VictorJuiz/thesis huggingface dataset:
Atrial Fibrillation: unravelling the significance of lysosomes in atria under normal and pathological conditions

Lysosomes are responsible for the degradation of intracellular and extracellular macromolecules. They also play roles in signalling relevant to cardiac function and cardiac disease, however, the extent of altered lysosomal function in Atrial fibrillation (AF) is unknown. This thesis describes the development of a fractionation method and label-free quantitative proteomics using guinea-pig atrial tissue lysate (TL), endo-lysosome (EL) and mitochondria (Mito) fractions. Over two thousand proteins were detected, of which 564 were more abundant in EL than TL. The resulting lysates contained atrial, mitochondrial and EL-specific proteins. Significant EL proteins recovered included catalytic activity proteins. Protein enrichment and networks were studied. The developed fractionation method was applied to goat left atrial AF and sham control samples, including network and pathway analysis. Regulated proteins discovered by proteomics were validated with Western blotting, including Ras-related protein 11 (RAB11). In addition, lysosomal assays (beta-galactosidase and beta-hexosaminidase) were performed. Out of 2104 proteins, levels of 340 proteins in TL, 113 in mito and 148 in EL were significantly altered. EL fractions showed enrichment for EL specific proteins including GAA, clathrin light chain B (CLTB), T-complex protein 1 subunit beta (CCT2), and vacuolar protein-sorting-associated protein 25 (VPS25). KEGG pathways analysis highlighted mitochondrial oxidative-phosphorylation OXPHOS, and AMPK pathway protein upregulation, indicating a potential increased ATP energy demand in AF samples. Upregulation of protein processing suggests increased vesicular trafficking, potentially related to increased metabolic energy demand. The downregulation of autophago-lysosome fusion proteins such as dynein, dynactin and dynamin indicate a possible disruption in the cellular degradation of macromolecules during chronic AF. The data presented in this thesis therefore provides evidence to support the role of the lysosome as an important organelle that may play a role in AF pathology.

Advisor: Burton, RAB
Platt, F
Model theory and rough approximate subgroups

The aim of this thesis is to use model theory to study rough approximate subgroups, generalising various known results about approximate subgroups.
Firstly, a systematic study of the structure of piecewise hyperdefinable sets is developed. In particular, we show the most significant properties of their logic topologies. Then, we study piecewise hyperdefinable groups, generalising and improving two of the main model-theoretic results of "Stable group theory and approximate subgroups" by E. Hrushovski. The first one is the existence of Lie models. The second one is the Stabilizer Theorem. In the process, we define the model theoretic components for piecewise hyperdefinable groups, and introduce a new component. We use these results to generalise the Lie Model Theorem, one of the main applications of model theory to study approximate subgroups, to the case of rough approximate subgroups.
Secondly, we focus on the case of metric approximate subgroups, i.e. rough approximate subgroups in metric groups. In this particular case, we show that ultraproducts of metric approximate subgroups satisfying some discretisation conditions have Lie models up to an infinitesimal thickening. We conclude using this result to get various combinatorial consequences.

Keywords: Hyperimaginaries
Lie models
Stabilizer theorem
Approximate subgroups
Advisor: Hrushovski, E
The interpretation of deep brain stimulation through diffusion-weighted magnetic resonance imaging

Advances in neuroimaging, particularly magnetic resonance imaging (MRI), have been fundamental to achieving improvements in clinical outcomes from deep brain stimulation (DBS). These improvements are essentially an increase in the reliability of the procedure as a result of improved accuracy in targeting a neuroanatomic structure of interest. However, many DBS procedures still result in highly variable outcomes between patients, raising the possibility that targeting remains suboptimal in these cases. These procedures may benefit from advanced forms of MRI that can extract unutilised anatomic features for a more individualised approach. Diffusion MRI tractography is a prime candidate for this but has to date mostly been applied to low outcome-variance procedures or with normative data which belies any project of individualisation. This thesis examines three cases of high outcome-variance DBS procedures and interprets them with patient-specific structural connectomes. DBS of the pedunculopontine nucleus in Parkinson’s patients with severe gait freezing was interpretable by stimulation-associated connectivity to primary motor cortex (M1), cerebellum, and caudal primary somatosensory cortex. This suggests connectivity maps of the ventrolateral pontine tegmentum could be useful as an adjunct to targeting. DBS of the ventrocaudal nucleus of thalamus (Vc) in patients with chronic neuropathic pain was interpretable through a homuncular framework superimposed on an individualised connectivity-based parcellation (CBP) of the thalamus aimed at segmenting the Vc. This suggests that CBP may have utility in targeting electrodes to Vc instead of relying on atlas coordinates. Lastly, DBS of the internal pallidum (GPi) for patients with cervical dystonia was interpretable through stimulation associated connectivity to the putamen, specifically the region of putamen characterised by dense input from M1. This was shown to be uncoupled from electrode coordinates, and therefore points to GPi connectivity maps as a promising tool with which to personalise the procedure. Retrospective data indicates diffusion MRI has promise to improve outcomes in DBS and underscores merit in the future pursuit of prospective work in this field.

