VictorJuiz/thesis huggingface dataset:
Statistical methods and analyses in autoimmune diseases

Type 1 diabetes (T1D) is a common, heritable autoimmune disease, with approximately 60 chromosome regions identified that show association with disease. Cases diagnosed at < 10 years most rapidly lose the ability to endogenously produce insulin and suffer the greatest complications of the disease, including decreased life expectancy.
I therefore analysed genotype data from 15, 645 cases and tested the association of each variant at a genome-wide level with age-at-diagnosis, in an attempt to reveal genes and pathways implicated in early-diagnosed T1D. Variants within the human leucocyte anti- gen (HLA) region, as expected, showed association with age-at-diagnosis, but I also found a novel T1D region on chromosome 6q22.33, which associated with both age-at-diagnosis and also disease risk if examining only cases diagnosed at < 5 years.
Based on prior pancreas histology results, which showed cases diagnosed at < 7 years have a distinct immune cell infiltration signature to those diagnosed at ≥ 13 years, I then predefined specific age-at-diagnosis groups, < 7, 7-13 and ≥ 13, and restricted my analysis to examine only known T1D regions, thereby reducing the multiple testing adjustment required in genome-wide studies. Six alleles within the HLA region were more strongly associated in individuals diagnosed at < 7 years compared to ≥ 13 years, as well as six regions outside the HLA. The identified candidate causal genes indicate effects not only in the immune system but also in the islet beta cells and thymus.
Finally, I performed an ImmunoChip-wide meta-analysis of 59, 974 individuals, approxi- mately twice the sample size of the previous largest T1D genetic analysis, and identified 74 chromosome regions associated with T1D, including 22 novel regions. I fine mapped each region and confirmed that prioritised variants were enriched in open chromatin re- gions in lymphoid cells.
Ongoing and future research aims to go from maps, to mechanisms, to medicines.

Advisor: Crouch, D
Todd, J
Claiming the state: the everyday lives of Palestinian refugee youth in East Jerusalem

An understudied yet central aspect of the failure of the Oslo Peace Process is the lived impact of this failure on the lives of young Palestinians who have grown up in its wake. By examining the everyday lives of youth in the Shu’fat refugee camp in East Jerusalem, this thesis explores the changing production and enactment of politics among third generation refugee youth. While the Palestinian political elite continue to strive for a two-state solution that many in reality know is impossible, this study offers an account of the ways that young refugees continue moving forward with their own lives in spite of political stagnation. Drawing on fieldwork conducted over an 18-month period, it explores how and why young refugees begin to make stronger political claims on the Israeli State. Young people in Shu’fat camp hold both refugee documents and permanent residency status, enabling them a partial access to the Israeli State. Planning regimes and discriminatory bureacractic processes in Jerusalem are incrementally excluding the population of Shu’fat camp and its surrounding neighborhoods from the demographic of the city. While the state operates against them, these young refugee, permanent residents are making strategically pragmatic claims on the state. It asks questions of what remains of nationalism for third generation refugees in Palestine, and specifically, what forms Palestinian nationalism takes when Israeli citizenship, however conditional, becomes a viable alternative. By exploring the ways Palestinian refugee youth in East Jerusalem experience, navigate, subvert and ultimately make claims on the Israeli State, this research hopes to further our understanding of youth aspiration and agency in a context of protracted violence and displacement. In so doing, it hopes to contribute to the rich discussion about the changing content and form of politics in Palestine, painting a nuanced picture of what oppression and freedom look like to third generation refugee youth.

Advisor: Boyden, J
Rethinking growth through trade: a two-tiered capabilities approach

Trade has been a concern of global justice theorists since Charles Beitz prominently cited it as a fundamental cause of global inequalities in his seminal 1979 book Political Theory and International Relations. Yet it is only recently that theorists are beginning to address trade in and of itself. Following David Miller, I define trade as “a practice that involves the voluntary exchange of commodities or services for mutual advantage. That means, self-evidently, that both trading partners expect to be better off as a result of their exchange.” Ultimately, the problem is, that despite this definition of trade, it does not always benefit both partners or at the very least benefit them to the full (expected) potential of the exchange. That is, trade, quite problematically, does not fulfill its normative potential; it is not doing what it was designed to do.
This thesis proposes and develops a normative theory of justice in international trade. Thus, it falls both within the fields of political theory and normative or welfare economics. Like other theorists of trade justice, I too seek to answer the question “what does it mean for trade to be fair?” Yet unlike other theorists of trade justice, I am not looking for a theory of specifically distributive justice within trade, instead I take inspiration from an older conception of justice, one where something must fulfill its function in order to be considered just. The normative economic aspect, then, becomes important because the ‘mutual advantage’ that countries gain from trade must be benefiting economically in some way. Namely, they must be benefitting in terms of growth and/or development.
After demonstrating that this is a reasonable interpretation of a function of international trade, I propose that this idea of growth and/or development is best understood in terms of what I call a ‘Two-Tiered Capabilities Approach’ focusing specifically on country-level capabilities that can be used to assess development. Using a capabilities framework allows us to identify practical functions of international trade and then subsequently assess whether or not trade is fulfilling its purpose and where exactly it falls short. I offer that this broad understanding of development through trade must not just be focused on gross domestic product (GDP), but also a tentative list of ‘capabilities’ such as labor standards, environmental sustainability, and human rights.

