VictorJuiz/thesis huggingface dataset:
Reducing mobile bearing dislocations in the Oxford Domed Lateral unicompartmental knee replacement implant
Keywords: Osteoarthritis
Lateral knee
Oxford Knee
Bearing dislocation
Knee arthroplasty

The Oxford Domed Lateral (ODL) mobile bearing Unicompartmental Knee Replacement (UKR) provides good clinical results, but the bearing dislocation rate is unacceptably high.
A systematic review and meta-analysis found that changing the articulating surface on the tibial component from a flat to a domed shape reduced the overall bearing dislocation rate from 17% to 3.7%. The risk of anterior/posterior (AP) dislocations was reduced substantially. Most dislocations were found to occur medially and with the knee in a flexed position.
Dislocations occur in flexion because when the knee is flexed, the lateral ligaments are lax. Therefore a mechanical rig, which allowed the relative position of components to be adjusted and the joint to be distracted, was used to determine the minimum Distraction required for a Dislocation (DD), which is related to the risk of dislocation. However, as testing with the rig was inefficient, a computational dislocation analysis tool based on the mechanical rig was developed and validated against results from the rig. The tool uses path planning algorithms from the field of robotics to allow the bearing to find a viable dislocation pathway. It was found that medial dislocations required a much lower DD than AP dislocations, which explains why medial dislocations are more common than AP dislocations. Further, changing the tibial surface from a flat to a dome increased the DD for AP dislocations substantially, which explains why this change primarily decreased AP dislocations.
A series of potential implant design changes were studied to see if they would decrease the DD for medial dislocations to that of AP dislocations as the risk of AP dislocation was considered acceptable. The simplest change to achieve this was to increase the tibial wall height by 2 mm, but to avoid the femoral and tibial components hitting if there is bearing wear, the minimum bearing thickness would have to be 5 mm. Alternatively if the centre of the femoral component sphere was moved laterally, the bearing made wider laterally and the wall height increased, then an acceptable dislocation rate would be achieved with a minimum bearing thickness of 4 mm. For both these modifications to be successful, surgeons must ensure that the bearing is not more than 4 mm from the tibial wall.
Cadaveric and clinical studies are required to assess the viability of the proposed changes. If the risk of dislocation can be minimised or reduced, more patients may benefit from the advantages of lateral mobile bearing UKRs.
Aspects of Hrusso Aka phonology and morphology
Keywords: Hruso
Underspecification
Aka (Hruso)
Complex consonants
Sentence-final particles
Tibeto-Burman languages
Featurally Underspecified Lexicon (FUL)

This thesis is part of a collective effort to support the Hrusso Aka language in its struggle for survival and revival. At a critical juncture in the history of this endangered language, this thesis addresses the pressing need for a systematic study of its phonology and morphology, necessary to lay the sound, scientific foundation, required by the newly emerging culture of written literature. It is also part of a larger scientific endeavour, paving the way for a future reference grammar and providing primary data and coherent phonological analysis for a diachronic study. As the title suggests, this work has two distinct parts. The first (Chapters 2-7) focusing on phonology, analyses the segmental structure of Hrusso Aka and, using the Featurally Underspecified Lexicon (FUL) model (Lahiri & Reetz 2010; Lahiri 2018), offers a detailed analysis of Hrusso Aka's sound system, explaining its "bewildering" complexity. In a chapter dedicated to tone, this thesis gives an account of the underlying tonal system and tone-stress interaction of the language. The second part (Chapters 8-9) deals with morphology, describing the word classes and word-building strategies of Hrusso Aka.
Characterisation of emergent and emerging human-infective RNA viruses
Keywords: SARS-CoV-2
zoonoses
clinical virology
arboviruses
virus evolution
molecular diagnostics

Improved understanding of the early adaptation of zoonotic, human-infective RNA viruses and the genetic factors leading to spillover will inform public health approaches attempting to limit the morbidity and mortality associated with these events. In this thesis, I use clinical microbiological methods to characterize the intra-host replicative and evolutionary dynamics of SARS-CoV-2 and bioinformatic approaches to investigate genetic factors associated with spillover of arboviruses.
Chapter one broadly reviews the field of virology.
Chapter two reviews the apolipoprotein B mRNA-editing enzyme, catalytic polypeptide (APOBEC) family of proteins, focusing on their emergence, diversification, and function, and summarizes the bioinformatic and functional evidence of their role in SARS-CoV-2 evolution.
Chapter three details the methods underlying the subsequent results chapters.
Chapter four describes the development and validation of single nucleotide polymorphism-based genotyping assays for identifying variants of concern in COVID-19 clinical samples. Their performance is compared to next-generation sequencing, demonstrating the superiority of the genotyping assays at a wide range of viral loads.
Chapter five uses amplification data generated from two COVID-19 clinical trials to explore factors associated with viral load and within-patient viral load dynamics, uses a novel polymerase chain reaction approach to quantify subgenomic RNA transcripts, and investigates the emergence and spread of the Alpha variant in the United Kingdom and the Zeta, Gamma, and Delta variants in Brazil.
Chapter six investigates the interaction between SARS-CoV-2 virological features and COVID-19 clinical outcomes leveraging patients admitted to intensive care within the REMAP-CAP convalescent plasma clinical trial. The null results in this chapter support severe COVID-19 pathology being primarily immune-mediated.
Chapter seven quantitatively tests the hypothesis that convalescent plasma treatment was responsible for the emergence of SARS-CoV-2 variants of concern using an intensively sampled cohort within the REMAP-CAP convalescent plasma trial. Using a variety of approaches, no evidence in support of convalescent plasma therapy as a general driver of immune-escape substitutions was found.
Chapter eight probes the genetic factors associated with human-human transmissibility of arboviruses, finding strong evidence for the role of CpG suppression in the host optimization of flaviviruses. The strong genetic barriers to spillover enable more focused surveillance of this informal classification of viruses.
Virtual court hearings: judicial perspective from Ontario judgments
Keywords: Covid-19
administration of justice
online hearings
online courts
remote hearings
online justice
judges
courts
pandemic
hybrid hearings
court technology
Ontario
virtual hearings
Canada
virtual justice

