gilthead sea bream. Fish reared at 21–22°C (range) were fed a commercial diet at 3% body mass d−1 (non-satiation feeding, NSF) for 4 weeks, fasted for 4d (F) and then fed to satiation (SF) for 21d. 13 out of 34 genes investigated showed consistent patterns of regulation between nutritional states. Fasting was associated with a 20-fold increase in MAFbx, and a 5-fold increase in Six1 and WASp expression, which returned to NSF levels within 16h of SF. Refeeding to satiation was associated with a rapid (<24 h) 12 to 17-fold increase in UNC45, Hsp70 and Hsp90α transcripts coding for molecular chaperones associated with unfolded protein response pathways. The growth factors FGF6 and IGF1 increased 6.0 and 4.5-fold within 16 h and 24 h of refeeding respectively. The average growth in diameter of fast muscle fibres was checked with fasting and significant fibre hypertrophy was only observed after 13d and 21d SF. To investigate developmental plasticity in growth responses we used the same experimental protocol with fish reared at either 17.5–18.5°C (range) (LT) or 21–22°C (range) (HT) to metamorphosis and then transferred to 21–22°C. There were persistent effects of development temperature on muscle growth patterns with 20% more fibres of lower average diameter in LT than HT group of similar body size. Altering the nutritional input to the muscle to stimulate growth revealed cryptic changes in the expression of UNC45 and Hsp90α with higher transcript abundance in the LT than HT groups, whereas there were no differences in the expression of MAFbx and Six1. It was concluded that myogenesis and gene expression patterns during growth are not fixed, but can be modified by temperature during the early stages of the life cycle. http://hdl.handle.net/10023/3333 Abstract: The Prins reaction was investigated using BF3 center dot OEt2 as a Lewis acid. It has been recently demonstrated, that if BF3 center dot OEt2 is used in stoichiometric amounts then these reactions generate fluorinated products where the BF3 center dot OEt2 contributes fluoride ion to quench the intermediate carbocations. In this study oxa- and aza-Prins reactions for the synthesis of 4-fluoro-pyrans and -piperidines were investigated. The products were obtained in good yields, but only with moderate diastereoselectivity. These Prins fluorination reactions can be accelerated under microwave conditions. The study extends the Prins fluorination methodology for the generation of the C-F bond in heterocycles. 2010-04-26T00:00:00Z Launay, Guillaume G. Slawin, Alexandra M. Z. O'Hagan, David The Prins reaction was investigated using BF3 center dot OEt2 as a Lewis acid. It has been recently demonstrated, that if BF3 center dot OEt2 is used in stoichiometric amounts then these reactions generate fluorinated products where the BF3 center dot OEt2 contributes fluoride ion to quench the intermediate carbocations. In this study oxa- and aza-Prins reactions for the synthesis of 4-fluoro-pyrans and -piperidines were investigated. The products were obtained in good yields, but only with moderate diastereoselectivity. These Prins fluorination reactions can be accelerated under microwave conditions. The study extends the Prins fluorination methodology for the generation of the C-F bond in heterocycles. http://hdl.handle.net/10023/3332 Abstract: St Andrews Cathedral is located on the East Coast of Scotland, construction started in 1160 and spanned Romanesque and Gothic architectural styles. It was consecrated in 1318, four years after the battle of Bannockburn in the presence of King Robert the Bruce. For several hundred years, the Cathedral was one of the most important religious buildings in Europe and the centre of religious life in Scotland. During the Scottish Reformation, John Knox lead reformers in divesting the Cathedral of much of its finery. Thereafter it fell into disuse and decline. Today the impressive remains only hint at the former glory of this important building. Cultural Heritage encompasses physical aspects such as architecture and artifacts along with less tangible culture such as music, songs and stories. Open virtual worlds offer an extensible collaborative environment for developing historic scenes against the background of which material and ephemeral aspects of cultural heritage associated with a site may be explored through engagement with historic narratives. They offer the potential to reconstruct within a 3D computer environment both the physical structures of the past and important aspects of the light, music and life that once filled those structures. Virtual reconstructions enable scenarios to be created where individual pieces of art can be located and appreciated within the audio, visual and spacial contexts for which they were originally created. Bringing together architecture, sculpture, illumination, stained-glass, music, procession and lighting into a scene which can be explored from multiple spatial perspectives enables holistic experience and appreciation. Historic reconstructions may be created upon virtual stages allowing new and engaging Cultural Heritage perspectives to be accessible to diverse audiences. Through the example of St Andrews Cathedral reconstruction this paper presents an example of Open Virtual Worlds as a technology for supporting the creation and use of virtual reconstructions as a platform that promotes understanding of and engagement with Cultural Heritage. The use contexts discussed range from research based exploration of 3D spaces, to primary schools students using the reconstructions as a backdrop for tag. The digital literacies of the audience and goals of the use case impact on the appropriateness of the user interface. A range of interfaces are explored including games controllers, touch screens, tablets that provide location aware views into the model and hands free gesture control systems. 2012-12-01T00:00:00Z Kennedy, Sarah Dow, Lisa Oliver, Iain Angus Sweetman, Rebecca Jane Miller, Alan Henry David Campbell, Anne Davies, Christopher John McCaffery, John Philip Allison, Colin Green, Daryl Luxford, Julian Marcus Fawcett, Richard St Andrews Cathedral is located on the East Coast of Scotland, construction started in 1160 and spanned Romanesque and Gothic architectural styles. It was consecrated in 1318, four years after the battle of Bannockburn in the presence of King Robert the Bruce. For several hundred years, the Cathedral was one of the most important religious buildings in Europe and the centre of religious life in Scotland. During the Scottish Reformation, John Knox lead reformers in divesting the Cathedral of much of its finery. Thereafter it fell into disuse and decline. Today the impressive remains only hint at the former glory of this important building. Cultural Heritage encompasses physical aspects such as architecture and artifacts along with less tangible culture such as music, songs and stories. Open virtual worlds offer an extensible collaborative environment for developing historic scenes against the background of which material and ephemeral aspects of cultural heritage associated with a site may be explored through engagement with historic narratives. They offer the potential to reconstruct within a 3D computer environment both the physical structures of the past and important aspects of the light, music and life that once filled those structures. Virtual reconstructions enable scenarios to be created where individual pieces of art can be located and appreciated within the audio, visual and spacial contexts for which they were originally created. Bringing together architecture, sculpture, illumination, stained-glass, music, procession and lighting into a scene which can be explored from multiple spatial perspectives enables holistic experience and appreciation. Historic reconstructions may be created upon virtual stages allowing new and engaging Cultural Heritage perspectives to be accessible to diverse audiences. Through the example of St Andrews Cathedral reconstruction this paper presents an example of Open Virtual Worlds as a technology for supporting the creation and use of virtual reconstructions as a platform that promotes understanding of and engagement with Cultural Heritage. The use contexts discussed range from research based exploration of 3D spaces, to primary schools students using the reconstructions as a backdrop for tag. The digital literacies of the audience and goals of the use case impact on the appropriateness of the user interface. A range of interfaces are explored including games controllers, touch screens, tablets that provide location aware views into the model and hands free gesture control systems. http://hdl.handle.net/10023/3330 Abstract: We calculate the photoluminescence spectrum and lifetime of a biexciton in a semiconductor using Fermi's golden rule. Our biexciton wavefunction is obtained using a Quantum Monte Carlo calculation. We consider a recombination process where one of the excitons within the biexciton annihilates. For hole masses greater than or equal to the electron mass, we find that the surviving exciton is most likely to populate the ground state. We also investigate how the confinement of excitons in a quantum dot would modify the lifetime in the limit of a large quantum dot where confinement principally affects the centre of mass wavefunction. The lifetimes we obtain are in reasonable agreement with experimental values. Our calculation can be used as a benchmark for comparison with approximate methods. Description: 6 pages, 2 figures 2013-01-07T00:00:00Z Bauer, M. Keeling, J. M. Parish, M. Lopez Rios, P. B. Littlewood, P. We calculate the photoluminescence spectrum and lifetime of a biexciton in a semiconductor using Fermi's golden rule. Our biexciton wavefunction is obtained using a Quantum Monte Carlo calculation. We consider a recombination process where one of the excitons within the biexciton annihilates. For hole masses greater than or equal to the electron mass, we find that the surviving exciton is most likely to populate the ground state. We also investigate how the confinement of excitons in a quantum dot would modify the lifetime in the limit of a large quantum dot where confinement principally affects the centre of mass wavefunction. The lifetimes we obtain are in reasonable agreement with experimental values. Our calculation can be used as a benchmark for comparison with approximate methods. http://hdl.handle.net/10023/3329 Abstract: Potato mop-top pomovirus (PMTV) is one of a few viruses that can move systemically in plants in the absence of the capsid protein (CP). Pomoviruses encode the triple gene block genetic module of movement proteins (TGB 1, 2, and 3) and recent research suggests that PMTV RNA is transported either as ribonucleoprotein (RNP) complexes containing TGB1 or encapsidated in virions containing TGB1. Furthermore, there are different requirements for local or systemic (long-distance) movement. Research suggests that nucleolar passage of TGB1 may be important for the long-distance movement of both RNP and virions. Moreover, and uniquely, the long-distance movement of the CP-encoding RNA requires expression of both major and minor CP subunits and is inhibited when only the major CP sub unit is expressed. This paper reviews pomovirus research and presents a current model for RNA movement. 2011-12-22T00:00:00Z Torrance, Lesley Wright, Kathryn M Crutzen, Francois Cowan, Graham H Lukhovitskaya, Nina I Bragard, Claude Savenkov, Eugene I Potato mop-top pomovirus (PMTV) is one of a few viruses that can move systemically in plants in the absence of the capsid protein (CP). Pomoviruses encode the triple gene block genetic module of movement proteins (TGB 1, 2, and 3) and recent research suggests that PMTV RNA is transported either as ribonucleoprotein (RNP) complexes containing TGB1 or encapsidated in virions containing TGB1. Furthermore, there are different requirements for local or systemic (long-distance) movement. Research suggests that nucleolar passage of TGB1 may be important for the long-distance movement of both RNP and virions. Moreover, and uniquely, the long-distance movement of the CP-encoding RNA requires expression of both major and minor CP subunits and is inhibited when only the major CP sub unit is expressed. This paper reviews pomovirus research and presents a current model for RNA movement. http://hdl.handle.net/10023/3328 Abstract: Background: Many fish species experience long periods of fasting in nature often associated with seasonal reductions in water temperature and prey availability or spawning migrations. During periods of nutrient restriction, changes in metabolism occur to provide cellular energy via catabolic processes. Muscle is particularly affected by prolonged fasting as myofibrillar proteins act as a major energy source. To investigate the mechanisms of metabolic reorganisation with fasting and refeeding in a saltwater stage of Atlantic salmon (Salmo salar L.) we analysed the expression of genes involved in myogenesis, growth signalling, lipid biosynthesis and myofibrillar protein degradation and synthesis pathways using qPCR. Results: Hierarchical clustering of gene expression data revealed three clusters. The first cluster comprised genes involved in lipid metabolism and triacylglycerol synthesis (ALDOB, DGAT1 and LPL) which had peak expression 3-14d after refeeding. The second cluster comprised ADIPOQ, MLC2, IGF-I and TALDO1, with peak expression 14-32d after refeeding. Cluster III contained genes strongly down regulated as an initial response to feeding and included the ubiquitin ligases MuRF1 and MAFbx, myogenic regulatory factors and some metabolic genes. Conclusion: Early responses to refeeding in fasted salmon included the synthesis of triacylglycerols and activation of the adipogenic differentiation program. Inhibition of MuRF1 and MAFbx respectively may result in decreased degradation and concomitant increased production of myofibrillar proteins. Both of these processes preceded any increase in expression of myogenic regulatory factors and IGF-I. These responses could be a necessary strategy for an animal adapted to long periods of food deprivation whereby energy reserves are replenished prior to the resumption of myogenesis. 2009-08-24T00:00:00Z Bower, Neil I. Taylor, Richard G. Johnston, Ian A. Background: Many fish species experience long periods of fasting in nature often associated with seasonal reductions in water temperature and prey availability or spawning migrations. During periods of nutrient restriction, changes in metabolism occur to provide cellular energy via catabolic processes. Muscle is particularly affected by prolonged fasting as myofibrillar proteins act as a major energy source. To investigate the mechanisms of metabolic reorganisation with fasting and refeeding in a saltwater stage of Atlantic salmon (Salmo salar L.) we analysed the expression of genes involved in myogenesis, growth signalling, lipid biosynthesis and myofibrillar protein degradation and synthesis pathways using qPCR. Results: Hierarchical clustering of gene expression data revealed three clusters. The first cluster comprised genes involved in lipid metabolism and triacylglycerol synthesis (ALDOB, DGAT1 and LPL) which had peak expression 3-14d after refeeding. The second cluster comprised ADIPOQ, MLC2, IGF-I and TALDO1, with peak expression 14-32d after refeeding. Cluster III contained genes strongly down regulated as an initial response to feeding and included the ubiquitin ligases MuRF1 and MAFbx, myogenic regulatory factors and some metabolic genes. Conclusion: Early responses to refeeding in fasted salmon included the synthesis of triacylglycerols and activation of the adipogenic differentiation program. Inhibition of MuRF1 and MAFbx respectively may result in decreased degradation and concomitant increased production of myofibrillar proteins. Both of these processes preceded any increase in expression of myogenic regulatory factors and IGF-I. These responses could be a necessary strategy for an animal adapted to long periods of food deprivation whereby energy reserves are replenished prior to the resumption of myogenesis. http://hdl.handle.net/10023/3327 Abstract: Organisms are affected by different DNA damaging agents naturally present in the environment or released as a result of human activity. Many defense mechanisms have evolved in organisms to minimize genotoxic damage. One of them is induced radioresistance or adaptive response. The adaptive response could be considered as a nonspecific phenomenon in which exposure to minimal stress could result in increased resistance to higher levels of the same or to other types of stress some hours later. A better understanding of the molecular mechanism underlying the adaptive response may lead to an improvement of cancer treatment, risk assessment and risk management strategies, radiation protection, e. g. of astronauts during long-term space flights. In this mini-review we discuss some open questions and the probable underlying mechanisms involved in adaptive response: the transcription of many genes and the activation of numerous signaling pathways that trigger cell defenses - DNA repair systems, induction of proteins synthesis, enhanced detoxification of free radicals and antioxidant production. 