VictorJuiz/thesis huggingface dataset:
Brain imaging in UK Biobank

UK Biobank is a large-scale prospective epidemiological study with all data accessible to researchers worldwide. It is currently in the process of bringing back 100,000 of the original participants for brain, heart and body MRI, carotid ultrasound and low-dose bone/fat x-ray. The brain imaging component covers six modalities (T1, T2 FLAIR, susceptibility-weighted MRI, Resting fMRI, Task fMRI and Diffusion MRI). Raw and processed data from the first ∼42,000 imaged subjects has recently been released for general research access. To help convert this data into useful summary information, we have developed an automated processing and QC (Quality Control) pipeline that is available for use by other researchers. In this work, we describe the tools and research we have developed in order to generate the data in a way that is readily usable for researchers worldwide. The first half of this thesis will give a brief overview of UK Biobank brain imaging and the acquisition protocol, and then describe the processing pipeline and QC pipeline in detail. We also describe several quantitative investigations carried out as part of the development of both the imaging protocol and the processing pipeline. The second part of this thesis will show the research we performed to come up with a set of recommendations to deal with confounds in brain imaging studies using UK Biobank. UK Biobank is a powerful resource for studying associations between imaging and non- imaging measures such as lifestyle factors and health outcomes, in part because of the large subject numbers. However, the resulting high statistical power also raises the sensitivity to confounding effects, which therefore have to be carefully considered. Here we describe a set of possible confounds (including non-linear effects and interactions) that researchers may wish to consider for their studies using such data. We include descriptions of how we can estimate the confounds, and study the extent to which each of these confounds affects the data, and the spurious correlations that may arise if they are not controlled.

Keywords: neuorinformatics
confounds
UK Biobank
machine learning
neuroimaging
processing pipeline
artificial Intelligence
quality control
Advisor: Jenkinson, M
Smith, SM
Nichols, TEP
Probability and nondeterminism in compositional game theory

We substantially extend previous work in the emerging field of compositional game theory.
We generalise work by Escardó and Oliva relating the selection monad to game theory. Escardó and Oliva showed that the tensor operation of selection functions computes a subgame perfect equilibirium of a sequential game. We investigate game theoretic interpretations of selection functions generalised over a monad. In particular we focus on the finite non-empty powerset monad which we use to model nondeterministic games. We prove a negative result: that nondeterministic selection functions do not com- pute the collection of all subgame perfect plays of a sequential game. We then define a solution concept related to the iterated removal of strongly dominated strategies, and then show that the tensor of nondeterministic selection functions computes the plays of strategy profiles satisfying this solution concept.
In the second part of this thesis we greatly expand the expressive power of open games, first introduced by Jules Hedges [Hed16]. In the current literature, open games are defined using the category of sets and func- tions as an ambient category. We define a category of open games that can use any symmetric monoidal category as an ambient category. This is accomplished using coend lenses which can be used to model certain bidirectional processes. Generalising open games to arbitrary symmetric monoidal categories allows us to, in particular, model probablistic games involving Bayesian agents in an open games formalism.

Keywords: category theory
open games
game theory
compositional game theory
Advisor: Hedges, J
Faithful decides: contemporary French thought and the eternal return of religion

