VictorJuiz/thesis huggingface dataset:
Methods for large-scale genome-wide association studies
Keywords: association
linear mixed model
heritability
GWAS
population stratification
rare variation
UK Biobank
SNP
sequencing
genealogies
identity-by-descent

Genome-wide association studies (GWAS) have led to the identification of thousands of associations between genetic polymorphisms and complex traits or diseases, facilitating several downstream applications such as genetic risk prediction and drug target prioritisation. Biobanks containing extensive genetic and phenotypic data continue to grow, creating new opportunities for the study of complex traits, such as the analysis of rare genomic variation across multiple populations. These opportunities are coupled with computational challenges, creating the need for the development of novel methodology.
This thesis develops computational tools to facilitate large-scale association studies of rare and common variation. First, we develop methods to improve the analysis of ultra-rare variants, leveraging the sharing of identical-by-descent (IBD) genomic regions within large biobanks. We compare ∼ 400k genotyped UK Biobank (UKBB) samples with 50k exome-sequenced samples and devise a score that quantifies the extent to which a genotyped individual shares IBD segments with carriers of rare loss-of-function mutations. Our approach detects several associations and replicates 11/14 loci of a pilot exome sequencing study. Second, we develop a linear mixed model framework, FMA, that builds on previous techniques and is suitable for scalable and robust association testing. We benchmark FMA and several state-of-the-art approaches using synthetic and UKBB data, evaluating computational performance, statistical power, and robustness to known confounders, such as cryptic relatedness and population stratification. Finally, we integrate FMA with recently developed methods for genealogical analysis of complex traits, enabling it to perform scalable genealogy-based estimation of narrow-sense heritability and association.
Engineering optoelectronics and smart sensors leveraging metal-organic framework materials
Keywords: metal-organic frameworks
near-field infrared spectroscopy
nanoscale analytics
density functional theory

Metal-organic frameworks (MOFs) have emerged as promising nanomaterials for the development of advanced sensing technologies. Indeed, their unparalleled features comprising structural diversity, tailorability, high porosity, large surface area, and adsorption affinities can offer superior sensing performance unattainable by the array of conventional materials for selective, fast, and sensitive detection of gases. However, for the integration of MOFs into sensor devices, a thorough understanding of the material’s underpinning properties and mechanisms is vital. In this integrated thesis, the key principles, which are used for functionalising MOFs with desired properties, are studied from the single-crystal level (Chapter 1). Herein, Chapter 2 introduces near-field infrared spectroscopy techniques for the chemical characterisation of individual MOF-type crystals at the nanoscale.
Based on this technique, Chapter 3 presents a new strategy to reveal the encapsulation of luminescent ‘guest’ molecules in the pores of the ‘host’ MOF framework. This so-called guest@MOF principle is a smart way to engineer novel material for sensors and optoelectronics, however, unambiguously proving the successful encapsulation in lieu of surface adsorption has been challenging thus far.
Turning to defect tuning - another strategy to tune MOF materials for sensing applications - Chapter 4 demonstrates how the combination of nanoscale analytics and density functional theory calculations can probe point defects in individual MOF crystals, further scrutinising their impact on mechanical properties.
Chapter 5 offers insights into the sensing mechanism itself by studying the exceptional response of a guest@MOF material towards volatile acetone. Herein, several spectroscopy techniques ranging from nanoscale analytics to in situ and operando techniques based on inelastic neutron scattering and synchrotron radiation, all corroborated by theoretical simulations, are used to explore the underlying principles of the unique sensing performance.
Building upon the findings of Chapter 3-5, Chapter 6 presents a detailed characterisation of a promising MOF material for sensing applications. Specifically, theoretical calculations and spectroscopy techniques can explain the interplay between the physical, chemical, and mechanical properties to provide a fundamental understanding of the material’s behaviour and structure-function relations.
Finally, Chapter 7 serves as a critical review of the presented findings, further highlighting their contribution to the future development of tailored MOF materials as next-generation sensors.
Can 'word' and 'sword' cooperate? Reforming Christian theo-political witness to Muslims
Keywords: David VanDrunen
Oliver O'Donovan
Christian-Muslim relations
Old Testament
Kenneth Cragg
establishment
Church discipline
theo-political witness
missiology
shari'a
political theology
Noahic Covenant
Dramaturgy
Ibn Taymiyya
Jonathan Leeman