2008-01-01T00:00:00Z Dimova, Evgeniya G Bryant, Peter Edward Chankova, Stephka G Organisms are affected by different DNA damaging agents naturally present in the environment or released as a result of human activity. Many defense mechanisms have evolved in organisms to minimize genotoxic damage. One of them is induced radioresistance or adaptive response. The adaptive response could be considered as a nonspecific phenomenon in which exposure to minimal stress could result in increased resistance to higher levels of the same or to other types of stress some hours later. A better understanding of the molecular mechanism underlying the adaptive response may lead to an improvement of cancer treatment, risk assessment and risk management strategies, radiation protection, e. g. of astronauts during long-term space flights. In this mini-review we discuss some open questions and the probable underlying mechanisms involved in adaptive response: the transcription of many genes and the activation of numerous signaling pathways that trigger cell defenses - DNA repair systems, induction of proteins synthesis, enhanced detoxification of free radicals and antioxidant production. http://hdl.handle.net/10023/3326 Abstract: Adult nervous systems are so complex that understanding how they produce behavior remains a real challenge. We chose to study hatchling Xenopus tadpoles where behavior is controlled by a few thousand neurons but there is a very limited number of types of neuron. Young tadpoles can flex, swim away, adjust their trajectory, speed-up and slow-down, stop when they contact support and struggle when grasped. They are sensitive to touch, pressure, noxious stimuli, light intensity and water currents. Using whole-cell recording has led to rapid progress in understanding central networks controlling behavior. Our methods are illustrated by an analysis of the flexion reflex to skin touch. We then define the seven types of neuron that allow the tadpole to swim when the skin is touched and use paired recordings to investigate neuron properties, synaptic connections and activity patterns. Proposals on how the swim network operates are evaluated by experiment and network modeling. We then examine GABAergic inhibitory pathways that control swimming but also produce tonic inhibition to reduce responsiveness when the tadpole is at rest. Finally, we analyze the strong alternating struggling movements the tadpole makes when grasped. We show that the mechanisms for rhythm generation here are very different to those during swimming. Although much remains to be explained, study of this simple vertebrate has uncovered basic principles about the function and organization of vertebrate nervous systems. 2010-06-24T00:00:00Z Roberts, Alan Li, Wen-Chang Soffe, Steve Adult nervous systems are so complex that understanding how they produce behavior remains a real challenge. We chose to study hatchling Xenopus tadpoles where behavior is controlled by a few thousand neurons but there is a very limited number of types of neuron. Young tadpoles can flex, swim away, adjust their trajectory, speed-up and slow-down, stop when they contact support and struggle when grasped. They are sensitive to touch, pressure, noxious stimuli, light intensity and water currents. Using whole-cell recording has led to rapid progress in understanding central networks controlling behavior. Our methods are illustrated by an analysis of the flexion reflex to skin touch. We then define the seven types of neuron that allow the tadpole to swim when the skin is touched and use paired recordings to investigate neuron properties, synaptic connections and activity patterns. Proposals on how the swim network operates are evaluated by experiment and network modeling. We then examine GABAergic inhibitory pathways that control swimming but also produce tonic inhibition to reduce responsiveness when the tadpole is at rest. Finally, we analyze the strong alternating struggling movements the tadpole makes when grasped. We show that the mechanisms for rhythm generation here are very different to those during swimming. Although much remains to be explained, study of this simple vertebrate has uncovered basic principles about the function and organization of vertebrate nervous systems. http://hdl.handle.net/10023/3325 Abstract: Spatial memory is a well-characterized psychological function in both humans and rodents. The combined computations of a network of systems including place cells in the hippocampus, grid cells in the medial entorhinal cortex and head direction cells found in numerous structures in the brain have been suggested to form the neural instantiation of the cognitive map as first described by Tolman in 1948. However, while our understanding of the neural mechanisms underlying spatial representations in adults is relatively sophisticated, we know substantially less about how this network develops in young animals. In this article we briefly review studies examining the developmental time scale that these systems follow. Electrophysiological recordings from very young rats show that directional information is at adult levels at the outset of navigational experience. The systems supporting allocentric memory, however, take longer to mature. This is consistent with behavioral studies of young rats which show that spatial memory based on head direction develops very early but that allocentric spatial memory takes longer to mature. We go on to report new data demonstrating that memory for associations between objects and their spatial locations is slower to develop than memory for objects alone. This is again consistent with previous reports suggesting that adult like spatial representations have a protracted development in rats and also suggests that the systems involved in processing non-spatial stimuli come online earlier. 2012-03-01T00:00:00Z Ainge, James A. Langston, Rosamund F. Spatial memory is a well-characterized psychological function in both humans and rodents. The combined computations of a network of systems including place cells in the hippocampus, grid cells in the medial entorhinal cortex and head direction cells found in numerous structures in the brain have been suggested to form the neural instantiation of the cognitive map as first described by Tolman in 1948. However, while our understanding of the neural mechanisms underlying spatial representations in adults is relatively sophisticated, we know substantially less about how this network develops in young animals. In this article we briefly review studies examining the developmental time scale that these systems follow. Electrophysiological recordings from very young rats show that directional information is at adult levels at the outset of navigational experience. The systems supporting allocentric memory, however, take longer to mature. This is consistent with behavioral studies of young rats which show that spatial memory based on head direction develops very early but that allocentric spatial memory takes longer to mature. We go on to report new data demonstrating that memory for associations between objects and their spatial locations is slower to develop than memory for objects alone. This is again consistent with previous reports suggesting that adult like spatial representations have a protracted development in rats and also suggests that the systems involved in processing non-spatial stimuli come online earlier. http://hdl.handle.net/10023/3324 Abstract: Autism spectrum condition (ASC) is recognized as having an inflammatory component. Post-mortem brain samples from patients with ASC display neuroglial activation and inflammatory markers in cerebrospinal fluid, although little is known about the underlying molecular mechanisms. Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) is a protein found in almost all cell types and mediates regulation of immune response by inducing the expression of inflammatory cytokines and chemokines, establishing a feedback mechanism that can produce chronic or excessive inflammation. This article describes immunodetection and immunofluorescence measurements of NF-κB in human post-mortem samples of orbitofrontal cortex tissue donated to two independent centers: London Brain Bank, Kings College London, UK (ASC: n = 3, controls: n = 4) and Autism Tissue Program, Harvard Brain Bank, USA (ASC: n = 6, controls: n = 5). The hypothesis was that concentrations of NF-κB would be elevated, especially in activated microglia in ASC, and pH would be concomitantly reduced (i.e., acidification). Neurons, astrocytes, and microglia all demonstrated increased extranuclear and nuclear translocated NF-κB p65 expression in brain tissue from ASC donors relative to samples from matched controls. These between-groups differences were increased in astrocytes and microglia relative to neurons, but particularly pronounced for highly mature microglia. Measurement of pH in homogenized samples demonstrated a 0.98-unit difference in means and a strong (F = 98.3; p = 0.00018) linear relationship to the expression of nuclear translocated NF-κB in mature microglia. Acridine orange staining localized pH reductions to lysosomal compartments. In summary, NF-κB is aberrantly expressed in orbitofrontal cortex in patients with ASC, as part of a putative molecular cascade leading to inflammation, especially of resident immune cells in brain regions associated with the behavioral and clinical symptoms of ASC. 2011-05-13T00:00:00Z Young, Adam Campbell, Elaine Catherine Lynch, Sarah Janice Suckling, John Powis, Simon John Autism spectrum condition (ASC) is recognized as having an inflammatory component. Post-mortem brain samples from patients with ASC display neuroglial activation and inflammatory markers in cerebrospinal fluid, although little is known about the underlying molecular mechanisms. Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) is a protein found in almost all cell types and mediates regulation of immune response by inducing the expression of inflammatory cytokines and chemokines, establishing a feedback mechanism that can produce chronic or excessive inflammation. This article describes immunodetection and immunofluorescence measurements of NF-κB in human post-mortem samples of orbitofrontal cortex tissue donated to two independent centers: London Brain Bank, Kings College London, UK (ASC: n = 3, controls: n = 4) and Autism Tissue Program, Harvard Brain Bank, USA (ASC: n = 6, controls: n = 5). The hypothesis was that concentrations of NF-κB would be elevated, especially in activated microglia in ASC, and pH would be concomitantly reduced (i.e., acidification). Neurons, astrocytes, and microglia all demonstrated increased extranuclear and nuclear translocated NF-κB p65 expression in brain tissue from ASC donors relative to samples from matched controls. These between-groups differences were increased in astrocytes and microglia relative to neurons, but particularly pronounced for highly mature microglia. Measurement of pH in homogenized samples demonstrated a 0.98-unit difference in means and a strong (F = 98.3; p = 0.00018) linear relationship to the expression of nuclear translocated NF-κB in mature microglia. Acridine orange staining localized pH reductions to lysosomal compartments. In summary, NF-κB is aberrantly expressed in orbitofrontal cortex in patients with ASC, as part of a putative molecular cascade leading to inflammation, especially of resident immune cells in brain regions associated with the behavioral and clinical symptoms of ASC. http://hdl.handle.net/10023/3323 Abstract: Our forward-facing eyes allow us the advantage of binocular visual information: using the tiny differences between right and left eye views to learn about depth and location in three dimensions. Our visual systems also contain specialized mechanisms to detect motion-in-depth from binocular vision, but the nature of these mechanisms remains controversial. Binocular motion-in-depth perception could theoretically be based on first detecting binocular disparity and then monitoring how it changes over time. The alternative is to monitor the motion in the right and left eye separately and then compare these motion signals. Here we used an individual differences approach to test whether the two sources of information are processed via dissociated mechanisms, and to measure the relative importance of those mechanisms. Our results suggest the existence of two distinct mechanisms, each contributing to the perception of motion-in-depth in most observers. Additionally, for the first time, we demonstrate the relative prevalence of the two mechanisms within a normal population. In general, visual systems appear to rely mostly on the mechanism sensitive to changing binocular disparity, but perception of motion-in-depth is augmented by the presence of a less sensitive mechanism that uses interocular velocity differences. Occasionally, we find observers with the opposite pattern of sensitivity. More generally this work showcases the power of the individual differences approach in studying the functional organization of cognitive systems. 2010-10-12T00:00:00Z Nefs, Harold O'Hare, Louise Harris, Julie Our forward-facing eyes allow us the advantage of binocular visual information: using the tiny differences between right and left eye views to learn about depth and location in three dimensions. Our visual systems also contain specialized mechanisms to detect motion-in-depth from binocular vision, but the nature of these mechanisms remains controversial. Binocular motion-in-depth perception could theoretically be based on first detecting binocular disparity and then monitoring how it changes over time. The alternative is to monitor the motion in the right and left eye separately and then compare these motion signals. Here we used an individual differences approach to test whether the two sources of information are processed via dissociated mechanisms, and to measure the relative importance of those mechanisms. Our results suggest the existence of two distinct mechanisms, each contributing to the perception of motion-in-depth in most observers. Additionally, for the first time, we demonstrate the relative prevalence of the two mechanisms within a normal population. In general, visual systems appear to rely mostly on the mechanism sensitive to changing binocular disparity, but perception of motion-in-depth is augmented by the presence of a less sensitive mechanism that uses interocular velocity differences. Occasionally, we find observers with the opposite pattern of sensitivity. More generally this work showcases the power of the individual differences approach in studying the functional organization of cognitive systems. http://hdl.handle.net/10023/3321 Abstract: We demonstrate a diode-pumped Cr:LiSAF laser with controllable and reliable fast switching between its continuous-wave and mode-locked states of operation using an optically-addressed semiconductor Bragg reflector, permitting dyed microspheres to be continuously trapped and monitored using a standard microscope imaging and on-demand two-photon-excited luminescence techniques. (C) 2012 Optical Society of America 2012-03-26T00:00:00Z Savitski, Vasili G. Metzger, Nikolaus K. Calvez, Stephane Burns, David Sibbett, W. Brown, C. T. A. We demonstrate a diode-pumped Cr:LiSAF laser with controllable and reliable fast switching between its continuous-wave and mode-locked states of operation using an optically-addressed semiconductor Bragg reflector, permitting dyed microspheres to be continuously trapped and monitored using a standard microscope imaging and on-demand two-photon-excited luminescence techniques. (C) 2012 Optical Society of America http://hdl.handle.net/10023/3320 Abstract: Efficient mode-locking in a Tm:KY(WO4)(2) laser is demonstrated by using InGaAsSb quantum-well SESAMs. Self-starting ultrashort pulse generation was realized in the 1979-2074 nm spectral region. Maximum average output power up to 411 mW was produced around 1986 nm with the corresponding pulse duration and repetition rate of 549 fs and 105 MHz respectively. Optimised pulse durations of 386 fs were produced with an average power of 235 mW at 2029 nm. (C) 2011 Optical Society of America 2011-05-09T00:00:00Z Lagatsky, A. A. Calvez, S. Gupta, J. A. Kisel, V. E. Kuleshov, N. V. Brown, C. T. A. Dawson, M. D. Sibbett, W. Efficient mode-locking in a Tm:KY(WO4)(2) laser is demonstrated by using InGaAsSb quantum-well SESAMs. Self-starting ultrashort pulse generation was realized in the 1979-2074 nm spectral region. Maximum average output power up to 411 mW was produced around 1986 nm with the corresponding pulse duration and repetition rate of 549 fs and 105 MHz respectively. Optimised pulse durations of 386 fs were produced with an average power of 235 mW at 2029 nm. (C) 2011 Optical Society of America http://hdl.handle.net/10023/3319 2012-01-01T00:00:00Z Jones, Chris http://hdl.handle.net/10023/3318 Abstract: Afterword 2012-01-01T00:00:00Z Kamusella, Tomasz Dominik Afterword http://hdl.handle.net/10023/3317 Abstract: The Silesians are an ethnic or national group that coalesced in the nineteenth century. During the subsequent century, they survived repeated divisions of their historical region of Upper Silesia among the nation-states of Czechoslovakia (or today its western half, that is, the Czech Republic), Germany, and Poland, which entailed Czechization, Germanization, and Polonization, respectively. The ideal of ethnolinguistic homogeneity, a typical goal of Central European nationalism, was achieved in post-war Poland. After the end of communism (1989) and the country‟s accession to the European Union (2004), this ideal is still aspired to, though it appears to stand in direct conflict with the values of democracy and rule of law. The Silesians are the largest minority in today‟s Poland and Silesian speakers are the second largest speech community in this country after Polish-speakers. Despite the Silesians‟ wish to be recognized as a minority, expressed clearly in their grassroots initiatives and in the Polish censuses of 2002 and 2011, Poland neither recognizes them nor their language. This inflexible attitude may amount to a breach of the spirit (if not the letter) of the Council of Europe‟s Framework Convention for the Protection of National Minorities and the European Charter for Regional or Minority Languages, both of which Poland signed and ratified. The case of the Silesians is a litmus test of the quality of Polish democracy. In order to resolve the debacle, the article proposes a genuine dialogue between representatives of Silesian organizations and the Polish administration under the guidance of observers and facilitators from the Council of Europe and appropriate international non-governmental organizations. 