VictorJuiz/thesis huggingface dataset:
E2F7: a member of the E2F family with a novel mechanism of transcriptional repression

The mammalian E2F family of transcription factors plays a crucial role in the regulation of cellular proliferation, apoptosis and differentiation. E2F7 and E2F8 are the most recently identified family members and have unusual features that distinguish them from other members in the E2F family, including two distinct DNA-binding domains that bind to DNA in a DP-independent manner. E2F7 and E2F8 have been shown to be transcriptional repressors. However, the mechanism by which E2F7 represses E2F responsive gene expression remains to be elucidated.
The results presented here provide the first insight into the E2F7-mediated transcriptional mechanism. E2F7 was shown to contain a CtBP binding motif and form a complex with CtBP in both HeLa and MCF7 cells. An E2F7 deletion mutant lacking the CtBP binding motif was unable to form a complex with CtBP and repress the transcription of E2F target genes in luciferase assays, suggesting that this motif is essential for E2F7-dependent repression. Furthermore, the E2F7-CtBP complex was shown to be stable under different types of damage, such as following etoposide and UV treatment, and under different cell redox states. Interestingly, however, E2F7 was unable to repress the transcriptional activity of E2F target genes following treatment with the CtBP substrate MTOB. Moreover, E2F7 endogenous immunoprecipitations showed that E2F7 forms a complex with the chromatin-modifying enzymes HDAC1, HDAC2 and LSD1 and the co-repressor CoREST. Interestingly, via chromatin immunoprecipitations, E2F7 was shown to recruit these co-repressors to a subset of E2F-responsive promoters where they affect the activity of these promoters in a target gene-specific manner. Furthermore, results presented here suggest that CtBP could play a dual role in E2F7 function, not only being involved in E2F7-mediated repression but also in the repression of E2F7 itself as siRNA mediated CtBP depletion was shown to cause an upregulation of E2F7 protein levels. These results implicate a repertoire of co-repressors in a target gene-specific E2F7 repression mechanism, and as such define a new level of complexity in cell cycle control.

Keywords: cell cycle
cancer
E2F
E2F7
Advisor: La Thangue, N
Geometric multigrid and closest point methods for surfaces and general domains

This thesis concerns the analytical and practical aspects of applying the Closest Point Method to solve elliptic partial differential equations (PDEs) on smooth surfaces and domains with smooth boundaries. A new numerical scheme is proposed to solve surface elliptic PDEs and a novel geometric multigrid solver is constructed to solve the resulting linear system. The method is also applied to coupled bulk-surface problems.
A new embedding equation in a narrow band surrounding the surface is formulated so that it agrees with the original surface PDE on the surface and has a unique solution which is constant along the normals to the surface. The embedding equation is then discretized using standard finite difference scheme and barycentric Lagrange interpolation. The resulting scheme has 2nd-order accuracy in practice and is provably 2nd-order convergent for curves without boundary embedded in &Ropf;2.
To apply the method to solve elliptic equations on surfaces and domains with boundaries, the "ghost" point approach is adopted to handle Dirichlet, Neumann and Robin boundary conditions. A systematic method is proposed to represent values of ghost points by values of interior points according to boundary conditions.
A novel geometric multigrid method based on the closest point representation of the surface is constructed to solve the resulting large sparse linear systems. Multigrid solvers are designed for surfaces with or without boundaries and domains with smooth boundaries. Numerical results indicate that the convergence rate of the multigrid solver stays roughly the same as we refine the mesh, as is desired of a multigrid algorithm.
Finally the above methods are combined to solve coupled bulk-surface PDEs with some applications to biology.

Keywords: multigird methods
Surface partial differential equations
Closest Point Method
finite difference methods
Advisor: Macdonald, C
Construction of national identities in Azerbaijan, Kazakhstan and Ukraine in Soviet historiography (1936-1953)