This thesis offers a fresh articulation of the gospel’s significance for the relationship between the church (the ‘word’) and the exercise of coercive rule (the ‘sword’) to Muslim audiences. Setting the stage, Chapter One proposes that Christian theo-political witness to Muslims be viewed through a dramaturgical lens, where the primary task is to adapt faithfully the ‘drama’ of the gospel for Muslims through study of its ‘script’ (Scripture) and previous adaptations. In this spirit, Chapter Two and Chapter Three offer a novel ‘performance review’ of historical Christian theo-political witness to Muslims. It shows how pre-modern Christian theo-political witness manifested an increasingly negative attitude towards the Old Testament, contributing to Muslims critiques that Christianity’s lack of faithfulness to the entirety of its Scriptures made it politically dysfunctional. These critiques have not been surmounted by the selective Old Testament retrievals found in modern and contemporary Christian theo-political witness, which present the gospel as creating an antithesis between the church and coercive rule. Chapters Four and Five offer a ‘performance reform’ in response to this inadequate incorporation of the Old Testament, retrieving the biblical themes of kingship and priesthood. By letting these themes shed light of the meaning of the gospel, Christian theo-political witness can move beyond presenting an antithesis between church and coercive rule to Muslims. It can instead present them as both authorized by the ascended Christ and capable of acknowledging one another’s authority through a modest form of religious establishment. Additionally, it can present the exercise of coercive rule by Christians as accountable to the church’s exercise of the keys of the kingdom, alleviating Muslim concerns about Christianity’s ‘other-worldliness’ and proneness to assimilation. In Chapter Six, the theological permissibility of religious establishment is defended against three critiques, strengthening the case for this thesis’ way of retrieving the Old Testament.
Education in the climate emergency: school sustainability practices, climate imaginaries, and teaching hope
Keywords: climate education
school sustainability
digital storytelling

The Intergovernmental Panel on Climate Change has reported with very high confidence that human activity is changing the climate, that climate change has severe impacts for human and natural systems, and that we have a limited window to dramatically reduce greenhouse gas emissions and limit global warming to 1.5 °C. Our future is being shaped by this crisis and our collective responses to mitigate and adapt to it. This article-based thesis presents interdisciplinary research on the response of secondary schools in England to climate change. The chapters first introduce a doctoral journey over 3.5 years, including adaptations in response to COVID-19. They then present a combined literature review, weave together the three academic articles, and end by exploring the contributions of this research and sharing future plans. The first paper (Chapter 3) was based on a large number of semi-structured interviews and focus group conversations with different school stakeholders at both state and independent schools. Theories of social practice and practice architectures were used to explore bundles of practices and the arrangements that support them related to sustainability, especially in terms of semantic (sayings), material (doings) and social (relatings) dimensions. The article, currently under peer review by the journal Energy Research and Social Science, argued for expanding whole-school approaches to sustainability to incorporate insights from practice architectures. The second paper (Chapter 4) involved data collection through a questionnaire distributed to Sixth Form students and teachers, primarily comprising measures of action competence and climate hope that were previously developed and validated by other researchers. Quantitative analysis of this data revealed the relationship between teacher practices and student reported hope, and compared responses based on students from independent versus state schools and students that identified as female versus male. This article was published in the journal Environmental Education Research. The third paper (Chapter 5) used the creative, participatory method of speculative digital storytelling, in which 16-18-year-olds in the UK and Ireland participated in workshops to produce a short ‘letter from the future’ in a video format. Through reflexive thematic and narrative analysis, themes related to the scripts and visuals were identified, as well as different narratives of climate futures. This article was published in the journal Children’s Geographies. The discussion (Chapter 6) outlines three threads that weave together the research – education, futures, storytelling – and offers a series of methodological, theoretical and empirical contributions, including speculative digital storytelling, practice-informed whole-school sustainability, and hope-based pedagogies in climate education.
'We are Muslims too': the politics of identity, practice, and discourse among British progressive Muslims
Keywords: hermeneutics
abolitionism
British Islam
counter-terrorism
queer Muslims
feminism
British Muslims
homonationalism
progressive Islam
counter-radicalisation
anthropology of Islam
sexuality
female imams
securitisation
police
progressive Muslims
LGBTQIA+ rights
Islamophobia
secularism
prevent
gender
queer theory
racism