2012-12-21T00:00:00Z Kamusella, Tomasz Dominik The Silesians are an ethnic or national group that coalesced in the nineteenth century. During the subsequent century, they survived repeated divisions of their historical region of Upper Silesia among the nation-states of Czechoslovakia (or today its western half, that is, the Czech Republic), Germany, and Poland, which entailed Czechization, Germanization, and Polonization, respectively. The ideal of ethnolinguistic homogeneity, a typical goal of Central European nationalism, was achieved in post-war Poland. After the end of communism (1989) and the country‟s accession to the European Union (2004), this ideal is still aspired to, though it appears to stand in direct conflict with the values of democracy and rule of law. The Silesians are the largest minority in today‟s Poland and Silesian speakers are the second largest speech community in this country after Polish-speakers. Despite the Silesians‟ wish to be recognized as a minority, expressed clearly in their grassroots initiatives and in the Polish censuses of 2002 and 2011, Poland neither recognizes them nor their language. This inflexible attitude may amount to a breach of the spirit (if not the letter) of the Council of Europe‟s Framework Convention for the Protection of National Minorities and the European Charter for Regional or Minority Languages, both of which Poland signed and ratified. The case of the Silesians is a litmus test of the quality of Polish democracy. In order to resolve the debacle, the article proposes a genuine dialogue between representatives of Silesian organizations and the Polish administration under the guidance of observers and facilitators from the Council of Europe and appropriate international non-governmental organizations. http://hdl.handle.net/10023/3316 Abstract: Duplication of genetic material is clearly a major route to genetic change, with consequences for both evolution and disease. A variety of forms and mechanisms of duplication are recognised, operating across the scales of a few base pairs upto entire genomes. With the ever-increasing amounts of gene and genome sequence data that are becoming available, our understanding of the extent of duplication is greatly improving, both in terms of the scales of duplication events as well as their rates of occurrence. An accurate understanding of these processes is vital if we are to properly understand important events in evolution as well as mechanisms operating at the level of genome organisation. Here we will focus on duplication in animal genomes and how the duplicated sequences are distributed, with the aim of maintaining a focus on principles of evolution and organisation that are most directly applicable to the shaping of our own genome. 2012-01-01T00:00:00Z Mendivil Ramos, Olivia Ferrier, David Ellard Keith Duplication of genetic material is clearly a major route to genetic change, with consequences for both evolution and disease. A variety of forms and mechanisms of duplication are recognised, operating across the scales of a few base pairs upto entire genomes. With the ever-increasing amounts of gene and genome sequence data that are becoming available, our understanding of the extent of duplication is greatly improving, both in terms of the scales of duplication events as well as their rates of occurrence. An accurate understanding of these processes is vital if we are to properly understand important events in evolution as well as mechanisms operating at the level of genome organisation. Here we will focus on duplication in animal genomes and how the duplicated sequences are distributed, with the aim of maintaining a focus on principles of evolution and organisation that are most directly applicable to the shaping of our own genome. http://hdl.handle.net/10023/3315 Abstract: Predicting how marine mammal populations act to habitat changes will be essential for developing conservation management strategies by marine mammal ecologists in the 21st century. Responses to previous environmental change may be informative in the development of predictive models. Here we describe the likely effects of the last ice age on grey seal population size and distribution. We use satellite telemetry data to define grey seal foraging habitat in terms of the temperature and depth ranges exploited by the contemporary populations. We estimate the available extent of such habitat in the North Atlantic at present and at the last glacial maximum (LGM); taking account of glacial and seasonal sea-ice coverage, estimated reductions of sea-level (123m) and seawater temperature hind-casts from GLAMAP-2000. Most of the extensive continental shelf waters (North Sea, Baltic Sea and Scotian Shelf), currently supporting >95% of grey seals, were unavailable at the LGM. A combination of lower sea-level and extensive ice-sheets, massively increased seasonal sea-ice coverage and southerly extent of cold water would have pushed grey seals into areas with no significant shelf waters. The habitat during the LGM might have been as small as 4%, when compared to today’s extent and grey seal populations may have fallen to similarly. An alternative scenario involving a major change to a pelagic/bathy-pelagic foraging niche cannot be discounted. However, hooded seals that appear to out-compete and effectively exclude grey seals from such habitat currently dominate that niche. If as seems likely, the grey seal population fell to very low levels it would have remained low for several thousand years before expanding into current habitats over the last 12000 years or so. 2012-12-26T00:00:00Z Boehme, Lars Thompson, David Fedak, Mike Bowen, Don Hammill, Mike Stenson, Gary Predicting how marine mammal populations act to habitat changes will be essential for developing conservation management strategies by marine mammal ecologists in the 21st century. Responses to previous environmental change may be informative in the development of predictive models. Here we describe the likely effects of the last ice age on grey seal population size and distribution. We use satellite telemetry data to define grey seal foraging habitat in terms of the temperature and depth ranges exploited by the contemporary populations. We estimate the available extent of such habitat in the North Atlantic at present and at the last glacial maximum (LGM); taking account of glacial and seasonal sea-ice coverage, estimated reductions of sea-level (123m) and seawater temperature hind-casts from GLAMAP-2000. Most of the extensive continental shelf waters (North Sea, Baltic Sea and Scotian Shelf), currently supporting >95% of grey seals, were unavailable at the LGM. A combination of lower sea-level and extensive ice-sheets, massively increased seasonal sea-ice coverage and southerly extent of cold water would have pushed grey seals into areas with no significant shelf waters. The habitat during the LGM might have been as small as 4%, when compared to today’s extent and grey seal populations may have fallen to similarly. An alternative scenario involving a major change to a pelagic/bathy-pelagic foraging niche cannot be discounted. However, hooded seals that appear to out-compete and effectively exclude grey seals from such habitat currently dominate that niche. If as seems likely, the grey seal population fell to very low levels it would have remained low for several thousand years before expanding into current habitats over the last 12000 years or so. http://hdl.handle.net/10023/3314 Abstract: Consistent individual differences (CIDs) in behaviour, indicative of behavioural types or personalities, have been shown in taxa ranging from Cnidaria to Mammalia. However, despite numerous theoretical explanations there remains limited empirical evidence for selective mechanisms that maintain such variation within natural populations. We examined behavioural types and fitness proxies in wild female grey seals at the North Rona breeding colony. Experiments in 2009 and 2010 employed a remotely-controlled vehicle to deliver a novel auditory stimulus to females to elicit changes in pup-checking behaviour. Mothers tested twice during lactation exhibited highly repeatable individual pup-checking rates within and across breeding seasons. Observations of undisturbed mothers (i.e. experiencing no disturbance from conspecifics or experimental test) also revealed CIDs in pup-checking behaviour. However, there was no correlation between an individuals’ pup-checking rate during undisturbed observations with the rate in response to the auditory test, indicating plasticity across situations. The extent to which individuals changed rates of pup-checking from undisturbed to disturbed conditions revealed a continuum of behavioural types from proactive females, who maintained a similar rate throughout, to reactive females, who increased pup-checking markedly in response to the test. Variation in maternal expenditure (daily mass loss rate) was greater among more reactive mothers than proactive mothers. Consequently pups of more reactive mothers had more varied growth rates centred around the long-term population mean. These patterns could not be accounted for by other measured covariates as behavioural type was unrelated to a mother’s prior experience, degree of inter-annual site fidelity, physical characteristics of their pupping habitat, pup sex or pup activity. These findings are consistent with the hypothesis that variation in behavioural types is maintained by spatial and temporal environmental variation combined with limits to phenotype-environment matching. 2012-11-16T00:00:00Z Twiss, Sean D Cairns, Charlotte Culloch, Ross Richards, Shane A Pomeroy, Patrick Consistent individual differences (CIDs) in behaviour, indicative of behavioural types or personalities, have been shown in taxa ranging from Cnidaria to Mammalia. However, despite numerous theoretical explanations there remains limited empirical evidence for selective mechanisms that maintain such variation within natural populations. We examined behavioural types and fitness proxies in wild female grey seals at the North Rona breeding colony. Experiments in 2009 and 2010 employed a remotely-controlled vehicle to deliver a novel auditory stimulus to females to elicit changes in pup-checking behaviour. Mothers tested twice during lactation exhibited highly repeatable individual pup-checking rates within and across breeding seasons. Observations of undisturbed mothers (i.e. experiencing no disturbance from conspecifics or experimental test) also revealed CIDs in pup-checking behaviour. However, there was no correlation between an individuals’ pup-checking rate during undisturbed observations with the rate in response to the auditory test, indicating plasticity across situations. The extent to which individuals changed rates of pup-checking from undisturbed to disturbed conditions revealed a continuum of behavioural types from proactive females, who maintained a similar rate throughout, to reactive females, who increased pup-checking markedly in response to the test. Variation in maternal expenditure (daily mass loss rate) was greater among more reactive mothers than proactive mothers. Consequently pups of more reactive mothers had more varied growth rates centred around the long-term population mean. These patterns could not be accounted for by other measured covariates as behavioural type was unrelated to a mother’s prior experience, degree of inter-annual site fidelity, physical characteristics of their pupping habitat, pup sex or pup activity. These findings are consistent with the hypothesis that variation in behavioural types is maintained by spatial and temporal environmental variation combined with limits to phenotype-environment matching. http://hdl.handle.net/10023/3313 Abstract: The performance of 16-electron ruthenium complexes with the general formula Cp*Ru(L)X (in which L = phosphine or N-heterocyclic carbene ligand; X = Cl or OCH2CF3) was explored in azide−alkyne cycloaddition reactions that afford the 1,2,3- triazole products. The scope of the Cp*Ru(PiPr3)Cl precatalyst was investigated for terminal alkynes leading to new 1,5-disubstituted 1,2,3-triazoles in high yields. Mechanistic studies were conducted and revealed a number of proposed intermediates. Cp*Ru- (PiPr3)(η2-HCCPh)Cl was observed and characterized by 1H, 13C, and 31P NMR at temperatures between 273 and 213 K. A rare example of N,N-κ2-phosphazide complex, Cp*Ru(κ2-iPr3PN3Bn)Cl, was fully characterized, and a single-crystal X-ray diffraction structure was obtained. DFT calculations describe a complete map of the catalytic reactivity with phenylacetylene and/or benzylazide. 2012-01-23T00:00:00Z Lamberti, Marina Fortman, George C. Poater, Albert Broggi, Julie Slawin, Alexandra M. Z. Cavallo, Luigi Nolan, Steven P. The performance of 16-electron ruthenium complexes with the general formula Cp*Ru(L)X (in which L = phosphine or N-heterocyclic carbene ligand; X = Cl or OCH2CF3) was explored in azide−alkyne cycloaddition reactions that afford the 1,2,3- triazole products. The scope of the Cp*Ru(PiPr3)Cl precatalyst was investigated for terminal alkynes leading to new 1,5-disubstituted 1,2,3-triazoles in high yields. Mechanistic studies were conducted and revealed a number of proposed intermediates. Cp*Ru- (PiPr3)(η2-HCCPh)Cl was observed and characterized by 1H, 13C, and 31P NMR at temperatures between 273 and 213 K. A rare example of N,N-κ2-phosphazide complex, Cp*Ru(κ2-iPr3PN3Bn)Cl, was fully characterized, and a single-crystal X-ray diffraction structure was obtained. DFT calculations describe a complete map of the catalytic reactivity with phenylacetylene and/or benzylazide. http://hdl.handle.net/10023/3312 2012-01-01T00:00:00Z Kamusella, Tomasz Dominik http://hdl.handle.net/10023/3311 2010-12-15T00:00:00Z Magurran, Anne E. http://hdl.handle.net/10023/3310 Abstract: The 2010 Biodiversity Target of the Convention on Biological Diversity (CBD), set in 2002, which stated that there should be ‘a significant reduction of the current rate of biodiversity loss' by 2010, highlighted the need for informative and tractable metrics that can be used to evaluate change in biological diversity. While the subsequent Aichi 2020 targets are more wide-ranging, they also seek to reduce the rate of biodiversity loss. The geometric mean of relative abundance indices, G, is increasingly being used to examine trends in biological diversity and to assess whether biodiversity targets are being met. Here, we explore the mathematical and statistical properties of G that make it useful for judging temporal change in biological diversity, and we discuss its advantages and limitations relative to other measures. We demonstrate that the index reflects trends in both abundance and evenness, and that it is not prone to bias when detectability of individuals varies by species. We note that it allows data from different surveys to be combined to generate a composite index. However, the index exhibits high variance and unstable behaviour when rarely-recorded species are included in the analyses. Read More: http://www.esajournals.org/doi/abs/10.1890/ES11-00186.1 2011-09-02T00:00:00Z Buckland, Stephen Terrence Studeny, Angelika Caroline Magurran, Anne Illian, Janine Baerbel Newson, Stuart The 2010 Biodiversity Target of the Convention on Biological Diversity (CBD), set in 2002, which stated that there should be ‘a significant reduction of the current rate of biodiversity loss' by 2010, highlighted the need for informative and tractable metrics that can be used to evaluate change in biological diversity. While the subsequent Aichi 2020 targets are more wide-ranging, they also seek to reduce the rate of biodiversity loss. The geometric mean of relative abundance indices, G, is increasingly being used to examine trends in biological diversity and to assess whether biodiversity targets are being met. Here, we explore the mathematical and statistical properties of G that make it useful for judging temporal change in biological diversity, and we discuss its advantages and limitations relative to other measures. We demonstrate that the index reflects trends in both abundance and evenness, and that it is not prone to bias when detectability of individuals varies by species. We note that it allows data from different surveys to be combined to generate a composite index. However, the index exhibits high variance and unstable behaviour when rarely-recorded species are included in the analyses. Read More: http://www.esajournals.org/doi/abs/10.1890/ES11-00186.1 http://hdl.handle.net/10023/3309 Abstract: Because most species in an ecological assemblage are rare, much of the species richness we value is due to taxa with few individuals or a restricted distribution. It has been apparent since the time of ecological pioneers such as Bates and Darwin that tropical systems have disproportionately large numbers of rare species, yet the distribution and abundance patterns of these species remain largely unknown. Here, we examine the diversity of freshwater fish in a series of lakes in the Amazonian várzea, and relate relative abundance, both as numbers of individuals and as biomass, to the occurrence of species in space and time. We find a bimodal relationship of occurrence that distinguishes temporally and spatially persistent species from those that are infrequent in both space and time. Logistic regression reveals that information on occurrence helps distinguish those species that are rare in this locality but abundant elsewhere, from those that are rare throughout the region. These results form a link between different approaches used to evaluate commonness and rarity. In doing so, they provide a tool for identifying species of high conservation priority in poorly documented but species rich localities. 2013-01-01T00:00:00Z Hercos, A Sobansky, M Queiroz, H Magurran, Anne Because most species in an ecological assemblage are rare, much of the species richness we value is due to taxa with few individuals or a restricted distribution. It has been apparent since the time of ecological pioneers such as Bates and Darwin that tropical systems have disproportionately large numbers of rare species, yet the distribution and abundance patterns of these species remain largely unknown. Here, we examine the diversity of freshwater fish in a series of lakes in the Amazonian várzea, and relate relative abundance, both as numbers of individuals and as biomass, to the occurrence of species in space and time. We find a bimodal relationship of occurrence that distinguishes temporally and spatially persistent species from those that are infrequent in both space and time. Logistic regression reveals that information on occurrence helps distinguish those species that are rare in this locality but abundant elsewhere, from those that are rare throughout the region. These results form a link between different approaches used to evaluate commonness and rarity. In doing so, they provide a tool for identifying species of high conservation priority in poorly documented but species rich localities. http://hdl.handle.net/10023/3308 Abstract: There is no universally accepted working linguistic definition of a language; the distinction between a dialect and a language is a political question. On the basis of a discussion of this problem, the article proposes that the ISO 639 family of standards, issued by the International Organization for Standardization (ISO), amounts to the backbone of an emerging global regime of language recognition. This regime is being rapidly coaxed into being by the booming IT industry and by the Internet, both of which require clear-cut and uniform standards on languages and their scripts in order to function efficiently and profitably. A potentially undesirable and divisive foundation of the regulatory regime, stemming from and meeting the distinctive sectoral purposes of the world of Evangelicalism and Bible translation, is a hurdle to be overcome in achieving a universally accepted system of language standards. Despite efforts by other actors, there is no viable secular alternative in prospect, because the religiously-grounded system has an established and substantial “first mover” advantage in the field. 