VictorJuiz/thesis huggingface dataset:
The interaction between HTLV-1 Tax protein and the proteasome

This thesis presents studies on the interaction between the human T cell lymphotropic virus type 1 (HTLV-1) Tax protein and the 20S proteasome and the role of the interaction in cellular processes and the cytotoxic T cell (CTL) response against HTLV-1.
The rapid translocation of Tax into the nucleus is described. Tax accumulates in the nucleus and forms unique bodies involved in transcriptional activation.
It was further found that Tax associated with assembled nuclear 20S proteasomes and stimulated the chymotryptic and tryptic activities of the 20S proteasome, independent of the induction of the LMP2 and LMP7 proteasome subunits. Confocal microscopy revealed a partial colocalisation of Tax with nuclear proteasomes.
A panel of Tax mutants was generated and their subcellular localisation and association with the 20S proteasome analysed. This analysis revealed that both the N- and C-terminus of Tax play a role in proteasome binding of Tax and further showed that proteasome binding was not sufficient for nuclear localisation of Tax. Therefore, Tax probably translocates into the nucleus prior to and independent of proteasome association.
Tax specific CTL clones were generated and characterised using tetrameric MHC class I/peptide complexes. These CTL clones were used to investigate the requirements for processing and presentation of Tax for recognition by CTL. It was found that Tax was a metabolically very stable protein and that the presentation of the immunodominant Tax 11-19 epitope was dependent on the transporter associated with antigen presentation (TAP), independent of the expression of LMP2 and LMP7 proteasome subunits and resistant to treatment with the proteasome inhibitor lactacystin.
It is proposed that the interaction between Tax and the 20S proteasome plays a role in Tax mediated transcriptional activation, leading to cellular activation and proliferation, and may not determine the immunodominance of Tax in the CTL response against HTLV-1.

Advisor: McMichael, A
Secularism in Salman Rushdie's Midnight's children and Vikram Seth's A suitable boy

This thesis is a comparative study of Salman Rushdie's Midnight's Children (1981) and Vikram Seth's A Suitable Boy (1993). It compares the novels' representations of the postcolonial Indian nation-state and of the conflict between secular and religious perspectives in the Indian public sphere. The novels are interpreted as responses to specific moments of crisis in the so-called "secular consensus" of the Indian state: Midnight's Children to the Emergency of 1975, A Suitable Boy to the rise of the Hindu right in the early 1990s. The aim of this study is to establish secularism as an interpretative concept in South Asian literature in English. Each chapter examines different aspects of the texts in relation to secularism. The first chapter outlines two different theoretical positions, Seth's "rationalist" and Rushdie's "radical" secularism. The second examines the question of minority identity in the two novels. The third explores the different narrative structures that shape their ideas of Indian citizenship. The fourth compares their differing versions of India's national past. The fifth interrogates the status of English as a secular language in the Indian context by examining the interaction between English and Indian vernaculars in the two texts. The dialogic form of the novel has been appropriated by postcolonial Indian writers in English in order to stage contrasting religious and secular worldviews. This dialogism, it is suggested, may offer the possibility of opening up the public sphere to different modes of communication not exclusively defined by rationalism.

Advisor: Mee, J
Modelling and correction of the non-linear transverse dynamics of the LHC from beam-based measurements

The non-linear beam dynamics of a circular accelerator, such as the Large Hadron Collider, can have a significant impact on its operation. In order to avoid limitations on the performance reach of the accelerator, and ensure machine protection, it is vital that the beam dynamics are well understood and controlled. This thesis presents the results of studies of non-linear beam dynamics undertaken on the Large Hadron Collider at CERN, during the 2010 to 2013 period. It sets out to quantify the understanding of the non-linear beam dynamics through the comparison of beam-based measurements to simulation, and where able and appropriate seeks to explain deviations of measurement from the model, and define corrections for relevant aspects of the dynamics.
The analyses presented in this thesis represent considerable advances in the understanding of the LHC beam dynamics which should allow for an improved operation of the machine in the coming years.

