VictorJuiz/thesis huggingface dataset:
The text and transmission of Cicero's Brutus

This thesis is composed of three parts: a study of the transmission of Cicero’s rhetorical work Brutus, a critical edition, and a textual commentary. I begin Part One with a catalogue of the c.109 extant manuscripts of Brut. The second chapter of this part is devoted to the oldest surviving manuscript, the Cremona fragment. I demonstrate, against the view of earlier scholars, that the Cremona fragment is a part of the long-lost Codex Laudensis (L), the archetype of the entire tradition. In the following chapters, I use the stemmatic method to establish the relationships between the fifteenth-century copies of L. In Chapter 3, I prove that there are three independent lines of descent from L for the first part of the text, and four for the second. In Chapters 4 and 5, I study the manuscripts and printed editions which derive from the independent descendants of L, placing them into families and sub-families. In particular, I show that one manuscript, F, copied by Niccolò Niccoli, is the source of the majority of the tradition. The final chapter of this part, Chapter 6, is a textual history of Brut.: I connect my conclusions from Chapters 3-5 to the historical data, shedding fresh light on the roles played by various humanists of the Italian Renaissance, including Gasparino Barzizza, Flavio Biondo, and Niccolò Niccoli, in the dispersion of the text. No comprehensive study of the transmission of Brut. has been undertaken before, and many of my conclusions are completely new.
In Part Two, I present a new text of Brut., together with an apparatus criticus. I diverge from Malcovati (1970) in c.100 places, sometimes reverting to the paradosis and sometimes printing a conjecture, whether my own or that of another scholar; these differences are listed in an appendix. In Part Three, I discuss all the most significant textual problems and explain many of my editorial decisions in a textual commentary.

Keywords: Textual Criticism
Textual Transmission
Brutus
Cicero
Advisor: Reinhardt, T
Explanations for ontology-mediated query answers

Ontology-mediated query answering is a paradigm that seeks to exploit the semantic knowledge expressed in terms of ontologies to improve query answers over incomplete data sources. In this thesis, we consider explanations for ontology-mediated query answers under the classical semantics. We provide a comprehensive complexity analysis of a wide range of computational problems, associated with explaining ontology-mediated query answers. We study explanations both for positive and negative ontology-mediated query answers under different minimality criteria, both for existential rules and description logics. This allows us to indicate similarities and point out differences in the complexity of explaining ontology-mediated query answers for these different settings.

Keywords: existential rules
description logics
computational complexity
ontology-mediated query answering
Advisor: Lukasiewicz, T
Ceylan, I
Courts and prisons: practices of criminal imprisonment in the London metropolis, 1750-1845

This dissertation looks at the development of criminal imprisonment and the evolution of prison systems in the London metropolis between the mid-eighteenth and mid-nineteenth centuries. It combines a study of the processes through which individuals came to be incarcerated with an examination into the regulation and experience of confinement with the aim of explaining the functions that London’s prisons came to serve and the forms that they assumed.
Drawing on court records, prison commitment books, and newspaper accounts of judicial hearings, this dissertation explores how committing bodies in London, from the lowest levels of justice to the highest, used imprisonment to detain and punish criminal offenders. It looks not only at how often imprisonment was used and for what sort of offenders, but also at the particular prisons where the sentences were carried out. It shows how magistrates, both as a bench making policy decisions and as individuals in their commitment practice, used their stock of prisons to target commitments and create distinctive penal regimes.
Though most studies of English imprisonment posit that the main criminal prisons effectively merged in form and function from the late seventeenth or early eighteenth century, this dissertation instead argues that the prisons became increasingly specialised. Specialisation was locally driven, so the particular arrangements adopted differed by jurisdiction, but in all parts of the metropolis, there was a general trend towards treating prisons as either custodial or punitive. As a result, prisoners for punishment increasingly served their sentences in prisons distinct from those where prisoners for detention were held.
These changes in commitment practice provide a crucial, but heretofore neglected, context for understanding changes in the administration and internal operation of London prisons. This dissertation draws on a wide range of surviving evidence relating to the administration of prisons and to the conditions of confinement—including parliamentary reports; quarter sessions’ books and papers; papers, minutes and reports of prison committees; journals of prison officers; prison plans; and codes of regulations—to detail and explain the particular shape that prisons took. It argues that this period saw the crystallisation of two distinct regimes of confinement: punitive imprisonment and custodial incarceration.