The onset of the Covid-19 pandemic has sparked a phenomenal rise in virtual hearings in Ontario (Canada), much like in many other jurisdictions around the world. While video court participation has been available for decades, hearings have, until recently, remained courtroom-centric events and the possibility of dematerialized courts had seemed far off, if not far-fetched. Inspired by the latest evolution of justice delivery, this thesis explores the views of Ontario judges on the implications of virtual justice. What judges have to say about video-enabled testimony and adjudication matters enormously given their role in the administration of justice. Through a systematic content analysis of reported judicial decisions from the superior trial court and appellate court in Ontario between 16 March 2017 and 17 December 2021, this thesis tackles the question: To what extent do reported decisions by Ontario judges confirm or challenge concerns about virtual hearings expressed in scholarly debates about the topic? The analysis suggests that judges share many of the concerns articulated by scholars about proceeding virtually, such as the loss of solemnity and the expanded opportunity it lends to remote participants to behave in ways that undermine the integrity of the trial. At the same time, judges agree that proceeding virtually can be effective, fair, and in some cases, a more efficient alternative to the in-person format. The findings further reveal how judges have adapted their hearing management practices to accommodate the virtual court environment and assert control over remote sites. Overall, judicial conceptions of the modern trial appear to have evolved to the point that it is no longer seen as inevitably a courtroom affair.
Investigating large-scale change in volcanic time series data using machine learning analysis
Keywords: Volcano-seismology
Machine learning
Active learning
Novelty detection
Volcanology

Volcanic eruptions are characterised by large-scale transitions in behaviour, which include the transitions governing repose to unrest, unrest to eruption, and eruption to quiescence. Identification of these transitions is a fundamental goal in volcanology. This thesis aims to explore the use of machine learning approaches which are established for the monitoring of critical systems, such as healthcare or jet engine monitoring, to better understand the timing of large-scale transitions in volcanic activity. The first research chapter is an application of machine learning approaches to better understand the timing of eruption end, which has no systematic definition. Multi-class machine learning methods were applied to time series derived from volcano-seismic data from two volcanoes with contrasting eruption styles: Nevado del Ruiz, Colombia and Telica, Nicaragua. The resulting eruption end-dates agreed with previous, generic definitions of eruption end and provide an independent constraint on the timescale of eruption cessation processes. The second research chapter is an extension of this methodology to multi-parameter datasets from the 2005 – 2006 unrest and eruption of Augustine, Alaska. Both multi-class and novelty detection approaches, in which models are trained only on non- eruptive data, are applied. The resulting transition from non-eruptive to eruptive identified from the modelling agrees with previous estimates of the timing of dike initiation prior to eruption. Additionally, I explored the use of different types of data and different seismic catalogues for distinguishing between eruptive and non-eruptive activity. The final research chapter is an application of deep active learning to automated volcano-seismic event classification. Active learning is the process by which a machine learning model actively selects the training data which it learns from. This approach has the potential to reduce the quantity of labelled data required to train a successful model. The deep active learning approach is applied to two datasets from Nevado del Ruiz, Colombia and Llaima, Chile. Active learning models performed better on unseen testing data for both datasets and achieved better performance during training for the Nevado del Ruiz dataset.
Rising powers, subordinate monopolization, and major interstate war
Keywords: revisionism
subordinate monopolization
rising powers
major power relations
norms
war

This dissertation argues that the association of rising powers with major interstate war is dependent on competition over subordinates. It develops the theory of subordinate monopolization, arguing that when rising powers seek to close and monopolize subordinates, this increases the probability of conflict with other major powers. By contrast, when rising powers pursue openness and common-pool approaches to subordinates, conflict is much less likely. This theory addresses two omissions in the field. Firstly, the failure to treat peaceful rises seriously, which problematizes the pathway between the existence of a rising power and revisionist approaches to the international order. Secondly, the absence of subordinates from accounts of major power politics, despite their value. Subordinate monopolization is compared and contrasted with three alternative approaches: the realist focus on relative power between major powers, the need for status recognition and reform of distributional and institutional structures, and locating foreign policy within a domestic political context. Through quantitative examination of rising power disputes between 1816 and 2010, and two pairs of case studies of rising power disputes in the long nineteenth century and early Cold War, robust evidence for the theory is found which is more consistent than for any of the alternatives. This leads to the conclusion that rising powers should be understood in terms of their interactions with subordinates, as well as with the major powers.
Modelling elements of microstructure in olivine
Keywords: recovery
olivine
plasticity
dislocation
dislocation creep
microstructure
annealing

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.
Gender, property and household in provincial English parish government, c. 1540-1660
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

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.
Translating Kōminka: shaping narratives of Japanese rule in Taiwan through translation post-1975
Keywords: Taiwan
colonial literature
postcolonial literature
Sinophone literature
translation
Japanophone literature
Japanese empire
women's history
women's literature

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.
Developing a computational high-resolution scATAC-seq platform to prioritize non-coding genetic variants

Keywords: non-coding genetic variants
epigenomics
data visualization
GWAS
computational pipeline
gene regulation
single-cell ATAC-seq

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.