VictorJuiz/thesis huggingface dataset:
Reception of Virgil in England and Scotland c. 1400-1550: manuscripts, editions, translations

This study examines understudied English and Scottish evidence for reading and translating Virgil in the years c. 1400-1550. Scholarship on Virgil’s reception has generally focused either on the Middle Ages or the Renaissance, but this straightforward periodisation suppresses the intellectual continuities and gradual pace of change between the two periods. The thesis assembles its broader narrative from close analyses of extant manuscripts, print editions, and translations. Using the evidence of glosses, it argues that Virgilian reading throughout the fifteenth and early sixteenth centuries was characterised more by a close attention to language than by allegory or moralisation. The linguistic focus is witnessed across a range of reading contexts both inside and outside schools, and these common glossing practices went on to shape practices of translation.
The first half of the thesis is a bibliographic study of surviving manuscripts and print copies of Virgil’s Latin texts. Chapter 1 surveys the various contexts of reading Virgil manuscripts, and establishes the consistent linguistic focus of readers’ glosses. Chapter 2 shows that printing caused technological and commercial changes in book-design, but did not see major intellectual changes in glossing practice and book-use. Chapter 3 uses De Worde’s sequence of four Bucolics editions (1512-1529) to demonstrate the incremental impact of humanism on English pedagogy and print culture. Chapter 4 posits that the most striking development in fifteenth- and sixteenth-century Virgil glosses was the gradual rise in using the vernacular as opposed to Latin.
The second half of the thesis demonstrates how these widespread and consistent glossing techniques influenced and informed three major Aeneid translations. William Caxton’s Eneydos (1490) is not usually considered a proper translation of Virgil, but Chapter 5 shows its frequent dependence on the Latin text and glosses. Chapter 6 demonstrates the continuities between Gavin Douglas’s Eneados (1513) and the translation practice of his fifteenth-century predecessors such as Caxton. Chapter 7 shows that the Earl of Surrey’s translations of Aeneid II and IV (c. 1543) look back to Douglas’s model, but also forward to the more rigorous formal experiments of later sixteenth-century Virgil translators.
In light of these findings, the Conclusion summarises the shortcomings of applying a simplistic ‘Middle Ages’ versus ‘Renaissance’ periodisation to the reception of Virgil. It also shows that close analysis of even minute grammatical and lexical glosses is necessary to reconstruct broader trends in reading and translating classical texts.

Advisor: Wakelin, D
Ghosh, K
Helping and harming

After Darwin (1858) presented the idea of evolution by natural selection scientists focused on the idea of fitness as the personal reproductive success of an individual. Hamilton (1964) gave birth to social evolution by defining what fitness means for a social trait, such as helping another individual by raising their young or harming them by stealing their food. In this thesis we look at the two most unintuitive forms of social behaviour: altruism and spite. In both an individual sacrifices its own personal fitness to help (altruism) or harm (spite) another individual. In my chapters I cover: (i) how the altruistic production of virulence factors in a pathogen can lead to strong frequency and density dependent effects when they are under a volunteer's dilemma, (ii) how these strong effects can lead to year-to-year fluctuations in bacterial virulence and the risk of epidemics, (iii) an argument against indiscriminate spite being possible in finite populations and argue that some previous examples are better classified as selfish indiscriminate harming, and (iv) how spiteful interactions between symbionts can lead to a host evolving higher relatedness amongst the symbionts and eventually result in close mutualisms between the symbiont and the host.