This dissertation aims to explain how Soviet national historiographies were constructed in Ukraine, Azerbaijan, and Kazakhstan, in 1936-1953 and what the political and ideological reasons were behind the way they were written. The dissertation aims to contribute to current scholarship on Soviet nationality policies; on Stalinist nation-building projects; and to the debate on whether the Soviet period was a project of developmentalist modernization or not. This dissertation aims to examine the process of national history writing in three republics from the local point of view, by using the local archival sources. For this research, archival materials that have been overlooked by scholars up to this point from the archives of the communist parties, academy of sciences, and central state archives in Kiev, Ukraine, Baku, Azerbaijan, and Almaty, Kazakhstan have been collected. The timeline starts with Zhdanov’s commission in 1936, which summoned historians and ideologues of the Communist Party in Moscow to write an all-Union history because a parallel campaign of writing national histories had been initialized by the local communist parties. The first two chapters cover the pre-war (1936-1941) period, when national histories were written after the demise of Pokrovskiian historiography. Although there was one ideology, there were different preferences in solving the problem of ethnogenesis, defining national heroes, and also different preferences among the sections of the past that national histories emphasized. The third chapter explains the construction of national histories during the war period (1941-1945). The chapter also presents how national histories were used for wartime propaganda. Finally, the last chapter is about the post-war discussions and the shift of emphasis from ‘national’ to ‘class’ that occurred in the non-Russian national narratives in the Zhdanovshchina period. While there was an ‘imperial design’ for the necessities of managing a multi-national state, the Soviet Union also appears as a modernization project for all three cases by constructing national narratives. Though non-Russian Soviet historiographies produced contradictory narratives in different decades, they also homogenized, codified and nationalized the narrative of the past. Regional, dynastic, religious, tribal figures and events incorporated into grandiose national narratives. Nations were primordialized and their national identities armed with spatial and temporal indigenousness within the borders of their national republics. Modern national identities of Azerbaijan, Kazakhstan and Ukraine gained from this homogenization and codification by the Soviet regime. Although modernism is not only about construction of national narratives, the latter points out the developmental and modernizing character of the Soviet period.

Keywords: Soviet Union
Azerbaijan
historiography
World War II
Stalinism
Kazakhstan
Russia
nationalism
Ukraine
Advisor: Service, R
Herzig, E
Threads to the past

This thesis describes the aboriginal and contemporary social organization of the Coast Salish people of southwestern British Columbia and northwestern Washington State, with a focus on the Squamish Nation whose Reserves are situated in North Vancouver and the Howe Sound area. It is based on field research undertaken over a 30-year period and on published and unpublished sources. The thesis explores the construction of kinship and social groups among the Coast Salish, and the transformation of these relationships over time and in various historical circumstances, from the mid-19th century to the present day.
Drawing upon the theoretical approaches of William Davenport (1959), Raymond Firth (1963) and Anthony Cohen (1985), among others, the thesis discusses key components of Coast Salish social organization and identity, including a group's contrasting identity and relation to the groups within its ambit of comparison, the association of specific social units with territory, and the expression of status in both traditional and contemporary society. Specific findings document a shift to nuclear family households, the adoption of English kinship terms, the development of hereditary and elected leadership, and the emergence of the Tribe and the First Nation as primary symbols of identity in the 20th century. Some current issues resulting from the impact of change are examined in the context of naming ceremonies and disputes over inherited property, including ancestral names.
The thesis argues that the diversity and complexity of neither the traditional nor transformed expressions of Coast Salish social organization find congruence with models of aboriginal society being deployed by contemporary Courts and Treaty negotiators. Issues of territorial "overlap" presently impeding treaty negotiation among BC's Coast Salish peoples were nevertheless predictable, for like some of the world's other cognatic societies, the Coast Salish could hold discrete notions of identity simultaneously.
In conclusion, the thesis examines briefly the application to the Coast Salish of Lévi-Strauss' "House-society" as a specific form of social organization.
Gauge theory on Calabi-Yau manifolds

We study complex analogues on Calabi-Yau manifolds of gauge theories on low dimensional real manifolds. In particular we define a holomorphic analogue of the Casson invariant, counting coherent sheaves on a Calabi-Yau 3-fold.

Keywords: holomorphic bundles
Gauge theory
moduli
Calabi-Yau
coherent sheaves
Advisor: Donaldson, S
The image of the state and the expansion of the international system

This thesis presents a history of the concept of the state as a political community. Beginning with the early-nineteenth century and using debates about state formation and state recognition as its source material, it uses the language of English-speaking policy makers and political commentators to explore understandings of statehood across different time periods.
The thesis argues that the meaning and connotations of the state have changed significantly in the past two hundred years, as it has become more salient in images of world politics. In particular, the state has evolved to incorporate the idea of the 'nation,' such that when governments act they are perceived to have their populations 'in tow.' These conceptual changes are surprisingly recent, solidified particularly since the Second World War.
Four broad themes structure the argument in each chapter. First, the historical 'nation' has become an increasingly dominant way of conceptualising the populations of states. Second, the state has come to be construed as the inevitable unit of world politics, corroborated by the assumption that each one arises out of a pre-existing 'nation.' Third, the state has increasingly been perceived as a unitary actor with its own consciousness, separate from 'government.' Finally, the state with its nationalist implications, has come to define the dynamics of international politics, a means of simplifying an ever more complex world.
The thesis roots contemporary (English language) understandings of the state in a particular historical and political context, defined by the contestation between 'American' and 'British' worldviews, the triumph of liberal internationalism and the multiple interests at stake in the image of the state as a nation. The thesis thus exposes the intensely political nature of language and the complacency of International Relations with regard to its own use of words and conventional narratives.