2012-11-21T00:00:00Z Kamusella, Tomasz Dominik There is no universally accepted working linguistic definition of a language; the distinction between a dialect and a language is a political question. On the basis of a discussion of this problem, the article proposes that the ISO 639 family of standards, issued by the International Organization for Standardization (ISO), amounts to the backbone of an emerging global regime of language recognition. This regime is being rapidly coaxed into being by the booming IT industry and by the Internet, both of which require clear-cut and uniform standards on languages and their scripts in order to function efficiently and profitably. A potentially undesirable and divisive foundation of the regulatory regime, stemming from and meeting the distinctive sectoral purposes of the world of Evangelicalism and Bible translation, is a hurdle to be overcome in achieving a universally accepted system of language standards. Despite efforts by other actors, there is no viable secular alternative in prospect, because the religiously-grounded system has an established and substantial “first mover” advantage in the field. http://hdl.handle.net/10023/3307 Abstract: The quality of contracting institutions has been thought to be of second-order importance next to the impact that good property rights institutions can have on long- run growth. Using a large range of proxies for each type of institution, we find a robust $negative$ link between the quality of contracting institutions and long-run growth when we condition on property rights and a number of additional macroeconomic variables. Although the result remains something of a puzzle, we present evidence which suggests that only when property rights institutions are good do contracting institutions appear also to be good for development. Good contracting institutions can reduce long-run growth when property rights are not secured, presumably because the gains from the (costly) contracting institutions cannot be realised. This suggests that contracting institutions can benefit growth, and that the sequence of institutional change can matter. 2012-01-01T00:00:00Z Trew, Alex William The quality of contracting institutions has been thought to be of second-order importance next to the impact that good property rights institutions can have on long- run growth. Using a large range of proxies for each type of institution, we find a robust $negative$ link between the quality of contracting institutions and long-run growth when we condition on property rights and a number of additional macroeconomic variables. Although the result remains something of a puzzle, we present evidence which suggests that only when property rights institutions are good do contracting institutions appear also to be good for development. Good contracting institutions can reduce long-run growth when property rights are not secured, presumably because the gains from the (costly) contracting institutions cannot be realised. This suggests that contracting institutions can benefit growth, and that the sequence of institutional change can matter. http://hdl.handle.net/10023/3306 Abstract: Integrated nested Laplace approximation (INLA) provides a fast and yet quite exact approach to fitting complex latent Gaussian models which comprise many statistical models in a Bayesian context, including log Gaussian Cox processes. This paper discusses how a joint log Gaussian Cox process model may be fitted to independent replicated point patterns. We illustrate the approach by fitting a model to data on the locations of muskoxen (Ovibos moschatus) herds in Zackenberg valley, Northeast Greenland and by detailing how this model is specified within the R-interface R-INLA. The paper strongly focuses on practical problems involved in the modelling process, including issues of spatial scale, edge effects and prior choices, and finishes with a discussion on models with varying boundary conditions. 2012-07-01T00:00:00Z Illian, Janine Baerbel Soerbye, S Rue, H Hendrichsen, D Integrated nested Laplace approximation (INLA) provides a fast and yet quite exact approach to fitting complex latent Gaussian models which comprise many statistical models in a Bayesian context, including log Gaussian Cox processes. This paper discusses how a joint log Gaussian Cox process model may be fitted to independent replicated point patterns. We illustrate the approach by fitting a model to data on the locations of muskoxen (Ovibos moschatus) herds in Zackenberg valley, Northeast Greenland and by detailing how this model is specified within the R-interface R-INLA. The paper strongly focuses on practical problems involved in the modelling process, including issues of spatial scale, edge effects and prior choices, and finishes with a discussion on models with varying boundary conditions. http://hdl.handle.net/10023/3305 Abstract: We consider spatial point pattern data that have been observed repeatedly over a period of time in an inhomogeneous environment. Each spatial point pattern can be regarded as a “snapshot” of the underlying point process at a series of times. Thus, the number of points and corresponding locations of points differ for each snapshot. Each snapshot can be analyzed independently, but in many cases there may be little information in the data relating to model parameters, particularly parameters relating to the interaction between points. Thus, we develop an integrated approach, simultaneously analyzing all snapshots within a single robust and consistent analysis. We assume that sufficient time has passed between observation dates so that the spatial point patterns can be regarded as independent replicates, given spatial covariates. We develop a joint mixed effects Gibbs point process model for the replicates of spatial point patterns by considering environmental covariates in the analysis as fixed effects, to model the heterogeneous environment, with a random effects (or hierarchical) component to account for the different observation days for the intensity function. We demonstrate how the model can be fitted within a Bayesian framework using an auxiliary variable approach to deal with the issue of the random effects component. We apply the methods to a data set of musk oxen herds and demonstrate the increased precision of the parameter estimates when considering all available data within a single integrated analysis. 2012-12-01T00:00:00Z King, Ruth Illian, Janine Barbel King, Stuart Edward Nightingale, Glenna Faith Hendrichsen, Ditte We consider spatial point pattern data that have been observed repeatedly over a period of time in an inhomogeneous environment. Each spatial point pattern can be regarded as a “snapshot” of the underlying point process at a series of times. Thus, the number of points and corresponding locations of points differ for each snapshot. Each snapshot can be analyzed independently, but in many cases there may be little information in the data relating to model parameters, particularly parameters relating to the interaction between points. Thus, we develop an integrated approach, simultaneously analyzing all snapshots within a single robust and consistent analysis. We assume that sufficient time has passed between observation dates so that the spatial point patterns can be regarded as independent replicates, given spatial covariates. We develop a joint mixed effects Gibbs point process model for the replicates of spatial point patterns by considering environmental covariates in the analysis as fixed effects, to model the heterogeneous environment, with a random effects (or hierarchical) component to account for the different observation days for the intensity function. We demonstrate how the model can be fitted within a Bayesian framework using an auxiliary variable approach to deal with the issue of the random effects component. We apply the methods to a data set of musk oxen herds and demonstrate the increased precision of the parameter estimates when considering all available data within a single integrated analysis. http://hdl.handle.net/10023/3304 Abstract: Scanning electron microscopy and high-resolution transmission electron microscopy have been used to investigate non-classic crystal growth of catalytic nanoparticles, such as zeolites, perovskites, metal and alloy particles. Growth mechanisms of some crystals with novel morphologies, for example, BiOBr flower-like particles and ZnO twin-crystals, have also been studied. A development of sampling method for soot particles inside a candle flame allows us to reveal all four well-known carbon forms, amorphous, graphitic, fullerenic and nanodiamond particles. This article demonstrates that electron microscopy is a powerful tool to study the microstructures of small particles, giving us more freedom to develop new materials. 2012-09-01T00:00:00Z Zhou, Wuzong Yu, Fengjiao Greer, Heather Frances Jiang, Zheng Edwards, Peter P. Scanning electron microscopy and high-resolution transmission electron microscopy have been used to investigate non-classic crystal growth of catalytic nanoparticles, such as zeolites, perovskites, metal and alloy particles. Growth mechanisms of some crystals with novel morphologies, for example, BiOBr flower-like particles and ZnO twin-crystals, have also been studied. A development of sampling method for soot particles inside a candle flame allows us to reveal all four well-known carbon forms, amorphous, graphitic, fullerenic and nanodiamond particles. This article demonstrates that electron microscopy is a powerful tool to study the microstructures of small particles, giving us more freedom to develop new materials. http://hdl.handle.net/10023/3303 Abstract: In the field of biomedical optics, Raman spectroscopy is a powerful tool for probing the chemical composition of biological samples. In particular, fiber Raman probes play a crucial role for in vivo and ex vivo tissue analysis. However, the high-fluorescence background typically contributed by the auto fluorescence from both a tissue sample and the fiber-probe interferes strongly with the relatively weak Raman signal. Here we demonstrate the implementation of wavelength-modulated Raman spectroscopy (WMRS) to suppress the fluorescence background while analyzing tissues using fiber Raman probes. We have observed a significant signal-to-noise ratio enhancement in the Raman bands of bone tissue, which have a relatively high fluorescence background. Implementation of WMRS in fiber-probe-based bone tissue study yielded usable Raman spectra in a relatively short acquisition time (∼30  s), notably without any special sample preparation stage. Finally, we have validated its capability to suppress fluorescence on other tissue samples such as adipose tissue derived from four different species. 2012-07-09T00:00:00Z Balagopal, Bavishna Ashok, Praveen Cheriyan Mazilu, Michael Riches, Andrew Clive Herrington, C Simon Dholakia, Kishan In the field of biomedical optics, Raman spectroscopy is a powerful tool for probing the chemical composition of biological samples. In particular, fiber Raman probes play a crucial role for in vivo and ex vivo tissue analysis. However, the high-fluorescence background typically contributed by the auto fluorescence from both a tissue sample and the fiber-probe interferes strongly with the relatively weak Raman signal. Here we demonstrate the implementation of wavelength-modulated Raman spectroscopy (WMRS) to suppress the fluorescence background while analyzing tissues using fiber Raman probes. We have observed a significant signal-to-noise ratio enhancement in the Raman bands of bone tissue, which have a relatively high fluorescence background. Implementation of WMRS in fiber-probe-based bone tissue study yielded usable Raman spectra in a relatively short acquisition time (∼30  s), notably without any special sample preparation stage. Finally, we have validated its capability to suppress fluorescence on other tissue samples such as adipose tissue derived from four different species. http://hdl.handle.net/10023/3302 Abstract: The removal of chemically damaged DNA bases such as 3-methyladenine (3-MeA) is an essential process in all living organisms and is catalyzed by the enzyme 3-MeA DNA glycosylase I. A key question is how the enzyme selectively recognizes the alkylated 3-MeA over the much more abundant adenine. The crystal structures of native and Y16F-mutant 3-MeA DNA glycosylase I from Staphylococcus aureus in complex with 3-MeA are reported to 1.8 and 2.2 angstrom resolution, respectively. Isothermal titration calorimetry shows that protonation of 3-MeA decreases its binding affinity, confirming previous fluorescence studies that show that chargecharge recognition is not critical for the selection of 3-MeA over adenine. It is hypothesized that the hydrogen-bonding pattern of Glu38 and Tyr16 of 3-MeA DNA glycosylase I with a particular tautomer unique to 3-MeA contributes to recognition and selection. 2012-06-01T00:00:00Z Zhu, Xiaofeng Yan, Xuan Carter, Lester G. Liu, Huanting Graham, Shirley Coote, Peter J. Naismith, James The removal of chemically damaged DNA bases such as 3-methyladenine (3-MeA) is an essential process in all living organisms and is catalyzed by the enzyme 3-MeA DNA glycosylase I. A key question is how the enzyme selectively recognizes the alkylated 3-MeA over the much more abundant adenine. The crystal structures of native and Y16F-mutant 3-MeA DNA glycosylase I from Staphylococcus aureus in complex with 3-MeA are reported to 1.8 and 2.2 angstrom resolution, respectively. Isothermal titration calorimetry shows that protonation of 3-MeA decreases its binding affinity, confirming previous fluorescence studies that show that chargecharge recognition is not critical for the selection of 3-MeA over adenine. It is hypothesized that the hydrogen-bonding pattern of Glu38 and Tyr16 of 3-MeA DNA glycosylase I with a particular tautomer unique to 3-MeA contributes to recognition and selection. http://hdl.handle.net/10023/3301 Abstract: Naval sonar has been accused of causing whale stranding by a mechanism which increases formation of tissue N2 gas bubbles. Increased tissue and blood N2 levels, and thereby increased risk of decompression sickness (DCS), is thought to result from changes in behavior or physiological responses during diving. Previous theoretical studies have used hypothetical sonar-induced changes in both behavior and physiology to model blood and tissue N2 tension PN2, but this is the first attempt to estimate the changes during actual behavioral responses to sonar. We used an existing mathematical model to estimate blood and tissue N2 tension PN2 from dive data recorded from sperm, killer, long-finned pilot, Blainville’s beaked, and Cuvier’s beaked whales before and during exposure to Low- (1–2 kHz) and Mid- (2–7 kHz) frequency active sonar. Our objectives were: (1) to determine if differences in dive behavior affects risk of bubble formation, and if (2) behavioral- or (3) physiological responses to sonar are plausible risk factors. Our results suggest that all species have natural high N2 levels, with deep diving generally resulting in higher end-dive PN2 as compared with shallow diving. Sonar exposure caused some changes in dive behavior in both killer whales, pilot whales and beaked whales, but this did not lead to any increased risk of DCS. However, in three of eight exposure session with sperm whales, the animal changed to shallower diving, and in all these cases this seem to result in an increased risk of DCS, although risk was still within the normal risk range of this species. When a hypothetical removal of the normal dive response (bradycardia and peripheral vasoconstriction), was added to the behavioral response during model simulations, this led to an increased variance in the estimated end-dive N2 levels, but no consistent change of risk. In conclusion, we cannot rule out the possibility that a combination of behavioral and physiological responses to sonar have the potential to alter the blood and tissue end-dive N2 tension to levels which could cause DCS and formation of in vivo bubbles, but the actually observed behavioral responses of cetaceans to sonar in our study, do not imply any significantly increased risk of DCS. 2012-05-10T00:00:00Z Kvadsheim, Petter H Miller, Patrick Tyack, Peter Lloyd Sivle, Lise D Lam, Frans Peter Fahlman, Andreas Naval sonar has been accused of causing whale stranding by a mechanism which increases formation of tissue N2 gas bubbles. Increased tissue and blood N2 levels, and thereby increased risk of decompression sickness (DCS), is thought to result from changes in behavior or physiological responses during diving. Previous theoretical studies have used hypothetical sonar-induced changes in both behavior and physiology to model blood and tissue N2 tension PN2, but this is the first attempt to estimate the changes during actual behavioral responses to sonar. We used an existing mathematical model to estimate blood and tissue N2 tension PN2 from dive data recorded from sperm, killer, long-finned pilot, Blainville’s beaked, and Cuvier’s beaked whales before and during exposure to Low- (1–2 kHz) and Mid- (2–7 kHz) frequency active sonar. Our objectives were: (1) to determine if differences in dive behavior affects risk of bubble formation, and if (2) behavioral- or (3) physiological responses to sonar are plausible risk factors. Our results suggest that all species have natural high N2 levels, with deep diving generally resulting in higher end-dive PN2 as compared with shallow diving. Sonar exposure caused some changes in dive behavior in both killer whales, pilot whales and beaked whales, but this did not lead to any increased risk of DCS. However, in three of eight exposure session with sperm whales, the animal changed to shallower diving, and in all these cases this seem to result in an increased risk of DCS, although risk was still within the normal risk range of this species. When a hypothetical removal of the normal dive response (bradycardia and peripheral vasoconstriction), was added to the behavioral response during model simulations, this led to an increased variance in the estimated end-dive N2 levels, but no consistent change of risk. In conclusion, we cannot rule out the possibility that a combination of behavioral and physiological responses to sonar have the potential to alter the blood and tissue end-dive N2 tension to levels which could cause DCS and formation of in vivo bubbles, but the actually observed behavioral responses of cetaceans to sonar in our study, do not imply any significantly increased risk of DCS. http://hdl.handle.net/10023/3300 Abstract: All eukaryotic organisms, single-celled or multi-cellular, produce a diverse array of natural anti-infective agents that, in addition to conventional antimicrobial peptides, also include proteins and other molecules often not regarded as part of the innate defences. Examples range from histones, fatty acids, and other structural components of cells to pigments and regulatory proteins. These probably represent very ancient defence factors that have been re-used in new ways during evolution. This review discusses the nature, biological role in host protection and potential biotechnological uses of some of these compounds, focusing on those from fish, marine invertebrates and marine micro-algae. 