VictorJuiz/thesis huggingface dataset:
Elucidating mechanisms of premature ovarian failure using a transgenic mouse model

Premature ovarian failure (POF) is a condition that affects around 1% of women of reproductive age. It is idiopathic in 74-90% of cases and the mechanisms involved remain unclear. Several mouse models of POF have been described, however new models are necessary to understand the aetiology of POF and to hopefully identify candidate molecules that can be used as targets for intervention. A mouse model of POF (DM) occurs from oocyte-specific deletion of two glycosyltransferases encoded by C1galt1 and Mgat1, thus oocytes lack core 1-derived O-glycans and complex N-glycans. DM females have POF by 3 months of age exhibiting follicle depletion, elevated gonadotropins and decreased sex steroids. Female mice are fertile prior to ovarian failure producing a single small litter and thus, the DM model provides an outstanding opportunity to explore the onset of POF. In addition, since ablation of these glycans occurs only in the oocyte generates a progressive ovarian failure and POF, this model provides a unique opportunity to further our understanding of the role of the oocyte in the regulation of ovarian function and fertility. In this thesis, the influence of the abnormal endocrine environment was discarded as the origin of the altered follicle development in DM. In vitro and in vivo analysis of follicle development using follicle culture and the reaggregated chimeric ovary technique has highlighted intra-ovarian factors as responsible for the onset of POF in DM females. Finally, ovary transcriptomic analysis revealed an accumulation of changes in gene expression with age consistent with the DM phenotype. These results have highlighted potential therapies as well as genes and pathways as candidate molecules to try to reverse POF in the DM mouse model.

Keywords: glycans
ovarian physiology
female infertility
oocyte
POF
Advisor: Williams, S
Cytochrome c biogenesis in bacteria

Cytochromes c are electron transfer proteins in which haem is covalently attached to the polypeptide chain via thioether bonds formed from thiol groups of the two cysteines and the two vinyl groups of haem. This attachment is a post translational process and in many species of bacteria as many as approximately twelve gene products, the functions of which are largely unknown, are required. In Gram-negative bacteria the assembly of the c-type cytochromes occurs in the periplasm. Cytochrome c552 from the thermophilic organism Hydrogenobacter thermophilus is known to be expressed in the cytoplasm of Escherichia coli. This unique example of cytoplasmic assembly of a c-type cytochrome has previously been postulated to result from insertion of haem into the folded apoform of the cytochrome followed by non-catalysed attachment of the haem. This postulate is supported by the present work which has shown that the cytoplasmic assembly of this cytochrome c552 continues in the absence of the E. coli ccm genes which are needed for 'normal' c-type cytochrome assembly in that organism. Attempts to test the postulate of spontaneous assembly of the cytochrome c552 with in vitro experiments require large amounts of cytochrome c552 and its apo protein. A number of procedures for preparing these proteins were investigated. Although a T7-based expression produced lower amounts than was expected, its use led to detection of the apo form of cytochrome c552 in E. coli. It was shown that this apoform has some secondary structure, whereas mitochondrial apocytochrome c has a random coil conformation. This observation is consistent with, but does not prove, the postulate for cytochrome c552 assembly. It was unexpectedly found that a strain of E. coli that produces abnormally large amounts of its endogenous c-type cytochromes also made large amounts of cytoplasmic cytochrome c552. NMR studies on this material are consistent with a single and 'normal' attachment of the haem to the polypeptide. Thus the unusual cytoplasmic assembly was not different from the usual periplasmic assembly that occurs in the H. thermophilus itself.
In E. coli there is a periplasmic cytochrome b562 that is presumed to acquire its haem in the periplasm. Some of the ccm genes, required for c-type cytochrome assembly, are postulated to code for a system that transports haem to the periplasm. Cytochrome b- 562 synthesis was not blocked by the absence of these genes. This implies that haem provision for cytochrome b562 synthesis occurs independently of the ccm system. Apocytochrome b562
could be detected in E. coli with the ratio apo:holo being higher in a strain that produces c-type cytochromes to relatively low levels. It is suggested that the synthesis of both cytochrome b562 and c-type cytochromes is at least partly a reflection of the rate of production of haem by the cells.
Aspects of branch groups

