VictorJuiz/thesis huggingface dataset:
Investigating fibrotic pathways in human rotator cuff tendon disease

Tendon disease begins with inflammation and results in an incomplete repair with fibrosis. IL- 1β is a pro-inflammatory cytokine related to tendinopathy and IL-4 is a pro-fibrotic cytokine implicated in torn tendons. TGF-β, BMPs and CTGF are key mediators of fibrosis and their expression is dysregulated in animal models of tendon injury and overuse. The aim of the thesis was to investigate the fibrotic pathways active in human tendon disease. TGF-β, BMP family and CTGF mRNA and protein expression were investigated in patient samples of healthy and diseased tendinopathic and torn supraspinatus tendons. Tendon stromal cells (TSCs) isolated from healthy and diseased (torn) tendons were treated with IL-1β and IL-4 to investigate mRNA expression of TGF-β, BMPs and CTGF. Cell signalling pathways driving cytokine-induced changes in their expression was determined. TSCs from healthy and diseased tendons were treated with TGF-β1 and BMP-2 to investigate how these treatments modulate the expression of extracellular matrix (ECM)-related genes. TGF-β1, BMPs and CTGF protein expression was reduced in diseased compared to healthy tendons, with marked suppression in tissues from torn tendons. IL-4 suppressed TGFB1, BMP2 and CTGF mRNA in TSCs from diseased tendons indicating the regulatory role of the inflammatory milieu in disease development. IL-1β induced TGFB1 and increased BMP2 mRNA expression in TSCs from diseased tendons that was negated by ERK1/2 inhibition. The suppressive or inductive effects of TGF-β1 and BMP-2 treatments on ECM-related genes were similar in TSCs from healthy and diseased tendons. However, the cells from diseased compared to healthy tendons showed reduced responsiveness to TGF-β1 and BMP-2. The induced TGFB1 and increased BMP2 mRNA expression by with IL-1β is possibly a compensatory mechanism for their diminished baseline expression and cellular effects in diseased tendon tissues.

Keywords: tendon
Advisor: Carr, A
Snelling, S
Dakin, S
Speculative politics: U.S. Economic policymaking towards China in the post-Cold War era

This dissertation develops a new speculative politics framework to explain the major shifts and enduring consistencies in U.S. economic policy toward China from 1989 to 2019. Building on behavioral economics, the speculative politics framework posits that just as investors face uncertainty about which stocks will yield the greatest returns, it is far from clear which policies will best promote one’s political interests, especially in the context of complex economics and politics, both foreign and domestic. Thus, causal stories help translate interests into policy preferences under uncertainty, helping actors diagnose problems and speculate about the effects of policy solutions.
Moreover, like financial markets, the market for causal stories and the policies they support suffers from systemic biases like the availability heuristic and belief inertia. These biases can lead to market failures, such as overconfidence in certain stories and policies, opportunities for foreign actors to manipulate policy debates, and the potential for speculative bubbles. During debates over China’s Most Favored Nation (MFN) status and later during China’s entry into the World Trade Organization (WTO), Chinese officials and pro-engagement U.S. actors sought to bolster the narrative that U.S. economic engagement with China would strengthen the cause of reform in China and promote international stability. However, mounting dissonance due to unmet promises will eventually pop a bubble, producing a backlash in perceptions and policies, as can be seen today in the combative shift in the U.S. approach to China and talk of a “reckoning” within the U.S. China-watching community.
This dissertation utilizes archives, interviews, and statistical analysis of Congressional voting and focuses on key policy issues across two main eras: China’s MFN status and WTO accession during the George H.W. Bush and Bill Clinton presidencies, and U.S. bilateral and plurilateral trade negotiations and escalating trade enforcement actions during the George H.W. Bush, Barack Obama, and Donald Trump presidencies. Thus, the dissertation makes important empirical and theoretical contributions, shedding light on the interplay between perceptions, power, and policies in U.S.-China economic relations.