Keywords: non-linear beam dynamics
Accelerator
LHC
Advisor: Bartolini, R
Tomas, R
Relations between Nigeria, France and selected francophone states in West Africa, 1960-1975

The thesis is concerned with the emergence of Nigeria as a regional power since 1966, through a study of political ' relations between Nigeria, France and selected francophone West African states between 1960 and 1975 - Ivory Coast, Niger and Dahomey. Until 1966, Nigeria's policy substantially contributed to the preservation of francophone influence in West Africa. The first change in Nigeria's relationship with its neighbours was prompted by its disagreements with. Ivory Coast during the Nigerian civil war. Subsequently, Nigerian influence spread into francophone West Africa at the expense of that of Ivory Coast, a change stimulated by shifts in France's policy towards Africa. The study concludes with the climax of this evolution, Nigeria's successful creation of the Economic Community of West African States in May 1975. This is seen as the embodiment of Nigeria's emergence as an active West African power, along with its corollary, the weakening of the historic francophone-anglophone division.
The study of Nigeria's changing relations with Ivory Coast in brought into sharper perspective by the inclusion of Dahomey and Niger into the analysis. Indeed, these two countries were closely bound to Nigeria in a subordinate relationship through unequal economic and social ties. Furthermore, they belonged to the core of the francophone group in Africa, for here were two of those states which, under the leadership of Ivory Coast, retained the closest links with France at the time, of their independence in 1960.
Facets of judgment: towards a reflexive political psychology

The knowledge base of empirical psychology is more expansive than ever before. So too is the impulse to integrate this factual knowledge into political theory. But how should this psychological turn be undertaken? What would a political psychology for political theorists look like? How could psychology credibly tackle the questions that political theorists characteristically ask, especially regarding the nature and consequences of prescriptive political judgment? In this thesis, I explore this issue through the framework of recent debates between political moralists—specifically, John Rawls, G. A. Cohen, and Peter Singer—and political realists—largely Bernard Williams. Deploying the insights of political realists, I argue that moralists cannot quarantine the relevance of psychological facts through the ideal of a 'pure' normative judgment. To explore what this empirical engagement might look like, I contrast these moralist ideals of judgment with Jonathan Haidt’s social intuitionism, which proposes a more affectively laden and pluralistic model of judgment. I then redeploy the insights of political realism to critique social intuitionism, to uncover its weaknesses from the perspective of existing political theory. Finally, to stabilize this critique, I lay out the framework for a reflexive political psychology, which acknowledges the co-constitutive relationship between the discipline of psychology and its subject matter: human psychology. This reflexive political psychology offers an agenda by which we can investigate the political usefulness of psychological and political theories.

Keywords: political psychology
philosophy of social sciences
judgment
Jonathan Haidt
Political realism
political philosophy
political ideology
Bernard Williams
moral psychology
Advisor: Frazer, E
The role of termites in the ecology of Tsavo National Park, Kenya

Tsavo National Park lies in an area of very dry country in South Eastern Kenya. Elephants live there in large numbers and in the early 2 1970's, they had a mean population density of about 1 km-2 . They have inflicted widespread destruction on the woodlands which originally covered the Park, leading to a complete change in the appearance of the habitat. This caused considerable anxiety about the future of the Park and all its animal populations so research was begun to try to elucidate the root causes of the "elephant problem" and to predict its consequences. The purpose of the present study was to find out what happens to dead wood in Tsavo and to gauge the importance of termites in the ecology of the area.
Section 1 gives a brief introduction to the history of Tsavo and sets out the main questions posed when this study was begun. In Section 2 the environment of the study area is described in terms of its topography and geology, the soils and their origins, the floristic and structural composition of the vegetation during this study, the climate and its variations in time and space and the role of fire in shaping the habitat. The species of termites found in the study area are listed in Section 3, followed by brief descriptions of their natural history.
Section 4 contains all the information on the turnover of dead wood. The standing crop and rates of wood fall and removal were measured directly at one site and extended by means of an index to measure consumption of dead wood by termites at other sites. Consumption is found to be related to rainfall. The results are discussed in relation to similar studies made elsewhere. A model is constructed relating the consumption of dead wood by termites to rainfall and comparing this with the consumption of grass and browse by large herbivorous mammals. A method is described for measuring the relative importance of different termite species as consumers of dead wood... [See PDF file for full abstract]

Advisor: Phillipson, J
Coe, M
Theft, patronage &amp; society in Western India

This thesis is an ethnography of a community of professional thieves called the Kanjar-a 'caste of thieves' by practice, public perception and self-designation-in the northern Indian province of Rajasthan. It is also an argument that spells out the broader logic of rank in local society. Insofar as it offers the first ethnography of the Kanjar community- and of caste-based, professional, hereditary theft-this study is new. My analytical concern with hierarchy and rank, however, is old, engaging in the once central, and now largely out-fashioned, discussion in the sociology of South Asia. My project began with a narrow set of concerns with the place of thieving and thieves in local society. In the course of my fieldwork, however, it became apparent that the received wisdom of South Asian sociology regarding the principles of rank did not offer useful explanatory tools and that a different conception of rank was necessary to make sense of what I observed, both about the social position of Kanjars and the hierarchical social formation at large. As is so often the case, what began as a study of historically and sociologically particular circumstances became an inquiry into the pervasive regnant aspects of the local order of things.