This ethnographic study explores organisations in the UK that identify with the label ‘progressive Muslim’. The main organisation it studies is the Inclusive Mosque Initiative (IMI) together with other organisations that offer points of contrast and similarities with the IMI. The thesis describes the key academic and theological principles of contemporary progressive Islam and the ways these are utilised in specific socio-historical contexts. Specifically, it explores through participant observation and interviews the key areas of debate where progressive Muslim theology and principles are applied within the British context: female ritual leadership; LGBTQIA+ rights; Islamophobia and racism; and the counterterrorism and criminal justice systems. The thesis claims that the same theological resources and hermeneutical approaches can lead to contrasting and oppositional political positions and practices, thereby challenging any essentialist understanding of ‘progressive Muslims’ as either pro- or anti- ‘secular’ state actors. Progressive Muslims engage with religious resources in diverse ways and with diverse goals, ranging from rational textual hermeneutics aimed at creating a new orthodoxy to somatic and affective personal mystical experiences aimed at projects of ‘self-care’. Furthermore, they often straddle the boundaries between discourses, practices, and identities that are constructed as ‘incompatible,’ creating unique challenges as well as opportunities for religious and political responses that are unavailable or ineffective for other social actors. The thesis claims that this positionality of progressive Muslims within Western socio-political contexts makes them valuable subjects to interrogate the fault-lines of sensitive public and academic debates on Islamophobia, racism, feminism, queer rights, secularism, religious violence and extremism, and the criminal justice system.
Late Holocene cultural dynamics and trans-Saharan connections in Southeastern Mauritani: a remote sensing approach
Keywords: satellite imagery
Mauritania
settlement patterns
Tichitt tradition
remote sensing
funerary archaeology
prehistoric archaeology
archaeology
African archaeology

This doctoral thesis investigates the prehistoric and medieval archaeological record of southeastern Mauritania (c. 2,000 BC to AD 1,100). The highlands of southeastern Mauritania present an extraordinary archaeological record for documenting the emergence, consolidation, and reorganisation of cultural dynamics. A remote sensing approach represents the most viable research methodology, politically and logistically, for this study. My work integrates quantitative methods and transdisciplinary theoretical developments to characterize and assess diachronic cultural trends in terms of regional settlement dynamics, the nature of funerary landscapes, and supra-regional connectivity. The results include the identification and spatial distribution mapping of >9,000 funerary tumuli and 1,140 settlements belonging to the Tichitt Tradition, many of which were previously unpublished or undocumented.
The Tichitt Tradition represents the growth and consolidation of a thriving agropastoral economy based on cattle-keeping and pearl millet (Pennisetum glaucum) cultivation throughout during the second millennium BC, structured around extensive, drystone settlements. I interpret these Late Holocene cultural dynamics through the lens of Complex Adaptive Systems, unfolding within the cultural milieu of pre-colonial African polities. The expansion of Tichitt Tradition communities was characterized a conservative but decentralized reproduction of material and ideological forms leading to high systemic coherence, conforming to Kopytoff’s Internal African Model. From the first millennium BC, Tichitt Tradition communities witnessed a drastic release and reorganisation of settlement patterns amidst severe aridification trends and the arrival of Lybico-Berber groups. This scenario led to migration outflows and the formation of interstitial communities with greater adaptive creativity, reflected in a greater diversity of settlement styles and the syncretism of pottery traditions described by Kevin MacDonald. The interplay between concepts of spatial and socio-political centrality and liminality—illustrated by the shifting trends of funerary monument clustering in relation to settlement centers—highlights issues of translocal resilience and landscape memorialisation among agropastoral communities in dryland ecosystems.
Transcription dynamics during metabolic changes
Keywords: yeast metabolic cycle
transcription dynamics
sub-populations
saccharomyces cerevisiae
RNA fluorescence in-situ hybridization

Temporal control of processes in cells such as metabolism, gene expression, and cell growth and division are ubiquitous in nature but how they are coordinated in single cells is poorly understood. The yeast Saccharomyces cerevisiae offers a tractable system in which to address these relationships, as growth rates, the number of cells in the cell division cycle (CDC), and their metabolism can be varied and linked to patterns of gene expression. Precise numbers of nascent and mature transcripts can be monitored in single cells using single-molecule RNA fluorescence in-situ hybridisation (smRNA-FISH). The Yeast Metabolic Cycle (YMC) is a model system of temporal compartmentalisation of cellular and metabolic processes in slow-growing synchronous cultures and can be compared with data from asynchronous cultures at different growth rates (exponential mid-log versus slow growth) and metabolic states.
These studies reveal that single cells from mid-log and YMC cultures possess an intrinsic metabolic and gene expression clock. Remarkably, individual cells are found to possess a high degree of variability in levels of expression of individual transcripts yet the oscillations in mean transcript levels over time are similar to those described at the population level using RNA-seq. Furthermore, although most yeast genes are proposed to show a constitutive mode of transcription initiation, the transcript distribution of oscillating transcripts along the YMC do not fit those predicted by a one-state mathematical model of constitutive transcription. Instead, the predicted “bursty” mode of expression could explain the variability in transcript levels in single cells. Cell-to-cell transcript heterogeneity was also observed for pre-rRNA transcripts during the YMC, despite population levels oscillating with periods of cell growth and ribosome biogenesis. The link to cell growth is supported by the observation that ribosomal RNA production is found to be temporally coordinated to TORC1-controlled Rps6 phosphorylation.
The examination of DNA content and cell diameters together with transcript numbers in single cells of YMC and mid-log populations indicates distinct sub-populations with different relationships between gene expression, proliferation and growth. In synchronous YMC cultures, metabolism and patterns of gene expression are proposed to alternate synchronously between phases of growth and quiescence, linked to metabolism by high or lower levels of oxygen consumption respectively. This study suggests that the organization of the culture is far more nuanced. It supports at least three distinct co-existing states in the population over each metabolic cycle, including small quiescent-like cells, slow-growing cells, and larger cells whose metabolism is remodelled, with increased oxygen consumption, to facilitate their entry and progression through the cell division cycle.
Sex, race and power: colonial and interracial sexuality in the French Empire in Morocco, 1912-1956
Keywords: global history
French empire
gender
history
sexuality
North Africa
imperialism
France
Morocco
prostitution
colonialism