Keywords: Legal history
British history
Prison and Imprisonment
London
Advisor: Innes, J
Development of single-molecule DNA hybridisation tools for high-content analysis of protein-DNA interactions and gene expression

This thesis presents results in the development of two single-molecule methods which use DNA hybridisation, in vitro and in vivo, to investigate protein-DNA interactions and processes.
Single-molecule DNA sequencing methods have made important contributions to genomics, diagnostics and functional analysis of genetic processes. Despite the fact that there are a large variety of single-molecule sequencing methods, there is currently no systematic way to connect the functional properties, with regards to protein interactions, of a single DNA molecule (single-molecule phenotype) with DNA sequence. In this thesis, I describe proof-of-principle experiments for ‘Gap-Seq’, a short-read single-molecule sequencing method that interrogates DNA sequence through the transient binding of short fluorescent DNA strands to surface-immobilised gapped-DNA substrates. A way to identify a base can be the dwell times of the short DNAs on the immobilised substrates: the correct base shows comparatively long dwells of the short DNAs on the substrates, whereas, non-complementary bases show no binding or comparatively shorter dwells on the substrates. I also show how single base DNA modifications affect protein-DNA interactions and a method for how Gap-Seq can be implemented to evaluate the DNA sequence at the protein binding site. Once developed further, Gap-Seq will fill a significant void in single-molecule DNA/RNA sequencing and will be important for both mechanistic work and screening libraries of nucleic acids against targets of biomedical importance.
I have also used DNA hybridisation to demonstrate the proof-of-principle for a new type of fluorescence in situ hybridisation (FISH) assay in live bacterial cells. Specifically, my work introduces ‘in vivo single-molecule FISH’ (in vivo smFISH), where short doubly labelled single-stranded DNAs are electroporated into cells and subsequently bind transiently or stably to target RNA. I establish that the electroporated probes exhibit site-specific binding and produce bright fluorescence signals that should lead to direct measurements of the kinetics of gene transcription on the chromosome, and advance the understanding of many fundamental processes involving RNA.

Advisor: Kapanidis, A
Isolation of Fibrillar Elastin Gel (FEG) and its application in heart valve tissue engineering

Elastin, although a small constituent of heart valves, plays a significant role in its functionality and the maintenance of tissue homeostasis. It is due to its low abundance that its significance has been overlooked in favour of collagen and glycosaminoglycans. However, repeatedly, the failure of biological prostheses has been associated with the disruption of elastic fibres. The incorporation of exogenous forms of elastin has been challenging due to the intrinsic insolubility and poor processability of polymeric forms. This has led to the precedence of applications of soluble forms of elastin, which, although are tailorable, do not offer sufficient structural integrity or bioactivity (once cross-linked).
This thesis reports a method for the isolation of a novel form of natural elastin, termed Fibrillar Elastin Gel (FEG), which was discovered during the course of the DPhil. A method was developed to modify polymeric elastin to a processable form with improved polymer-solvent interactions. FEG is a thermally induced aggregated gel, composed of rod-like fibres (4-6µm) with improved intermolecular interactions as shown by the appearance of a shoulder at 1618cm-1 by infrared spectroscopy. The material exhibits a low loss factor (~0.1 at 1Hz) and has been hypothesised to be applicable as a biomaterial for tissue engineering of heart valves.
Porous (>94%) scaffolds of multiple compositions were fabricated by freeze-casting. Swelling studies revealed a negative thermosensitivity and contraction of FEG above the inverse transition temperature (30°C). Tensile testing showed a strong positive correlation between the concentration of FEG and the strain-to-failure of composites which increased from 37% to 94% as the concentration increased. In vitro studies revealed FEG contains cell-binding sites and did not hinder the attachment or viability of induced pluripotent stem cell-derived cardiomyocytes. The elastogenic capability of FEG was assessed by studying the gene expression of lysyl oxidase (LOX), elastin (ELA), and fibrillin-1 (FIB-1) which upregulated significantly on scaffolds with higher FEG content, suggesting that FEG would be a suitable material to use to design templates that promote elastogenesis. In addition, layer-specific tri-layer scaffolds were shown to stimulate layer-specific gene expression of extracellular matrix markers such as collagen type I (COL), hyaluronan synthase-2 (HAS-2) and ELA. Tri-layer scaffolds exhibited a non-linear mechanical response as well as bending anisotropy, a key deformation characteristic of native valves.