Keywords: Trade
international political economy
U.S.-China relations
China
Advisor: Hall, T
Belonging at the margins: nation, religion, and the Ahmadiyya Muslim Jama'at in colonial and postcolonial India, c. 1930-74

This thesis examines the history of the Ahmadiyya Muslim Jama’at in India, c. 1930-1974 through archival and printed sources in Urdu and English. It considers the multiple sites of belonging of nation, sect, and religion that the Ahmadiyya negotiated whilst remaking itself after it was devastated by Partition. The Jama’at’s strategies of self-presentation are assessed via its newspaper, al-Badr, to trace the formation of a distinct Indian Ahmadi identity in the early postcolonial period.
Chapters 1 and 2 suggest the received wisdom of the Ahmadiyya’s political neutrality needs revision by looking at its early history under colonial rule and its active engagement in its fate as Partition became increasingly likely. Chapter 3 explores the impact of suspicion of Punjabi Ahmadis in the aftermath of Partition and during wars with Pakistan to consider how Ahmadis projected themselves as loyal and patriotic Indian citizens. Chapter 4 examines two High Court judgements from 1922 and 1970 through the prism of gender and personal law. It proposes continuities between the colonial and postcolonial periods in how the state responded when Ahmadi claims to Muslimness were challenged. The final two chapters are anchored by anti-Ahmadi events in Pakistan in 1953 and 1974 respectively. Chapter 5 assesses Ahmadi efforts to put forward an idea of Muslim political unity to thrive under secular, non-Muslim rule, whilst not losing sight of sectarian differences. Chapter 6 considers how the Ahmadiyya’s missionary efforts and narratives of growth sat alongside intensifying opposition against them from other Muslims and how this opposition reinforced representations of themselves as followers of True Islam.
The conclusion considers how this thesis contributes to wider scholarly efforts to deepen and broaden understandings of the legacies of Partition and suggests the implications of its intersectional analysis, especially for conversations about the dynamics of Muslim identity during this time of flux.

Keywords: Indian Muslims
respectability
belonging
newspapers
tabligh
Urdu
Partition
religious minority
postcolonial India
patriotism
Muslim Personal Law
proselytising
Qadian
loyalty
sectarianism
Ahmadiyya Muslim Jama'at
intersectionality
Advisor: Devji, F
The white-collar hustle: academic writing & the Kenyan digital labour economy

This study seeks to understand the experiences of young academic writers in Kenya, within the context of the new digital economy of educated-youth labour and global microwork exchanges. It situates academic writing in their wider lives and career trajectories; exploring the nature of their work, and the types of knowledge, skills and capital (if any) being developed through writing. The research design featured a case study of 27 current and former academic writers, and employed several methods, including; semi-structured interviews using WhatsApp, non-participant observation, Facebook data ‘scraping’, and document analysis of written samples.
Drawing on Thieme (2013), the thesis argues that academic writing acts as a ‘white-collar hustle’ for current undergraduate students and recent graduates in Kenya. It is an informal and precarious form of employment- facilitated through the digital economy- which affords Kenyan youth an avenue for developing academic and professional skills, while earning an income. Academic writing is primarily used as a part-time job alongside full-time studies, as a ‘place-holder’ during periods of would-be unemployment, and as a supplement to formal employment. Moreover, the writers have created an informal ‘community’ and ‘marketplace’ to their collective benefit, by leveraging existing personal and professional networks.
As such, the thesis challenges dominant narratives of youth (un)employment by suggesting that periods of transition are characterized by very active ‘making do’. Therefore, the study contends that the academic writing industry offers insights into the present and future of educated-youth work in Africa, and globally. In so doing, the study connects the global economy to local polities through the lens of contemporary experiences of youth; navigating assumptions and realities about Kenya’s place in a globalized world, and the young writers’ place in a newly-formed knowledge economy.