Advisor: Green, A
Payne, S
Aziz, T
The reception of Ariosto's Orlando furioso (1532) by three Italian women writers of the sixteenth century

The thesis aims to bridge a gap in the current re-evaluation of women’s contribution to the literature of Renaissance Italy, by focussing on the reception of Ariosto’s epic poem Orlando Furioso - published in its ‘final’ version in 1532 - by three female poets of the sixteenth century: Isabella di Morra (1516/18-45/46), Laura Bacio Terracina (c.1519-77) and Moderata Fonte (1555-92). The thesis examines how the ‘Ariostism’ of all three women writers challenges the model of Petrarch as benchmark for female literary production during the Cinquecento.
Chapter One outlines some of the gender-related issues raised in the Furioso, with which the three female poets may subsequently be said to engage. The chapter looks at both narratorial statements and constructions of masculinity and femininity within the text, revealing Ariosto’s complex relationship with the question of gender.
Chapter Two considers the Ariostan echoes present within Isabella di Morra’s Rime, first published in full in an anthology of 1559. Her small canzoniere - not typically Petrarchan in its themes and tone - is re-considered in light of the Furioso, especially with regard to the topos of the ‘abandoned woman’ and the twin themes of harsh landscape and malevolent Fortune which are central to her poetics.
Chapter Three discusses Laura Bacio Terracina’s Discorso sopra tutti i primi canti d’Orlando Furioso (1549), a moralizing commentary in ottava rima which constitutes one of the most direct responses to Ariosto’s poem. Terracina’s bold appropriation of the model of the Furioso incorporates aims of both a poetic and an ideological nature, since her engagement also revolves around moral issues that are mostly gendered in their emphasis.
Chapter Four considers Moderata Fonte’s Tredici canti del Floridoro (1581), the first ‘original’ romance epic to be written and published by a woman. The Floridoro contains strong thematic and structural parallels with the Furioso; yet the chapter also highlights the ways in which Fonte diverges from the Ariostan precedent re-writing the epic genre in feminine - and ‘feminist’ - key.
The thesis concludes that the poetic model of the Furioso would play an increasingly important role in the development of the female literary canon as the century progressed.

Keywords: Ariosto
Italy
Terracina
Orlando furioso
Italian women writers
Tredici canti del Floridoro
women writers
Lodovico
reception
16th century
Fonte
Moderata
sixteenth century
Morra
Discorso sopra il principio de tutti i canti d'Orlando furioso
Advisor: McLaughlin, M
Dorigatti, M
Irish women's lives in the United States, c. 1850-1914

This work examines the lives and wellbeing of Irish women in the United States from 1850 until 1914, encompassing the end of the famine and the age of mass European migration. Irish migration in this period has been the subject of a large body of research, but existing studies have focused primarily on men, despite Irish female migrants often outnumbering male migrants in the late nineteenth century. The decision to emigrate in this period has frequently been explained by wage differentials between Ireland and destination countries, but this was only one factor in a multifaceted process. The importance of the family and the home is usually overlooked, despite their centrality to the decision to emigrate; and insufficient attention has been paid to how the experiences and circumstances of Irish émigrés changed over time. Most glaringly, the particular experiences of female migrants have not been given sufficient attention, with the result that our knowledge of this exceptional group of women is scanty, and their seminal impact on the broader history of Irish emigration is underplayed.
This thesis takes a new and innovative approach to Irish emigration research, an approach which questions many of the assumptions underlying existing analysis. It does so in four main ways. First, this thesis places women at the centre of the analysis, considering their life in Ireland and, for emigres, their life in the United States. Second, it adopts a broad approach to wellbeing that extends beyond the typical and androcentric focus on real wages. Third, it considers how the lives of Irish women evolved over their life course, as workers, wives, mothers and widows. Fourth, it adopts a multi-level approach which combines numbers with narratives. The former includes United States micro-census data which provides information on all individuals in 1880, allowing for a new, national and comparative picture of women’s lives. The latter includes parliamentary papers, newspaper articles, philanthropic studies of urban life, and charity reports. Moreover, this thesis employs letters of Irish women, to extrapolate how these women themselves perceived their own lives.
Through this examination, this thesis shows the multidimensional nature of women’s wellbeing, and how women’s lives often deteriorated as migrant women aged. Although many women found independence and wellbeing in the US in their youth, many older women were left alone and destitute. Yet these women and their voices are central to our understanding of the history of Ireland, migration, and the making of the modern America.

