VictorJuiz/thesis huggingface dataset:
The shuzi gua corpus and the Yi traditions: a critical study

My dissertation explores the technical, theoretical, and philosophical aspects of divination practice in early China as found in the so-called shuzi gua 數字卦 (‘numerical cypher’ or simply ‘numerical gua’) corpus. Chapter 1 is a state of field of the relevant issues discussed in the present work: knowledge transmission in early China, divination, and the historiography of the shuzi gua corpus. In chapter 2, I introduce the shuzi gua corpus and establish the methodology for the assessment of the primary sources, namely the Analytical Map, a three-fold grid built around the following criteria: material, visual and linguistic. They each focus on three aspects of the evidence: objects, layout, and language. Chapter 3 is the Analytical Map divided into three criteria. Chapter 4 is comprised of two main parts: part I (Writing Orality) revisits the stronghold of oralism—the formula—and examines the interplay between the oral and the written in the language of the shuzi gua materials. I argue that formulae should be considered a scribal device, a set of common phrases and technical terms used by scribes to record the divination results. Thus, the formula is intended to facilitate the production of written records on hard media. Part II (Computational Methods) discusses the ‘two stalk system hypothesis’, first proposed by Li Xueqin 李學勤 (1992), and later elaborated by Jia Lianxiang 賈連翔 (2014) with respect to the Shang 商 (c. 1600-1046 BCE) and Western Zhou 西周 (1045-771 BCE) shuzi gua material. After discussing the shortcomings of this hypothesis, the analytical criteria described above are used to extend the statistical methods applied by Bréard & Cook (2020). By tracing the instances of 1 and 7, I provide important arguments for the 1-7 debate by looking at local communities where specific practices of generating numbers prevail. Chapter 5 focuses on the relationship between the shuzi gua and the Xici 繫辭 ([Commentary to the] Appended Sentences; c. mid-4th century BCE). First, it explores the strategies of philosophical meaning construction by analysing its textual macrostructure and lexical usage. Finally, I discuss how the Xici relates to different shuzi gua traditions.

Keywords: shuzi gua corpus
manuscript cultures
Yi traditions
textual analysis
divination
Advisor: Meyer, D
Understanding precipitation responses to externally driven climate change

Precipitation plays a fundamental role in transferring water and energy in the climate system. Human activities significantly impact the hydrological cycle, but the magnitude of global and regional changes remains uncertain due to the complex nature of microphysical-dynamical interactions. This thesis aims to improve the understanding of precipitation responses to climate change through a combination of bottom-up (process-driven) and top-down (energetic) approaches.
The relationship between aerosol-induced changes in atmospheric energetics and precipitation responses across different scales is studied in terms of fast (radiatively or microphysically mediated) and slow (temperature-mediated) responses. This thesis proposes an energetic framework to decompose rainfall changes into contributions from clouds, aerosols, and clear-clean sky (without aerosols and clouds). It provides a way to better interpret and quantify the precipitation changes caused by aerosol perturbations. Further investigations show that the increase rate in global-mean precipitation with temperature (hydrological sensitivity; η) is dependent on the spatial pattern of sea surface temperature (SST) change, which has been overlooked before. Warming in strong tropical ascending regions can produce large η via enhanced global circulation and atmospheric radiative cooling. The warming pattern effect significantly contributes to the spread of η in the current generation of general circulation models (GCMs). After accounting for the pattern effect, the reconstructed global-mean precipitation agrees much better with observations, evidencing the importance of SST patterns on global-mean precipitation changes. Furthermore, we extend the analysis to regional rainfall by showing that anthropogenic aerosols modulate the Sahel rainfall variability through their impacts on regional SST. We show analysis supporting the chain of processes whereby changes in anthropogenic aerosol emissions alter net radiative fluxes and sea surface temperature variability in the North Atlantic Ocean, leading to a shift of the intertropical convergence zone (ITCZ), changes in the West African monsoon, and eventually changes in Sahel rainfall. These findings highlight the importance of accurate representation of regional aerosol radiative effects for the simulation of Sahel rainfall variability.