2010-04-14T00:00:00Z Smith, Valerie Jane Desbois, Andrew Paul Dyrynda, Elisabeth All eukaryotic organisms, single-celled or multi-cellular, produce a diverse array of natural anti-infective agents that, in addition to conventional antimicrobial peptides, also include proteins and other molecules often not regarded as part of the innate defences. Examples range from histones, fatty acids, and other structural components of cells to pigments and regulatory proteins. These probably represent very ancient defence factors that have been re-used in new ways during evolution. This review discusses the nature, biological role in host protection and potential biotechnological uses of some of these compounds, focusing on those from fish, marine invertebrates and marine micro-algae. http://hdl.handle.net/10023/3299 Abstract: Six silver(I) coordination complexes have been prepared and structurally characterised. Mixed chalcogen-donor acenaphthene ligands L1–L3 [Acenap(EPh)(E'Ph)] (Acenap = acenaphthene-5,6-diyl; E/E' = S, Se, Te) were independently treated with silver(I) salts (AgBF4/AgOTf). In order to keep the number of variables to a minimum, all reactions were carried out using a 1:1 ratio of Ag/L and run in dichloromethane. The nature of the donor atoms, the coordinating ability of the respective counter-anion and the type of solvent used in recrystallisation, all affect the structural architecture of the final silver(I) complex, generating monomeric, silver(I) complexes {[AgBF4(L)2] (1 L = L1; 2 L = L2; 3 L = L3), [AgOTf(L)3] (4 L = L1; 5 L = L3), [AgBF4(L)3] (2a L = L1; 3a L = L3)} and a 1D polymeric chain {[AgOTf(L3)]n 6}. The organic acenaphthene ligands L1-L3 adopt a number of ligation modes (bis-monodentate μ2-η2-bridging, quasi-chelating combining monodentate and η6-E(phenyl)-Ag(I) and classical monodentate coordination) with the central silver atom at the centre of a tetrahedral or trigonal planar coordination geometry in each case. The importance of weak interactions in the formation of metal-organic structures is also highlighted by the number of short non-covalent contacts present within each complex. 2012-11-08T00:00:00Z Knight, Fergus Ross Randall, Rebecca Amy Michele Wakefield, Lucy Slawin, Alexandra Martha Zoya Woollins, J Derek Six silver(I) coordination complexes have been prepared and structurally characterised. Mixed chalcogen-donor acenaphthene ligands L1–L3 [Acenap(EPh)(E'Ph)] (Acenap = acenaphthene-5,6-diyl; E/E' = S, Se, Te) were independently treated with silver(I) salts (AgBF4/AgOTf). In order to keep the number of variables to a minimum, all reactions were carried out using a 1:1 ratio of Ag/L and run in dichloromethane. The nature of the donor atoms, the coordinating ability of the respective counter-anion and the type of solvent used in recrystallisation, all affect the structural architecture of the final silver(I) complex, generating monomeric, silver(I) complexes {[AgBF4(L)2] (1 L = L1; 2 L = L2; 3 L = L3), [AgOTf(L)3] (4 L = L1; 5 L = L3), [AgBF4(L)3] (2a L = L1; 3a L = L3)} and a 1D polymeric chain {[AgOTf(L3)]n 6}. The organic acenaphthene ligands L1-L3 adopt a number of ligation modes (bis-monodentate μ2-η2-bridging, quasi-chelating combining monodentate and η6-E(phenyl)-Ag(I) and classical monodentate coordination) with the central silver atom at the centre of a tetrahedral or trigonal planar coordination geometry in each case. The importance of weak interactions in the formation of metal-organic structures is also highlighted by the number of short non-covalent contacts present within each complex. http://hdl.handle.net/10023/3298 Abstract: WbdD is a bifunctional kinase/methyltransferase that is responsible for regulation of lipopolysaccharide O antigen polysaccharide chain length in Escherichia coli serotype O9a. Solving the crystal structure of this protein proved to be a challenge because the available crystals belonging to space group I23 only diffracted to low resolution (>95% of the crystals diffracted to resolution lower than 4 angstrom and most only to 8 angstrom) and were non-isomorphous, with changes in unit-cell dimensions of greater than 10%. Data from a serendipitously found single native crystal that diffracted to 3.0 angstrom resolution were non-isomorphous with a lower (3.5 angstrom) resolution selenomethionine data set. Here, a strategy for improving poor (3.5 angstrom resolution) initial phases by density modification and cross-crystal averaging with an additional 4.2 angstrom resolution data set to build a crude model of WbdD is desribed. Using this crude model as a mask to cut out the 3.5 angstrom resolution electron density yielded a successful molecular-replacement solution of the 3.0 angstrom resolution data set. The resulting map was used to build a complete model of WbdD. The hydration status of individual crystals appears to underpin the variable diffraction quality of WbdD crystals. After the initial structure had been solved, methods to control the hydration status of WbdD were developed and it was thus possible to routinely obtain high-resolution diffraction (to better than 2.5 angstrom resolution). This novel and facile crystal-dehydration protocol may be useful for similar challenging situations. 2012-10-01T00:00:00Z Hagelueken, Gregor Huang, Hexian Harlos, Karl Clarke, Bradley R. Whitfield, Chris Naismith, James H. WbdD is a bifunctional kinase/methyltransferase that is responsible for regulation of lipopolysaccharide O antigen polysaccharide chain length in Escherichia coli serotype O9a. Solving the crystal structure of this protein proved to be a challenge because the available crystals belonging to space group I23 only diffracted to low resolution (>95% of the crystals diffracted to resolution lower than 4 angstrom and most only to 8 angstrom) and were non-isomorphous, with changes in unit-cell dimensions of greater than 10%. Data from a serendipitously found single native crystal that diffracted to 3.0 angstrom resolution were non-isomorphous with a lower (3.5 angstrom) resolution selenomethionine data set. Here, a strategy for improving poor (3.5 angstrom resolution) initial phases by density modification and cross-crystal averaging with an additional 4.2 angstrom resolution data set to build a crude model of WbdD is desribed. Using this crude model as a mask to cut out the 3.5 angstrom resolution electron density yielded a successful molecular-replacement solution of the 3.0 angstrom resolution data set. The resulting map was used to build a complete model of WbdD. The hydration status of individual crystals appears to underpin the variable diffraction quality of WbdD crystals. After the initial structure had been solved, methods to control the hydration status of WbdD were developed and it was thus possible to routinely obtain high-resolution diffraction (to better than 2.5 angstrom resolution). This novel and facile crystal-dehydration protocol may be useful for similar challenging situations. http://hdl.handle.net/10023/3297 Abstract: The essential histone variant H2A.Z localises to both active and silent chromatin sites. In embryonic stem cells (ESCs), H2A.Z is also reported to co-localise with polycomb repressive complex 2 (PRC2) at developmentally silenced genes. The mechanism of H2A.Z targeting is not clear, but a role for the PRC2 component Suz12 has been suggested. Given this association, we wished to determine if polycomb functionally directs H2A.Z incorporation in ESCs. We demonstrate that the PRC1 component Ring1B interacts with multiple complexes in ESCs. Moreover, we show that although the genomic distribution of H2A.Z co-localises with PRC2, Ring1B and with the presence of CpG islands, H2A.Z still blankets polycomb target loci in the absence of Suz12, Eed (PRC2) or Ring1B (PRC1). Therefore we conclude that H2A.Z accumulates at developmentally silenced genes in ESCs in a polycomb independent manner. 2012-04-09T00:00:00Z Illingworth, Robert S. Botting, Catherine H. Grimes, Graeme R. Bickmore, Wendy A. Eskeland, Ragnhild The essential histone variant H2A.Z localises to both active and silent chromatin sites. In embryonic stem cells (ESCs), H2A.Z is also reported to co-localise with polycomb repressive complex 2 (PRC2) at developmentally silenced genes. The mechanism of H2A.Z targeting is not clear, but a role for the PRC2 component Suz12 has been suggested. Given this association, we wished to determine if polycomb functionally directs H2A.Z incorporation in ESCs. We demonstrate that the PRC1 component Ring1B interacts with multiple complexes in ESCs. Moreover, we show that although the genomic distribution of H2A.Z co-localises with PRC2, Ring1B and with the presence of CpG islands, H2A.Z still blankets polycomb target loci in the absence of Suz12, Eed (PRC2) or Ring1B (PRC1). Therefore we conclude that H2A.Z accumulates at developmentally silenced genes in ESCs in a polycomb independent manner. http://hdl.handle.net/10023/3296 Abstract: We use magnetic force microscopy (MFM) to measure the local penetration depth λ in Ba(Fe0.95Co0.05)2As2 single crystals and use scanning superconducting quantum interference device susceptometry to measure its temperature variation down to 0.4 K. We observe that superfluid density ρs over the full temperature range is well described by a clean two-band fully gapped model. We demonstrate that MFM can measure the important and hard-to-determine absolute value of λ, as well as obtain its temperature dependence and spatial homogeneity. We find ρs to be uniform on the submicron scale despite the highly disordered vortex pinning. 2010-03-01T00:00:00Z Luan, Lan Auslaender, Ophir Lippman, Thomas M Hicks, Clifford William Kalisky, Beena Chu, Jiun-Haw Analytis, James G Fisher, Ian R Kirtley, John R Moler, Kathryn A We use magnetic force microscopy (MFM) to measure the local penetration depth λ in Ba(Fe0.95Co0.05)2As2 single crystals and use scanning superconducting quantum interference device susceptometry to measure its temperature variation down to 0.4 K. We observe that superfluid density ρs over the full temperature range is well described by a clean two-band fully gapped model. We demonstrate that MFM can measure the important and hard-to-determine absolute value of λ, as well as obtain its temperature dependence and spatial homogeneity. We find ρs to be uniform on the submicron scale despite the highly disordered vortex pinning. http://hdl.handle.net/10023/3295 Abstract: We measure the penetration depth λab(T) in Ba(Fe1-xCox)2As2 using local techniques that do not average over the sample. The superfluid density ρs(T)≡1/λab(T)2 has three main features. First, ρs(T=0) falls sharply on the underdoped side of the dome. Second, λab(T) is flat at low T at optimal doping, indicating fully gapped superconductivity, but varies more strongly in underdoped and overdoped samples, consistent with either a power law or a small second gap. Third, ρs(T) varies steeply near Tc for optimal and underdoping. These observations are consistent with an interplay between magnetic and superconducting phases. 2011-02-09T00:00:00Z Luan, Lan Lippman, Thomas M Hicks, Clifford William Bert, Julie A Auslaender, Ophir M Chu, Jiun-Haw Analytis, James G Fisher, Ian R Moler, Kathryn A We measure the penetration depth λab(T) in Ba(Fe1-xCox)2As2 using local techniques that do not average over the sample. The superfluid density ρs(T)≡1/λab(T)2 has three main features. First, ρs(T=0) falls sharply on the underdoped side of the dome. Second, λab(T) is flat at low T at optimal doping, indicating fully gapped superconductivity, but varies more strongly in underdoped and overdoped samples, consistent with either a power law or a small second gap. Third, ρs(T) varies steeply near Tc for optimal and underdoping. These observations are consistent with an interplay between magnetic and superconducting phases. http://hdl.handle.net/10023/3294 Abstract: We present scanning superconducting quantum interference device microscopy data on the superconductors Sr2RuO4 (Tc=1.5 K) and PrOs4Sb12 (Tc=1.8 K). In both of these materials, superconductivity-related time-reversal symmetry-breaking fields have been observed by muon spin rotation; our aim was to visualize the structure of these fields. However, in neither Sr2RuO4 nor PrOs4Sb12 do we observe spontaneous superconductivity-related magnetization. In Sr2RuO4, many experimental results have been interpreted on the basis of a px±ipy superconducting order parameter. This order parameter is expected to give spontaneous magnetic induction at sample edges and order parameter domain walls. Supposing large domains, our data restrict domain wall and edge fields to no more than ∼0.1% and ∼0.2% of the expected magnitude, respectively. Alternatively, if the magnetization is of the expected order, the typical domain size is limited to ∼30 nm for random domains or ∼500 nm for periodic domains. 2010-06-01T00:00:00Z Hicks, Clifford William Kirtley, John R Lippman, Thomas M Koshnick, Nicholas C Huber, Martin E Maeno, Yoshiteru Yuhasz, William M Maple, M Brian Moler, Kathryn A We present scanning superconducting quantum interference device microscopy data on the superconductors Sr2RuO4 (Tc=1.5 K) and PrOs4Sb12 (Tc=1.8 K). In both of these materials, superconductivity-related time-reversal symmetry-breaking fields have been observed by muon spin rotation; our aim was to visualize the structure of these fields. However, in neither Sr2RuO4 nor PrOs4Sb12 do we observe spontaneous superconductivity-related magnetization. In Sr2RuO4, many experimental results have been interpreted on the basis of a px±ipy superconducting order parameter. This order parameter is expected to give spontaneous magnetic induction at sample edges and order parameter domain walls. Supposing large domains, our data restrict domain wall and edge fields to no more than ∼0.1% and ∼0.2% of the expected magnitude, respectively. Alternatively, if the magnetization is of the expected order, the typical domain size is limited to ∼30 nm for random domains or ∼500 nm for periodic domains. http://hdl.handle.net/10023/3293 Abstract: The search for potent and selective sirtuin inhibitors continues as chemical tools of this type are of use in helping to assign the function of this interesting class of deacetylases. Here we describe SAR studies starting from the unselective sirtuin inhibitor tenovin-6. These studies identify a sub-micromolar inhibitor that has increased selectivity for SIRT2 over SIRT1 compared to tenovin-6. In addition, a H-1-NMR-based method is developed and used to validate further this class of sirtuin inhibitors. A thermal shift analysis of SIRT2 in the presence of tenovin-6, -43, a control tenovin and the known SIRT2 inhibitor AGK2 is also presented. 2012-10-01T00:00:00Z Pirrie, Lisa McCarthy, Anna R. Major, Louise L. Morkunaite, Vaida Zubriene, Asta Matulis, Daumantas Lain, Sonia Lebl, Tomas Westwood, Nicholas J. The search for potent and selective sirtuin inhibitors continues as chemical tools of this type are of use in helping to assign the function of this interesting class of deacetylases. Here we describe SAR studies starting from the unselective sirtuin inhibitor tenovin-6. These studies identify a sub-micromolar inhibitor that has increased selectivity for SIRT2 over SIRT1 compared to tenovin-6. In addition, a H-1-NMR-based method is developed and used to validate further this class of sirtuin inhibitors. A thermal shift analysis of SIRT2 in the presence of tenovin-6, -43, a control tenovin and the known SIRT2 inhibitor AGK2 is also presented. http://hdl.handle.net/10023/3292 Abstract: The Escherichia coli serotype O9a O-antigen polysaccharide (O-PS) is a model for glycan biosynthesis and export by the ATP-binding cassette transporter-dependent pathway. The polymannose O9a O-PS is synthesized as a polyprenol-linked glycan by mannosyltransferase enzymes located at the cytoplasmic membrane. The chain length of the O9a O-PS is tightly regulated by the WbdD enzyme. WbdD first phosphorylates the terminal non-reducing mannose of the O-PS and then methylates the phosphate, stopping polymerization. The 2.2?angstrom resolution structure of WbdD reveals a bacterial methyltransferase domain joined to a eukaryotic kinase domain. The kinase domain is again fused to an extended C-terminal coiled-coil domain reminiscent of eukaryotic DMPK (Myotonic Dystrophy Protein Kinase) family kinases such as Rho-associated protein kinase (ROCK). WbdD phosphorylates 2-a-d-mannosyl-d-mannose (2a-MB), a short mimic of the O9a polymer. Mutagenesis identifies those residues important in catalysis and substrate recognition and the in vivo phenotypes of these mutants are used to dissect the termination reaction. We have determined the structures of co-complexes of WbdD with two known eukaryotic protein kinase inhibitors. Although these are potent inhibitors in vitro, they do not show any in vivo activity. The structures reveal new insight into O-PS chain-length regulation in this important model system. 