Keywords: internet-mediated research
hustle
contract cheating
informal economy
youth
higher education
WhatsApp
digital economy
academic writing
unemployment
Kenya
Functional genomics studies of cancer and cells of origin: from pan-cancer to single-cell

The development of stratification systems and therapeutical targets is critical for cancer research. Recent advances in high-throughput sequencing enable the gener- ation of a large amount of cancer genomic and transcriptomic data, which can be used to answer the questions on cancer diagnosis and treatment. However, it is still a great challenge to interpret a mass of data and get reliable conclusions.
In this study, I used the functional genomics methodologies to study cancer and cells of origin. In the pan-cancer study, I developed an algorithm, Masonmd, to predict the targets of nonsense-mediated decay (NMD). This algorithm identified over 140 thousand NMD-elicit mutations from the genomic data of The Cancer Genome Atlas (TCGA) pan-cancer cohort. Further analysis showed that NMD was prevalent across cancer types and, more notably, it could play a permissive role in cancer progression. The results support the notion that the inhibition of NMD is a promising therapeutic strategy.
In the work on single-cell RNA sequencing (scRNA-seq), I first developed a differential- expression-based clustering algorithm, ClinCluster, tailored for clinical scRNA-seq data. The benchmarking analysis demonstrated that ClinCluster outperformed other commonly used pipelines in both simulated and real datasets. I next gen- erated and analysed the scRNA-seq data from human fallopian tubes, which certain high-grade serous ovarian cancer (HGSOC) arose from. The analysis constructed a cell atlas of human fallopian tubes and identified four novel secretory subtypes. Based on the discovery of cell phenotypic repertoire, the deconvolution analysis of the TCGA data refined the molecular subtyping of HGSOC. This gave rise to a robust prognostic predictor, which was validated in eight independent expression datasets. Together, the evidence suggests that the phenotypic heterogeneity in cells of origin can be inherited by tumour cells, which affects patients’ overall survival. It shed light on a refined molecular diagnosis for HGSOC.

Keywords: cancer
functional genomics
cells of origin
fallopian tube
pan-cancer analysis
ovarian cancer
single-cell RNA sequencing
Advisor: Ahmed, AA
Yau, C
Family and school factors on educational outcomes in contemporary Brazil

This thesis investigates how family and school factors affect selected educational outcomes in Brazil. In particular, the effectiveness of two nationwide compensatory policies - the National Fund for Basic Education and Bolsa Família - in improving and equalizing educational outcomes is assessed. Three main research questions are answered. First, what are the trends in Inequality of Educational Opportunities (IOE) during the twentieth and beginning of the twentieth-first centuries in Brazil? Second, is there stability or change in average scholastic performance as measured by test scores in language and mathematics over time? Do changing school resources predict average scholastic performance over time? Third, does the Bolsa Família programme improve test scores performance in language and mathematics of poor beneficiary pupils? The Brazilian National Household Sample Survey, Prova Brasil (or Brazil Exam), School Census, Single Registry, and the Attendance System are used to answer these questions. The key findings from the observational studies are as follows. First, there is an equalisation in early educational transitions (completing some and graduating primary education), followed by a strengthening in the association between parental education and the completion of secondary and some tertiary education respectively. We also observe a stable but very unequal trend for completing university degree over time. Second, there are positive gains in average school performance between 2009 and 2015 (compared to the same schools in 2007): from 4 to 24 of a standard deviation for mathematics, and from 19 to 37 of a standard deviation for language. Moreover, increasing selected school resources have significant effects on average school achievement in language and mathematics over time, but the effects are very small, between 0.3 and 2.3 of a standard deviation. Third, there is a positive effect of the Bolsa Família programme on test scores in language and mathematics, but the effect is very small: between 1 and 3 of a standard deviation. This thesis addresses the influence of family and school on inequalities in selected educational outcomes accounting for socioeconomic differences observed by region and school type in a large and unequal developing country. The findings have important implications for future research and policy on this topic.

