VictorJuiz/thesis huggingface dataset:
Epigraphic form, from Ann Radcliffe to George Eliot
Keywords: paratext
Walter Scott
history of reading
history of the novel
epigraphs
George Eliot
Ann Radcliffe

My thesis charts a history of the chapter epigraph through the eighteenth-century periodical, and the novels of Ann Radcliffe, Walter Scott, and George Eliot. It examines the formal developments and stylistic variations of epigraph composition practiced by these authors, shedding light on the content and aims of their fiction, and on how they sought to moderate the imagined relationship between reader and writer. I argue that while Radcliffe, Scott, and Eliot, used the epigraph to different ends, consistent with their respective genres, all three attempted to correct some version of exclusionary politics. In particular, I sketch out a long tradition in which the epigraph has been used for highly gendered purposes, and explore how the practice laid the foundations for the modernist and, indeed, feminist, use of the fragment.
The emergence and popularisation of epigraphs in the eighteenth and nineteenth centuries was concomitant with the expansion of the British reading audience. Whereas books had once been scarce and expensive, read several times over, and often aloud to friends and families, reading materials, such as books, newspapers, and periodicals, began to proliferate at this time. In turn, reading became a solitary, silent, and fast-paced activity. While we may think of the ‘slow’ movement, from slow cooking to slow reading, as a response to postmodern life, my research reveals how an earlier age confronted similar challenges. Then, as now, authors used epigraphs to fasten attention in a society devoted to haste and speed. In tracing the development of the epigraph from the eighteenth century to the present, my thesis therefore offers one possible approach to thinking about the cultural work of the novel and its effect on the mind of the reader.
The scholar at work: Varro's study of the Latin language
Keywords: ancient scholarship
Hellenistic philosophy
morphology
Varro
De lingua Latina
Roman grammar
analogy
Crates of Mallus
Alexandrian grammarians
Stoics
ancient grammar
antiquarianism
derivation
etymology
anomaly
Epicureans
Latinitas
inflection
philosophy of language
Cratylus
Latin language

As part of a bigger project to investigate the history and features of Roman culture, Varro set out to study the Latin language in all its components: where its vocabulary came from, and what such derivation revealed about the history of Latin speakers; how its words were arranged into classes based on their morphological features, and to what extent this arrangement was rationally motivated and self-consistent; and how various people used language differently, some employing distinct sections of its lexicon depending on their backgrounds or professions, others bending grammatical rules either out of ignorance or for literary purposes.
My thesis focuses on some of the main subjects explored in Varro’s linguistic writings: “nature” as a criterion for Latinitas; the notion of “kinship” in language; etymology (both the theories underpinning it and the methods used to reconstruct the origin of a word); analogy and anomaly (notoriously the focal points of an ancient controversy and a vexata quaestio in Varronian scholarship). For each of these subjects, I inquire into how Varro engaged with the scholarship produced before him, what principles and methods he absorbed, and how he re-worked previous material to make it suitable for his own goals and readership. I use my findings to piece together a portrait of Varro as a scholar who had extensive knowledge of previous treatments of the subjects he tackled and drew on a multitude of sources, combining philosophical, literary critical, philological, and historical-antiquarian influences. I also highlight how Varro’s production was aimed at contributing to the conversations ongoing in cultural circles in his own time, in which he was actively involved.
Dance and social bonding: synchrony and the endogenous opioid system
Keywords: endogenous opioids
dance
synchrony
social bonding