Keywords: American History
Irish History
Women's History
Gender History
Nineteenth Century
Wellbeing
Economic History
Census
Migration
Advisor: Paseta, S
Oxley , D
The history of the Amalgamated Society of Railway Servants, 1871-1913

Trade Unionism among British railwaymen developed in the course of the second wave of trade union growth which occurred during the prosperous years towards the end of the third quarter of the Nineteenth Century. Until then self-organisation among railwaymen had been hampered by certain features of the industry in its period of expansion.
An exceptionally authoritarian tradition of management, a high proportion of young and unsettled workers, the policy of recruiting new entrants from the ranks of agricultural labourers, and a tendency among different grades of railwaymen to keep aloof from one another - these factors hindered the growth of trade unionism, The Locomotive grade possessed a scarcity value which made its members more susceptible to organisation. But they also cultivated an attitude of exclusiveness. The history of the Amalgamated Society of Railway Servants is largely a story of a struggle to maintain a trade union in spite of these handicaps.
Continued in thesis ...

Keywords: railways
trade unions
Britain
labor unions
Amalgamated Society of Railway Servants
An edition with introduction and commentary of John Blount's English translation of Nicholas Upton's De studio militari

This thesis presents an edition, with introduction and commentary, of John Blount’s early sixteenth century English translation of Nicholas Upton’s De Studio Militari, a highly influential chivalric text written in 1446. It was comprised of four books, the first two provide a legal justification and discussion of conflict, and the last two a discussion of the theory and practice of heraldry. The translation survives in one copy, which is held in the Bodleian Library (Bodl. MS Eng.misc.d.227). The thesis is presented in two volumes: the first is the introduction and commentary, the second the text itself. The introduction begins with a biography of Upton and Blount and places the production of both the original De Studio Militari and the translation in context. After the biographies, each of the four books is introduced each with a chapter to itself, with Book Four divided into two chapters; one examining Upton’s discussion of beasts and the other examining Upton’s discussion of inanimate charges. These chapters outline sources used by Upton for the information he presented and compare the discourse Upton made with contemporary literature and an evaluation of De Studio Militari in its historical context. This ends volume one of the thesis. The second volume opens with a discussion of the families of De Studio Militari manuscripts and the position of John Blount’s translation in relation to these, and the individual characteristics of Blount’s translation. After this I outline the editorial conventions that I have used in the presentation of the manuscript: this is followed by the description of the manuscript of the English translation of De Studio Militari. After this is a list of all identified surviving manuscripts of De Studio Militari. There follows the text of the translation itself, transcribed word for word from the manuscript. I have inserted illustrations and modern punctuation into the transcript, and have added references that were omitted from the translation, which appear in the Latin versions of the text. Upton’s introduction to De Studio Militari which is not in the translation, a section missed by Blount from chapter eighteen of Book One, and a list of the authorities which Upton cited are included as appendices.

Keywords: De studio militari
Nicholas Upton
John Blount
Advisor: Keen, M
Royal administration and the keeping of the seas, 1422-1485

This work is concerned With naval activity between 1422 and 1485 in which the English government was involved, chiefly with that initiated or undertaken by the administration, and with the organisation of any such activity.
The Introduction deals with the nature of the evidence used ~ this being particularly the records of the central government (notably of the Exchequer), certain local records, for instance of King's Lynn and Sandwich, and the various printed sources, such as the Howard Household accounts, the Paston letters, the chronicles of the period, and the other narratives, correspondence and treatises in which the time is comparatively rich - with what was meant in the 15th century by the term ‘the keeping of the sea’, both by the men who used it or had reason to comment on it, and in practice, and (arising from this) what might be called naval strategy.
Continued in thesis ...

