VictorJuiz/thesis huggingface dataset:
Contagions and manifolds

A spreading process on a network can be influenced by the network’s underlying spatial structure. In particular, if a network’s nodes are embedded in a manifold and connected by both ‘geometric edges’, which respect the geometry of the underlying manifold, and ‘non-geometric edges’ that are not constrained by that geometry, a threshold contagion can either propagate as a wave along the network or jump via long non-geometric edges to remote areas of the network. In this thesis, we study so-called ‘contagion maps’, which are defined via spreading dynamics on such ‘noisy geometric networks’. We take two complementary perspectives: In the first part of this thesis, we use contagion maps to examine the spreading of a threshold contagion on a class of networks that are embedded in a torus. We analyse the dimensionality, geometry, and topology of point clouds produced by contagion maps to examine qualitative properties of this spreading process. We conduct a bifurcation analysis to identify a region in parameter space in which the contagion propagates predominantly via wavefront propagation and find that this region aligns with our computational analysis of the point clouds produced by contagion maps. We also consider different probability distributions for constructing non-geometric edges — reflecting different decay rates with respect to the distance between nodes in the underlying manifold — and examine how qualitative properties of the spreading dynamics are affected by these choices. Moreover, we incorporate an approach for calibrating persistent homology barcodes of different scales. This approach is applicable in various other applications that use persistent homology, and the Wasserstein distance between barcodes in particular. In the second part of this thesis, we test contagion maps as a manifold learning tool on a variety of data sets. In particular, we compare the performance of contagion maps on these data sets to that of Isomap and find that, under certain conditions, contagion maps are able to reliably detect underlying manifold structure in noisy data, when Isomap is prone to noise-induced error. Our work consolidates contagion maps both as a tool for investigating spreading behaviour on spatial networks and as a technique for manifold learning.

Advisor: Tillmann, U
Modelling elements of microstructure in olivine

To solve problems in the Earth and planetary sciences ranging from mantle convection and plate tectonics, magma dynamics, glacial-isostatic adjustment, post-seismic creep, seismic attenuation, and tidal dissipation, we require a deep understanding of the rheological, seismic, and chemical properties of silicate materials. Elements of microstructure, such as grain size and dislocation density, exert a strong control on these properties. In this thesis, I apply novel approaches to modelling the time evolution of these quantities.
I begin by examining grain-size evolution in the regime of normal grain growth, which is driven by surface energy reduction. I extend the canonical model of normal grain growth by limiting the interactions of a grain to its neighbourhood. In this extended model, heterogeneity in the local environments of grains is accounted for using a stochastic process. The model predicts the existence of a normal grain growth regime that evolves according to accepted grain-growth kinetics. Moreover, this regime is characterised by a grain-size distribution that agrees with observed distributions, in direct contrast to the distribution predicted by the canonical model.
I then examine dislocation-density evolution. I construct a new theory of the physical processes affecting dislocations: storage and recovery. The evolution of dislocation density is fundamentally connected to intracrystalline plastic deformation, and thus also makes predictions about viscosity. We calibrate our theoretical framework for olivine using data from steady-state deformation experiments. This model explains the empirical relationships among strain rate, applied stress, and dislocation density in disparate laboratory regimes. Indeed, it predicts the previously unexplained dependence of dislocation density on applied stress in olivine. The predictions of our model for geological conditions differ from direct extrapolations from experimental data. For example, the calibrated model predicts rapid, transient deformation in the upper mantle, consistent with recent measurements of post-glacial rebound.
The calibrated model of dislocation-density evolution sets out the hypothesis that dislocation recovery in olivine is controlled by pipe diffusion. This assumption is in direct contrast with previous work, which has assumed that dislocation recovery in olivine is controlled by lattice diffusion instead. The recovery process can be inferred from annealing experiments that track the decrease in dislocation density with time. Through statistical analysis of data from new annealing experiments, combined with previously published data from the literature, I determine that the dominant dislocation recovery process in olivine is likely controlled by pipe diffusion.