Dance – movement to music – is a ubiquitous and ancient human activity, which may serve important adaptive functions. In this thesis I focus on the suggestion that dance may encourage social bonding amongst co-actors by stimulating the production of endorphins in the Endogenous Opioid System (EOS).
Studies have demonstrated that performing similar movements in a predictable, rhythmic fashion makes dyads feel more socially close, likely due to a merged sense of ‘self’ and ‘other’. Synchronising movements with other people has also been investigated with regard to its neurochemical effect. People performing exertive synchronised movements in a social context experience increased pain threshold (a proxy measure of endorphin release by the EOS) compared to those performing the same movements alone or out of synchrony.
This thesis brings together these two bodies of literature to address a number of outstanding questions regarding the effects of dance in a naturalistic context (i.e. groups rather than dyads moving to music rather than a metronome). Firstly, does dance make people feel more socially bonded? Secondly, what role does exertion play in the relationship between synchrony, social bonding and endorphin release? Thirdly, what aspects of synchrony (similar movement and/or mere temporal entrainment to music) are associated with this social bonding and endorphin release? Finally, does endogenous opioid uptake mediate the social bonding effects in dance?
In experiment 1, I compare participants’ self-reported closeness and generosity in an economic game before and after either a real-world dance class or gym session and find that either activity can have an effect on some measures of social bonding between strangers. In experiment 2, conducted in Brazil, I find both synchrony and exertion have significant and independent main effects on self-reported bonding amongst non-strangers, and on pain threshold (a proxy measure of endorphin levels). The subsequent two experiments are laboratory-based studies in the UK, and utilise silent disco technology to better manipulate the audio-visual experience of synchrony between strangers, and Actiwatches to measure exertion. Participants in synchrony with one another experience elevated pain threshold and higher levels of social bonding and in experiment 4, naltrexone- (an endorphin antagonist) treated participants experience suppressed analgesic effects, confirming that exertive synchronous movement activates the EOS.
In conclusion, this thesis presents novel research on and preliminary support for the endorphin-mediated social bonding hypothesis of dance. The results lay the foundation for further investigation into the complex neurohormonal underpinnings of these human social behaviours, and contribute to our understanding of the atavistic nature of group dance.
Modelling thermoregulation for prosthetic design
Keywords: lower-limb prosthesis
finite element analysis
theromoregulation
prosthetic socket
muscle temperature
bioheat model
sweat
discomfort
multiphysics modelling
exercise
hot climate

Conventional manufacture of prosthetic sockets is artisanal, relying on limited objective data, which often leads to discomfort and tissue damage. Thermal discomfort is a key concern identified by amputees, particularly in hot climates. Despite this, it has had little research attention. This research increases knowledge of the body’s heat transfer mechanisms and the effect of amputation and wearing a prosthesis on heat transfer and thermal discomfort through reviewing literature, running a clinical study with amputees and developing a computational bioheat model. A questionnaire on discomfort, completed by 42 amputees in Bangalore, found heat and perspiration in the prosthetic socket were the most prevalent causes of discomfort. Skin temperatures and thermal discomfort measurements were collected from 30 lower-limb prosthesis users during exercise. After exercise, thermal discomfort was greater on the amputated leg, despite the skin on both legs cooling. The discomfort might signal that the heat generated by the muscles in the residual limb during exercise is stored in the muscles. To explore the effect of the environment on muscle temperatures during exercise and post-exercise recovery, a cylindrical isolated-segment bioheat model of the thigh was developed in COMSOL Multiphysics and compared to empirical data of muscle temperatures. This model is the first to use finite element analysis to determine temperature distributions through the thigh during exercise and post-exercise recovery. It showed that thermal responses of individuals are varied and complex. From this understanding of the temperature responses of a healthy leg, the possible effects of amputation and prosthesis-use are discussed. The model increases knowledge of the heat transfer factors to consider in developing user-specific prosthetic sockets that reduce the body’s thermal load. The feasibility of integrating simulations, such as this model, with computer-aided design and 3D printing technology to improve customisation of prosthetic sockets was assessed by systematically reviewing the effectiveness of 3D printing prosthetics and other medical devices. The technology shows promise for supporting data-driven prosthetic socket design and manufacture but lacks research and clinical validation.
A Jewish lawgiver in a Greek world: Moses in Josephus' Antiquities in light of Plutarch's Lives
Keywords: Hellenistic Judaism
lawgivers
Plutarch
Jewish Antiquities
Josephus
Moses