At a time when religious fundamentalisms fight on all continents for the monopoly of religious truth, no definition seems as uncertain as that of religion. To be sure, the definitions proposed by Edward Burnett Tylor, William James and Emile Durkheim in the nineteenth and early twentieth centuries, which all revolve around the notion of transcendent belief, have been used in social sciences for more than a century and still constitute the theoretical ground on which secularism rests in the modern West. In the past few decades, however, globalisation and the emergence of spiritual approaches to environmentalism and mindfulness in Western countries have raised the question of whether non-theistic devotion and ritual practices detached from supernatural belief should be considered as religious. Reformist currents of the Abrahamic religions have also contributed to challenging the idea that transcendent belief is conditio sine qua non of religion by emphasising ‘lived experienced’ and ‘reflective faith’. These definitional transformations go hand in hand with the urgency felt by political leaders and sociologists to distinguish religion from what is presented as its terrorist caricature. In this thesis, I argue that a way out of this definitional crisis may be found in the work of four of France’s most original contemporary philosophical voices. Through their respective non-dialectical engagements with the concept of the death of God, Georges Bataille, Jacques Derrida, Gilles Deleuze, and Jean-Luc Nancy inaugurate a thinking of the religious that does not depend on transcendent belief, but rather unfolds as an open-ended trust in otherness. Over the course of four chapters, I demonstrate that, by designating faith in difference as the lowest common denominator of transcendent religions and immanent spiritualities found across the world, these thinkers lay the ground for a more inclusive approach to religious pluralism than the one currently secured by Western secularism.

Keywords: French thought
eternal return
Georges Bataille
Jean-Luc Nancy
Jacques Derrida
deconstruction
continental philosophy
Gilles Deleuze
return of religion
Advisor: Maclachlan, I
Understanding immunity differences induced by whole cell and acellular pertussis vaccines in a paediatric population

Bordetella pertussis causes whooping cough, a life-threatening disease in infants. Both whole cell (wP) and acellular (aP) vaccines are used for infant immunisation with aP providing less robust long-term population protection. To further understand differences between wP and aP, this thesis aims: to characterise the immune response to an aP-booster in a UK cohort by age and priming backgrounds (wP/aP) using a broad variety of assays of humoral immunity; to investigate effect of HLA-DRB1-233Thr previously associated with pertussis toxin (PT) IgG antibody levels in wP-primed infants and protection from disease; to evaluate the use of continuous temperature monitoring as an objective method of evaluating reactogenicity.
An aP booster gave the best responses in adolescents (aP-primed) and adults (wP-primed) in terms of antibody (highest for pertactin (Prn) and filamentous haemagglutinin (FHA) IgG), memory B-cells and novel functional assays (SBA, OPA, CDA). Prn-IgG was the antigen most closely correlated with novel functional antibody assays (SBA, OPA, CDA). For all antigens, IgA baseline and booster response increased with age, unlike IgG, suggesting a role of continued antigen exposure in generating this response.
The association of HLA-DRB1-233Thr variant with PT-IgG antibody levels was replicated in wP-primed Asian infants and European adolescents. There was no indication of an additional association with any functional antibody assays assessed. However, an association with PT-IgG avidity and PT-IgA, suggested a role of this variant in enhancing immunological memory in addition to initial antibody production.
Continuous temperature monitoring identified a higher number of fever episodes, characterising more accurately fever, a marker of innate immune response, post-vaccination.
This thesis provides data supporting the introduction of Prn-containing aP in adolescents and adults. Investigation of the mechanisms associated to HLA-DRB1-233Thr and protection in wP-primed individuals may give further insight into differences between aP and wP vaccine responses associated with protection.

Keywords: Acellular vaccine
Immunity
Bordetella pertussis
Whole cell vaccine
Advisor: Clutterbuck, E
Mentzer, A
Kelly, D
"Subjection for the sake of virtue": voluntary slavery in Plato's Symposium and the Laws

What is to be made of Plato’s provocative and perplexing claim in the Laws that both Athenian citizens and citizens of Magnesia, Plato’s second-best city, should be thought of as “voluntary slaves to the laws”? How is it possible that ordinary citizens attain virtue by mimicking the subordination of those who lack the capacity for knowledge and independent reasoning? How can a state of dependence and subordination to legal authority be compatible with the acquisition of ordinary civic virtue? Approaching the Laws via the Symposium, I propose to elucidate the paradox of voluntary slavery by examining the striking but overlooked use of a similar phrase –“voluntary slavishness”– in Pausanias’s speech in Plato’s Symposium. In this novel reading of the Laws, I propose that understanding the citizens’ voluntary slavery to the laws in parallel with the beloved’s willing slavery to the lover reveals that Plato envisions ordinary citizens of Magnesia as passive beloveds. Like the beloved in Pausanias’s speech, who is permanently subjected to the training and guardianship by the lover despite being a fully-grown man, I suggest that the ordinary citizens of Magnesia are attributed a permanent status of minority and slavishness with relation to the laws because they are incapable of achieving or sustaining independent virtue. I argue that ordinary citizens of Magnesia have a status that parallels that of minors and slaves vis-à-vis the legal authority. Based on this analogy between the beloved in Pausanian paiderastia and the ordinary citizen in the Laws, I cast doubt on the idea that the Laws embodies a ‘democratic turn’ in Plato’s political thought. In contrast to much recent scholarship, I suggest that the Laws preserves, not undermines, the divide between philosophic rulers and non-philosophic ordinary citizens found in the Republic.