Keywords: greenhouse gases
aerosols
precipitation responses
climate change
Advisor: Stier, P
Investigating the role of homologous recombination in the maintenance of chromosome stability

Homologous recombination (HR) is an essential DNA break repair pathway that maintains genome stability. BRCA2, PALB2, and RAD51 are key modulators of this pathway, mutations within which are associated with tumourigenesis. Centromeres are large repetitive DNA regions in the genome, defined through the presence of CENP-A. There is increasing evidence that centromeres experience instability across the cell cycle, impeding their function.
In this thesis, I first demonstrate a role for de novo RAD51 loading in mitosis after mild replication stress to promote mitotic DNA synthesis (MiDAS). Utilising RAD51 separation-of-function mutant cell lines, I present evidence suggesting that RAD51’s single stranded DNA binding activity is important to promote MiDAS at undamaged loci. Failure to complete MiDAS in RAD51 deficient cells leads to mitotic defects and increased aberrant centromere recombination and fragility. I next explored the role of HR factors: BRCA2, PALB2, and RAD51 at centromeres RPE1 cells. Here, I show evidence of a role for BRCA2 and RAD51, but not PALB2, in maintaining centromeric CENP-A levels and, using Exo-FISH, show that BRCA2 may have a distinct role in minimising centromeric single stranded DNA accumulation in a cell cycle-dependent manner. Finally, I generated and validated an auxin-inducible degron system to rapidly degrade BRCA2 and PALB2 in the mismatch repair defective, colorectal cancer cell line, HCT116. Using these tools, I highlight the impact of short-term and long-term BRCA2 and PALB2 depletion on chromosome stability, providing an insight into a potential mechanism for tumourigenesis. Investigations into the role of BRCA2 and PALB2 in centromere identity and stability further identified BRCA2 as important for maintaining centromere stability, different from RPE1 cells, highlighting their different genetic backgrounds. Hence, I propose a role for BRCA2 and RAD51 in preserving centromere stability and function, collectively increasing our comprehension of the importance of HR factors at centromeres and how different cellular and chromatin contexts may influence repair at this region to limit tumourigenesis.

Advisor: Esashi, F
Graph reconstruction and structure

This thesis explores the difficulties of capturing graph structure, and the recent approaches that have been able to do so effectively in some settings.
The famous Graph Reconstruction Conjecture (Kelly-Ulam, 1941) states that every graph on at least 3 vertices is uniquely determined by its deck of vertex-deleted subgraphs. Despite sustained efforts, it remains wide open. In Part I, we break new ground on several variants of this reconstruction problem. Two such settings are even harder than the classical case; we reconstruct graphs or their properties from decks of k-vertex-deleted subgraphs as well as from incomplete decks where l subgraphs are missing. While most general results in literature only apply when k and l are small constants, in both cases we develop techniques that facilitate significant leaps to even handle deficits that are linear in the number of vertices. For the third variant, we introduce axioms to define a family of reconstruction problems in which decks are defined by ‘switching’ at a vertex instead of deletions. This encompasses a well-known problem of Stanley from 1985. Our key result is a new sufficient condition for switching-reconstructibility that applies under this generic framework.
Part II examines the problem of formulating approximate characterisations of graphs in terms of simpler building blocks. A recent focal point has been on graph product structure theory, which allows many graph classes to be described using graphs of bounded treewidth. Having first appeared in 2019, this theory is still actively under development, but has already facilitated progress on longstanding problems. As a new application in the intersection of structural and geometric graph theory, we use it to prove that all proper minor-closed classes of graphs have touching representations by comparable boxes in bounded dimensions. We also show that product structure can, in turn, describe the bounded treewidth building blocks from the original theorems using even simpler parts.

Keywords: structural graph theory
graph reconstruction
Advisor: Scott, A
Fast quasi-centroid molecular dynamics

Imaginary time path integrals are a proven way of accounting for quantum effects in theoretical chemistry. Despite considerable interest, and for a variety of reasons, no path integral method has been suggested that is able to robustly simulate vibrational dynamics. The best attempt so far is quasi-centroid molecular dynamics (QCMD), but this still has some major problems: it is quite slow, and the only gas-phase molecules it has been shown to work for so far are H2O and NH3. This thesis presents fast quasi-centroid molecular dynamics (f-QCMD), a new implementation that is simple, efficient and demonstrably applicable to more complex molecules. Furthermore, this thesis develops and tests two additional methods that compliment f-QCMD. The first is a simple way of correcting the intensities of overtone and combination bands in infrared spectroscopy, which trajectory-based methods like f-QCMD tend to get wrong. The second is an extremely versatile force-based technique for calculating any type of distribution function quickly and with arbitrary precision.

Keywords: quantum dynamics
spectroscopy
path integrals
molecular dynamics
vibrational dynamics
Advisor: Manolopoulos, D
The genetics of participation and some aspects of genetic data