Keywords: Rajasthan
India
Kanjars
thieves
patronage
criminal tribes
criminality
hierarchy
crime
patron-client relations
rank
Advisor: Dresch, P
Gellner, D
Essays on the economics of reputation

This thesis is comprised of three essays. These essays model facets of illicit markets using economic theories of reputation and go on to develop new theories of reputation.
In chapter 1, we start by defining illicit markets. We build a model of trade in an illicit market where honesty is enforced through reputation. We then show how criminals' heterogeneity in their ability to avoid detection can have interesting consequences. In particular, such heterogeneity can explain why illicit market participants might sometimes adopt surprisingly blatant trading strategies. Heterogeneity among criminals in terms of how they are affected by enforcement can give rise to counter-intuitive market reactions to changes in the level of enforcement.
Chapter 2 considers the market for stolen payment data such as credit card numbers. The central observation is that stealing financial data and using it for personal gain are two very different skills. An online market exists through which those who steal data can sell it to those who can
cash in''. The low prices in these markets are not evidence of a failure of the reputational system, but of large outside options on one side of the market.
Finally chapter 3 considers reputation more generally. We find folk theorem and incomplete information models place too much faith in the knowledge and rationality of short-lived players. We propose instead a new model with more realistic assumptions about the information available to short-lived players and their ability to use it. This model generates natural cycles in the reputation of the rational long-lived player.

Keywords: Illicit trade
Reputation
Illegal behavior and the enforement of law
Advisor: Young, H
Challenges to meritocracy? A study of the social mechanisms in student selection and attainment at the University of Oxford

Educational transitions in the UK are related to social background characteristics such as social class and, to a lesser extent, ethnicity and gender. This thesis presents a case study of admission to the University of Oxford to understand why, conditional on application, admissions patterns into selective higher eduction in Britain show an advantage for already privileged strata of society. Specifically, net of attainment, the professional middle class, white, male and state school applicants fare particularly well in securing offers for undergraduate study at Oxford. With the exception of the state school effect, the admissions privilege advantages already privileged strata of society.
Development of novel hyperpolarized magnetic resonance techniques and compounds for perfused organs

Hyperpolarization via the Dynamic Nuclear Polarization (DNP) technique has revolutionized our ability to study metabolic changes in real time. The aim of this thesis was to build upon previous work centered around the use of DNP within the isolated perfused rat heart, a well established model system for the study of cardiac metabolism, to enhance the information that can be obtained through the combination of DNP with perfused organs. Initially this was done by using the widely studied DNP probe, [1-13C]pyruvate, to generate images of metabolism within the isolated perfused rat heart. The developed technique was then successfully demonstrated in two models of myocardial infarction. The thesis then proceeds to develop an understanding of how the supra-physiological concentrations of [1-13C]pyruvate commonly used in DNP experiments can affect metabolism in the isolated perfused rat heart, and the way in which the myocardium responds to those changes if it is not adequately supplied with substrates ordinarily present in vivo, namely fatty acids. New methods of providing the heart with these required substrates were developed, without significant interference to the biochemical information acquired from DNP experiments. As [1-13C]pyruvate only provides information on a small subset of carbohydrate metabolism, the next chapter develops new compounds to be used with DNP, which would allow the exploration of short chain fatty acid metabolism (butyrate) as well as ketone body metabolism (β-hydroxybutyrate and acetoacetate), and other aspects of carbohydrate metabolism (lactate and alanine). These compounds were developed and then tested for their potential usefulness in the isolated perfused heart. Finally, as the isolated perfused rat heart lacks the diversity of genetic disease models available in the mouse, the final chapter expanded the use of DNP to the isolated perfused mouse heart with all the size challenges that this entails, and makes the transition from the heart to the liver, in order to provide an alternative metabolic viewpoint on the biochemistry of disease models. This thesis thereby permits studies involving isolated perfused organs to be carried out whilst exploiting all the tools that DNP has to offer and consequentially, allows for a vast array of physiologically derived information to help us better understand metabolic diseases.