In the preface to the Antiquities, Josephus introduces Moses, the lawgiver, as the central figure in Jewish history. Moses is presented in terms which are familiar from the traditions about lawgivers in the Greek world, but Josephus also adapts the category of lawgiver itself to fit Moses in particular. This pattern of appeal and adaptation persists in the account of Moses’ life which appears in Antiquities II to IV. In order to formulate a historically grounded picture of what a Greek audience would expect, this thesis uses Plutarch’s Lives, particularly of Lycurgus, Numa, and Solon. The core chapters of the thesis analyse the narrative of Moses’ life in the Antiquities through this lens, finding that on the levels both of narrative motifs and theoretical assumptions about the process of legislation Josephus imagines an audience with expectations similar to those presupposed in Plutarch’s Lives. Narrative motifs added to the stories of Moses’ birth, exile, and death reveal Josephus’ attempt to conform to Greek models of founding and legislating. When we consider Moses’ actions as lawgiver, comparison with Plutarch uncovers unexpected ambivalence about the ultimate source of the Jewish law, while also laying bare some core differences in emphasis in relation to the medium through which law is transmitted, and the categories of life managed by a “constitution”. Even where there are differences, however, the investigation finds a consistent concern on Josephus’ part to ensure his text appeals to readers who expected an approach like that in Plutarch’s Lives. The few exceptions expose core issues about which Josephus may have wished to provoke his audience: the place of communal worship in a nation’s “constitution”, the legislator’s need to be a part of the community for which he legislates, and the limited power of persuasion to deal with existential threats. The thesis argues that in his portrait of Moses as Jewish lawgiver, Josephus uses and challenges Greek models.
Communities and homology in protein-protein interactions
Keywords: networks
homology
protein interactions
proteomics
community detection

Knowledge of protein sequences has exploded, but knowledge of protein function is needed to make use of sequence information, and this lags behind. A protein’s function must be understood in context and part of this is the network of interactions between proteins. What are the relationships between protein function and the structure of the interaction network? In the first part of my thesis, I investigate the functional relevance of clusters, or communities, of proteins in the yeast protein interaction network. Communities are candidates for biological modules. The work I present is the first to systematically investigate this structure at multiple scales in such networks. I develop novel tests to assess whether communities are functionally homogeneous, and demonstrate that almost every protein is found in a functionally homogeneous community at some scale.
The evolution of protein sequences is well-studied, but comparatively little is known about the evolution of protein function. Such knowledge is needed to understand when it is appropriate to annotate newly sequenced proteins by transferring functional information from homologs–i.e. evolutionarily related proteins. In the second part of my thesis, I assess the success of transferring protein-protein interactions across species and use this to estimate the rate at which interactions are lost in evolution. At levels of sequence similarity associated with functional annotation transfer, I demonstrate that protein-protein interaction transfer is unreliable.
The relevance of community structure for understanding protein function and the low conservation of individual interactions, suggests a possible role for communities in the evolution of cellular function. I discuss this possibility in my conclusions.
Virtually inconceivable: Ontological insecurities and the rise of geopolitics and sovereignty in EU cybersecurity policy
Keywords: European Union
delegitimization
sovereignty
cyberspace
ontological security
cybersecurity
geopolitics