Advisor: Dr Jennifer Welsh, D
Systematic review of suicidal behaviour and related issues of wellbeing in the veterinary profession

Population-based studies of suicide prevalence have identified certain occupational groups to be at particularly high risk of suicide. There is recent evidence that rate of suicide may also be significantly elevated in the veterinary profession. However, relatively little is known about the contributory factors that may explain this phenomenon. The present study is the first systematic review of the research literature on the prevalence of, and factors associated with, suicidal behaviour in the veterinary profession. An extensive search strategy was performed in order to identify studies that presented data on these issues. Studies were categorised into two main groups: those that presented epidemiological data from observational studies of suicide prevalence and those that were survey-based studies of suicidal behaviour and associated issues of wellbeing in the veterinary profession. In total, 89 papers were included in the final review. Nineteen studies of suicide prevalence were identified and 11 of these provided data on the relative risk of suicide in the veterinary profession. All but one of these studies found suicide to be significantly elevated in the veterinary profession. Interpretation of studies of highest quality found that the proportion of suicide in the veterinary profession was at least four times that of the general population. Data from 70 survey-based papers identified the prevalence of various aspects of suicidal behaviour in veterinary populations and the psychiatric, occupational and psychological risk factors that may help explain the reasons for the elevated rate of suicide in the veterinary profession. Knowledge of suicidal behaviour and wellbeing in the veterinary profession is still very much in its early stages. The limitations of research studies reviewed have been identified and suggestions made about the direction of future research. Suggestions for methods of preventing suicide in this high-risk group are also made, based on the current research reviewed, and existing strategies in other groups at high risk of suicide.

Keywords: epidemiology
suicide
wellbeing
occupation
Advisor: Hawton, K
Mellanby, RJ
A study of ammonia borane and its derivatives

This thesis reports the investigation of molecular materials for hydrogen storage applications with a particular emphasis on alkali-metal amidoboranes. I have developed new routes for the synthesis of alpha-LiNH2BH3 and NaNH2BH3, and have studied their hydrogen storage properties by thermogravimetric analysis, variable temperature X-ray and neutron diffraction and inelastic neutron scattering. I report the synthesis and full structural characterization of two new materials, KNH2BH3 and beta-LiNH2BH3, and have performed initial studies on a tetragonal phase of a variant of LiNH2BH3 with a preliminary structure solution. I have also performed variable temperature neutron diffraction on ammonium borodeuteride, ND4BD4, and report the full structural characterisation of the three phases identified as a result of these measurements. Furthermore, variable temperature inelastic neutron scatting (INS) measurements were performed on ammonia borane, NH3BH3, and the results are discussed in terms of crystallographic phase changes.

Keywords: neutron scattering
ammonia borane
hydrogen storage
Advisor: David, W
Edwards, P
Mathematical models of respiratory control in humans

This thesis is concerned with modelling the properties of human ventilation during steady-state conditions and during acute and sustained isocapnic hypoxia.
Chapter 1 reviews some of the relevant studies in animals and humans.
Chapter 2 describes the origins of the data studied in this thesis. In particular, it describes the experimental apparatus and the technique of dynamic end-tidal forcing used to gather the data, as well as the particular protocols employed.
Chapter 3 studies the breath-to-breath variations in ventilation during steady breathing in both rest and during light exercise with the end-tidal gases controlled. The results suggest that: 1) both simple ARMA models and a simple state-space model can describe the autocorrelation present in the data; 2) variations in spectral power were present in the data which cannot be described by these models; and 3) these variations were often due to a uniform modulation and did not significantly affect the coefficients of the models. For these kinds of data, a heteroscedastic form of state-space model provides an attractive theoretical structure for the noise processes.
Chapter 4 studies human ventilation during sustained isocapnic hypoxia. Two models are used. The first, developed by Painter et al. (J. Appl. Physiol. 74:2007-2015, 1993) describes hypoxic ventilatory decline (HVD) as a decline in peripheral chemoreflex sensitivity. The second is an extended model which incorporates a component of HVD that is independent of peripheral chemoreflex sensitivity. The models incorporate a parallel noise structure. It is concluded that, in some subjects but not others, there is a component of HVD which is independent of peripheral chemoreflex sensitivity.
Chapter 5 studies the human ventilatory response to cyclic isocapnic hypoxia. Both a simple proportional dynamic model suggested by Clement and Robbins (Respir. Physiol. 92:253-175, 1993), and an extended model with an additional non-linear rate-sensitive component are studied. The models incorporate a parallel noise structure. The results show that, although the extended model improves the fit to the data for some subjects, both models failed to explain the data fully, especially the occasional large breaths, which were shown to occur more frequently in some parts of the hypoxic cycle than other parts.
Studies in electrode kinetics