Keywords: fair trade
capabilities approach
Advisor: Wolff, J
A comparative study of the dress, food and leisure of domestic servants in France and Britain, 1900-1939

This thesis is a comparative study of the everyday lives of French and British female domestic servants between 1900 and 1939. Despite making-up nearly half of the female workforce in both countries, the experiences of servants are hard to access. To overcome this problem, the thesis relies on a large sample of French and British servants’ autobiographies. Autobiographies have been used by historians primarily to document the economic struggles these women faced and the social trajectories they followed. However, autobiographies are also bursting with revealing digressions and significant little details about servants’ lives. This thesis seizes upon these insights by actively reading at the margins of servants’ stories. It concentrates on three themes which were most present in servants’ accounts: dress, food and leisure. What servants wore, what they ate and what they did in their free time played a key role in their negotiations of authority and the construction of class, gender, generational and regional identities. The thesis combines this focus on the micro-level of domestic servants’ lives with a comparative analysis which contextualises servants’ testimonies within two different social, cultural and economic environments. It shows how contrasting levels of industrialisation, urbanisation and land ownership as well as divergent forms of family structures and gender norms shaped French and British servants’ world and identities. Ultimately, this comparative study of French and British servants’ experiences with dress, food and leisure leads us to interrogate what it meant to be a servant and deconstruct the category of ‘servanthood’ in the first half of the twentieth century.

Keywords: France
autobiographies
domestic service
Britain
Advisor: Hopkin, D
Humphries, J
3-D printing: adding a new dimension to intellectual property?

3D printing is a phrase often seen in the media in relation to wondrous or troubling developments in manufacturing, health, arms and myriad other areas. The growth of 3D printing has the potential to have a major economic impact, and while we may be at a tilting point with regard to the relationship between 3D printing and intellectual property law, whether the future will see it as a truly ‘disruptive’ element remains to be seen.
This dissertation identifies three key issues for intellectual property and highlights how 3D printing raises both old and new questions in the areas of copyright, trade mark and patent law. In looking at these focal areas it analyses the extent to which existing regimes are capable of answering some of the difficult questions 3D printing may raise. It does so with the aim of questioning whether the newness of these issues is primarily fuelled by media buzz and a fear regarding the status quo, or whether 3D printing is inherently disruptive.
While the idea of printing a car or a watch may be as novel to the layman as the Star Trek Replicator, the host of issues that come with this new technology are not so fantastic or beyond comprehension. In dealing with many of the questions raised by 3D printing we need to keep a mind to questions that IP law has addressed in the past in relation to disruptive technologies. Some areas may benefit from new legislation or amendments. For others, it is clear that what is required is a re-interpretation of existing legal principles. Either way, while the technology may be new, it does not require us to re-write our IP law. At least not yet.

Keywords: Trade Mark
Copyright
3D Printing
IPR
Intellectual Property Rights
Patent
Monopile foundations under complex cyclic lateral loading

The vast majority of offshore wind turbines are supported on monopile foundations. These foundations experience lateral loading which is both cyclic and complex: continuously varying in amplitude, direction, frequency and eccentricity with the environmental and turbine operation conditions. The effect of cyclic loading on the accumulated rotation (ratcheting), strength and stiffness of the foundation must be considered, while advanced structural dynamic modelling requires prediction of the cyclic hysteretic response. However, there are currently no commonly accepted design methods for predicting the cyclic response of monopile foundations, particularly under the complex loading to which they are exposed.
This thesis explores the response of monopile foundations to cyclic lateral loading through laboratory-scale physical modelling in dry sand, principally at 1g. The development of novel laboratory apparatus allows the application of complex, continuously varying cyclic loading. Regular, unidirectional tests complement previous studies and explore the impact of load amplitude and asymmetry in detail. Regular, multidirectional tests provide novel insight into the response to loading with multiple direction components. And irregular, multi-amplitude and multidirectional tests reveal the response to realistic loading, highlighting the dominance of large load events. Throughout, the monopile response is characterised in terms of ratcheting, evolution of hysteresis loop shape and the post-cyclic reloading response. Behaviour in very loose and dense sand is found to be qualitatively similar.
A complementary study using centrifuge modelling explores the impact of stress-level on the monopile response, to establish the relevance of 1g modelling and inform comparison of monopile responses observed at different stress-levels. Qualitatively similar behaviour is observed at multiple stress-levels, although the rate of ratcheting and stiffening reduce with increasing stress-level.
Together, the physical modelling results inform the design of monopile foundations under cyclic lateral loading. In particular, the results facilitate demonstration and development of numerical models in the Hyperplastic Accelerated Ratcheting Model (HARM) framework, which can capture ratcheting and evolution of the hysteretic response, and can respond to arbitrary loading. Models in the HARM framework are shown to capture key features of the response to complex - irregular, multi-amplitude and multidirectional - cyclic loading in dry sand of various densities and at multiple stress-levels. The results build confidence in the application of models in the HARM framework for full-scale monopile design.