This thesis is a study of the subgroup structure of some remarkable groups of automorphisms of rooted trees. It is divided into two parts. The main result of the first part is seemingly of an algorithmic nature, establishing that the Gupta--Sidki 3-group G has solvable membership problem. This follows the approach of Grigorchuk and Wilson who showed the same result for the Grigorchuk group. The proof, however, is not algorithmic, and it moreover shows a striking subgroup property of G: that all its infinite finitely generated subgroups are abstractly commensurable with either G or G × G. This is then used to show that G is subgroup separable which, together with some nice presentability properties of G, implies that the membership problem is solvable. The proof of the main theorem is also used to show that G satisfies a "strong fractal" property, in that every infinite finitely generated subgroup acts like G on some rooted subtree.
The second part concerns the subgroup structure of branch and weakly branch groups in general. Motivated by a natural question raised in the first part, a necessary condition for direct products of branch groups to be abstractly commensurable is obtained. From this condition it follows that the Gupta--Sidki 3-group is not abstractly commensurable with its direct square. The first main result in the second part states that any (weakly) branch action of a group on a rooted tree is determined by the subgroup structure of the group. This is then applied to answer a question of Bartholdi, Siegenthaler and Zalesskii, showing that the congruence subgroup property for branch and weakly branch groups is independent of the actions on a tree. Finally, the information obtained on subgroups of branch groups is used to examine which groups have an essentially unique branch action and why this holds.

Keywords: Branch groups
subgroup structure
commensurability
congruence subgroup property
automorphisms of rooted trees
Advisor: Wilson, JS
The politics of compensation under trade: openness, economic geography and spending

This thesis examines the conditions under which democratically elected policymakers are more likely to provide policies that compensate individuals that lose from international trade. It develops and empirically tests a theoretical framework of compensation in open economies that accounts for differences in the degree to which governments benefit losers from trade. It first develops a theory of preference formation based on economic geography, and then argues that electoral and legislative institutions jointly condition the supply of compensation. The theoretical analysis provides three sets of observable implications evaluated using micro- and macro-level data in Europe and Latin America. First, exposure to international competition increases demand for policy that compensates for the costs of trade, but this effect is more pronounced among those individuals in economically specialised and uncompetitive contexts where reemployment in the event of a shock is difficult. Second, policymakers in proportional electoral systems face weak incentives to target trade losers in geographically concentrated and uncompetitive regions. In contrast, majoritarian institutions generate incentives to increase compensation when trade losers are geographically concentrated. Another implication is that under some conditions, the presence of a strong upper house that represents regional interests dampens the provision of compensation, and the relative effect of electoral rules.
The empirical implications of the argument are tested using a multi-method research strategy that combines cross-national and case study analyses and draws on quantitative and qualitative techniques. Chapter 3 tests the micro-level implications of the model using survey data for European regions over 2002-2006. The findings indicate that regional economic specialization and regional competitiveness jointly condition the impact of trade on preferences for compensation. Chapter 4 systematically tests the extent to which the geographical concentration of trade losers conditions the effect of electoral institutions on levels of compensation. It uses panel data from 14 European countries from 1980 to 2010. The findings indicate that where trade losers are concentrated, lower district magnitude leads to more compensation. Chapters 5 and 6 conduct case studies of compensation in Spain and Argentina, both countries that underwent deep liberalisation and offer significant variation at the regional and institutional level. Chapter 5 explores preferences over compensation in selected regions in Spain and Argentina, and shows that regional specialisation and competitiveness were important in shaping levels of support for compensation. Chapter 6 examines the role of electoral institutions and legislative veto bargaining in shaping the politics of compensation in Spain and Argentina.