This thesis examines Morocco under French rule (1912-1956) through experiences of gender, sexuality and race. It argues that colonial power was experienced intimately on a large scale through the body and through emotions. This regulation of sexuality extended from sex work into consensual relationships and through attempts to intervene into emotions and sexual desire to police racial boundaries and the limits of whiteness. This thesis outlines how French colonial authorities attempted to regulate sexuality and gender in Morocco in five chapters. The first chapter shows the exploitative sex work system introduced by French health authorities in Morocco that trapped women in brothels to protect the health of European men and women. The second chapter offers a case study of how the French military trafficked 211 Moroccan women to France to work in military brothels in 1947 to prevent interracial sexuality after brothels had been banned in France, comparing this case study to French women who moved to North Africa to sell sex in the same period and moral panics about the “white slave trade”. The third chapter examines letters from European women to their Moroccan lovers, which were used as proof that these women were “dangerous to public security” and should be expelled from Morocco for threatening racial hierarchies. The fourth chapter compares these relationships with “desert romance” novels and films from the 1920s onwards to argue that European women sought to recreate elements of fictional relationships with Moroccan men and that French authorities heavily censored films in Morocco to attempt to regulate the space of sexual fantasy. The fifth chapter looks at queerness, arguing that colonial understandings that sex between men was “traditional” to Moroccan society meant that French authorities avoided intervening when European men bought sex exploitatively from Moroccan boys, but did police gender roles and binaries.
Carroll's regress, Bradley's regress, and the incoherence of logical consequence
Keywords: Carroll's regress
Bradley's regress
logic
normativity
principle of sufficient reason

§1 frames Carroll's regress as a problem of metaphysical grounding, i.e. as an instance of Bradley's regress, and attempts to provide it the strongest possible defence. §2 applies this regress to accounts of logical consequence, and argues that all such accounts ultimately fail to explain why modus ponens is valid. §3 argues that rejecting logical consequence as incoherent amounts to rejecting the analytic/synthetic distinction as incoherent, and discusses the devastating consequences of doing so. §4 shows that the self-undermining nature of such a view has its roots in the Principle of Sufficient Reason, and works towards a way of resolving the paradox that is exemplified in §5.
Theories of mind in international relations: why individuals' inferences about states' motives vary
Keywords: experimental social science
motives
perception and misperception
attribution
signaling
international conflict
political psychology

In international politics, communication about motives can make the difference between bargaining and war, policies of mutual reassurance and arms races, a state of perpetual conflict and the pursuit of a shared vision for international society. However, despite its centrality, empirical research on the communication of motives has long lagged behind theoretical scholarship, and fundamental questions about the microfoundations of motives remain: how do individuals infer a state’s motives from its actions, and why do individuals’ inferences dynamically vary, sometimes converging, other times diverging, in response to a state’s signal? This thesis draws on psychology and the philosophy of mind to explore these questions. First, I examine the theoretical foundations of a recent wave of psychological research in International Rela- tions and show that this research shares with rationalism a conception of the mind as computer. In order to explain variation in belief formation and updating about motives, I argue, we must move beyond this conception and integrate rationalist and psychological approaches to information processing with constructivist insights into social facts and systems of meaning. Second, I develop a domain-specific theory of attribution to explain how individuals infer motives in international politics. Combining a cross-national survey experiment with an in-depth analysis of evolving perceptions of Soviet motives during the Carter Administration, I find support for the costly signaling hypothesis, yet also show that the way individuals infer motives is shaped by their ontological assumptions about the target. Importantly, differences in these assumptions do not always result in divergent responses to costly signals: whether or not they do depends on the signal in question. Offering novel evidence on the attributional processes that underpin costly signaling, this thesis has important implications for the risk of escalatory dynamics between states and the study of the mind in International Relations.