Keywords: Tissue Engineering
Elastin
Viscoelastic
Elastogenesis
Biomaterials
Advisor: Czernuszka, J
Exploring the factors and mechanisms involved in triggering the alternative lengthening of telomeres pathway

Maintaining replicative immortality is a crucial step in the development of cancers and is achieved by activating a telomere lengthening mechanism. While the majority of cancers rely on upregulation of telomerase, approximately 10-15% of cancers achieve telomere length maintenance through a telomerase-independent mechanism referred to as the Alternative Lengthening of Telomeres (ALT) pathway. ALT cancers exhibit a number of characteristic markers and recent work has sought to understand the mechanisms that underly the generation of these markers and of ALT telomere maintenance.
Previous work has also highlighted the striking loss of the chromatin remodelling protein ATRX and its histone chaperon partner DAXX in ALT cancers, and the ability of ATRX and DAXX to suppress the ALT pathway. Until now, however, it has remained unclear as to the mechanisms by which ATRX loss drives ALT development given that ATRX loss alone is generally insufficient to generate the ALT phenotype.
In this thesis a novel marker of ALT, the presence of Replication Protein A coincident with telomeric sequences, is shown. This marker is dependent on the presence of the endonuclease Mus81, which is known to cleave stalled replication forks. In conjunction, evidence is presented showing that the telomeric replication stress or lesions on telomeric DNA when combined with loss of ATRX or DAXX are able to trigger ALT pathway induction. This induction can be triggered both through artificial means with genotoxic agents, but also through loss of the histone lysine methyltransferase SETD2, which is responsible for the methylation of Histone H3.3 at lysine 36. Together these observations provide critical understanding of a possible route of ALT development, given the frequent co-occurrence of histone H3.3 G34R/V mutations, which are known to be detrimental to SETD2 activity, and ATRX/DAXX mutations in ALT cancers.

Keywords: ALT
ATRX
RPA
telomere
Cohesion
replication stress
DNA repair
alternative lengthening of telomeres
Advisor: Gibbons, R
Clynes, D
An examination of scar modelling and assessment methods for the evaluation of treatments

Scarring is the final common pathway for healing within the skin irrespective of age, gender and race. Scars can be itchy, painful, tight and above all, cosmetically disfiguring. Despite advances in surgery and trauma management, there is currently no reliably effective treatment for reducing or preventing scarring. The primary aim of this thesis is to assess the currently available models for scarring and evaluate/further develop the utility of current assessment tools, in an effort to design a pilot randomised control trial for silicone gel treatment of scars.
Review of scar models in humans and animals demonstrated the limitations and drawbacks of many existing methods to assess scar treatments. Examination of currently used subjective and objective scar assessment tools in a plastic surgery clinic helped to develop protocols and methodology for a scar treatment research trial. Long-term scar outcomes assessed using a novel subjective patient reported outcome measure for paediatric burn patients demonstrated no statistically significant difference between those treated surgically, and those treated conservatively. A pilot randomised control trial to produce high quality evidence for silicone gel sheeting in the treatment of scars was set up and successful in recruitment.
Scarring remains a difficult condition for clinicians to manage, with many treatments utilised on a poor evidence basis. Here, we have demonstrated difficulties in establishing a scientific scar treatment model; and created a pilot study that will help to provide high quality evidence for the efficacy of silicone gel sheeting as a treatment for scars.