Keywords: paiderastia
education
Symposium
virtue
Laws
Plato
voluntary slavery
Advisor: Srinivasan, A
Rational inattention in macroeconomics

In many markets, acquiring and processing the information needed to make optimal decisions costs agents time, effort, and/or money. This thesis is concerned with the macroeconomic implications of the way households behave in the face of these costs, which is known as rational inattention. The thesis consists of three self-contained chapters.
The first and second chapters both explore limited household attention to the choice between different savings products. Regulators (e.g. FCA, 2015) have found that households who gather more information when choosing savings products obtain higher interest rates, and the chapters explore two implications of this.
The first chapter studies how the attention decision varies over the business cycle, and the impact that then has on the cycle. I find in both theory and data that attention to savings product choice is countercyclical. This amplifies business cycle fluctuations, because it introduces a countercyclical wedge between policy rates and the interest rate faced by households. In an estimated DSGE model this amplification is substantial, increasing the variance of consumption by 17%. Policies that reduce the cost of information weaken this amplification and so reduce business cycle volatility.
The second chapter explores the implications of rational inattention to savings choices for inequality and fiscal policy. In a model related to that in chapter 1, I find that poorer households pay less attention to saving choices because they have less to gain from higher interest rates. They therefore face lower interest rates, so have less asset income and less desire to save. I show that this feedback between wealth and attention renders the representative agent steady state of the model unstable with respect to idiosyncratic household income shocks. The stable steady state has a two-agent structure, with poor households at the borrowing constraint paying no attention, while wealthy households pay attention and earn high returns. As the steady state inequality is driven by endogenous attention choices, it responds to policy. I find that aggregate consumption has a smaller and more persistent response to large fiscal expansions in this model than a comparable model where inequality is driven by exogenous discount factor heterogeneity.
The third chapter, co-authored with Martin Ellison, moves away from attention to savings choices, considering the information households choose to acquire about the future of the labour market. We find that introducing rational inattention into a model with uninsurable unemployment risk can generate multiple steady states, where with full information the model has a unique steady state. Large mutations in the distribution of household beliefs can shift the economy between steady states. Labour market beliefs in the model are heterogeneous and persistent, consistent with survey evidence.

Keywords: Rational inattention
Advisor: Ellison, M
Brevard Childs’ canonical approach: an evaluation of its main elements

This thesis aims to provide an evaluation of Brevard Childs’ canonical approach, which is an approach to Theological Interpretation that aims to utilise the Bible as a vehicle to know the Christian God. This thesis is located in the academic discipline of Biblical Studies and has a substantial lean towards Old Testament (hereafter ‘OT’)/Hebrew Bible (hereafter ‘HB’) Studies as this was Childs’ specialism and is also mine today. This thesis was not initially devoted to a study of Childs’ approach, but his approach is so extensive that it warrants a thesis in itself. My argument is twofold: (i) Childs’ approach consists of three main elements that were variously developed and implemented over time, and (ii) these elements, though rich and informed, ultimately fail to complete the aim that Childs set out to achieve. Regarding originality, this thesis introduces the idea that Childs’ canonical approach is composed of these three main elements and provides what I hope is the most detailed evaluation of Childs’ approach in light of Biblical Studies. A conclusion was established by firstly identifying that the canonical approach consists of three main elements. I then undertook detailed analyses of each of these elements and evaluated them in accordance with their reasonableness and in light of the evidence from Biblical Studies. This thesis is structured in two parts. Part A aims to provide the reader with a helpful foundation before one engages in a detailed study of Childs’ canonical approach. Part B is then the main body of the thesis which analyses and evaluates each of the approach’s main elements.