Keywords: recovery
olivine
plasticity
dislocation
dislocation creep
microstructure
annealing
Advisor: Katz, R
Hansen, L
Kumamoto, K
Kohlstedt, D
Gender, property and household in provincial English parish government, c. 1540-1660

The political structure of early modern England was, definitively, patriarchal. And yet, women wielded direct authority on the local level in the sixteenth and seventeenth centuries at a scale not seen in the periods before or after. While historians have long recognised that early modern parishes occasionally elected female officers, this thesis is the first full-length study of female office-holding in the rural parish. As such, it reveals that we have underestimated the frequency of female nomination to parish office throughout this period, requiring a reevaluation of current historical knowledge on custom, state formation, gender relations and the nature of parish government.
This thesis begins with a simple question: why were women chosen, and why were they chosen more often in some parishes than in others? By mapping female office-holding over time and space, we find that the nomination of women was firmly linked to specific local customs of election which privileged landholding. Examined intersectionally, instances of female nomination allow us to deepen our understanding of these electoral customs, why they were developed and the extent of their authority. First, we consider why householding and landholding might come before gender in considerations of eligibility for parish office, concluding that office-holding was a liability attached to the land, regardless of who held it. Property-based customs of election, it is argued, developed as a way of spreading financial risk among substantial tenements, which provided security to parish transactions. Finally, patterns of nomination and deputyship in the seventeenth century suggest that these customs were carefully preserved, even as they came to have less bearing on who carried out the duties of the office. Thus, the nomination of women to parish office in early modern England was, more than anything else, a byproduct of their neighbours' ongoing dedication to custom.

Keywords: local politics
church history
electoral systems
wardenship
southwest England
family reconstitution
early modern credit
moneylending
Devon
rural communities
gender history
deputyship
early modern England
vestry
women in government
widows
manorial custom
female officeholding
local history
churchwardens
early modern
householding
political geography
overseers of the poor
local government
housewifery
custom
landholding
parish
land liability
sidesmen
churchwardens' accounts
state formation
female officers
women in politics
land custom
officeholding
property
women's history
husbandry
early modern rural economy
local elections
early modern Britain
rural credit
Advisor: Gunn, S
Translating Kōminka: shaping narratives of Japanese rule in Taiwan through translation post-1975

This thesis explores the role of translators in shaping historical, political and cultural narratives of Japanese colonial rule in Taiwan (1895-1945). It focuses on the translation into Mandarin Chinese of Japanese-language texts written by Taiwanese women between 1934 and 1943, drawing on a corpus of short stories and literary essays with themes ranging from infertility and free love to the choice between a life of work and life as a housewife. The circumstances of their publication gives these texts great political significance. Written under intensified assimilation policies that saw Japanese enforced as the language of Taiwan’s textual culture from the mid-1930s, their language of composition was a direct consequence of Japan’s imperial presence in Taiwan. Then, after 1945, laws enforced by Taiwan’s Chinese Nationalist Party (KMT) government subjected these stories and essays to censorship and cultural erasure on account of their symbolic relationship with the former regime. This thesis shows how translation has played a central part in the recovery and repositioning of these texts, providing a medium of mediation on the significance of Taiwan’s colonial history to more contemporary times. Through close analysis of translation, retranslation and adaptation carried out by Taiwanese literary scholars, as well as relatives of the women authors concerned, this study shows how translated text is used to comment on linguistic politics in colonial society, as well as on Taiwanese femininity and its history. It finds that rather than engaging in sweeping interventions that wholly alter the content of texts at the level of plot, translators instead employ subtle reframing devices to reshape the political significance of a text in their care. This analysis showcases literature’s significant contribution to Taiwan-centric histories of the twentieth century, whilst characterising translation as a history-making force in the context of Taiwan’s Japanese-language literature. By taking as its foci both source text and translation, this thesis considers the linguistic designs of the Japanese colonial project both during and after the imperial moment, showing how works written in its throes possess a cultural influence that stretches beyond 1945, expressed through the medium of translation.

Keywords: Taiwan
colonial literature
postcolonial literature
Sinophone literature
translation
Japanophone literature
Japanese empire
women's history
women's literature
Advisor: Hillenbrand, M
The role of cis-acting elements in regulating 3D structure and gene expression

Precise spatial-temporal gene expression is essential for normal development and differentiation, and, as such, must be tightly controlled. Cis-acting regulatory elements (enhancers, promoters and boundary elements) play a key role in gene regulation, either by enhancing transcription directly or by altering the 3D chromatin conformation to modify interactions between enhancers and promoters. Neither the contributions of individual elements to these processes, nor the complex interplay between them is fully understood. In this thesis, I have specifically investigated the ability of an ectopic CTCF binding site to shape the 3D genome and perturb gene expression. Furthermore, I have studied which aspects of gene activation and transcription depend on the enhancers using a model of the alpha-globin locus from which all enhancers have been removed. The mouse alpha-globin locus provides a well-characterised model of mammalian gene expression. Five enhancer elements regulate the expression of the alpha-globin genes, which lie in a ~65 kb sub-TAD flanked by largely convergent CTCF binding sites. First, I have studied the effect of restricting the 3D interactions of the enhancers by placing an insulator element between the alpha-globin enhancers and genes. This single CTCF binding site significantly reduces enhancer-promoter interactions and strongly decreases the expression of the alpha-globin genes. I created two CTCF insertion models, with the site either oriented to predominantly block loop extrusion from the direction of the enhancers or from the direction of the genes. Gene expression is most strongly affected in the model that is predominantly blocking cohesin coming from the direction of the enhancers. In this orientation, there is a prominent accumulation of cohesin at the insertion site, which is absent in the other orientation. I have also characterized a model in which all five alpha-globin enhancer elements have been deleted. This had a much stronger effect on gene expression than restricting enhancer interactions and sheds light on the role that the enhancers play in activating the locus: for example, the binding of transcription factors and co-factors was almost completely lost from the alpha-globin promoters. This all enhancer knockout model provides a “blank” slate that will be valuable resource for re-building the enhancers and establishing the precise role of each element and their combinations in the future.