Keywords: treatments
silicone
Scarring
Advisor: Issa, F
Furniss, D
Meditative practices - correlates and consequences for political attitudes

While meditative practices have become increasingly common in both science and society, many questions remain about their correlates and consequences for political attitudes. This is what will be examined in this thesis.
Part One of this thesis uses survey data from the United States and Britain to investigate awareness and experience of mindfulness, both overall and across groups. The results from the first empirical chapter suggest that five per cent of adults in the United States in 2017 had used mindfulness during the 12 months prior to the survey interview and mindfulness use was less likely among married adults and more likely among women, sexual minorities, young and middle-aged adults, white adults, employed adults, adults without minor children in the family, adults from the West of the United States, adults with access barriers to healthcare, adults with cost barriers to healthcare, adults with mental illness, and adults with physical pain. The results from the second empirical chapter suggest that fifteen per cent of adults in Britain in 2018 had learnt to practise mindfulness and awareness of mindfulness was more likely among women, unmarried adults, adults from middle and high-income households, and adults who voted Remain in the 2016 Brexit Referendum; and higher levels of engagement with mindfulness was more likely among young and middle-aged adults, but otherwise not concentrated in any particular groups.
Part Two of this thesis uses data from randomized controlled trials conducted in the United States and Britain to investigate the causal effects of mindfulness-based and kindness-based interventions on political attitudes. The results show that: (1) participation in an eight-week compassion-based program increased liberal political attitudes; and (2) a brief befriending meditation reduced affective polarization between Democrats and Republicans. Taken together, the findings suggest that kindness-based practices and programs increase tolerant and other-regarding attitudes more generally.

Keywords: political
mindfulness
meditation
compassion
polarization
Advisor: Stephen, F
Maryanne, M
Subjugation angst: memory and Europeanisation of foreign policymaking in Slovenia and Croatia

The past and its remembrance possess an incredible power to influence the present. The field of foreign policy is not immune to the forces of history and a vast body of literature invokes collective memory—an intersubjectively shared narrative construction of the past—to explain states’ international and foreign policy behaviour. The European Union is often called a community of memory, yet EU Members’ national collective memories differ substantially and persistently. Similarly, although the EU strives for unity in foreign policymaking, a truly Europeanised foreign policy has not yet emerged. To determine whether the parallel fractures in the EU’s respective memory and foreign policy communities are interrelated, this dissertation investigates the question: How does national collective memory influence EU Members’ Europeanisation of foreign policymaking? Whilst conventional scholarship emphasizes the influence of collective memory on foreign policy outcomes, the remembrance approach advanced in this dissertation reveals its influence on the foreign policymaking process. More specifically, I argue that national collective memory shapes national role conception which influences the extent of EU Member’s Europeanisation of foreign policymaking, as well as its crystallisation through uploading or downloading. The research design features an asymmetric comparative case study of the principal case of Slovenia and supplementary case of Croatia. It utilises a plethora of documentary primary sources, as well as conducts original empirical research in the form of elite interviews and questionnaire responses. Empirical findings support the theorised influence of collective memory on the Europeanisation of foreign policymaking and unveil that it is particularly remembrance of co- opted subjugation in Slovenia and Croatia that is informative for state practice.

