VictorJuiz/thesis huggingface dataset:
Imperialism and localism in provincia Asia: The development of Roman provincial administration, 133 BCE - c. 20 CE
Keywords: political and social institutions
ideology
Asia Minor
Provincial government
Roman Republic

This thesis contributes to the study of Roman imperialism, providing an investigation of the development of Roman provincial administration in western Asia Minor in the period between 133 BCE and c. 20 CE. It investigates the evolving institutional and ideological frameworks put in place by the Roman state and its representatives and local reactions to them.
Chapter 1 focuses on the institutions which the Roman state established in the province of Asia. Employing models of institutional dynamics from the social sciences, it argues that Roman approaches to provincial administration were initially ad hoc and situational and that ‘governance’ developed in an unplanned fashion. The critical role played by individuals such as L. Cornelius Sulla and C. Iulius Caesar, whose influence and power allowed them more flexibility in dealing with institutional constraints, is emphasised.
Chapter 2 examines the role of Roman official communication in creating an imperial ideology. It stresses that the establishment of Roman hegemony interrupted long-standing modes of interaction between poleis and Hellenistic rulers and argues that structural factors hindered the establishment of a new framework for negotiating power.
Chapter 3 shifts the perspective to the responses of Asian communities to these institutional and ideological realities of Roman rule. It argues that in the absence of a secure discursive framework and faced with an evolving institutional landscape, poleis experimented to maximise their own agency. Addressing the specific strategies of issuing honorific decrees, engaging in diplomacy and monumentalising Roman normative documents, it suggests that communities played a critical role in integrating themselves within a Roman administrative framework.
Overall, this thesis makes the case that the Roman state had minimal administrative ambitions vis-à-vis provincia Asia. Consequently, institutional and ideological developments establishing governance were driven by combination of individual Roman actors and, in the longer term, local responses to empire.
A study of non-linear thermochemical wave propagation in fixed-bed gas-solid reactors
Keywords: Coherence
Non-linear Wave Theory
Thermochemical waves
Reactive flow

The flow of a reactive fluid in a fixed-bed reactor, where a fluid-solid reaction takes place, can be described as a progression of thermal and thermochemical fronts that have a wave-like character. These waves are characterised by their dynamics such as their spatio-temporal patterns, constant pattern behaviour, temperature plateaus, and wave velocities.
A wave model is developed for determining approximate thermal and material profiles in the reactor, which is significantly simpler and less time-consuming to compute than the integration of a complete set of highly stiff, non-linear partial differential equations. The wave model can only be applied when the waves become coherent. Guidelines to predict the transient time to coherence are outlined for the specific reacting systems in the thesis.
A full numerical model for irreversible, exothermic and endothermic, and reversible exothermic, gas-solid reactions has also been developed and applied to the decoking of fixed bed reactors, reduction of iron pyrite and oxidation of magnetite respectively. The results of the numerical model reveal that, regardless of the combination of kinetic and transport parameters, wave propagation eventually assumes a stable, constant pattern form independent of time. The wave model matches the numerical simulations reasonably well; in particular, the width and position of thermal and thermochemical wave fronts, and the temperature plateau in the bed, are accurately predicted. The current work provides a simple and efficient tool essential to understanding, designing and controlling slowly reacting systems through non-linear wave theory and the theory of coherence. A new simple, mechanistic, and conceptually appealing way of looking at reactor dynamics in gassolid reactions. The wave model is a powerful tool for pre-design problems and screening potential operating schemes/strategies. The reduced heating strategy developed using the wave model saves 36.6% of the energy required to heat the injected oxygen in the decoking process. Pre-heat strategy involves injecting concentrated hydrogen whilst still pre-heating the fixed bed of pyrite particles with nitrogen. The strategy saves 10.4% of the energy required to preheat the pyrite.
Genotype imputation methods for next generation datasets
Keywords: impute5
genotyping
snparrays
imputation

The advent of genome-wide association studies (GWAS) revolutionized the field of complex disease genetics. The primary goal of these studies is to achieve a better understanding of the biology of a complex disease and use this knowledge for prevention or better treatment of diseases. Genotype imputation is one of the key steps in such studies. The contribution of genotype imputation is to increase the power of study by boosting the coverage of genetic variation and to provide a natural framework for combining results across association studies that rely on different genotyping platforms.
Genotype imputation is the process of statistical inference of unobserved genotypes in a sample of individuals. In the typical scenario, a reference panel of haplotypes is used to infer ungenotyped variants in a set of study samples. Increasing the sample size in the reference panel improves imputation accuracy, especially for variants with low minor allele frequencies, but big reference panels are also a computational challenge for imputation methods. The goal of this dissertation is to develop methods and protocols that scale genotype imputation to very large next generation reference panels.
The main contribution of this dissertation is a genotype imputation method named IMPUTE5. It achieves fast, accurate, and memory-efficient imputation by selecting a small number of reference panel haplotypes using the Positional Burrows-Wheeler Transform. Imputation is performed only using the selected haplotypes, leading to a dramatic speed-up with no loss in accuracy compared to other methods. In order to facilitate other researchers to perform GWAS, a protocol to impute from a reference panel of phased haplotypes into a genome-wide association dataset is also described.
We also present an efficient C++ implementation of the Positional Burrows-Wheeler Transform which allows fast string matching in a set of haplotypes. An evaluation of previous state selection algorithms is provided together with a qualitative measure of the accuracy of chromosome painting performed by IMPUTE5.
A major application is the imputation of the UK Biobank dataset using the 100,000 Genomes Project reference panel. We show how the reference panel has been created and how imputation will be performed. Imputation of the UK Biobank represents an extremely valuable resource for researches, potentially providing new highlights for genome-wide association studies.
Investigating fibrotic pathways in human rotator cuff tendon disease
Keywords: tendon

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.
Speculative politics: U.S. Economic policymaking towards China in the post-Cold War era
Keywords: Trade
international political economy
U.S.-China relations
China

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.
Belonging at the margins: nation, religion, and the Ahmadiyya Muslim Jama'at in colonial and postcolonial India, c. 1930-74
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

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.
The white-collar hustle: academic writing & the Kenyan digital labour economy
Keywords: internet-mediated research
hustle
contract cheating
informal economy
youth
higher education
WhatsApp
digital economy
academic writing
unemployment
Kenya

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.
Functional genomics studies of cancer and cells of origin: from pan-cancer to single-cell
Keywords: cancer
functional genomics
cells of origin
fallopian tube
pan-cancer analysis
ovarian cancer
single-cell RNA sequencing

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.
Twisted coadmissible equivariant D-modules on rigid analytic spaces
Keywords: Geometric representation theory

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.
Fair division of the commons
Keywords: computational social choice
fair allocation
preferences
voting
resource allocation
computational complexity
public goods

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.