Advisor: Higgs, D
Beagrie, R
Developing a computational high-resolution scATAC-seq platform to prioritize non-coding genetic variants


A genome-wide association study (GWAS) is a standard approach for understanding the relationship between genetic variants and disease, resulting in a better understanding of disease mechanisms. However, despite the vast contribution of GWAS to our knowledge and understanding of human biology, our ability to interpret these findings has not yet been fully developed. This is primarily because most disease-disposed regions are found within the non-coding regions of the genome, which affect regulatory elements such as enhancers and promoters. There is currently no clear path to identify causal regulatory SNPs and to link these to the genes and cell types they affect.
This thesis work focuses on first understanding scATAC-seq as a technology and its outputs and then taking advantage of its potential power to prioritise non-coding genetic variants and cell types. I have deeply reviewed and explored single-cell open chromatin epigenetics, which led to discovering the effect of the Tn5 cutting pattern on providing different levels of information from scATAC-seq. I developed a mathematical strategy to remove nucleosomal background from scATAC-seq data, increasing the data resolution and enabling the accurate identification of TF-bound regions. We successfully built an analytical platform, Avocato, which provides a complete solution to understand the relationship between non-coding genetic variants and their affected diseases. Avocato is not only capable of analysing and visualising scATAC-seq data but also removes background noise resulting in high-resolution data to be used in prioritising non-coding genetic variants and cell types. Additionally, Avocato allows users to interact with their analysis and prioritisation results interactively in a user-friendly interface.
Together this thesis builds on existing technologies, bringing us one step closer to fully understanding GWAS findings and functional studies and elucidating the mechanisms of common human diseases.

Keywords: non-coding genetic variants
epigenomics
data visualization
GWAS
computational pipeline
gene regulation
single-cell ATAC-seq
Advisor: Hughes, J
Lunter, G
Explaining the rise and fall of trust in India's relations with Pakistan and China in the 1950s

Jawaharlal Nehru’s trust-building efforts with his Pakistani and Chinese counterparts in the 1950s are important moments in global history to shed light on the nature of trust-building between rivals in international relations. Due to their inattention to its socially-contingent nature, existing theories of trust in IR cannot provide compelling explanations for how rivals can build trust in the absence of costly signals, institutions, and shared identities. To address this, I offer a “thick description” of trust and argue that social factors, which exist in the micro-environments of elites—such as discrepant information, the personal reputations of leaders, shared weaknesses, and initial reciprocity—are integral to explaining the trust-building process between rivals [something I refer to as “strategic trust”]. Uncovering them allows us to better understand when face-to-face diplomacy is likely to be more effective as a medium of trust-building and why there is variation in trusting outcomes even as actor’s dispositional traits remain constant. I also limit the scope conditions for these social factors by showing that trust can either be “blocked” by spoilers (leading to disappointment) or “overridden” if actors are unable to live up to positive expectations of behaviour (leading to betrayal). I use historical methods, case study research, and interpretive process tracing to study two cases of trusting success in India-Pakistan and India-China relations, viz. the Nehru-Liaquat Agreement [1950] and The Panchsheel Phase [1954-1957], and two cases of trusting failure, viz. Nehru-Bogra talks on Kashmir [1953-1955] and Nehru-Zhou border talks [1960]. I argue that trust is as much a social relationship as it is a psychological state of being and actors consider social factors associated with their counterparts before making trusting choices. However, while widening the possibilities of trust-building, I also caution against the risks of disappointment and betrayal. Trust is a useful tool to overcome rivalries, but only if leaders are equally attuned to its promises as well as pitfalls.