One of the major challenges in human genetic studies is to differentiate between results that reflect biological mechanisms and those that reflect data specific properties. If genetics play a role in determining who would participate in a study that includes DNA collection, the genotypes of the participants would not be representative of the target population. By its very nature, this bias cannot be investigated by comparing genotypes of participants and non-participants. In this thesis I introduce a new method that enables one to investigate participation bias using only the genetic samples of the participants. The method involves comparing shared and non-shared alleles of first-degree relatives and is sensitive only to direct genetic effects, i.e. there is no confounding with population stratification or indirect genetic effects. Applying this method to perform a genome-wide association analysis using data of first-degree relative pairs in the UK Biobank, I demonstrate simultaneously that the method works and there is a very substantial genetic component underling participation in UK Biobank. The demonstration is achieved by showing that a polygenic score constructed from the association analysis can, in a non-overlapping sample, significantly predict traits and behaviour that include educational attainment, BMI, age at first birth and participation in follow-up studies. The method includes three separate test statistics that each captures real participation effects, but are affected by data artefacts in a very different manner. Consequentially, data artefacts could potentially be identified through comparison of the three statistics, an alternative utility of the method. The thesis also includes investigating the effectiveness of using principal components to adjust for population stratification, and the many possible causes of deviation from Hardy-Weinberg equilibrium. Together with studying participation bias, these investigations have a common goal of potentially improving the many analyses that are, or can be, performed using a large dataset such as the UK Biobank.

Keywords: participation bias
genetic studies
Advisor: Kong, A
Lindgren, C
Galapagos farmers: risk and the coexistential rift

Galapagos farmers are generally invisible in global discourses and remain understudied from an anthropological perspective. Drawing on a year of ethnographic fieldwork during the 2020-2021 global pandemic, this thesis focuses on their main worries and livelihood challenges. The liminal period created during the Covid-19 pandemic brought back many aspects of life prior to the arrival of the archipelago’s tourism industry and led farmers to yearn for a nostalgic, utopian past when they coexisted more harmoniously with each other and the environment. Unfortunately, many elements of that idealized life are currently unattainable due to compounding risks, including pests, climate change, and Covid-19. The everyday threats to farmers’ livelihoods have led to market dependence, indebtedness, alienation, and cumulative anxiety. I explore each risk ethnographically, whilst also showing the ways in which they are part of a causal framework that alters farmers’ values and behaviours. This thesis formulates the coexistential rift concept to explain how both the materiality of risks and their perception accelerate a treadmill syndrome where farmers must focus on making money to lessen their insecurity. This vicious cycle is reinforced by the slow violence of political abandonment, economic inequality, fortress conservation, legal and bureaucratic obstacles, and predominant metanarratives that blame and exclude the archipelago’s inhabitants. Both Galapagueño society and the environment would benefit from addressing the agricultural sector’s long-standing problems. Finally, this thesis points to how human and political ecological studies can better conceptualize and incorporate risks into their analysis and causal frameworks to elucidate their impact on everyday life.

Keywords: pests
risk
coexistential rift
Galapagos Islands
Covid-19
farmers
climate change
Advisor: Ewart, E
Thornton, T
Constructing military alliance: shared language as a determinant of alliance sharing, design & duration


This dissertation comprises three papers investigating the impact of shared language among states on various aspects of their military alliance relations. The first paper establishes that states sharing a common language are more likely to maintain alliance ties, particularly evident in defensive alliances. The second paper delves into how a shared language among two or more states influences alliance design. The proposed "Sociolinguistic Theory of Alliance Design" posits that states with a shared language have a higher likelihood in opting for alliance features that do not encourage credible commitments when compared to states without a shared language. Achieving credible commitment-enhancing designs also entails a more strenuous negotiation process among language-sharing states, compared to their counterparts that do not share a common language. Four out of five alliance design dimensions among states sharing a language demonstrate these tendencies, with one anomaly that is also explainable. The third paper addresses the question of how a shared language might impact the likelihood of premature alliance termination. The findings suggest that alliances involving states sharing a language tend to be shorter-lived. These results stem from the multifaceted role of language—functionally aiding communication while also carrying a heuristic function that influences alliance sharing, design choices, and duration in both expected and unexpected ways. This research contributes to International Relations scholarship in several ways. It introduces language as an often- overlooked variable in military alliance literature. It bridges a gap in the literature’s paradigms by employing the rational choice method- ology to substantiate the explanatory power of language—an element more associated with constructivist scholarship.

Keywords: constructivism
linguistic similarity
rational design
international institution
international organization
social identity
shared identity
alliance design
alliance
international cooperation
language
military alliance
Advisor: Snidal, D
Prediction of disease severity in patients with febrile illnesses in resource-limited settings