Keywords: Kin Selection
Social Evolution
Inclusive Fitness
Mathematical Biology
Advisor: West, S
Bonsall, M
Whole genome sequencing and resistance in Escherichia coli

Rising antimicrobial resistance is an increasing problem worldwide. Escherichia coli presents a particular challenge as it spreads resistance rapidly via mobile genetic elements. Combatting this requires fast, detailed identification of resistance to prevent its spread and inform treatment. Culture-based antimicrobial susceptibility testing (AST) is limited by the time required for bacterial growth and does not directly identify mechanisms of resistance. However, many molecular techniques require specific targets, limiting their routine use in clinical microbiology. Whole genome sequencing (WGS) offers an alternative, solving many of these issues. However, evidence of WGS’s ability to identify clinically significant resistance in E. coli is limited. This thesis investigates this in detail.
Using methods similar to those from “proof-of-principle” studies, beta-lactam resistance was predicted from WGS data in several sets of E. coli, including a large set of unselected bloodstream infection isolates. While agreement between WGS-predicted and observed AST was high for many antibiotics, for some, including several commonly used broad spectrum antibiotics, there was significant discrepancy. Focussing on amoxicillin-clavulanate resistance due to the extent of disparity and its clinical significance, the causes of discrepancy were investigated. Instead of the discrepancy being due to the bioinformatic approach, incomplete knowledge of resistance mechanisms or phenotyping errors as is commonly believed, results suggested oversimplifications of both phenotype and genotype were the major cause. Future work is needed to investigate WGS-based prediction for other antibiotic and antimicrobial combinations.
This work demonstrates the feasibility of WGS-based prediction for a phenotype widely regarded as one of the most complex. However, it also highlights many barriers WGS-based prediction will need to overcome prior to clinical implementation. These include not only technical problems such as how to best curate and use genetic data for resistance prediction, but also non-technical problems such as the need to challenge long held assumptions regarding the nature of antimicrobial susceptibility testing.

Keywords: Escherichia coli
Beta-lactam
Whole Genome Sequencing
Antimicrobial Resistance
Advisor: Walker, S
Peto, T
Anjum, M
Stoesser, N
Woodford, N
Liquid-liquid phase separation of germline proteins

Spatial organization of chemical processes is a widely accepted requirement for living systems. Cells have developed a great variety of mechanisms to achieve spatial and temporal organization of which many rely on lipid membranes to separate biochemical processes from bulk phases. However, studies in recent years have shown that membraneless organelles are highly dynamic entities that can organize and facilitate chemical reactions. Membraneless organelles are known to consist of a diverse population of different proteins and nucleic acids. Many studies focus on the phase behaviour and properties of single protein regions. We therefore investigated the phase behaviour of more complex systems using the well-characterized germ granule protein Ddx4 and the uncharacterized N-terminal regions of Piwi proteins. We show that the interplay of these disordered regions has differential effects on the phase properties and the propensity to phase separate. Furthermore, we find that liquidliquid phase separation of Piwi protein N-terminal regions is dependent on folded domains. The evolution of disordered proteins is not well understood and experimental data is scarce. Therefore, we compared the phase behaviour of human germ granule proteins to Drosophila melanogaster proteins. We show that the propensity to phase separate, phase properties and interactions of composite systems are evolutionarily conserved between Homo sapiens and Drosophila melanogaster homologues, even though sequence similarity is remarkably low.

Keywords: Biomolecular condensates
Intrinsically disordered proteins
Ddx4
Liquid-liquid phase separation
Evolution
Piwi
Advisor: Nott, T
Deep learning for communication: emergence, recognition and synthesis

Human intelligence is a social phenomenon tightly coupled to the act and process of communication. Ever since the early prehistoric period, humans have been able to communicate amongst themselves at an unprecedented and unparalleled level compared to all other living species. Communication led humans to develop media such as the spoken and written word to effectively convey the meanings of concrete and abstract concepts, and still today a substantial part of human life is spent communicating and sharing information. The scientific study of communication began in Classical Greece with the work of Aristotle and was to evolve through time into the work on information theory by Claude E. Shannon. This work proposes three novel methods for studying the processes of emergence, recognition, synthesis and enhancement of communication, using recent advances in deep learning. The first method investigates the emergence of communication among agents, and introduces a differentiable way of learning communication protocols. The second studies speech recognition in visual verbal communication, and for the first time solves sentence-level lipreading with deep neural networks trained end-to-end. The third and final method proposes a meta-learning approach for sample efficient verbal communication via text-to-speech synthesis. This thesis advances deep learning in these areas, and defines the premises for the creation of novel technologies for the greater good of society.