Keywords: Global South
betrayal
trust-building between rivals
India's relations with China
spoilers and disappointment
India's relations with Pakistan
Responding to shocks: cash, transfers and imagery

This thesis consists of three standalone chapters that speak to the broad theme of responding to shocks in low- and middle-income countries. Chapter 1 investigates the impact of receiving cash transfers in anticipation of an extreme climate disaster, thereby enabling low-income households to cope with the shock on their own terms. We present quasi-experimental evidence showing the effectiveness of a timelier forecast-based cash transfer delivered to low-income households just before the peak of severe flooding in Bangladesh. We find that the `anticipatory’ cash transfer enabled households to change their behaviour and improve their welfare, both during the flood and three months after the intervention. Chapter 2 explores the role of mental imagery in overcoming trauma – largely induced by exposure to violence – by fostering the ability to imagine the future. We design and test a ten-session entrepreneurship training curriculum that teaches mental imagery in business decision making through a randomised control trial in Colombia. We find that mental imagery can be taught as a skill and those who receive imagery training improve their earnings, relative to those who receive a placebo entrepreneurship training. Chapter 3 explores the interaction between public and private cash transfers, recognising that social protection may interact with existing coping strategies. I estimate the extent to which receiving an old-age pension crowds out remittances in post-Apartheid South Africa, using a regression discontinuity design. I find evidence of substantial crowding out in a middle-income country context: for every 1 rand of pension received, 0.22 rand of remittances are displaced on average.

Keywords: remittances
cash transfers
entrepreneurship
anticipatory action
imagery
disasters
social protection
Advisor: Dercon, S
Labour market institutions, skill and the (re)production of wage inequality: the stratification process in comparative perspective

This thesis is concerned with how labour market institutions and policies at the country level shape the stratification processes. Two topical questions are at the basis of the presented research: First, how do institutional frameworks impact the linkages between job positions and wage, and between individuals and jobs? Second, what do these linkages reveal about the underlying mechanisms that continue to generate wage inequality in the labour market? The interest lies in the sizes of statistical effects or associations, and in the extent of conformity to predictions based on different theorical approaches. All three of the empirical chapters in this thesis draws upon the Programme for the International Assessment of Adult Competencies (PIAAC) data from OECD. Combining data from this cross-national survey with country-level data on employment protections, union strengths and work-family policies, this thesis investigates cross-national variation in wage inequality by contract type and skill distribution, and the gender gap in skill specialization. Confirming the broad argument of new institutionalism, the thesis identifies labour market institutions as an important factor shaping the structure of wage inequality. Besides, the results suggest that the wage premium to permanent contracts compared to temporary contracts is likely to reflect employment rent by virtue of higher termination costs for the employers, rather than higher productivity due to skill specialization. Power relations crystalized in union strength may distort the market pressure for returns to both specialized and general skills. The gender gap in job-specific skills can be shaped by women’s expectations of the possibility of achieving work-family balance, over and beyond the level of job interruptions.

Advisor: Jonsson, J
Micromechanics, microstructure and formation of zirconium hydrides in nuclear fission applications

Hydride formation in zirconium based nuclear fuel cladding can lead to reduction of ductility and fracture toughness. This detrimental effect of hydrogen embrittlement is critically dependent on the morphology of hydrides in microscale and the Zr/hydride dual-phase microstructure. In this work Zr hydride thin film samples were prepared for microstructural and micromechanical characterisation. The microstructure near the Zr/hydride interface was examined with the use of scanning electron microscopy (SEM) and electron backscatter diffraction (EBSD). A new model was developed to account for the effect of concentration-dependent diffusion on the formation of hydride precipitates. Microcantilever tests and nanoindentation were carried out to compare the deformation properties of the δ-hydride with those of the α Zr. Pre-notched microcantilevers were fabricated in the individual phases and across the phase boundary with the use of focused ion beam (FIB). The experimental results show that the δ-hydride exhibits isotropic micromechanical properties. All the 2-4 μm wide δ-hydride microcantilevers underwent brittle fracture and the conditional fracture toughness is 1.8-2.0 MPam^1/2 in a variety of crystallographic directions. The Young’s modulus of the δ-hydride is 88-94 GPa and its proportional limit in microscale (1016-1189 MPa) is approximately double that of the α-Zr (401-600 MPa). The indentation size effect (ISE) was experimentally investigated and the hardness increased by 65% to 5.1 GPa when the indenter penetration depth was reduced from 5 µm to 0.5 µm. Despite interfacial microvoids and secondary hydride microcracks were observed after applying the bending load, the interface-notched dual-phase microcantilevers predominantly underwent plastic deformation without primary crack propagation.

Keywords: EBSD
microcantilever
micromechanical testing
SEM
hydrogen embrittlement
zirconium hydride
fracture toughness
indentation size effect
microstructure characterisation
micromechanics
XRD
FIB
nanoindentation
Advisor: Roberts, S
Gong, J