Advisor: Chan, T
Orbital transmissions: affect and musical public-making in London

This thesis is a multi-sited ethnography of live music audiences in London. Drawing insight from four broadly defined field sites—classical music, sound art, dub reggae, and electronic/dance music—the thesis investigates the role of affect in the formation of musical and sonic publics. Music’s affective propensities refer to its ability to generate visceral states and adrenal surges that elude obvious discursive representation, and that often seem pre-conscious. The importance of these somatic feelings lies in their ‘public-making’ capacities: their ability to bind us to or separate us from others in ways that can transform or reinforce broader social relations. The central contribution of the thesis is that it advances new empirically grounded ways of understanding the workings and potentials of musical and sonic affect, offering insight into the social and affective processes by which music and sound generate collectivities, the extent to which such collectivities endure, evolve, or evaporate over time, and the opportunities they present for putting existing social orders into question. Above all, the thesis demonstrates through rich ethnographic and historical research how musically incited affect has to be analysed by reference to social, cultural, historical and political conditions. I show that affect, as it is engendered by music and sound, is an ambivalent mechanism, able to strengthen as well as challenge dominant social orders.
On the basis of this ethnographic work, the thesis simultaneously develops a new theoretical framework to critique influential theories of affect derived from the humanities and social sciences that portray affect as pre-mediated and involuntary: as an emancipatory force operating autonomously from subjectivity and social identity. The thesis is thus committed to the generative effects of putting theory and empiricism in dialogue, employing a ‘post-positivist’ empiricist methodology (Born, 2010a) that moves constantly between speculative theory and historically informed ethnography. Arguing that an empirically grounded theorisation of affect is central to an understanding of musical and sonic experience, musical and sonic publics, and therefore also to a musical and sonic politics, the thesis acts as a rejoinder to theories of listening and live audiencing in musicology and sound studies, while also advancing several secondary themes that cut across the thesis as a whole. These themes include questions of genre and creativity, specifically the contingent relations between musical producers and their publics; music and community vis-à-vis wider critical discourses on community and inclusivity; theories of temporality and the aesthetic; and musical taste and social stratification. Finally, in the Conclusion, the thesis suggests possible new directions for thinking about the affective politics of music and sound, oriented around three logics: antagonism-agonism; community-collaboration; and emergence-divergence.

Advisor: Born, G
Twisted coadmissible equivariant D-modules on rigid analytic spaces

We aim to extend the results of Ardakov and Wadsley on representations of p-adic Lie groups and sheaves of equivariant D-modules on rigid analytic spaces. Our main results are a canonical dimension estimate for coadmissible representations of a semisimple p-adic Lie group in a p-adic Banach space, and a Beilinson-Bernstein-type localisation for coadmissible equivariant Dλ -modules, where λ is a ρ-dominant ρ-regular infinitesimal central character.
This thesis is split into two principal sections. The first section contains results on the structure of the dual nilpotent cone of a semisimple Lie algebra g over an algebraically closed field K of positive characteristic p. When p is small, the structure of the adjoint and coadjoint orbits of G on g and g∗ respectively changes. We relax the hypotheses on p and prove that, under certain technical conditions, the dual nilpotent cone is a normal variety. Using this, we show that the canonical dimension of a coadmissible representation of a semisimple p-adic Lie group in a p-adic Banach space is either zero or at least half the dimension of a non-zero coadjoint orbit.
The second section extends the work of Ardakov on coadmissible equivariant D-modules on rigid analytic spaces, by defining the category of coadmissible equivariant twisted D-modules. We classify sheaves of differential operators on a rigid analytic variety X and use this to define the category CλX/G in the case where λ is a regular ρ-dominant ρ-integral central character. In this particular case, we show that CλX/G is equivalent to Ardakov’s category CX/G and use this to prove a twisted analogue of locally analytic equivariant Beilinson-Bernstein localisation on rigid analytic spaces.
The final part of this thesis is concerned with removing the integrality condition. We construct the enhanced completed skew-group algebra D(X, G) and realise the twisted completed skew-group algebra Dλ (X, G) as a quotient, providing a natural framework to view coadmissible Gequivariant DλX-modules as coadmissible modules over this algebra. We give a general definition of C λX/G for arbitrary ρ-dominant ρ-regular central character and discuss how to check this agrees with the definition given for the integral case. Following this, we show this category is equivalent to the category of U(g, G)-modules with fixed infinitesimal central character λ.