Keywords: lipreading
speech
lipnet
communication
machine learning
deep learning
Advisor: de Freitas, N
Whiteson, S
Electrochemical sensors for the detection and quantification of toxic metal ions

This thesis presents experimental work with the primary aim of developing sensors for the detection and quantification of the toxic metal ions Hg2+, Al3+, Zn2+, and Li+ through electrochemical methods. Chapter 1 describes the fundamentals of electrochemistry, including voltammetric and nano-impact methods. Chapter 2 provides information about chemical reagents, instrumentation and experimental procedures used in this thesis. Chapter 3 outlines the development of a sensor for inorganic Hg2+ in aqueous solution using silver nanoparticles with galvanic displacement under a suitable applied potential.
Chapter 4 and Chapter 5 demonstrate the utilization of tannic acid (TA) as a capping agent of gold nanoparticles for the sensitive detection of Al3+ and Hg2+ toward complexation, respectively. Chapter 6 generalizes and extends these chapters, defining the role of the TA capping agent in the redox activity for Hg2+ and Zn2+ detection by using the nano-impact method. Chapter 7 outlines the electrochemical dissolution of the citrate-capped gold nanoparticle in cyanide-containing solution, where an understanding of the dissolution mechanism is of great importance for the optimization of gold nanoparticle recovery or refinery via oxidative cyanidation. Finally, Chapter 8 outlines the development of an electrochemical sensor for Li+ in authentic human saliva at lithium manganese oxide (LiMn2O4)-modified electrodes. The sensing strategy is based on an initial galvanostatic delithiation of LiMn2O4 followed by linear stripping voltammetry to detect Li+ in the sample.
Overall, the sensing methodology reported in this thesis makes a significant contribution to the application of voltammetric methods for the detection and quantification of toxic metal ions. All sensors reported in this thesis are specifically suitable for routine environmental monitoring, for drinking water and food products quality assessment, or for clinical monitoring and diagnosis applications.

Advisor: Compton, R
Adventures in low-valent germanium chemistry

This thesis explores the use of boryl, terphenyl and amido ligands in a variety of interesting areas of low-valent germanium chemistry.
In Chapter 1, a general introduction to the state of the art in this field is provided. The ligands that have proven pivotal in recent decades in germanium chemistry are introduced, and the developments that they have facilitated are then described. Finally, the field of germanium cations is introduced.
In Chapter 2, the general methods deployed in this thesis’ work are described; modified literature procedures for the syntheses of a variety of starting materials that were used in this work are also detailed.
In Chapter 3, the synthesis of novel germylium-ylidenes is examined, utilising a strategy of chloride abstraction from chlorogermylenes substituted by a combination of N-heterocyclic carbene and anionic ligand. The structural characterisation of the first isolable germylium-ylidenes featuring boryl, terphenyl, primary amido, and borylamido ligands is reported, and the influence of these ligands on the structure of these compounds is discussed in detail. For instance, concerning terphenyl-substituted cations, the effect of subtle variation in ligand steric bulk is explored, in terms of changing the degree of aggregation, and leading to secondary interactions with the ligand peripheries.
In Chapter 4, the reactivity of these germylium-ylidenes is then explored. The first activation of E-H bonds by isolable germylium-ylidenes is reported, as well as novel onward reactivity of some of the products as a result of their charge. For instance, oxidative addition of certain cations with ammonia leads to a subsequent elimination. Attempts towards the synthesis of multiple bonds is described, and the novel compounds this leads to discussed; for instance, reaction of a boryl-substituted cation with trimethylsilylazide leads to the formation of the first germylium azide.
In Chapter 5, the synthesis of compounds featuring boryl-substituted germanium-transition metal bonds
is investigated, and the first examples of such compounds for the cases of molybdenum, cobalt and iron are reported.
In Chapter 6, conclusions are drawn from the work of this thesis, and suggestions for future work are made.