2012-11-01T00:00:00Z Hagelueken, Gregor Huang, Hexian Clarke, Bradley R. Lebl, Tomas Whitfield, Chris Naismith, James H. The Escherichia coli serotype O9a O-antigen polysaccharide (O-PS) is a model for glycan biosynthesis and export by the ATP-binding cassette transporter-dependent pathway. The polymannose O9a O-PS is synthesized as a polyprenol-linked glycan by mannosyltransferase enzymes located at the cytoplasmic membrane. The chain length of the O9a O-PS is tightly regulated by the WbdD enzyme. WbdD first phosphorylates the terminal non-reducing mannose of the O-PS and then methylates the phosphate, stopping polymerization. The 2.2?angstrom resolution structure of WbdD reveals a bacterial methyltransferase domain joined to a eukaryotic kinase domain. The kinase domain is again fused to an extended C-terminal coiled-coil domain reminiscent of eukaryotic DMPK (Myotonic Dystrophy Protein Kinase) family kinases such as Rho-associated protein kinase (ROCK). WbdD phosphorylates 2-a-d-mannosyl-d-mannose (2a-MB), a short mimic of the O9a polymer. Mutagenesis identifies those residues important in catalysis and substrate recognition and the in vivo phenotypes of these mutants are used to dissect the termination reaction. We have determined the structures of co-complexes of WbdD with two known eukaryotic protein kinase inhibitors. Although these are potent inhibitors in vitro, they do not show any in vivo activity. The structures reveal new insight into O-PS chain-length regulation in this important model system. http://hdl.handle.net/10023/3291 2012-12-20T00:00:00Z Jones, Chris http://hdl.handle.net/10023/3290 Abstract: Whole genome sequencing (WGS) promises to be transformative for the practice of clinical microbiology, and the rapidly falling cost and turnaround time mean that this will become a viable technology in diagnostic and reference laboratories in the near future. The objective of this article is to consider at a very practical level where, in the context of a modern diagnostic microbiology laboratory, WGS might be cost-effective compared to current alternatives. We propose that molecular epidemiology performed for surveillance and outbreak investigation and genotypic antimicrobial susceptibility testing for microbes that are difficult to grow represent the most immediate areas for application of WGS, and discuss the technical and infrastructure requirements for this to be implemented. 2012-08-02T00:00:00Z Koeser, Claudio U. Ellington, Matthew J. Cartwright, Edward J. P. Gillespie, Stephen H. Brown, Nicholas M. Farrington, Mark Holden, Matthew T. G. Dougan, Gordon Bentley, Stephen D. Parkhill, Julian Peacock, Sharon J. Whole genome sequencing (WGS) promises to be transformative for the practice of clinical microbiology, and the rapidly falling cost and turnaround time mean that this will become a viable technology in diagnostic and reference laboratories in the near future. The objective of this article is to consider at a very practical level where, in the context of a modern diagnostic microbiology laboratory, WGS might be cost-effective compared to current alternatives. We propose that molecular epidemiology performed for surveillance and outbreak investigation and genotypic antimicrobial susceptibility testing for microbes that are difficult to grow represent the most immediate areas for application of WGS, and discuss the technical and infrastructure requirements for this to be implemented. http://hdl.handle.net/10023/3287 Abstract: Independent studies have shown that candidate genes for dyslexia and specific language impairment (SLI) impact upon reading/language-specific traits in the general population. To further explore the effect of disorder-associated genes on cognitive functions, we investigated whether they play a role in broader cognitive traits. We tested a panel of dyslexia and SLI genetic risk factors for association with two measures of general cognitive abilities, or IQ, (verbal and non-verbal) in the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort (N>5,000). Only the MRPL19/C2ORF3 locus showed statistically significant association (minimum P = 0.00009) which was further supported by independent replications following analysis in four other cohorts. In addition, a fifth independent sample showed association between the MRPL19/C2ORF3 locus and white matter structure in the posterior part of the corpus callosum and cingulum, connecting large parts of the cortex in the parietal, occipital and temporal lobes. These findings suggest that this locus, originally identified as being associated with dyslexia, is likely to harbour genetic variants associated with general cognitive abilities by influencing white matter structure in localised neuronal regions. 2012-11-28T00:00:00Z Scerri, Thomas S. Darki, Fahimeh Newbury, Dianne F. Whitehouse, Andrew J. O. Peyrard-Janvid, Myriam Matsson, Hans Ang, Qi W. Pennell, Craig E. Ring, Susan Stein, John Morris, Andrew P. Monaco, Anthony P. Kere, Juha Talcott, Joel B. Klingberg, Torkel Paracchini, Silvia Independent studies have shown that candidate genes for dyslexia and specific language impairment (SLI) impact upon reading/language-specific traits in the general population. To further explore the effect of disorder-associated genes on cognitive functions, we investigated whether they play a role in broader cognitive traits. We tested a panel of dyslexia and SLI genetic risk factors for association with two measures of general cognitive abilities, or IQ, (verbal and non-verbal) in the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort (N>5,000). Only the MRPL19/C2ORF3 locus showed statistically significant association (minimum P = 0.00009) which was further supported by independent replications following analysis in four other cohorts. In addition, a fifth independent sample showed association between the MRPL19/C2ORF3 locus and white matter structure in the posterior part of the corpus callosum and cingulum, connecting large parts of the cortex in the parietal, occipital and temporal lobes. These findings suggest that this locus, originally identified as being associated with dyslexia, is likely to harbour genetic variants associated with general cognitive abilities by influencing white matter structure in localised neuronal regions. http://hdl.handle.net/10023/3286 Abstract: Site-directed spin labeling and pulsed electron–electron double resonance (PELDOR or DEER) have previously been applied successfully to study the structure and dynamics of nucleic acids. Spin labeling nucleic acids at specific sites requires the covalent attachment of spin labels, which involves rather complicated and laborious chemical synthesis. Here, we use a noncovalent label strategy that bypasses the covalent labeling chemistry and show that the binding specificity and efficiency are large enough to enable PELDOR or DEER measurements in DNA duplexes and a DNA duplex bound to the Lac repressor protein. In addition, the rigidity of the label not only allows resolution of the structure and dynamics of oligonucleotides but also the determination of label orientation and protein-induced conformational changes. The results prove that this labeling strategy in combination with PELDOR has a great potential for studying both structure and dynamics of oligonucleotides and their complexes with various ligands. 2013-01-01T00:00:00Z Reginsson, Gunnar Widtfeldt Shelke, Sandip Rouillon, Christophe White, Malcolm F Sigurdsson, Snorri T Schiemann, Olav Site-directed spin labeling and pulsed electron–electron double resonance (PELDOR or DEER) have previously been applied successfully to study the structure and dynamics of nucleic acids. Spin labeling nucleic acids at specific sites requires the covalent attachment of spin labels, which involves rather complicated and laborious chemical synthesis. Here, we use a noncovalent label strategy that bypasses the covalent labeling chemistry and show that the binding specificity and efficiency are large enough to enable PELDOR or DEER measurements in DNA duplexes and a DNA duplex bound to the Lac repressor protein. In addition, the rigidity of the label not only allows resolution of the structure and dynamics of oligonucleotides but also the determination of label orientation and protein-induced conformational changes. The results prove that this labeling strategy in combination with PELDOR has a great potential for studying both structure and dynamics of oligonucleotides and their complexes with various ligands. http://hdl.handle.net/10023/3285 Abstract: Based on our previous work (Vidotto et al. 2009a), we investigate the effects on the wind and magnetospheric structures of weak-lined T Tauri stars due to a misalignment between the axis of rotation of the star and its magnetic dipole moment vector. In such configuration, the system loses the axisymmetry presented in the aligned case, requiring a fully 3D approach. We perform 3D numerical MHD simulations of stellar winds and study the effects caused by different model parameters. The system reaches a periodic behavior with the same rotational period of the star. We show that the magnetic field lines present an oscillatory pattern and that by increasing the misalignment angle, the wind velocity increases. Our wind models allow us to study the interaction of a magnetized wind with a magnetized extra-solar planet. Such interaction gives rise to reconnection, generating electrons that propagate along the planet's magnetic field lines and produce electron cyclotron radiation at radio wavelengths. We find that a close-in Jupiter-like planet orbiting at 0.05AU presents a radio power that is ~5 orders of magnitude larger than the one observed in Jupiter, which suggests that the stellar wind from a young star has the potential to generate strong planetary radio emission that could be detected in the near future with LOFAR. This radio power varies according to the phase of rotation of the star. We also analyze whether winds from misaligned stellar magnetospheres could cause a significant effect on planetary migration. Compared to the aligned case, we show that the time-scale tau_w for an appreciable radial motion of the planet is shorter for larger misalignment angles. While for the aligned case tau_w~100Myr, for a stellar magnetosphere tilted by 30deg, tau_w ranges from ~40 to 70Myr for a planet located at a radius of 0.05AU. (Abridged) Description: 21 pages, 16 figures, 2 tables (emulateapj.cls). 2010-08-19T00:00:00Z A. Vidotto, A. Opher, M. Jatenco-Pereira, V. I. Gombosi, T. Based on our previous work (Vidotto et al. 2009a), we investigate the effects on the wind and magnetospheric structures of weak-lined T Tauri stars due to a misalignment between the axis of rotation of the star and its magnetic dipole moment vector. In such configuration, the system loses the axisymmetry presented in the aligned case, requiring a fully 3D approach. We perform 3D numerical MHD simulations of stellar winds and study the effects caused by different model parameters. The system reaches a periodic behavior with the same rotational period of the star. We show that the magnetic field lines present an oscillatory pattern and that by increasing the misalignment angle, the wind velocity increases. Our wind models allow us to study the interaction of a magnetized wind with a magnetized extra-solar planet. Such interaction gives rise to reconnection, generating electrons that propagate along the planet's magnetic field lines and produce electron cyclotron radiation at radio wavelengths. We find that a close-in Jupiter-like planet orbiting at 0.05AU presents a radio power that is ~5 orders of magnitude larger than the one observed in Jupiter, which suggests that the stellar wind from a young star has the potential to generate strong planetary radio emission that could be detected in the near future with LOFAR. This radio power varies according to the phase of rotation of the star. We also analyze whether winds from misaligned stellar magnetospheres could cause a significant effect on planetary migration. Compared to the aligned case, we show that the time-scale tau_w for an appreciable radial motion of the planet is shorter for larger misalignment angles. While for the aligned case tau_w~100Myr, for a stellar magnetosphere tilted by 30deg, tau_w ranges from ~40 to 70Myr for a planet located at a radius of 0.05AU. (Abridged) http://hdl.handle.net/10023/3284 Abstract: Growing concern about biodiversity loss underscores the need to quantify and understand temporal change. Here, we review the opportunities presented by biodiversity time series, and address three related issues: (i) recognizing the characteristics of temporal data; (ii) selecting appropriate statistical procedures for analysing temporal data; and (iii) inferring and forecasting biodiversity change. With regard to the first issue, we draw attention to defining characteristics of biodiversity time series—lack of physical boundaries, uni-dimensionality, autocorrelation and directionality—that inform the choice of analytic methods. Second, we explore methods of quantifying change in biodiversity at different timescales, noting that autocorrelation can be viewed as a feature that sheds light on the underlying structure of temporal change. Finally, we address the transition from inferring to forecasting biodiversity change, highlighting potential pitfalls associated with phase-shifts and novel conditions. 2013-01-01T00:00:00Z Dornelas, Maria Magurran, Anne Buckland, Stephen Terrence Chao, Anne Chazdon, Robin L Colwell, Robert K Curtis, Tom Gaston, Kevin J Gotelli, Nicolas J Kosnik, Matthew A McGill, Brian McCune, Jenny L Morlon, Hélène Mumby, Peter J Øvreås, Lise Studeny, Angelika Vellend, Mark Growing concern about biodiversity loss underscores the need to quantify and understand temporal change. Here, we review the opportunities presented by biodiversity time series, and address three related issues: (i) recognizing the characteristics of temporal data; (ii) selecting appropriate statistical procedures for analysing temporal data; and (iii) inferring and forecasting biodiversity change. With regard to the first issue, we draw attention to defining characteristics of biodiversity time series—lack of physical boundaries, uni-dimensionality, autocorrelation and directionality—that inform the choice of analytic methods. Second, we explore methods of quantifying change in biodiversity at different timescales, noting that autocorrelation can be viewed as a feature that sheds light on the underlying structure of temporal change. Finally, we address the transition from inferring to forecasting biodiversity change, highlighting potential pitfalls associated with phase-shifts and novel conditions. http://hdl.handle.net/10023/3283 Abstract: The introduction of non-native species into new habitats poses a major threat to native populations. Of particular interest, though often overlooked, are introductions of populations that are not fully reproductively isolated from native individuals and can hybridize with them. To address this important topic we used different approaches in a multi-pronged study, combining the effects of mate choice, shoaling behaviour and genetics. Here we present evidence that behavioural traits such as shoaling and mate choice can promote population mixing if individuals do not distinguish between native and foreign conspecifics. We examined this in the context of two guppy (Poecilia reticulata) populations that have been subject to an introduction and subsequent population mixing event in Trinidad. The introduction of Guanapo River guppies into the Turure River more than 50 years ago led to a marked reduction of the original genotype. In our experiments, female guppies did not distinguish between shoaling partners when given the choice between native and foreign individuals. Introduced fish are therefore likely to benefit from the protection of a shoal and will improve their survival chances as a result. The additional finding that male guppies do not discriminate between females on the basis of origin will further increase the process of population mixing, especially if males encounter mixed shoals. In a mesocosm experiment, in which the native and foreign populations were allowed to mate freely, we found, as expected on the basis of these behavioural interactions, that the distribution of offspring genotypes could be predicted from the proportions of the two types of founding fish. This result suggests that stochastic and environmental processes have reinforced the biological ones to bring about the genetic dominance of the invading population in the Turure River. Re-sampling the Turure for genetic analysis using SNP markers confirmed the population mixing process and showed that it is an on-going process in this river and has led to the nearly complete disappearance of the original genotype. 2012-05-31T00:00:00Z Sievers, Caya Willing, Eva-Maria Hoffmann, Margarete Dreyer, Christine Ramnarine, Indar Magurran, Anne The introduction of non-native species into new habitats poses a major threat to native populations. Of particular interest, though often overlooked, are introductions of populations that are not fully reproductively isolated from native individuals and can hybridize with them. To address this important topic we used different approaches in a multi-pronged study, combining the effects of mate choice, shoaling behaviour and genetics. Here we present evidence that behavioural traits such as shoaling and mate choice can promote population mixing if individuals do not distinguish between native and foreign conspecifics. We examined this in the context of two guppy (Poecilia reticulata) populations that have been subject to an introduction and subsequent population mixing event in Trinidad. The introduction of Guanapo River guppies into the Turure River more than 50 years ago led to a marked reduction of the original genotype. In our experiments, female guppies did not distinguish between shoaling partners when given the choice between native and foreign individuals. Introduced fish are therefore likely to benefit from the protection of a shoal and will improve their survival chances as a result. The additional finding that male guppies do not discriminate between females on the basis of origin will further increase the process of population mixing, especially if males encounter mixed shoals. In a mesocosm experiment, in which the native and foreign populations were allowed to mate freely, we found, as expected on the basis of these behavioural interactions, that the distribution of offspring genotypes could be predicted from the proportions of the two types of founding fish. This result suggests that stochastic and environmental processes have reinforced the biological ones to bring about the genetic dominance of the invading population in the Turure River. Re-sampling the Turure for genetic analysis using SNP markers confirmed the population mixing process and showed that it is an on-going process in this river and has led to the nearly complete disappearance of the original genotype. http://hdl.handle.net/10023/3282 Abstract: One of the initial steps of modern drug discovery is the identification of small organic molecules able to inhibit a target macromolecule of therapeutic interest. A small proportion of these hits are further developed into lead compounds, which in turn may ultimately lead to a marketed drug. A commonly used screening protocol used for this task is high-throughput screening (HTS). However, the performance of HTS against antibacterial targets has generally been unsatisfactory, with high costs and low rates of hit identification. Here, we present a novel computational methodology that is able to identify a high proportion of structurally diverse inhibitors by searching unusually large molecular databases in a time-, cost- and resource-efficient manner. This virtual screening methodology was tested prospectively on two versions of an antibacterial target (type II dehydroquinase from Mycobacterium tuberculosis and Streptomyces coelicolor), for which HTS has not provided satisfactory results and consequently practically all known inhibitors are derivatives of the same core scaffold. Overall, our protocols identified 100 new inhibitors, with calculated Ki ranging from 4 to 250 μM (confirmed hit rates are 60% and 62% against each version of the target). Most importantly, over 50 new active molecular scaffolds were discovered that underscore the benefits that a wide application of prospectively validated in silico screening tools is likely to bring to antibacterial hit identification. 