Advisor: Byrne, B
Houlsby, G
Geometric aspects of twisted 3d supersymmetric gauge theories

We study geometric aspects of 3d N = 2 and N = 4 supersymmetric gauge theories on the product of a line and a Riemann surface. Performing the topological twist on the Riemann surface, the theories preserve a supersymmetric quantum mechanics on the line. The quantum mechanics has an eﬀective description where its target space is a moduli space of conﬁgurations that satisfy generalized vortex equations on the Riemann surface. We propose a construction of the space of supersymmetric ground states of selected N = 2 theories as a graded vector space in terms of a certain cohomology of the moduli spaces. This exhibits a rich dependence on deformation parameters compatible with the topological twist, including superpotentials, real mass parameters, and background vector bundles associated to ﬂavour symmetries. By matching spaces of supersymmetric ground states, we perform new checks of 3d abelian mirror symmetry. We go on to the study of the twisted indices of a 3dN = 4 quiver gauge theories that have isolated vacua under generic mass and FI parameter deformations. These can be viewed as virtual Euler characteristics of the moduli spaces of generalized vortex equations, which in this case can be understood algebraically as quasi-maps to the Higgs branch. We demonstrate that this description agrees with the contour integral representation introduced in previous work. We then investigate 3d N = 4 mirror symmetry in this context, which implies an equality of enumerative invariants associated to mirror pairs of Higgs branches under the exchange of equivariant and degree counting parameters.

Keywords: Quasi-maps
Riemann surface
Vortex equations
Hilbert space
3d
Topological
Advisor: Mason, L
Design issues and challenges in clinical trials with a surgical and non-surgical comparison

Conducting surgical trials is essential to establish evidence based practice and inform health policy, particularly in the face of economic pressures. Randomised controlled trials (RCT) evaluating surgical interventions can be difficult to design and conduct, especially when including a non-surgical comparison. Only around half of initiated surgical trials reach their recruitment target, and failure to recruit is cited as the most frequent reason for premature closure of surgical RCTs.
The aim of the thesis was to gain a greater understanding of the main methodological challenges to the design and conduct of trials that directly compare surgical and non-surgical interventions, explore potential solutions, and provide guidance for use in future studies.
The work contained in the thesis purposefully used several different methodologies; a systematic review, case study, qualitative evidence synthesis and two qualitative interview studies. This approach provided insight from different perspectives in order to more fully understand the challenges involved in this type of trial, and therefore contribute to the design of future trials.
Several methodological challenges were identified in these types of trials related to; difficulty implementing blinding, recruitment difficulties, complexity of intervention content and delivery, imbalance in timing of follow-up, non-compliance with treatment allocation, and differential loss to follow-up. The dichotomy between several aspects of the surgical and non-surgical interventions, for example, level of invasiveness, risk, and perceived mechanism of effect, were seen to contribute to strong preferences of both patients and clinicians, making recruitment particularly challenging. The potential benefits of undertaking pre-trial qualitative research to identify potential issues of patients’ and clinicians’ treatment preferences in these types of trials, was also identified.
Several methodological issues were identified in this thesis that have the potential to impact on the design, conduct and analysis of these types of trials. If not adequately addressed, these issues may introduce significant bias and threaten the viability of the trial, and also the validity of the results. Consideration of these specific challenges should be made in the planning and design of future studies to optimise trial conduct.