Keywords: Christianity
hermeneutics
biblical theology
biblical studies
theological interpretation
Brevard Childs
Advisor: Barton, J
Extraterritorial court jurisdiction in the corporate anthropocene: a comparative enquiry

Corporations are notoriously powerful actors in the current configuration of our globalised economy. As such, they have assumed a key role in shaping a new age of ecological precarity—the Anthropocene. Indeed, the transnational scope of corporate activities often results in environmental harm elsewhere on the planet. Disheartened by host states’ perceived inability to deliver environmental justice locally, several recent lawsuits have tested the willingness of European home state judiciaries to adjudicate the extraterritorial conduct of domestic corporations. The fate of such litigation crucially hinges upon a procedural legal modality: jurisdiction. This thesis investigates when, how, and why European courts assume jurisdiction over civil environmental wrongs centred abroad (extraterritorial jurisdiction). Methodologically, it analyses two legal sagas in the UK (Lungowe v Vedanta) and the Netherlands (Akpan et al. v Shell) and contrasts these to a third lawsuit in Germany (Lliuya v RWE). This comparative enquiry reveals the contingency of extraterritorial jurisdiction as a socio-legal construct, as well as its opportunities and limits in confronting the corporate Anthropocene. Ultimately, the advent of unilateral judicial interventions in the environmental affairs of other countries raises concerns over the international and institutional legitimacy of such an exercise. In order to dispel these concerns, a re-imagination of the role and functionality of jurisdiction within an increasingly polycentric environmental governance landscape is required.

Advisor: Bogojević, S
A study of CP violation and measurement of the CKM angle γ in B0→ DK∗0 decays

Two measurements of CP observables in B0 → DK∗0 decays are presented, where D represents a superposition of D0 and D0-bar states. The measurements use samples of proton-proton collision data collected with the LHCb detector at centre-of-mass energies of 7, 8, and 13 TeV.
The first measurement uses 5 fb−1 of data with the D meson reconstructed in the two-body final states K+π−, π+K−, K+K-, and π+π−, and, for the first time, in the four-body final states K+π−π+π−, π+K−π+π-, and π+π-π+π−. First observations of the decays B0 → D(π+K−)K∗0 and B0 → D(π+π−π+π−)K∗0 are obtained, and a set of observables comprising yield ratios and asymmetries is studied. The second measurement studies D-meson decays to the three-body final states KS0π+π− and KS0K+K− in a binned Dalitz plot analysis using 9 fb−1 of data.
The CP observables from both measurements are interpreted together to determine the CP-violating weak phase γ = (77+8-9)◦. This is the world’s most precise determination using only B0-meson decays and is in agreement with the prediction of the Standard Model. The world’s best measurements of the hadronic parameters r_B = 0.258+0.022-0.023 and δB0 = (200 ± 8)◦ are also presented.

Keywords: CP violation
B mesons
Large Hadron Collider
CKM triangle
Advisor: Wilkinson, G
Feeling all the (partisan) feels: Exploring the drivers of affective polarization at the individual-level