2012-12-07T00:00:00Z Ballester, Pedro Mangold, Martina Howard, Nigel Marchese Robinson, Richard Abell, Chris Blumberger, Jochen Mitchell, John B. O. One of the initial steps of modern drug discovery is the identification of small organic molecules able to inhibit a target macromolecule of therapeutic interest. A small proportion of these hits are further developed into lead compounds, which in turn may ultimately lead to a marketed drug. A commonly used screening protocol used for this task is high-throughput screening (HTS). However, the performance of HTS against antibacterial targets has generally been unsatisfactory, with high costs and low rates of hit identification. Here, we present a novel computational methodology that is able to identify a high proportion of structurally diverse inhibitors by searching unusually large molecular databases in a time-, cost- and resource-efficient manner. This virtual screening methodology was tested prospectively on two versions of an antibacterial target (type II dehydroquinase from Mycobacterium tuberculosis and Streptomyces coelicolor), for which HTS has not provided satisfactory results and consequently practically all known inhibitors are derivatives of the same core scaffold. Overall, our protocols identified 100 new inhibitors, with calculated Ki ranging from 4 to 250 μM (confirmed hit rates are 60% and 62% against each version of the target). Most importantly, over 50 new active molecular scaffolds were discovered that underscore the benefits that a wide application of prospectively validated in silico screening tools is likely to bring to antibacterial hit identification. http://hdl.handle.net/10023/3281 Abstract: Languages are made and unmade, as nations are. The vagaries of history and politics that create the fluctuating framework in which human groups exist, influence these groups’ thinking about their own speech. Over the course of history Upper Silesia’s Slavophones (a group who, in the modern period, were predominantly bilingual in German) were divided up at different times between Prussia, Austria (that is, the Habsburg lands), Germany, Czechoslovakia (today, the Czech Republic) and Poland, and they had to adapt to these changes. During the last two centuries, with the rise of ethnolinguistic nationalism in Central Europe, it meant either accepting a dominant ethnolinguistic national identity, complete with its specific standard language (especially in the dark period of authoritarianisms and totalitarianism between 1926 and 1989), or inventing a Silesianness, frequently buttressed by the concept of a Silesian language. Against this backdrop, the article considers the emergence of the Silesian (regional, ethnic, national?) movement during the last two decades, with the main focus on efforts to standardize Silesian and have it recognized as a language in its own right. 2013-01-01T00:00:00Z Kamusella, Tomasz Dominik Languages are made and unmade, as nations are. The vagaries of history and politics that create the fluctuating framework in which human groups exist, influence these groups’ thinking about their own speech. Over the course of history Upper Silesia’s Slavophones (a group who, in the modern period, were predominantly bilingual in German) were divided up at different times between Prussia, Austria (that is, the Habsburg lands), Germany, Czechoslovakia (today, the Czech Republic) and Poland, and they had to adapt to these changes. During the last two centuries, with the rise of ethnolinguistic nationalism in Central Europe, it meant either accepting a dominant ethnolinguistic national identity, complete with its specific standard language (especially in the dark period of authoritarianisms and totalitarianism between 1926 and 1989), or inventing a Silesianness, frequently buttressed by the concept of a Silesian language. Against this backdrop, the article considers the emergence of the Silesian (regional, ethnic, national?) movement during the last two decades, with the main focus on efforts to standardize Silesian and have it recognized as a language in its own right. http://hdl.handle.net/10023/3280 Abstract: Background: Bunyamwera orthobunyavirus is both the prototype and study model of the Bunyaviridae family. The viral NSs protein seems to contribute to the different outcomes of infection in mammalian and mosquito cell lines. However, only limited information is available on the growth of Bunyamwera virus in cultured mosquito cells other than the Aedes albopictus C6/36 line. Methodology and Principal Findings: To determine potential functions of the NSs protein in mosquito cells, replication of wild-type virus and a recombinant NSs deletion mutant was compared in Ae. albopictus C6/36, C7-10 and U4.4 cells, and in Ae. aegypti Ae cells by monitoring N protein production and virus yields at various times post infection. Both viruses established persistent infections, with the exception of NSs deletion mutant in U4.4 cells. The NSs protein was nonessential for growth in C6/36 and C7-10 cells, but was important for productive replication in U4.4 and Ae cells. Fluorescence microscopy studies using recombinant viruses expressing green fluorescent protein allowed observation of three stages of infection, early, acute and late, during which infected cells underwent morphological changes. In the absence of NSs, these changes were less pronounced. An RNAi response efficiently reduced virus replication in U4.4 cells transfected with virus specific dsRNA, but not in C6/36 or C7/10 cells. Lastly, Ae. aegypti mosquitoes were exposed to blood-meal containing either wild-type or NSs deletion virus, and at various times post-feeding, infection and disseminated infection rates were measured. Compared to wild-type virus, infection rates by the mutant virus were lower and more variable. If the NSs deletion virus was able to establish infection, it was detected in salivary glands at 6 days post-infection, 3 days later than wild-type virus. Conclusions/Significance: Bunyamwera virus NSs is required for efficient replication in certain mosquito cell lines and in Ae. aegypti mosquitoes. 2012-09-01T00:00:00Z Szemiel, Agnieszka M. Failloux, Anna-Bella Elliott, Richard M. Background: Bunyamwera orthobunyavirus is both the prototype and study model of the Bunyaviridae family. The viral NSs protein seems to contribute to the different outcomes of infection in mammalian and mosquito cell lines. However, only limited information is available on the growth of Bunyamwera virus in cultured mosquito cells other than the Aedes albopictus C6/36 line. Methodology and Principal Findings: To determine potential functions of the NSs protein in mosquito cells, replication of wild-type virus and a recombinant NSs deletion mutant was compared in Ae. albopictus C6/36, C7-10 and U4.4 cells, and in Ae. aegypti Ae cells by monitoring N protein production and virus yields at various times post infection. Both viruses established persistent infections, with the exception of NSs deletion mutant in U4.4 cells. The NSs protein was nonessential for growth in C6/36 and C7-10 cells, but was important for productive replication in U4.4 and Ae cells. Fluorescence microscopy studies using recombinant viruses expressing green fluorescent protein allowed observation of three stages of infection, early, acute and late, during which infected cells underwent morphological changes. In the absence of NSs, these changes were less pronounced. An RNAi response efficiently reduced virus replication in U4.4 cells transfected with virus specific dsRNA, but not in C6/36 or C7/10 cells. Lastly, Ae. aegypti mosquitoes were exposed to blood-meal containing either wild-type or NSs deletion virus, and at various times post-feeding, infection and disseminated infection rates were measured. Compared to wild-type virus, infection rates by the mutant virus were lower and more variable. If the NSs deletion virus was able to establish infection, it was detected in salivary glands at 6 days post-infection, 3 days later than wild-type virus. Conclusions/Significance: Bunyamwera virus NSs is required for efficient replication in certain mosquito cell lines and in Ae. aegypti mosquitoes. http://hdl.handle.net/10023/3277 Abstract: Housing has been unjustifiably neglected in comparative welfare state research. The banking crisis of 2007–08, however, revealed how important housing, especially home ownership and the institutional structures of the mortgage market, has become to welfare state change. Securitisation of mortgages created a new circuit of global capital, while national mortgage markets became the conduit through which home owners were connected to this wave of globally sourced capital. In the UK, equity stored in owner-occupied property became much more fungible because of the very open/liberal mortgage market. As a result home owners began to ‘bank’ on their homes using it not only for consumption but increasingly as a financial safety net, a cushion against adversity and a means for securing access to privately supplied services and supporting their family’s welfare needs across the life-course. This welfare state change – a move towards assetbased welfare – was historically and today remains underpinned by the emergence of the UK as a home-owning society. 2012-01-01T00:00:00Z Lowe, Stuart Searle, Beverley Ann Smith, Susan J Housing has been unjustifiably neglected in comparative welfare state research. The banking crisis of 2007–08, however, revealed how important housing, especially home ownership and the institutional structures of the mortgage market, has become to welfare state change. Securitisation of mortgages created a new circuit of global capital, while national mortgage markets became the conduit through which home owners were connected to this wave of globally sourced capital. In the UK, equity stored in owner-occupied property became much more fungible because of the very open/liberal mortgage market. As a result home owners began to ‘bank’ on their homes using it not only for consumption but increasingly as a financial safety net, a cushion against adversity and a means for securing access to privately supplied services and supporting their family’s welfare needs across the life-course. This welfare state change – a move towards assetbased welfare – was historically and today remains underpinned by the emergence of the UK as a home-owning society. http://hdl.handle.net/10023/3276 Abstract: ABSTRACT: Massive coral species play a key role in coral reef ecosystems, adding significantly to physical integrity, long term stability and reef biodiversity. This study coupled the assessment of the distribution and abundance of 4 dominant massive coral species, Diploastrea heliopora, Favia speciosa, F. matthaii and Porites lutea, with investigations into species-specific photoacclimatory responses within the Wakatobi Marine National Park of southeast Sulawesi, Indonesia, to determine the potential of photoacclimation to be a driver of biological success. For this, rapid light curves using pulse amplitude modulated (PAM) chlorophyll a fluorescence techniques were employed with additional manipulations to circumvent differences of light quality and absorption between species and across environmental gradients. P. lutea was examined over a range of depths and sites to determine patterns of photoacclimation, and all 4 species were assessed at a single depth between sites for which long-term data for coral community structure and growth existed. Light availability was more highly constrained with depth than between sites; consequently, photoacclimation patterns for P. lutea appeared greater with depth than across environmental gradients. All 4 species were found to differentially modify the extent of non-photochemical quenching to maintain a constant photochemical operating efficiency (qP). Therefore, our results suggest that these massive corals photoacclimate to ensure a constant light-dependent rate of reduction of the plastoquinone pool across growth environments. 2008-10-13T00:00:00Z Hennige, S.J. Smith, D.J. Perkins, R. Consalvey, M Paterson, David Maxwell Suggett, D.J. ABSTRACT: Massive coral species play a key role in coral reef ecosystems, adding significantly to physical integrity, long term stability and reef biodiversity. This study coupled the assessment of the distribution and abundance of 4 dominant massive coral species, Diploastrea heliopora, Favia speciosa, F. matthaii and Porites lutea, with investigations into species-specific photoacclimatory responses within the Wakatobi Marine National Park of southeast Sulawesi, Indonesia, to determine the potential of photoacclimation to be a driver of biological success. For this, rapid light curves using pulse amplitude modulated (PAM) chlorophyll a fluorescence techniques were employed with additional manipulations to circumvent differences of light quality and absorption between species and across environmental gradients. P. lutea was examined over a range of depths and sites to determine patterns of photoacclimation, and all 4 species were assessed at a single depth between sites for which long-term data for coral community structure and growth existed. Light availability was more highly constrained with depth than between sites; consequently, photoacclimation patterns for P. lutea appeared greater with depth than across environmental gradients. All 4 species were found to differentially modify the extent of non-photochemical quenching to maintain a constant photochemical operating efficiency (qP). Therefore, our results suggest that these massive corals photoacclimate to ensure a constant light-dependent rate of reduction of the plastoquinone pool across growth environments. http://hdl.handle.net/10023/3275 Abstract: Background: Akirins are nuclear proteins that form part of an innate immune response pathway conserved in Drosophila and mice. This studies aim was to characterise the evolution of akirin gene structure and protein function in the eukaryotes. Results: akirin genes are present throughout the metazoa and arose before the separation of animal, plant and fungi lineages. Using comprehensive phylogenetic analysis, coupled with comparisons of conserved synteny and genomic organisation, we show that the intron-exon structure of metazoan akirin genes was established prior to the bilateria and that a single proto-orthologue duplicated in the vertebrates, before the gnathostome-agnathan separation, producing akirin1 and akirin2. Phylogenetic analyses of seven vertebrate gene families with members in chromosomal proximity to both akirin1 and akirin2 were compatible with a common duplication event affecting the genomic neighbourhood of the akirin proto-orthologue. A further duplication of akirins occurred in the teleost lineage and was followed by lineage-specific patterns of paralogue loss. Remarkably, akirins have been independently characterised by five research groups under different aliases and a comparison of the available literature revealed diverse functions, generally in regulating gene expression. For example, akirin was characterised in arthropods as subolesin, an important growth factor and in Drosophila as bhringi, which has an essential myogenic role. In vertebrates, akirin1 was named mighty in mice and was shown to regulate myogenesis, whereas akirin2 was characterised as FB11 in rats and promoted carcinogenesis, acting as a transcriptional repressor when bound to a 14-3-3 protein. Both vertebrate Akirins have evolved under comparably strict constraints of purifying selection, although a likelihood ratio test predicted that functional divergence has occurred between paralogues. Bayesian and maximum likelihood tests identified amino-acid positions where the rate of evolution had shifted significantly between paralogues. Interestingly, the highest scoring position was within a conserved, validated binding-site for 14-3-3 proteins. Conclusion: This work offers an evolutionary framework to facilitate future studies of eukaryotic akirins and provides insight into their multifaceted and conserved biochemical functions. 