Keywords: Cationic
Small molecule activation
Main group
Germanium
Advisor: Aldridge, S
Automorphic compatible systems of Galois representations

This thesis investigates properties of compatible systems of Galois representations, mainly focusing on the compatible systems which are attached to certain classes of automorphic representations of GLn.
We develop a general method to prove independence results for algebraic monodromy groups in abstract compatible systems of representations, and give applications both in characteristic zero and in positive characteristic settings. In the case of automorphic compatible systems (and actually for a slightly larger class of geometric compatible systems), we apply our method to deduce an independence result, assuming a classical irreducibility conjecture. In addition, we also deduce an independence result in the case of compatible systems of lisse sheaves on normal varieties over finite fields.
We then focus on the study of the geometry of (pseudo)deformation spaces of Galois representations and definite unitary groups eigenvarieties at points corresponding to certain classical automorphic representations. In this context, we present smoothness results known in the literature, and suggest possible implications for automorphic compatible systems.

Advisor: Wiles, A
Policing the camp: refugees and the geographies of humanitarian enforcement in Kenya

Humanitarianism is a morally charged project that vacillates between the alleviation of hardship and the re-inscription of further violence. Nowhere is this more pronounced than in the global archipelago of camps that houses millions of displaced people and thus appears as a beacon of protection, safety, and peace. This doctoral thesis questions this deceptive image and ethnographically explores the geographies of enforcing order in the paradigmatic humanitarian space of the refugee camp. It focuses specifically on the Kakuma refugee camp in north-western Kenya but offers a reading of the spatial, governmental, and discursive effects of policing camps and non-citizen populations that resonates with order-making practices elsewhere in the colonial present. African societies have been subjected to innumerable humanitarian interventions, emergency responses, and disaster relief operations over the past few decades. Forced displacement has arguably been one of the most visible results of political turmoil, civil war, economic devastation, persecution and has hence led to encampment on an unprecedented scale throughout the continent. Viewed through the prism of containment and control, African camps are the southernmost outposts of a global system of immobilisation, border policing, and closure that is not novel but has rather reached unrivalled proportions in recent years. Based on fifteen months of ethnographic research in Kakuma camp, this study delves into three interrelated facets of humanitarian enforcement by discussing (i) the militarised spatialities of the camp in which Kenya’s state violence has merged seamlessly with the contemporary humanitarian need for unobstructed aid management, (ii) the multiple technologies of government which enlist refugees themselves into upholding camp order, and (iii) the discursive practices of camp administrators who envision refugees as governable subjects that require constant policing and disciplinary checks. The study contributes to scholarship on humanitarian violence, camp geographies, refugee management, policing and local security governance in Africa, and the imaginative geographies of displacement. It counters the reification of the political technology of the camp and concludes with a discussion on the coloniality of policing refugees that exposes the illiberal disposition of humanitarianism in the global South. Policing thereby seems as integral to the workings of refugee camps as the provision of food, shelter, and legal aid. Paradoxically, it is only through uniformed officers, the baton, the gun, and the prison cell that humanitarians are able to make their promise of protection.

Advisor: Daley, P
Owen, O
Due diligence on conservation organisations: what should we be asking?