Affective polarization—hostility and aversion between rival political groups—is an increasingly salient feature of Western democratic politics. While scholars agree that this trend raises serious concerns for public life, its underlying drivers are still debated. This thesis enriches this line of research by clarifying some of the mechanisms shaping affective polarization at the individual level. My overarching research question is: What drives affective polarization at the individual level? I tackle this question through three distinct empirical studies that engage with separate aspect of this phenomenon. Study I leverages survey data to show that, among UK partisans, perceived conflict with their in-party on policy issues curbs affective polarization. Moving on to the digital sphere, Study II deploys computational methods to reveal the existence of affective biases in online political discussions between ideologically opposed Reddit users, and shows how the tone of their exchanges can both mitigate and worsen these patterns. Study III, finally, provides experimental evidence that only exposure to certain forms of online partisan messages have downstream consequences for affective polarization: those that explicitly threaten and devalue an individual’s own political party. Taken together, these findings reveal the drivers of affective polarization to be contingent on both situational and dispositional factors, including how ideologically aligned partisans are with their own political party, how their perceived political rivals engage with them in online conversations, and whether they are made to feel threatened by them.

Keywords: social identity theory
partisanship
political communication
affective polarization
Advisor: Bright, J
Howard, P
Characterising the cardiac effects of dysregulated propionate metabolism using a mouse model of propionic acidaemia

Propionate is a naturally-occurring monocarboxylate short-chain fatty acid in humans derived from the mitochondrial metabolism of multiple substrates. There is evidence for dysregulated propionate metabolism (and hence its accumulation), in common metabolic disorders, such as diabetes and obesity. However, the most extreme accumulation of propionate occurs in the inherited metabolic disease, propionic acidaemia (PA). Despite its rarity, PA is one of the commonest organic acidaemias. PA results from a defect in mitochondrial propionyl-CoA carboxylase, the rate-limiting step to propionate metabolism (as propionyl-CoA), resulting in the accumulation of propionate, and other related metabolites such as propionyl-carnitine and 2-methylcitrate. Interestingly, diastolic dysfunction, cardiomyopathy and arrhythmias account for significant morbidity and mortality in PA patients. However, the underlying mechanisms are yet to be fully elucidated.
The aim of this thesis was to characterise the effects of dysregulated propionate metabolism on the heart. This was primarily addressed by using a mouse model of PA (Pcca-/- A138T), in which the levels of propionate generated in vivo are sufficient to produce a metabolic signature of the human disease, but allows the animal to reach adulthood, thereby facilitating the study of cardiac physiology in vivo and in isolated cells.

Keywords: Organic anions
Excitation-contraction coupling
Cardiac dysfunction
Propionate
Organic acidaemia
Propionic acidaemia
Epigenetics
Advisor: Swietach, P
Smart, N
Adventures on the isle of adolescence: forms of contemporary American girlhood

This thesis examines how a revised version of the coming-of-age narrative has emerged in a range of contemporary novels, which offer feminist revisions of American girlhood through formal, thematic, and ideological departures from the traditional gendered narrative conventions of adolescence. Through this examination, this thesis argues that the American girl has been transformed from a flat aesthetic object in earlier iterations of the coming-of-age narrative, to a dynamic socio-political subject whose narrative centres upon the promotion of a range of feminist agendas in the contemporary novel.
The coming-of-age narrative has chiefly explored the development of adolescent boys, charting their ‘growing up’ into a world of masculine dominance and opportunity as they mature into men. In opposition to the expansive worlds of their male counterparts, girls’ coming-of-age narratives have routinely depicted an experience of ‘growing down’ into future womanhood, where the maturation from girl to woman charts a protagonist’s personal diminishment. In this story of the female coming-of-age experience, girls learn nothing more than how to acquiesce to the normative dictates governing gender identity.
However, this thesis argues that contemporary literature foregrounds new visions of American girlhood that explicitly destabilise the constricting conventions of the coming-of-age narrative. As a result of this generic reconfiguration, this thesis examines how the coming-of-age narrative has shifted from being an essentially conservative form that predominantly focused on the narratives of middle-class, white, heterosexual girls, to instead being used as a cultural vehicle to expand understandings of girlhood as an identity that is shaped by questions of gender, sexuality, race, disability, class, and religion in the post-1990 era.

Keywords: Girls
Girlhood
Novel
Contemporary literature
Identity
Gender
American literature
Advisor: Pratt, L
Emre, M