Keywords: labour market policies
international political economy
economic geography
comparative political economy
electoral institutions
globalization
Advisor: Rueda, D
Analysis of the immune evasion mechanisms of varicella zoster virus

Varicella zoster virus (VZV) is an alpha herpes virus that causes primary infection with varicella (chicken pox), establishes latency in ganglia and may later reactivate as herpes zoster (shingles). Innate immune effectors are thought to control initial viral replication, but it is the adaptive immune system, involving T cells that mediates eventual control of viraemia and the associated clinical disease. Although both CD4+ and CD8+ T cells mediate viral clearance during acute illness, memory responses are dominated by CD4+ T cells.
We tested the hypothesis that the paucity in memory CD8+ T cell effectors is partly attributed to immune evasion mechanisms that are mounted by VZV. We confirmed that VZV readily down regulates cell surface HLA-A and HLA-C but spares HLA-B onVZV infected keratinocytes and VZV infected Mewo cells. Analysis of intracellular HLA protein expression and gene transcription showed global down regulation of all HLA subtypes. Further analysis showed that VZV inhibits IFN-γ mediated up regulation of HLA expression and augments IFN-γ mediated up regulation of HLA-E and CD71 expression.
Furthermore, we show that acute VZV infection lowers the frequency of circulating peripheral blood myeloid dendritic cells (mDC), reduces the expression of the DC activation marker HLA-DR and impairs inflammatory cytokine secretion in blood DC populations. Inhibition of DC cytokine secretion was found to be dependent on viral replication as irradiated virus resulted only in mild inhibition of IFN-α and TNF-α secretion.
Lastly, we observed that VZV infection results in increased expression of host peptides, including MHC derived leader sequences that potentially bind to HLA-E. Cell surface HLA-E is known to be a ligand for the natural killer (NK) cell inhibitory receptor CD94/ NKG2A identifying a novel mechanism of viral immune escape from NK cell surveillance.
In conclusion, our data reiterates the fact that VZV targets different aspects of antigen presentation to evade the immune system with implications for pathogenesis and approaches to improved vaccination and treatment.

Keywords: herpesviruses
human immunology
immune evasion
Advisor: Ogg, G
Investigating the conformal  window of SU(N) gauge theories

In this thesis we are concerned with the existence of infrared fixed points and the conformal window for gauge theories with fermions. We are particularly interested in those theories that are candidates for walking technicolor. We discuss the background of technicolor and the techniques relevant to a theoretical understanding of the conformal window. Following this we extend the ideas of metric confinement and causal analyticity to theories with fermions in non-fundamental representations. We use these techniques to, respectively, provide a lower bound on the lower end of the conformal window and to provide a measure of perturbativity. As well as analytic calculations we use lattice techniques to investigate two particular candidate theories for walking technicolor - SU(2) with two adjoint fermions and with six fundamental fermions. We use Schrodinger Functional techniques to investigate the running of the theory across a wide range of scales. We measure both the running of the coupling and an estimator for the fermion mass anomalous dimension, gamma. We find that both theories are consistent with an infrared fixed-point. However, paying particular attention to our error estimates, we are unable to absolutely confirm their existence. This is a not unexpected result for SU(2) with two adjoint fermions but is rather surprising for SU(2) with only six fundamental fermions. In the region where we are consistent with a fixed point we find $0.05

Keywords: lattice gauge theory
technicolor
conformal window
Advisor: Teper, M
Hepatocellular lipid metabolism in Hepatitis C virus infection