Keywords: Europeanisation
Collective Memory
EU
Foreign Policymaking
Subjugation
‘It would be very much better if they never had children’: Eugenic Ideas and Policy-making in Edwardian Britain

‘What I want to insist upon is, that a state of things in which not two out of five of the population below a certain standard of life are fit to bear arms is a national danger, which cannot be met by any mere schemes of enlistment, and that true patriotism requires that that danger should be recognised’ (Miles, 1902: 81).1 Thus warned General J F Maurice writing under an alias in 1902 and sounding the alarm that the surprisingly poor performance of the British military in the Second Boer War (1899-1902), and its rejection of a worrying number of volunteers as physically unfit, might signal the end of British hegemony. General Maurice’s pronouncements launched a debate that would transform British politics in the twentieth century: the debate over physical deterioration and national efficiency.
His views were not entirely new. Investigators, philanthropists, doctors and others, had been warning for decades that the physical condition of the British people, and especially its poorer sections, was disconcerting. General Maurice’s contribution was in explicitly linking these concerns to the burning issue of the day: the military setbacks of the Second Boer War and the realisation that Britain’s predominance had become fragile (Gilbert, 1965). Amid this doubt over ‘whether English ways of doing things were any longer invariably the best’ (Ibid: 143), the Balfour government reluctantly initiated a series of thorough investigations on the various failings of British society and politics, among them the Inter-departmental Committee on Physical Deterioration (1903-1904), the Royal Commission on the Care and Control of the Feeble-Minded (1904- 1908), and the Royal Commission on the Poor Laws and Relief of Distress (1905-1909).
[Introduction continued in thesis]

Keywords: Social Science
Boer Wars
Britain
Poor Laws
Public Policy
Mental Health
Eugenics
Edwardians
Ideas
Disability
Advisor: Owen, N
King, D
Reasoning and normativity

This thesis addresses three questions: (I) What is theoretical and practical reasoning? (II) What is it to respond to normative reasons? (III) What are standards of evaluation for reasoning? Regarding (I), I first critically assess two views which have recently dominated the debate on the nature of the mental activity of reasoning. I argue that different versions of the Rule-Following View, according to which reasoning is essentially a rule-following activity, are problematic. Further, I argue that the Reasons View, which holds that reasoning consists in responding to normative reasons, is assumed by many but defended by few and remains underdeveloped. In particular, it is explanatorily unsatisfactory because, while it explains reasoning in terms of responding to normative reasons, it lacks an account of what it is to respond to normative reasons. I then provide a new theory of the nature of reasoning, the Approval Account. Reasoning is a transition in thought from some attitudes to another which the agent approves of. Regarding question (II), I propose a novel account of what it is to respond to normative reasons: it is a mental process that leads an agent from some attitudes to a response, where this process manifests the agent’s implicit conception of what is right to believe and do, and is under the agent’s (virtual) control. This account of responding to reasons allows me to systematically establish the claim that reasoning is a way of responding to normative reasons. With regards to question (III), it follows that correct reasoning is correctly responding to (supposed) normative reasons. I further argue that we must distinguish between the correctness, the goodness and the aim of reasoning.

Keywords: normative reasons
practical reasoning
theoretical reasoning
responding to reasons
Advisor: Broome, J
Bader, R
Ruling reasons: a defense of constructivism about reasons and objectivism about welfare

I argue in this thesis in favor of a position that combines constructivism about reasons and objectivism about welfare. In Chapter 1, I define reasons constructivism, on the basis of the Kantian origin of the view. I argue that reasons constructivism is a claim about the perspective-relativity of normative reasons for action. Furthermore, I argue that reasons constructivism, as I define the view, is distinct from both reasons objectivism and reasons subjectivism. In Chapters 2 and 3, I offer an argument in favor of reasons constructivism. I argue that in interpersonal reasoning, one agent can only offer reasons to another by engaging in the “if I were you” mode of reasoning. I show that these considerations support reasons constructivism, rather than other meta-ethical views about reasons. Finally, in Chapter 4, I argue that reasons constructivism can be combined with welfare objectivism. I show that this approach allows constructivists to generate the right reasons for agents with fundamentally corrupt judgments. Furthermore, I argue that this mixed position is coherent.

Keywords: welfare
interpersonal reasoning
reasons
constructivism
objectivism
Advisor: Fix, J