This thesis is concerned with the study of electrode kinetics, which we shall examine via comparison between theory with experiment. As such the first two chapters outline the basic principles of electrochemical experiments and their simulation.
First, we examine the properties of voltammetry at porous electrodes by means of both simulations and experiments.
We then introduce the symmetric Marcus-Hush (SMH) model of electrode kinetics as an alternative to the empirical Butler-Volmer model. First, we examine different methods for modeling the voltammetry of kinetically inhomogeneous electroactive monolayers. Next, we perform a critical evaluation of the SMH model for solution-phase systems through extensive comparison to experiments under diffusion-only and convective mass transport conditions using both cyclic and square wave voltammetry. The model is compared with the Butler-Volmer model throughout and is ultimately found to be poorly suited to the parameterisation of electrode kinetics, despite its foundations in the microscopic Marcus theory.
We then introduce the asymmetric Marcus-Hush model, which removes the assumption that the Gibbs energy curves for reactant and product have the same curvature. This modification results in an additional parameter which quantifies the asymmetry of the system. A similar evaluation of this model is then undertaken for both surface-bound and solution phase systems and the asymmetric model is found to be a great deal more successful than its symmetric predecessor.
Finally we outline a novel technique for extracting kinetic information directly from experimental cyclic voltammetry. The method is simple to implement and is general to all electrode geometries with one-dimensional symmetry.

Keywords: Simulation
Electrode kinetics
Marcus theory
Advisor: Compton, R
Formal structures of sensory/perceptual experience

This thesis deals primarily with metaphysical issues concerning human sensory/ perceptual experiences, and with questions about the formal representation of these experiences. In this respect it is similar to N. Goodman's The Structure of Appearance, which is discussed at some length. I establish a way of des- cribing and formally representing certain structures which must occur in sensory/ perceptual experiences, regardless of how the features of these experiences are categorized in terms of being physical or being mental. A special ("ontological- ly neutral") conceptual scheme which reflects the neutrality with respect to these categorizations, and which is particularistic in the sense of admitting sensory/per- ceptual individuals (sensations), is introduced for this purpose. The choice of a particularistic conceptual scheme in this context is supported by an argument which shows that the so-called adverbial approach is insufficient for describing sensory/perceptual experiences. To achieve the desired formal representation, I introduce an original generalization of the standard formalism for semantic 1st -order predicate theories which involves incomplete models, and a type of structured primitive predicates.
Based on a Kantian view of the function of concepts in experience, I then give an account of experiential colour-predicates (like x looks red) in ontologi- cally neutral terms. This account, involving a special class of sensory/perceptual individuals (colour-tokens), has the particular advantage of avoiding the short- comings of both sense-datum theories and the views held by C. Peacocke in Sense and Content. This is followed by an account of experiential intentionality (in ontologically neutral terms) which shows how intentionality, as occurring in the context of sensory/perceptual experiences, can have a relational nature, des- pite the well-known problems of substitutivity and intentional inexistence which are traditionally associated with intentional relations.
Torre Abbey: locality, community, and society in medieval Devon

Torre Abbey was a rural Premonstratensian monastery in south-east Devon. Although in many ways atypical of its order, not least in the quality and quantity of its surviving source material, Torre provides an excellent case study of how a medium-sized medieval monastery interacted with the world around it, and how the abbey itself was affected by that interaction. Divided into three broad sections, this thesis first examines the role of local landowners and others as patrons of the house in the most obvious sense, that of the bestowal of lands or other assets upon the house. Torre was relatively successful in this regard, and an examination of the architectural and archaeological record indicates a continuation of that relationship after the thirteenth century. The second section notes areas of conflict with the laity. Disputes could and did arise over both temporal and spiritual affairs, as well as through the involvement of a number of lay figures in the administration and patronage of the house. In both respects, notable incidents in the mid-fourteenth century highlight the complexities of the canons’ relationships with the secular world. These are further explored in an analysis of the abbey’s role during the Hundred Years’ War and the Wars of the Roses, two conflicts which greatly affected the locality, but required vastly differing approaches by the canons. Finally, the effect of society on the canons themselves is considered. It is possible to recover some picture of their origins, both social and geographic, as well as some idea of the size of the community in the fifteenth century, and discuss the repercussions for an understanding of monastic recruitment. Finally, the dynamic of the community over the entire history of the abbey is considered in terms of the scattered source material, utilising both architectural and documentary evidence.

Keywords: Devon
Premonstratensian Order
monasteries
Advisor: Thompson, B
Blair, J