Advisor: Beard, D
Toye, F
Cook, J
Price, A
Automatic verification of stochastic processes: certification of building automation systems

Smart buildings are key to reducing greenhouse gas emissions in the face of the continuous and fast-paced growth of urbanisation. The performance criteria for the optimal operation of such intelligent systems require the coupling of certification goals with the design of both the modelling framework and control algorithms. In the first part of this thesis we demonstrate the use of Fault Maintenance Trees (FMTs): a qualitative description that embeds component degradation, maintenance policies and the relationship between components leading to a failure. We provide semantics to FMTs using continuous-time Markov chains and employ efficient probabilistic model checking to analyse the performance of heating, ventilation and air-conditioning unit, against certification metrics, under different maintenance schemes. The method is also benchmarked against the application of statistical model checking for analysis. The second part introduces the modelling framework of discrete-time Stochastic Hybrid Systems (SHS): probabilistic models suitable for describing the dynamics of variables presenting interleaved and interacting continuous and discrete components. We present algorithms and techniques for performing scalable verification and control synthesis of SHS. The kernel of the methods is a novel abstraction procedure that makes use of interval Markov decision processes. The method embeds the exact abstraction error within the abstraction itself. Consequently reducing the number of states required significantly and allowing us to analyse SHS with more than 10 continuous variables. Furthermore, the applicability of the framework is shown via the construction and analysis of a library of models for building automation systems with different certification goals. Finally, we embed the models and algorithms within StocHy: a new tool aimed at simplifying the analysis of \shs. The tool is written in C++ and allows for simulation, verification and synthesis of stochastic and hybrid systems, in a manner that is accessible to general end-users.

Keywords: verification
Advisor: Abate, A
Analogy in morphological change

This thesis focusses on the tendencies of morphological change, as a source of evidence for how linguistic knowledge is stored and structured in the mind, and how speakers access and use this knowledge. I empirically test various hypotheses that morphological change is directed towards the optimisation of synchronic grammar. In chapter 4, I test the common claim that diachrony is guided by a universal preference for one-to-one mapping of meaning and form in language, implemented via Universal Grammar, and in chapter 5, I consider the diachronic implications of a set of claims by Carstairs-McCarthy (1998), that the degree to which synchronic systems of inflectional morphology deviate from this ideal meaning-form relationship is limited by a set of constraints on the acquisition of lexical semantics. I test the predictions made by these teleological theories against systematic data from synchronic verbal paradigms in classical Greek, and their subsequent diachronic restructuring, and show that the theories are not supported by this evidence. On the other hand, using the same data, I demonstrate two important factors influencing morphological change: the type frequency of formal patterns of implication between paradigm cells (chapter 4), and the token frequency of inflected words (chapter 6). I argue that this is best understood if we view diachronic tendencies as by-products of language use, and I make a case for a synchronic theory of morphology in which words are the fundamental stored units of language, and analogy is a psychologically real mechanism of both synchronic productivity and change.

Keywords: Analogy
Greek
Historical linguistics
Morphological change
Morphology
Advisor: Barber, P
Early Christian scripture and the Samaritan Pentateuch: a study in hexaplaric manuscript activity

EARLY CHRISTIAN SCRIPTURE AND THE SAMARITAN PENTATEUCH is a study exploring Christian interaction with the Samaritan Pentateuch as evinced by hexaplaric sources. Despite the claims of some previous scholarship, the manuscript evidence for the Samaritan Pentateuch in Greek attests two distinct, textually unrelated groups of readings: a σαμ΄-type (i.e., the Samareitikon) and a μονον-type. Only the latter, the subject of the present study, is hexaplarically derived and predates, considerably, any attributed attestation of the former. The extant hexaplaric colophons and scholia found in the books of Exodus, Numbers, and Deuteronomy reveal that at some point the Caesarean Library acquired a copy of the Samaritan Hebrew Pentateuch. This copy was then collated, quantitatively, against the hexaplaric Septuagint. As the Samaritan text is often longer than the Septuagint due to a number of ‘expansions’, taken from various pre-existing passages of the Pentateuch, the Caesarean critics ‘translated’ these expansions into Greek with the aid of the Septuagint (as opposed to the recentiores). No evidence was found that the socalled Samareitikon (i.e., Greek Samaritan Pentateuch) was either known to or used by the Caesarean critics; no evidence was found indicating Samaritans, or native Hebrew speakers, had created these ‘translations’. The ‘translations’ bear no trace of Samaritan exegesis. Instead, the translator(s) cribbed the Septuagint, something evident not only from certain scholia supplied by the translator(s) themselves, but also the remnants of the ‘translation’ which betray specific, septuagintal linguistic features vis-à-vis the translated Hebrew base. It is hypothesized here, that the collation and ‘translation’ process was made possible through the use of the multi-columned Hexapla. Taking the results of this effort, the Christian critic(s) added these data to the margins of the Caesarean Septuagint edition. It is posited that Eusebius—not Origen, as is commonly supposed—was the one responsible for this work.

Advisor: Salvesen, AG