Keywords: Geometric representation theory
Advisor: Ardakov, K
Fair division of the commons

A group of agents controls a common budget or owns some common resources. The agents need to decide how to divide this budget across various projects, or to distribute the resources among themselves. Each agent has their own preferences about the best use of the resources. We study ways in which the agents can make these decisions in a fair manner. By fairness, we will mean that for every group member, a proportional part of the common budget is spent in accordance with the member's interests. We will also be interested to take into account the interests of subgroups, and when appropriate aim to avoid envy between group members.
We consider several settings in this thesis, capturing different types of potential uses of the common budget. For example, we distinguish between projects that come with a fixed cost (and can be either fully funded or not at all), and projects that can flexibly scale with the amount of funding received. We also distinguish between uses that potentially benefit several or all group members (public goods) or uses that benefit only one agent (private goods).
For each scenario we consider, we formalise what we might mean by a "fair" outcome, and then design decision rules that guarantee fairness. Where possible, we additionally aim for rules that make Pareto-efficient use of the common budget. Unfortunately, many of our rules can be exploited by strategic agents who misreport their preferences. In these cases, we prove impossibility theorems which imply that no fair decision rule can be resistant to such strategic manipulation. These impossibility theorems are proved using a computer-aided technique based on SAT solvers, which allows us to obtain computer-generated but human-readable proofs. Further, we consider the computational complexity of the decision rules we consider. In most cases, they can be evaluated using efficient algorithms. In other cases, there are NP-completeness results, but we can show that efficient algorithms exist that work when preferences are well-behaved, in the sense of exhibiting underlying structure.

Keywords: computational social choice
fair allocation
preferences
voting
resource allocation
computational complexity
public goods
Advisor: Elkind, E
Statistical models of gene-environment interactions

Despite longstanding interest in gene-by-environment (GxE) interactions, the contribution of GxE interactions to complex disease in humans remains poorly characterised. Studies of GxE interaction are statistically challenging due to the inherent high dimensionality of environmental exposures, the increased sample size required to robustly detect GxE effects and the historic lack of large datasets that combine genetic and environmental data. In this thesis I introduce a new approach for GxE interactions with multiple environmental variables on biobank scale datasets called LEMMA (Linear Environment Mixed Model Analysis). LEMMA uses a Bayesian whole genome approach to jointly model SNP marginal effects and SNP GxE interaction effects with an Environmental Score (ES). The ES is a linear combination of multiple environmental variables, and 'interaction weights' used to construct the ES are learnt in the same Bayesian framework. The ES can subsequently be interpreted directly, used in single SNP hypothesis or used for heritability estimation. Using variational inference to fit the model and a distributed computational architecture allows LEMMA to be computationally tractable on Biobank scale datasets.
LEMMA is compared to existing single-SNP approaches that jointly model the effects of multiple environmental variables at each locus. Results suggest that LEMMA has substantially greater power to detect GxE effects when the underlying model assumptions hold.
I have applied LEMMA to model GxE interactions in body mass index, systolic, diastolic and pulse pressure, using 42 environmental variables and approximately 280,000 white British individuals from the UK Biobank. LEMMA uncovered 3 loci with GxE interactions at genome wide significance levels, and estimated that 9.3%, 3.9%, 1.6% and 12.5% of phenotypic variance is explained by GxE interactions, and that rare variants explain most of this variance.
In my final chapter I suggest a new model, referred to as RHE-NLS, that promises to achieve many of the same objectives as LEMMA with improved computational complexity.

Keywords: Bayesian statistics
Advisor: Sharp, K
Steinsaltz, D
Marchini, J