2009-02-06T00:00:00Z Macqueen, Daniel J. Johnston, Ian A. Background: Akirins are nuclear proteins that form part of an innate immune response pathway conserved in Drosophila and mice. This studies aim was to characterise the evolution of akirin gene structure and protein function in the eukaryotes. Results: akirin genes are present throughout the metazoa and arose before the separation of animal, plant and fungi lineages. Using comprehensive phylogenetic analysis, coupled with comparisons of conserved synteny and genomic organisation, we show that the intron-exon structure of metazoan akirin genes was established prior to the bilateria and that a single proto-orthologue duplicated in the vertebrates, before the gnathostome-agnathan separation, producing akirin1 and akirin2. Phylogenetic analyses of seven vertebrate gene families with members in chromosomal proximity to both akirin1 and akirin2 were compatible with a common duplication event affecting the genomic neighbourhood of the akirin proto-orthologue. A further duplication of akirins occurred in the teleost lineage and was followed by lineage-specific patterns of paralogue loss. Remarkably, akirins have been independently characterised by five research groups under different aliases and a comparison of the available literature revealed diverse functions, generally in regulating gene expression. For example, akirin was characterised in arthropods as subolesin, an important growth factor and in Drosophila as bhringi, which has an essential myogenic role. In vertebrates, akirin1 was named mighty in mice and was shown to regulate myogenesis, whereas akirin2 was characterised as FB11 in rats and promoted carcinogenesis, acting as a transcriptional repressor when bound to a 14-3-3 protein. Both vertebrate Akirins have evolved under comparably strict constraints of purifying selection, although a likelihood ratio test predicted that functional divergence has occurred between paralogues. Bayesian and maximum likelihood tests identified amino-acid positions where the rate of evolution had shifted significantly between paralogues. Interestingly, the highest scoring position was within a conserved, validated binding-site for 14-3-3 proteins. Conclusion: This work offers an evolutionary framework to facilitate future studies of eukaryotic akirins and provides insight into their multifaceted and conserved biochemical functions. http://hdl.handle.net/10023/3274 Abstract: Background. Gene families typically evolve by gene duplication followed by the adoption of new or altered gene functions. A different way to evolve new but related functions is alternative splicing of existing exons of a complex gene. The chemosensory gene families of animals are characterised by numerous loci of related function. Alternative splicing has only rarely been reported in chemosensory loci, for example in 5 out of around 120 loci in Drosophila melanogaster. The gustatory receptor gene Gr39a has four large exons that are alternatively spliced with three small conserved exons. Recently the genome sequences of eleven additional species of Drosophila have become available allowing us to examine variation in the structure of the Gr39a locus across a wide phylogenetic range of fly species. Methodology/Principal Findings. We describe a fifth exon and show that the locus has a complex evolutionary history with several duplications, pseudogenisations and losses of exons. PAML analyses suggested that the whole gene has a history of purifying selection, although this was less strong in exons which underwent duplication. Conclusions/Significance. Estimates of functional divergence between exons were similar in magnitude to functional divergence between duplicated genes, suggesting that exon divergence is broadly equivalent to gene duplication. 2008-01-30T00:00:00Z Gardiner, Anastasia Barker, Daniel Butlin, Roger K. Jordan, William C. Ritchie, Michael G. Background. Gene families typically evolve by gene duplication followed by the adoption of new or altered gene functions. A different way to evolve new but related functions is alternative splicing of existing exons of a complex gene. The chemosensory gene families of animals are characterised by numerous loci of related function. Alternative splicing has only rarely been reported in chemosensory loci, for example in 5 out of around 120 loci in Drosophila melanogaster. The gustatory receptor gene Gr39a has four large exons that are alternatively spliced with three small conserved exons. Recently the genome sequences of eleven additional species of Drosophila have become available allowing us to examine variation in the structure of the Gr39a locus across a wide phylogenetic range of fly species. Methodology/Principal Findings. We describe a fifth exon and show that the locus has a complex evolutionary history with several duplications, pseudogenisations and losses of exons. PAML analyses suggested that the whole gene has a history of purifying selection, although this was less strong in exons which underwent duplication. Conclusions/Significance. Estimates of functional divergence between exons were similar in magnitude to functional divergence between duplicated genes, suggesting that exon divergence is broadly equivalent to gene duplication. http://hdl.handle.net/10023/3273 Abstract: Background: MyoD is a muscle specific transcription factor that is essential for vertebrate myogenesis. In several teleost species, including representatives of the Salmonidae and Acanthopterygii, but not zebrafish, two or more MyoD paralogues are conserved that are thought to have arisen from distinct, possibly lineage-specific duplication events. Additionally, two MyoD paralogues have been characterised in the allotetraploid frog, Xenopus laevis. This has lead to a confusing nomenclature since MyoD paralogues have been named outside of an appropriate phylogenetic framework. Methods and Principal Findings: Here we initially show that directly depicting the evolutionary relationships of teleost MyoD orthologues and paralogues is hindered by the asymmetric evolutionary rate of Acanthopterygian MyoD2 relative to other MyoD proteins. Thus our aim was to confidently position the event from which teleost paralogues arose in different lineages by a comparative investigation of genes neighbouring myod across the vertebrates. To this end, we show that genes on the single myod-containing chromosome of mammals and birds are retained in both zebrafish and Acanthopterygian teleosts in a striking pattern of double conserved synteny. Further, phylogenetic reconstruction of these neighbouring genes using Bayesian and maximum likelihood methods supported a common origin for teleost paralogues following the split of the Actinopterygii and Sarcopterygii. Conclusion: Our results strongly suggest that myod was duplicated during the basal teleost whole genome duplication event, but was subsequently lost in the Ostariophysi ( zebrafish) and Protacanthopterygii lineages. We propose a sensible consensus nomenclature for vertebrate myod genes that accommodates polyploidization events in teleost and tetrapod lineages and is justified from a phylogenetic perspective. Description: DJM was supported by a Natural Environment Research Council studentship (NERC/S/A/2004/12435). 2008-02-06T00:00:00Z Macqueen, Daniel J. Johnston, Ian A. Background: MyoD is a muscle specific transcription factor that is essential for vertebrate myogenesis. In several teleost species, including representatives of the Salmonidae and Acanthopterygii, but not zebrafish, two or more MyoD paralogues are conserved that are thought to have arisen from distinct, possibly lineage-specific duplication events. Additionally, two MyoD paralogues have been characterised in the allotetraploid frog, Xenopus laevis. This has lead to a confusing nomenclature since MyoD paralogues have been named outside of an appropriate phylogenetic framework. Methods and Principal Findings: Here we initially show that directly depicting the evolutionary relationships of teleost MyoD orthologues and paralogues is hindered by the asymmetric evolutionary rate of Acanthopterygian MyoD2 relative to other MyoD proteins. Thus our aim was to confidently position the event from which teleost paralogues arose in different lineages by a comparative investigation of genes neighbouring myod across the vertebrates. To this end, we show that genes on the single myod-containing chromosome of mammals and birds are retained in both zebrafish and Acanthopterygian teleosts in a striking pattern of double conserved synteny. Further, phylogenetic reconstruction of these neighbouring genes using Bayesian and maximum likelihood methods supported a common origin for teleost paralogues following the split of the Actinopterygii and Sarcopterygii. Conclusion: Our results strongly suggest that myod was duplicated during the basal teleost whole genome duplication event, but was subsequently lost in the Ostariophysi ( zebrafish) and Protacanthopterygii lineages. We propose a sensible consensus nomenclature for vertebrate myod genes that accommodates polyploidization events in teleost and tetrapod lineages and is justified from a phylogenetic perspective. http://hdl.handle.net/10023/3272 Abstract: The growth in the range of disciplines that Virtual Worlds support for educational purposes is evidenced by recent applications in the fields of cultural heritage, humanitarian aid, space exploration, virtual laboratories in the physical sciences, archaeology, computer science and coastal geography. This growth is due in part to the flexibility of OpenSim, the open source virtual world platform which by adopting Second Life protocols and norms has created a de facto standard for open virtual worlds that is supported by a growing number of third party open source viewers. Yet while this diversity of use-cases is impressive and Virtual Worlds for open learning are highly popular with lecturers and learners alike immersive education remains an essentially niche activity. This paper identifies functional challenges in terms of Management, Network Infrastructure, the Immersive 3D Web and Programmability that must be addressed to enable the wider adoption of Open Virtual Worlds as a routine learning technology platform. We refer to specific use-cases based on OpenSim and abstract generic requirements which should be met to enable the growth in use of Open Virtual Worlds as a mainstream educational facility. A case study of a deployment to support a formal education curriculum and associated informal learning is used to illustrate key points. 2012-11-25T00:00:00Z Allison, Colin Campbell, Anne Davies, Christopher John Dow, Lisa Kennedy, Sarah McCaffery, John Philip Miller, Alan Henry David Oliver, Iain Angus Perera, Galhenage Indika Udaya Shantha The growth in the range of disciplines that Virtual Worlds support for educational purposes is evidenced by recent applications in the fields of cultural heritage, humanitarian aid, space exploration, virtual laboratories in the physical sciences, archaeology, computer science and coastal geography. This growth is due in part to the flexibility of OpenSim, the open source virtual world platform which by adopting Second Life protocols and norms has created a de facto standard for open virtual worlds that is supported by a growing number of third party open source viewers. Yet while this diversity of use-cases is impressive and Virtual Worlds for open learning are highly popular with lecturers and learners alike immersive education remains an essentially niche activity. This paper identifies functional challenges in terms of Management, Network Infrastructure, the Immersive 3D Web and Programmability that must be addressed to enable the wider adoption of Open Virtual Worlds as a routine learning technology platform. We refer to specific use-cases based on OpenSim and abstract generic requirements which should be met to enable the growth in use of Open Virtual Worlds as a mainstream educational facility. A case study of a deployment to support a formal education curriculum and associated informal learning is used to illustrate key points. http://hdl.handle.net/10023/3271 Abstract: Little is known about mate choice preferences outside Western, educated, industrialised, rich and democratic societies, even though these Western populations may be particularly unrepresentative of human populations. To our knowledge, this is the first study to test which facial cues contribute to African perceptions of African female attractiveness and also the first study to test the combined role of facial adiposity, skin colour (lightness, yellowness and redness), skin homogeneity and youthfulness in the facial attractiveness preferences of any population. Results show that youthfulness, skin colour, skin homogeneity and facial adiposity significantly and independently predict attractiveness in female African faces. Younger, thinner women with a lighter, yellower skin colour and a more homogenous skin tone are considered more attractive. These findings provide a more global perspective on human mate choice and point to a universal role for these four facial cues in female facial attractiveness. 2012-10-29T00:00:00Z Coetzee, Vinet Faerber, Stella J Greeff, Jaco M Lefevre, Carmen Emilia Re, Daniel Perrett, David Ian Little is known about mate choice preferences outside Western, educated, industrialised, rich and democratic societies, even though these Western populations may be particularly unrepresentative of human populations. To our knowledge, this is the first study to test which facial cues contribute to African perceptions of African female attractiveness and also the first study to test the combined role of facial adiposity, skin colour (lightness, yellowness and redness), skin homogeneity and youthfulness in the facial attractiveness preferences of any population. Results show that youthfulness, skin colour, skin homogeneity and facial adiposity significantly and independently predict attractiveness in female African faces. Younger, thinner women with a lighter, yellower skin colour and a more homogenous skin tone are considered more attractive. These findings provide a more global perspective on human mate choice and point to a universal role for these four facial cues in female facial attractiveness. http://hdl.handle.net/10023/3270 Abstract: The Cas4 protein is one of the core CRISPR-associated (Cas) proteins implicated in the prokaryotic CRISPR system for antiviral defence. Cas4 is thought to play a role in the capture of new viral DNA sequences for incorporation into the host genome. No biochemical activity has been reported for Cas4, but it is predicted to include a RecB nuclease domain. We show here that Cas4 family proteins from the archaeon Sulfolobus solfataricus utilise four conserved cysteine residues to bind an iron-sulfur cluster in an arrangement reminiscent of the AddB nuclease of Bacillus subtilis. The Cas4 family protein Sso0001 is a 5' to 3' single stranded DNA exonuclease in vitro that is stalled by extrahelical DNA adducts. A role for Cas4 in DNA duplex strand resectioning to generate recombinogenic 3' single stranded DNA overhangs is proposed. Comparison of the AddB structure with that of a related bacterial nuclease from Eubacterium rectales reveals that the iron-sulfur cluster can be replaced by a zinc ion without disrupting the protein structure, with implications for the evolution of iron-sulfur binding proteins. 2012-10-08T00:00:00Z Zhang, Jing Kasciukovic, Taciana White, Malcolm F. The Cas4 protein is one of the core CRISPR-associated (Cas) proteins implicated in the prokaryotic CRISPR system for antiviral defence. Cas4 is thought to play a role in the capture of new viral DNA sequences for incorporation into the host genome. No biochemical activity has been reported for Cas4, but it is predicted to include a RecB nuclease domain. We show here that Cas4 family proteins from the archaeon Sulfolobus solfataricus utilise four conserved cysteine residues to bind an iron-sulfur cluster in an arrangement reminiscent of the AddB nuclease of Bacillus subtilis. The Cas4 family protein Sso0001 is a 5' to 3' single stranded DNA exonuclease in vitro that is stalled by extrahelical DNA adducts. A role for Cas4 in DNA duplex strand resectioning to generate recombinogenic 3' single stranded DNA overhangs is proposed. Comparison of the AddB structure with that of a related bacterial nuclease from Eubacterium rectales reveals that the iron-sulfur cluster can be replaced by a zinc ion without disrupting the protein structure, with implications for the evolution of iron-sulfur binding proteins. http://hdl.handle.net/10023/3269 Abstract: Background: Predators can have profound impacts on the dynamics of their prey that depend on how predator consumption is affected by prey density (the predator's functional response). Consumption by a generalist predator is expected to depend on the densities of all its major prey species (its multispecies functional response, or MSFR), but most studies of generalists have focussed on their functional response to only one prey species. Methodology and principal findings: Using Bayesian methods, we fit an MSFR to field data from an avian predator (the hen harrier Circus cyaneus) feeding on three different prey species. We use a simple graphical approach to show that ignoring the effects of alternative prey can give a misleading impression of the predator's effect on the prey of interest. For example, in our system, a “predator pit” for one prey species only occurs when the availability of other prey species is low. Conclusions and significance: The Bayesian approach is effective in fitting the MSFR model to field data. It allows flexibility in modelling over-dispersion, incorporates additional biological information into the parameter priors, and generates estimates of uncertainty in the model's predictions. These features of robustness and data efficiency make our approach ideal for the study of long-lived predators, for which data may be sparse and management/conservation priorities pressing. 2010-05-27T00:00:00Z Smout, Sophie Caroline Asseburg, C Matthiopoulos, Jason Fernández, Carmen Redpath, S Thirgood, S Harwood, John Background: Predators can have profound impacts on the dynamics of their prey that depend on how predator consumption is affected by prey density (the predator's functional response). Consumption by a generalist predator is expected to depend on the densities of all its major prey species (its multispecies functional response, or MSFR), but most studies of generalists have focussed on their functional response to only one prey species. Methodology and principal findings: Using Bayesian methods, we fit an MSFR to field data from an avian predator (the hen harrier Circus cyaneus) feeding on three different prey species. We use a simple graphical approach to show that ignoring the effects of alternative prey can give a misleading impression of the predator's effect on the prey of interest. For example, in our system, a “predator pit” for one prey species only occurs when the availability of other prey species is low. Conclusions and significance: The Bayesian approach is effective in fitting the MSFR model to field data. It allows flexibility in modelling over-dispersion, incorporates additional biological information into the parameter priors, and generates estimates of uncertainty in the model's predictions. These features of robustness and data efficiency make our approach ideal for the study of long-lived predators, for which data may be sparse and management/conservation priorities pressing.