The policy domain of cybersecurity has become inundated with geopolitical concepts and sovereignty appeals over the last decade, arousing the interest of scholars and policymakers alike regarding how such a notable shift has implicated the behaviour of actors in cyberspace. Scholarship conventionally expects state actors with cyberwarfare and intelligence capabilities to voice geopolitical reasoning and sovereigntist claims, overlooking the presence of such discourse within the European Union’s (EU) cyber policies. Yet, the EU’s agenda of ‘technological sovereignty’ and its invocation of geopolitical metaphors have become increasingly prevalent in its cybersecurity policy, whereupon ‘European sovereignty’ has emerged as a priority—defying expectations based upon the EU’s traditional eschewal of geopolitics, and scholarly assumptions about its capabilities as a cyber actor. Thus, to explore this development, I ask how, and why, such geopolitical and sovereigntist language has emerged in EU cybersecurity policy, and the implications of such language upon the EU’s self-conception as a cyber actor. Adhering to an interpretive- qualitative methodology, I develop a chronology of EU cybersecurity policy development from 2009-2020 and conduct discourse analyses of documents and elite interviews. My dissertation undertakes a sustained focus upon the ontological dimension to cyber policymaking, particularly ontological insecurity—an approach not yet leveraged in this empirical context. Through the lens ontological insecurity, I argue that the emergence of geopolitical and sovereigntist language in EU cybersecurity policy is a consequence of how EU cybersecurity policy has centred upon the management of particular ontological insecurities in cyberspace, for which policymakers have leveraged discursive strategies oriented around the delegitimization, and later legitimization, of geopolitics. Sovereignty, in turn, emerged as a response to insecurities elicited by the EU’s decision to ‘speak in geopolitical terms’, and has become prevalent as a means of differentiating the EU from geopolitical actors in cyberspace. Overall, my dissertation illustrates how insecurities about the EU’s past, cyberspace as an environment, and relations with cyber actors have shaped the dominant ideas and policy responses over the course of 2009-2020, enabling the emergence of sovereigntist and geopolitical language in this contemporary stage of the EU’s development. Significantly, it unmasks a key tension underlying EU cybersecurity policy: while the EU has increasingly articulated traditional, state-centric assumptions about geopolitics in cyberspace; simultaneously, EU policymakers have sought to represent the EU as transcendent of this dynamic for which the vocabulary of ‘European sovereignty’ has been leveraged to differentiate the EU from geopolitical actors in cyberspace.
Vulnerable bodies: the poetics of protection in the Old English Metrical Charms
Keywords: history of medicine
Old English
metre
gender
metrical charms
style
poetics

This thesis offers the first complete metrical and stylistic analysis of the twelve Old English metrical charms. The verse found in these texts is rife with apparent irregularities, and scholars have historically labeled them poor verse, or have neglected discussions of style in favour of anthropological and source studies. Those who have addressed the poetics of the charms have largely dismissed them as meaningless features meant only to hypnotise the listener. Yet this thesis argues the metrical charms are not arbitrary sound, but narrative verse, containing powerful imagery that invokes themes appearing elsewhere in the Old English literary corpus. They also feature significant rhetorical and ornamental features lauded as aesthetic achievements in other Old English verse.
Drawing on past scholarship on Old English style and merging close reading with rigorous metrical analysis, this thesis argues that the unusual metrical and stylistic features of the charms are not defects but a function of their genre, the substance of a meaningfully different Old English poetic style. This study explores the ways in which the charms’ stylistic ornamentation, imagery, and word choice highlight their central ideologies and anxieties, and the ways in which supposed metrical ‘irregularities’ in fact serve aesthetic purposes and accommodate prescribed magical formulae. It invites us to reconsider the criteria by which we judge Old English verse, and to challenge dichotomies of ‘correct’ and ‘incorrect’ metre, rigorous ‘classical’ verse and ‘decayed’ late verse.
Stylometric analysis and close reading offer literary insight into the charms as well, and this thesis explores the ways in which the charms safeguard human individuals and communities against invasive agents. I argue that the charms equate disease, physical and spiritual dangers, and even falling victim to theft, with submission, defeat, or loss of control in intimate conflict with the Other. These texts seek to reinstate boundaries that have been violated — civilization and wilderness, inside and outside — by maintaining or restoring human bodies and spaces as inviolate wholes.
Investigating the roles of CDA and DCTD in cancer nucleotide metabolism
Keywords: nucleotide
cancer
metabolism