The work described in this thesis investigates the lipid metabolism of human hepatocytes in the context of Hepatitis C Virus (HCV) infection. This includes lipoprotein signalling and cholesterol metabolism targeted analysis of gene expression as well as the influence of polyunsaturated ER targeting liposomes (PERLs) on infection.
These analyses indicate that HCV suppresses the expression of key regulators throughout the cholesterol biosynthesis pathway. This effect was quantified and the influence of liposome treatment evaluated. The latter resulted in the formulation of the hypothesis that PERL treatment interfers with virus-induced abberations of the cholesterol biosynthesis pathway and normalises the expression of four genes directly involved in cholesterol regulation. In addition, the lipidome of isolated lipid droplet was analysed by mass spectrometry. These data, combined with microscopy data suggest that PERLs interfere with S-palmitoylation of the HCV core protein resulting in dissociation of core from lipid droplets. This is likely to interrupt the viral assembly process, leading to inhibition of the production of infectious viral particles.
Further described here are two different yet unsuccessful approaches to fluorescently label HCV RNA for live cell microscopy studies, namely an MS2 coat protein mediated approach, and Alexa®UTP labelling.

Keywords: virology
lipid metabolism
Hepatitis C virus
Advisor: Zitzmann, N
Left-wing theatre in Japan

This thesis is a historical account of left-wing theatre in Japan from its early beginnings in the 1910s to the collapse of the organised proletarian drama movement in 1934. It is set within the context of the general history of shingeki from the earliest attempts to reform existing traditional theatre soon after the Meiji restoration.
The choice of this subject was encouraged by several factors. The Japanese classical theatre has much of interest to the foreign scholar and several substantial studies of its various forms have boon published. Shingeki, on the other hand, has as yet not been studied seriously by any Eastern scholar and it was at least portly a curiosity concerning the problems that would have confronted a modern drama in Japan that prompted this study of left-wing drama.
The subject was limited to left-wing drama for several reasons. Firstly some limitation was required. The history of shingeki can now be said to extend over approximately one hundred years and such have been its vicissitudes and the volume of work contributed to it by its practitioners that only a very choral history would be possible in the limited scope of a thesis. Within the one hundred years of shingeki five separate periods can be discerned: the Meiji period, when the idea of a new drama for the new state was discussed and developed; the late Heiji and early Taisho periods, when the first experiments at a practical realization of new drama took place; the 1920s and early 1930s, when shingeki became an exciting new cultural form in the eyes of young intellectuals and when it became left-wing, as they did; the later 1930s, when a more sober approach to drama was taken by socialists and a more self-confident attitude was observable in those theatre people who were not left-wing; and the post-war period, with its complex mixture of self-examination and experiment. The 1920s and early 1930s - the left- wing period - were chosen because this can be confidently described as the formative period of modern Japanese drama. The struggle with the past was mainly over and the legacy left to future shingeki artists by these years was greater than that of any other period.
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The formal semantics of a domain-specific modelling language

The Specification and Description Language (SDL) was developed by the telecommunications industry as a common language for the design of asynchronous communicating systems. Designs expressed in SDL can be given a formal, mathematical interpretation to facilitate analysis and to guide correct implementation. The standard formalisation of SDL is adequate for the purposes of language definition, but is not oriented towards either analysis or implementation of specific designs. This thesis investigates alternative approaches to the formalisation of SDL. A specific, constrained version of the language is considered: one more amenable to code generation. A statebased formalisation is presented using the Z notation, together with a process-based account using the language of Communicating Sequential Processes. A more abstract, elegant solution is then proposed, in terms of a calculus of buffered systems, itself given an interpretation using Hoare and He's Unifying Theories of Programming. A case study is presented to demonstrate the practical application of the formalisations.