Keywords: hyperpolarization
DNP
perfusion
Advisor: Tyler, D
Studies on basement membrane permeation

The effects of the biological cross-linker transglutaminase, the neutrophil oxidant hydrogen peroxide, and neutrophil proteinases on glomerular basement membrane permeability have been examined using an in vitro model of glomerular ultrafiltration. The main focus of the study lies in determining whether any of the test agents were able to render glomerular basement membrane more permeable to protein.
Guinea pig liver transglutaminase was used as a model enzyme to test for the effect of biological cross-linkers on glomerular basement membrane permeability. It cross-linked glomerular basement membrane proteins, caused membrane contraction, and rendered glomerular basement membrane less permeable both to water and the low molecular weight protein marker myoglobin but had no effect on the membrane permeability to the high molecular weight marker protein bovine serum albumin or serum protein. The pathophysiological relevance of the effect is discussed.
Hydrogen peroxide increased glomerular basement membrane permeability to water and proteins but the effect depended on hydrogen peroxide concentration and incubation time. The minimum concentration needed to render glomerular basement membrane more permeable to bovine serum albumin and serum protein was 1 M and the minimum incubation time needed was 6 hrs. A respiratory burst analysis of activated neutrophils showed that the average concentration of hydrogen peroxide that could be generated by the neutrophils was less than 50 mM and the time taken for extracellular hydrogen peroxide concentration to fall off to zero was less than 1 hr. Therefore, neutrophils seemed unable to generate and sustain a sufficiently high hydrogen peroxide concentration to render glomerular basement membrane more permeable to protein in vivo.
Proteinases extracted from pig neutrophil granules were used to assess their effect on glomerular basement membrane permeability. The extract showed activity against glomerular basement membrane and the activity was primarily attributed to the serine proteinases elastase and cathepsin G, judged from substrate and inhibitor analyses. The proteinase extract also contain latent metalloproteinases, activatable by the organomercurial 4-aminophenyl mercuric acetate and calcium ions. Once activated, they also showed activity against glomerular basement membrane. The extract rendered glomerular basement membrane more permeable to water, myoglobin, bovine serum albumin, and serum protein. The increase in membrane permeability to water and proteins was due to membrane thinning and an increase in the intrinsic porosity of the membrane. When the serine and metalloproteinases were allowed to act in concert, they synergistically degraded glomerular basement membrane and increased the membrane permeability to serum protein and water. The study provides the first direct evidence that pathophysiological amounts of serine and metalloproteinases are able to render glomerular basement membrane more permeable to protein and suggests they may be capable of promoting proteinuria in neutrophil-dependent forms of immune glomerulonephritis.

Advisor: Robinson, G
Building common knowledge: a cultural-historical analysis of pedagogical practices at a rural primary school in Rajasthan, India

The centralised control over curriculum framing and pedagogy, the generally poor quality of teaching with little sensitivity to children’s sociocultural environment; and very high drop out rates, even at the primary school level, are some of the challenges facing school education in many of the regions of India. However, one of the successful approaches to these challenges has been the Digantar school system, working in rural communities. The study is based in one Digantar School in Rajasthan and employs concepts derived from the Vygotskian tradition to interrogate the methods employed in Digantar school system.
The study took Edwards’ (2010a, 2011, 2012) idea of common knowledge and Hedegaard’s (2008, 2012, 2013) idea of institutional demand in practices as conceptual lenses through which to investigate the components of the pedagogical practices that help Digantar teachers to align the motives of the school with those of the child in classroom activities. In doing so it analyses the institutional practices that lead to the development of common knowledge that in turn facilitates how teachers engage pupils as learners.
Data were gathered over six months and comprised around 120 hours of school-based video data together with interviews and detailed observations with teachers and community members. Data were gathered in classrooms, teacher meetings, meetings between parents and teachers and at school-community meetings. Analyses focused on the construction of common knowledge and the use made of it by the school to achieve a mutual alignment of motives between the practices of the school with the community and the families.
The study has revealed that teachers’ engagement with the knowledge and motives of other teachers and community members helped to create common knowledge, i.e. an understanding of what mattered for each participating group, which facilitated teaching-learning in the school. The analysis also points towards a form of democracy, which enhances children’s participation in their learning. It was found that building and sharing of common knowledge and creating a socially articulated ‘space of reasons’ (Derry 2008) produced a pedagogical model that engaged children in creating their social situation of development, seeking and recognising the curriculum demands being placed on them.

Keywords: primary education
funds of knowledge
space of reasons
learning
Vygotsky
Hedegaard
common knowledge
child development
cultural-historical activity theory
motives
Advisor: Edwards, A