Keywords: keeping of the seas
Great Britain
15th century
fifteenth century
Lancaster
Royal administration
York
Royal Navy
Studies on neural networks: Information propagation at initialisation and robustness to adversarial examples

Over the last decade, the academic and industrial communities have become increasingly involved in the field of Deep Learning, leading these algorithms to become the drivers of the AI revolution that has allowed “machines” to attain increasingly extraordinary results. However, despite the impressive results achieved, there is still room for these algorithms to improve, and the use of mathematical techniques is central to this advancement. In this thesis we focus on two different themes in this space: the initialisation and the robustness of neural networks.
Currently the training of these algorithms is becoming an always more expensive procedure, not only financially, but also ecologically. To speed-up this process and therefore alleviate the above problems, one can focus on trying to more optimally initialise the neural networks. In this thesis we focus on defining this optimality with measures taken from information theory. Specifically, we introduce a lower-bound on the mutual information of the neural networks and find that there is an initialisation procedure that allows signals to propagate through the neural networks with less loss of information.
Finally, neural networks are vulnerable to adversarial attacks, meaning that regular inputs with small perturbations, although appearing to be insignificant to humans, can cause undesired model behaviours. In particular, we focus on identifying the methods that generate these adversarial perturbations, considering the neural networks as black-boxes. To do this, we consider the state-of-the-art methods and compare them for the first time in the same exact settings. We also introduce a further method to ensure that all the most common derivativefree-optimisation techniques have been tested on this problem. Thanks to our experiments, we are able to show how there is a class of methods that is particularly effective at generating these adversarial perturbations, but also how the various methods are affected differently by the setting in which they are deployed, therefore indicating that there is not a one-size-fits-all solution.

Keywords: Black-box adversarial attacks
Initialisation of Neural Networks
Advisor: Tanner, J
The limits of religious and cultural claims in fundamental rights cases: A judicial framework

In secular, constitutional democracies, religion and culture are assumed to be of legal importance only for deciding the scope of religious and cultural freedom, maintaining communal harmony, and determining the scope of minority protection laws. However, across jurisdictions, courts have been influenced by religion and culture in determining other human rights as well. This phenomenon is especially observed in, but not restricted to, gender and sexuality cases: abortion, sexual orientation and gender identity, marital rape, sex work, euthanasia, bar dancing, surrogacy, etc.
This thesis examines the limits of religious and cultural influence on fundamental rights questions under secular and liberal constitutions, and proposes a judicial framework to determine the same. Using intensity sampling, I select the population of cases (31 in number) pertaining to the above-mentioned themes in the Indian jurisdiction. I perform a systematic content analysis on these cases to extract the religious and cultural claims and record various attributes. I find that, even though the law has mandated no role for them, such claims determine the outcome in 29% of the cases in which 78.5% of those claims are judicially noticed, i.e., admitted without proof. This makes it imperative to investigate the institutional limits upon the judiciary when dealing with religious and cultural claims.
The judicial framework that I propose has three pillars: 1. a theory of constitutional interpretation which discusses constitutional restrictions on the judge when considering religious and cultural arguments in fundamental rights cases; 2. a theory of judicial notice to determine when such claims can be admitted without proof; and 3. A theory of secularism and public reason which argues that once a religious or cultural claim has been admitted, it should be given weight in the final decision only if it matches defensible conceptions of constitutional values.
The thesis makes the following significant contributions to the field: 1. it identifies a unique class of human rights cases that are influenced by religious and cultural claims; and 2. it provides an empirically driven judicial framework to determine the limits of these claims in the outcome of those cases.

Keywords: Constitutional Interpretation
Religion
Public Reason
Fundamental Rights
Secularism
Judicial Notice
Culture
Systematic Content Analysis
Empirical Legal Research
Advisor: Craig, P
Causality and the arrow of time in process theories

The objective of this thesis is to study the concept of causality and its interplay with the arrow of time in quantum process theories and beyond. The framework of process theories is particularly intuitive since it is accompanied by a diagrammatic formalism. Its formal underpinnings lie in Categorical Quantum Mechanics, a field which has recently seen enormous success both in the foundations of physics and in quantum information theory.
Taking a process-theoretic viewpoint we examine possible ways to time-symmetrize quantum theory. We identify the causality condition as the root of the asymmetry and we proceed by eliminating it in a variety of ways. We furthermore view that process theories can be faithfully captured by operad algebras, which is an alternative to their identification with symmetric monoidal categories. The landscape of operad algebras allows us to introduce novel notions of process theories, namely time neutral process theories. To provide more intuition about them, we establish a link with compact closed categories. Finally, we present an algebraic framework to describe the evolution of fields, perceived as causal process theories, in discretised spacetimes. We form connections with algebraic quantum field theory (AQFT) as well as quantum cellular automata (QCA).

Keywords: causality
quantum foundations
operads
quantum cellular automata
time symmetry
fields
algebraic quantum field theory
Advisor: Gogioso, S
Barrett, J