Keywords: SDL
language
PLEX
Z
Java
CSP
specification
Ericsson
description
telecomunications
UML
Advisor: Davies, J
Empresses, religious practice and the imperial image in Ming China: the ordination scroll of Empress Zhang (1493)

The Ordination Scroll of Empress Zhang (1493) in the San Diego Museum of Art, a highlight at the Taoism and the Arts of China exhibition in 2000, is an unusual object among surviving visual material from Ming dynasty China (1368 – 1644). At over twenty-seven metres long, the scroll contains meticulously painted images and a detailed inscription that records the Daoist ordination of Empress Zhang (1470 – 1541), consort of the Hongzhi emperor (r. 1488 – 1505) by the Orthodox Unity institution. The event it documents, which elevates the empress into the celestial realm, would be unknown to history if not for the survival of this scroll. This dissertation is an in-depth study of the Ordination Scroll that also considers its implications for understanding the activities of empresses and their representations during the Ming dynasty.
The first three chapters of this dissertation closely examine the material, visual and textual aspects of the Ordination Scroll. The remaining two chapters situate the scroll within the broader activities of Ming empresses. A complete translation of the main inscription in the scroll is provided in the appendix.

Keywords: Daosim
empress
Ming dynasty
China
Zhengyi
Advisor: Clunas, C
The spirit of the Phenomenology

The aim of the thesis is to investigate Hegel's attempt to resurrect metaphysics in the Phänomenologie des Geistes. Chapter 1 sets forth Hegel's general strategy for the resurrection of metaphysics: to justify knowledge of reality as a whole through epistemology or the critique of knowledge. Chapter 2 then examines why Hegel thinks that the resurrection of metaphysics is necessary after its destruction by the Kantian critique of knowledge. Chapter 3 turns to Hegel's argument for the necessity of a critical justification of metaphysics. It reconstructs his arguments in behalf of the critique of knowledge, and it analyses his polemic against Schelling's postulate of intellectual intuition. The task of chapters 4 and 5 is to explain how Hegel resolves the problems that confront his ambition to justify metaphysics through the critique of knowledge. Chapter 4 considers the objections raised by the meta-critical campaign of Hamanm, Herder, Schulze, Schlogel and Reinhold, and it examines how Hegel attempts to re-establish tho programme of the critique of knowledge after the meta-critique. Chapter 5 discusses the problem of solipsism, and interprets the dialectic of chapters IV and IV.A of the Phänomenologie as Hegel's reply to the solipsist. Finally, chapter 6 is a historical study of Hegel's development toward the Phänomenologie in Jena. It describes the stages by which Hegel came to conceive his programme for the critical resurrection of metaphysics.
Paternal depression and infant outcomes: the role of expressed emotion

Introduction: The aim of this study was to examine expressed emotion (EE) in depressed fathers one year postpartum. Paternal depression in the postnatal period has been shown to place children at risk for emotional and behavioural problems. However, the mechanism through which the risk is transmitted remains unidentified. EE, a measure of family environment, has been investigated in children and adolescents and has been associated to child psychopathology. EE has also been found to mediate the relationship between maternal depression and child externalizing behaviours. There exists no research however examining EE in the context of paternal depression. The primary aims of the study were: a) To examine differences in EE in depressed and non-depressed fathers and b) To investigate whether EE mediates the relationship between paternal depression and child externalizing behaviours.
Methods: EE was examined in families of one year old infants, whose fathers (n=24) had experienced an episode of major depression within the first postnatal year and were compared to families whose fathers (n=79) had no history of depression. EE was measured using the preschool version of the Five-Minute Speech Sample (pFMSS). Both parents completed the EE assessment and the externalizing scale of the Child Behavior Checklist.
Results: Depressed fathers expressed fewer positive comments towards their infants than non-depressed fathers but did not differ in other aspects of EE. Depression predicted externalizing behaviours, but the relationship was not mediated by EE. Maternal EE revealed no differences in families with a depressed and non-depressed father.
Discussion: This is the first study to examine EE in the context of paternal depression and to report depressed fathers to be less positive towards their infants. The low rates of high EE in both mothers and fathers indicates that further adaptations are necessary to the pFMSS for use with one year old infants. Even though EE did not mediate the relationship between paternal depression and child externalizing behaviours; the low rates of positivity in families of depressed fathers may negatively impact on child development and therefore warrant further exploration.

Keywords: paternal depression
infant
expressed emotion
Advisor: Ramchandani, P
Psychogiou, L