This inductive study explores what criteria could be used to identify conservation organisations more likely to achieve their goals. In addition to information gathered from the academic and grey literature, primary data was obtained from three main sources: semi-structured interviews with 74 conservation practitioners; an online survey completed by 154 conservation practitioners; and review of 35 non-profit organisational effectiveness frameworks.
Interviews identified barriers to conservation success, allowing a typology of barriers to be developed. Risks to success can be internal (arising inside an organisation), external (completely outside of an organisation’s control) or operational (outside of individual organisational control, but within the control of the conservation community). Because the list was long, statistical procedures were applied to the survey data to reduce the number of barriers needed to understand operating context.
The framework review and survey explored organisational deficiencies that might present internal barriers to effectiveness. I found four dimensions to an effective organisation: governance; finance; leadership; and management. There was less agreement as to which criteria are present in effective organisations. Differences between frameworks used to guide effectiveness and those used to judge it were noted and discussed. Finally, survey results were compared to framework review results to compare viewpoints on effectiveness criteria. Ranked lists were not significantly different, but correlation between them was weak.
This study provides the first empirically based conceptual model of barriers to conservation as perceived by conservation practitioners, and a first attempt to identify which barriers, internal and external, may be most important in identifying more effective conservation organisations. My findings also suggest that current criteria applied in funding decisions might be counter-productive: insisting on the presence of unproven effectiveness criteria stretches already pressurised conservation organisations even further and hampers their effectiveness. Instead, the donors could collaborate more and work towards less onerous and untested methods of decision- making.

Keywords: conservation
organisational effectiveness
non-profit organisation
barriers
typology
Advisor: Rogers, A
Bhagwat, S
Discrimination in modern asymmetric conflict: a Christian moral analysis

The task of discrimination in war is a non-static phenomenon. It changes with the character of war, which itself changes with developments in cultures, international relations, how states organise for war, innovations in doctrines, technologies and tactics etc. Fundamental changes to war’s character necessitate some moral revision, and modern asymmetric conflict (MAC) is the latest fundamental change. MAC is characterised by forces from developed countries fighting unconventional, often non-state adversaries that flout moral and legal norms, and deliberately exploit immoral, unlawful and repugnant tactics.
My analysis of the relevant ethics of Paul Ramsey, the US Conference of Catholic Bishops and James Turner Johnson – which, respectively, treats the form of war most similar to MAC, addresses an earlier fundamental change in the character of war, and comprises an important assessment of MAC – as well as touching on other Christian and secular contributions, discerns that there is insufficient Christian moral guidance to address the questions raised about discrimination in MAC. Thinking out of Christian just-war tradition, I focus on the Improvised Explosive Device (IED) network to expose novel ethical issues concerning discrimination in MAC. I argue that by not revealing their combatant status, those enabling the prosecution of IED attacks, and by extension broader combat functions, should lose or at least jeopardise any absolute non-combatant immunity.
I then proceed to explain how conventional forces can discriminate morally, while their irregular and less scrupulous adversaries do not. This includes enhancing the rule of double effect by exploiting predictive analytics; overcoming the enemy’s erosion of non-combatant immunity and the inviolability of national borders; empowering soldiers to act discriminately through a simple, moral foundation; equalising the legal accountability of the opposing forces, rather than unfairly pursuing soldiers only from developed countries; and, finally, establishing a level of military supererogation that reflects this new form of conflict, where minimising civilian casualties is a key measure of success.

Keywords: Discrimination
Collateral Damage
Just War
Improvised Explosive Device
Double Effect
Modern Asymmetric Conflict
Advisor: Biggar, N
Single-molecule imaging of cholesterol-dependent cytolysin assembly

Cholesterol-dependent cytolysins (CDCs) are amongst the primary virulence factors for several important pathogens. Their typical function is to lyse cells by forming large pores in target membranes, often up to 40 nm in diameter and comprised of around 30-50 subunits. Pores assemble from diffusing monomers bound to the target membrane, via a prepore intermediate. Previous work on the mechanism of pore assembly has focused on structural and ensemble fluorescence information, complemented by atomic force microscopy. The experiments described herein present the application of single-molecule total internal reflection fluorescence microscopy to the study of CDC assembly, using droplet interface bilayers as a felicitous in vitro system. This technique supported millisecond temporal resolution imaging of CDC monomers and individual CDC complexes assembling in parallel. The recorded videos enabled quantification of assembly kinetics and further insight into the governing mechanism of assembly.