Nucleotides play essential roles in cellular function, including as components of the nucleic acids DNA and RNA. Cancer cells have elevated proliferation and DNA replication, necessitating a reliable supply of nucleotides from the nucleotide de novo synthesis and salvage pathways. These have consequently been exploited as targets for nucleotide analogue chemotherapy. Resistance to chemotherapy can arise from enzymes in the synthesis and salvage pathway, including upregulation of the pyrimidine salvage enzyme cytidine deaminase (CDA). CDA functionally overlaps with the salvage enzyme deoxycytidylate deaminase (DCTD), and it is uncertain whether either enzyme is the principal deaminase and whether they deaminate cytidine nucleotides derived from nucleotide synthesis, in crosstalk between the synthesis and salvage pathways. I investigated these queries by setting up and optimising targeted HPLC-MS/MS systems for nucleic acid composition and nucleotide pool analysis, using them to measure isotopically labelled nucleotide precursor incorporation into cell lines and observe effects of CDA and DCTD siRNA knockdown (KD). The nucleoside analysis platform I developed is capable of sensitive analysis of nearly 20 nucleosides, whereas the free nucleotide analysis platform has analyte sensitivity comparable to or lower than those reported in literature and can detect most nucleotide phosphates without sample purification steps. The KD and pulse-chase experiment provided evidence that CDA and DCTD are mutually redundant in deaminated 2’-deoxycytidine nucleotides and validates previous reports that DCTD has low activity against cytidine monophosphate. Additionally, there was no impact of CDA and DCTD KD on L-glutamine labelling of cytidine nucleotides, suggesting that de novo synthesis-derived cytidine nucleotides are not dephosphorylated and deaminated in significant amounts. It was also observed that nucleotide phosphate interconversion occurs at much shorter timeframes than one hour.
Taken together, the studies in this thesis, using targeted and sensitive MS analytical methods, support the theory of redundancy of the CDA and DCTD, with implications for their roles in resistance to cancer chemotherapy as well as in other disease states.
Computational analysis of host/pathogen coevolution
Keywords: homing endonuclease gene
Denisovans
HIV
HLA
virophage
polinton
linguistics
Neanderthals
phylogenetics

In this thesis, I present my research on host/pathogen coevolution in several different systems and on different time scales. The thesis comprises multiple parts and shows how advances in computational methods can be applied to a broad range of questions, from basic research to issues of immediate clinical relevance.
Chapter 1 examines this host pathogen coevolution in a nonhuman system, looking at giant viruses, satellite viruses, related transposable elements found in eukaryotes and giant viruses, and individual 'jumping' homing endonuclease genes (HEGs) found in all three. Unfortunately, due to enormous amounts of time over which some of the elements involved have diverged, it is difficult to draw reliable conclusions here. However, the novel identification of HEGs in satellite and giant viruses shows a likely solution to the question of the mechanism for the horizontal gene transfer of HEGs between dissimilar phyla.
Chapter 2 focuses on the coevolution of humans with pathogens. This can be seen in the influence of archaic hominid immune genes on the modern immune system, and what appears to be the introgression of archaic hominids' granular adaptation to local pathogens when modern humans expanded out of Africa. The fact that these archaic HLAs have retained this regional granular adaptation for tens of thousands of years suggests some sort of survival advantage. While previous work has shown that there is different selective pressures acting on different class I HLAs, this chapter shows that this relationship is retained when looking exclusively at archaic derived HLAs. Selective pressures acting on HLA-A but not HLA-B have not previously been described, and Chapter 2 identifies the suppression of endogenous retroviruses as possibly being one such selective pressure.
Chapter 3 examines the granular adaptation of HIV-1M to humans in Sub-Saharan Africa by looking at correlations between human genetic diversity and HIV diversity. Unfortunately, widespread genotyping of HIV patients in Sub-Saharan Africa is not available, but linguistic diversity has previously been specifically shown to correlate with human genetic diversity in Sub-Saharan Africa, providing a useful proxy with which to make comparisons. My results show that linguistic diversity, and by extension human genetic diversity, does indeed correlate with both HIV subtype and amino acid sequence diversity in the region. This runs contrary to the dominant paradigm that HIV subtypes are artefacts of founder effects and may explain some of the difficulties in creating an HIV vaccine despite over 30 years of research on the subject.