Febrile illnesses present unique challenges for health systems with scarce resources. Large volumes of mostly self-limiting diseases accompanied by high case-fatality rates for the small proportion of serious infections mean that risk stratification tools must have high sensitivities and/or specificities according to their proposed contexts of use. Unfortunately, accuracy and reliability of existing tools are sub-optimal and they are often impractical for deployment in resource-limited settings.
This thesis explores the development and application of prediction tools for the management of febrile illnesses across a range of resource-constrained settings in South and Southeast Asia. It aims to combine the best prediction model science with a pragmatic field-based reality to address locally-important health issues. Recognising that evaluation of prediction tools should be set in their intended contexts of use, each analysis is framed in a particular clinical use-case, yet draws upon approaches to allow exploration of the generalisability of the findings.
Using a variety of research methodologies, this thesis identifies prognostic factors amongst febrile children presenting to different levels of the health system, and uses these data to externally validate existing severity scores and develop new clinical prediction models suitable for resource-limited settings. Prospective work evaluates the relative contributions of clinical and biomarker-based approaches for the referral of children with respiratory infections from a resource-limited community setting on the Thailand-Myanmar border, whilst retrospective work develops a prognostic model for critically ill children on admission to a paediatric intensive care unit in northern Cambodia. Finally, in response to the arrival of the SARS-CoV-2 pandemic, this thesis reports the development and external validation of prognostic models at two sites in India to support the safe outpatient management of patients presenting with moderate Covid-19.
Important challenges and potential solutions to developing prediction tools in resource-limited settings are discussed, including application of the classical prediction paradigm to the assessment of disease severity, comparative analyses of the clinical utility of different models, and the differential importance of various predictors for identifying both patients who are sick at the time of clinical assessment and those whose illnesses will progress later in their disease course.

Keywords: Fever
Triage
Prognosis
Resource-limited
Risk stratification
Children
Febrile illness
Paediatric
Severity
Prediction
Advisor: Turner, P
Lubell, Y
Perera-Salazar, R
Day, N
Turner, C
Transparency politics and its limits: rethinking hermeneutical injustice

I draw on work in social epistemology, feminist philosophy, trans philosophy, queer theory, and ethics to rethink what hermeneutical injustices are, who suffers them, and what can be done to prevent them. I identify several problems with Miranda Fricker’s original account of what hermeneutical injustices are and how they arise, and argue for a number of revisions and clarifications in order to solve these problems. One upshot of these revisions is that more people suffer hermeneutical injustices than Fricker’s account acknowledges. I then outline a novel, more materialist sort of strategy for preventing hermeneutical injustices, and argue that the provision of gender-affirming healthcare is one context in which such a strategy ought to be pursued. Finally, I criticize the hermeneutical injustice literature for what I call its implicit commitment to transparency politics. By this I mean its implicit commitment to the view that when it comes to the hermeneutical dimension of people’s lives, the satisfaction of their interests in things about themselves being intelligible is all that matters. I argue that this view is mistaken, not least because it ignores the existence of two other important sorts of distinctly hermeneutical interest.

Keywords: Hermeneutical marginalization
Gender-affirming healthcare
Epistemic injustice
Transparency
Hermeneutical injustice
Opacity
Miranda Fricker
Advisor: Srinivasan, A
Fraser, R
Nithura Sivarajah - Thesis submitted in partial fulfilment of the degree of Doctor of Clinical Psychology (DClinPsych)

Background and objectives: Distressing mental images are common experiences in people with psychosis. Imagery based interventions have been found to be effective in directly targeting properties of distressing mental images. Given the central role of metacognitive deficits in psychosis, it appears that metacognitive techniques with imagery properties could play a central role in managing distressing mental imagery. A brief imagery-based metacognitive intervention was developed to target the control mechanism of distressing mental images in people with persecutory delusions. A fixed baseline case series was designed to investigate whether the protocol was feasible, acceptable, and evaluate preliminary signs of effectiveness effective.
Methods: Eight participants who met criteria for a schizophrenia spectrum diagnosis who experienced distressing non-trauma related mental images completed a brief metacognitive intervention which consisted of three phases; a baseline phase which comprised of an assessment, Psychoeducation and Microformulation, an intervention phase which included learning, developing and consolidating metacognitive techniques targeting the control mechanism of mental images and a follow up phase which included gathering qualitative feedback about the intervention. Characteristics of the image were assessed throughout the intervention. Symptoms of anxiety, depression, persecutory delusions, and schemas were assessed pre- and post- intervention.
Results: The metacognitive intervention was feasible, acceptable, and rated as highly satisfactory, successful, and useful. One participant dropped out at the baseline phase. No adverse events were reported throughout the intervention. Reliable change was reported for anxiety, depression, persecutory delusions, and schemas. Tau-U analysis showed positive trends and high effect sizes when comparing characteristics of distressing mental images at baseline compared to intervention and follow up.
Conclusion: Participants described positive symptomatic changes following the intervention and high satisfaction levels with their experience of engaging with the intervention. Our present findings suggest that it is feasible and acceptable to engage people with persecutory delusions in brief imagery based metacognitive interventions and that positive change can be achieved. However, the study is limited by an absence of a control group and rater-blinding so future studies are needed to replicate and clarify this finding.

Keywords: Mental images
persecutory delusions
flash-forwards
novel intervention
metacognitive intervention
Advisor: Steel, C
Taylor, C