VictorJuiz/thesis huggingface dataset:
Computational framework for multiscale investigation of pro-arrhythmic mechanisms in the human cardiac Purkinje system

Ventricular arrhythmias are a major cause of sudden cardiac death, which accounts for about 50% of cardiovascular mortality worldwide. Understanding the mechanisms underlying arrhythmias generations is crucial to improve its diagnosis and treatment. Cardiac Purkinje cells constitute the peripheral conduction system of the electrical stimulation in ventricles and are responsible for the correct contraction pattern of the heart. Experimental studies on animal models pointed out that drug actions, mutations or cardiac diseases might alter the electrical activity of Purkinje cells and lead to arrhythmia onsets. However, the pro-arrhythmic mechanisms in Purkinje cells are not entirely understood, and results obtained in animal studies do not always translate to humans, due to inter-species differences.

The aim of this thesis is to develop an experimentally-informed computational framework to mechanistically investigate the role of human Purkinje cells in arrhythmia onset, and predict Purkinje cells electrophysiological response to pharmacological therapy. Multiscale simulations are used to identify the mechanisms underlying electrical abnormalities in human Purkinje cell and tissue models, as well as to evaluate drug safety and efficacy on cardiac Purkinje electrophysiology in humans, also accounting for biological variability.

Keywords: computer modeling
arrhythmias
cardiac Purkinje
in silico trials
human cardiac electrophysiology
Advisor: Rodriguez, B
Passini, E
Right atrial deformation through speckle tracking echocardiography and feature tracking CMR

The right atrium (RA) plays a vital role in the electromechanical regulation of the heart. Various invasive and non-invasive techniques have been used to elucidate right atrial structure and function. One such novel technique is speckle-tracking echocardiography (STE). Speckle tracking-derived deformation is a relatively new parameter, which is less dependent on loading conditions. STE tracks acoustic scatters (speckles) of myocardium, frame by frame, to calculate the strain or deformation indices of the myocardium. The right atrium is a relatively neglected chamber as it is mostly studied for assessment of atrial mass lesions, congenital and acquired valve lesions and for electro physiological studies. However, its role in the systolic and diastolic function of the right ventricle of the heart has been less explored. I have adapted the STE technique, designed for left ventricular analysis, for use in the right atrial analysis. I undertook a reproducibility study for right atrial deformation parameters and defined normal reference ranges for longitudinal deformation parameters. I have found the analysis approach used generates similar values to those reported in the limited number of previous studies on right atrial STE. I then compared STE derived strain with cardiovascular magnetic resonance feature tracking derived measures of right atrial strain and found moderate agreement between the two techniques. Finally, I investigated whether there are differences in right atrial longitudinal deformation parameters in different patient disease groups. I studied those with Heart Failure with Normal Ejection Fraction (HFNEF) and found a decrease in right atrial function. Whereas, in another cohort of patients with Rheumatoid Arthritis (RhA) there was no statistical difference compared to healthy controls. This thesis therefore demonstrates the feasibility of using STE to measure right atrial strain and provides evidence that right atrial strain does vary in certain disease conditions.

Keywords: speckle tracking echocardiography
feature tracking Cardiac Magnetic resonance
Advisor: Neubauer, S
Leeson, P
The streams of knowledge: Organising the Siku Quanshu 四庫全書

This thesis is about the order of knowledge in the Siku Quanshu, the Complete Writings of the Four Repositories, the largest ‘encyclopaedic’ compilation of texts in pre-modern China. While contemporary scholarship has concentrated on what was included in the compilation, the question of how it was organised remains largely unexplored. Divided in five chapters, this thesis explores the understanding of knowledge and its organisation in the Qianlong era (1736–1796 CE). In the Introduction, I interrogate the methodological viability of a cross-cultural investigation and argue for a new conceptual framework to undertake such line of inquiry in the Chinese context. In Chapter 1, I show how the antecedent poetic understanding of knowledge as water determined the order of the Complete Writings. I provide an account of its impact on classification and briefly sketch its historical origins and development. By way of comparison to the western notion of knowledge as tree, I tease out the properties and cultural specificity of each system. In Chapter 2, I explore the intellectual, non-political purposes behind the collection. I provide a short overview of past bibliographic classifications and their impact on the editors’ scholarly objectives and show how the order of the Complete Writings was envisioned as an advising guide to scholarship. In Chapter 3, I identify the ascribed socio-scholarly function of texts as the fundamental principle of order and investigate the different ways in which it was expressed. I also show how the Qianlong-era conception of order differs from Aristotelian and Wittgensteinian notions of classification. In the Conclusion, I summarise the main findings of this thesis and offer some reflections on the nature of bibliographic divisions, imperial scholarship, and the Complete Writings.

Advisor: Meyer, D
The rationality and normativity of intention

This thesis develops a Neo-Humean, functionalist account of practical rationality and normativity. On this view, principles of practical rationality are grounded in the proper function of our agency, while the normative force of a normative reason in calling for a certain response on our part consists in its capacity to engage the function of that response. This functionalist picture, I contend, undermines three long-held and widely-accepted views about practical rationality and normativity. Contra orthodox Humeanism about practical rationality, the functionalist account shows that the rational principles governing our intention are not limited to instrumental and formal coherence principles. Contra rationalists about the nature of rationality, the functionalist account supports an environmentally-embedded conception of practical rationality and demonstrates that the requirements of practical rationality are not necessary, a priori requirements. Finally, contra externalists about normative reasons for action, the functionalist account reveals that the normative force involved in normative reasons for action is best captured not by externalist considerations, but instead by our intentions or volitional states.

Keywords: agency
intention
rationality
normativity
Advisor: Irwin, TH
Hills, AE
Effects of conflict on resistance and cooperation in hierarchical groups

Many social organisms engage in collective actions in which there is a mismatch between individual and common interest. Such problems may include competition with other groups or collaborative efforts to secure resources from the environment. In this thesis I test novel theoretical predictions which see hierarchy as one potential solution to the collective action problem at hand. More specifically, models have shown that high-rank individuals in hierarchical groups are expected to contribute more toward the group’s success than low-rank individuals during inter-group conflict. This pattern of contribution by the high-rank group members is expected to increase the group effort of hierarchical groups in comparison to egalitarian groups. However, the increased individual effort of high-rank individuals is expected to reduce their net benefits in comparison to individuals with lower rank.
To study these effects, I devised eight behavioural experiments with more than 2300 participants from three national cultures which operationalized hierarchy in both political and economic terms. In these experiments, I utilized a behavioural game theory paradigm called the contest game, which simulates an inter-group collective action problem in experimental settings. Results from the thesis suggest that in economic hierarchy high-rank players may contribute more than low-rank players, while in political hierarchy this may not be the case. Groups with economic hierarchy exerted less effort than groups without such hierarchy (e.g. egalitarian), mainly due to a reduced contribution of the low-rank players. However, groups with political hierarchy usually exerted more effort than politically egalitarian groups. These findings suggest that the type of hierarchy is important, as it leads to different results in terms of contribution both at the individual and at the group level.
Further to the these questions, I studied the effect of the collective action problem type, gender, and cognitive processing on the contribution preferences of players. Results suggest that usually inter-group conflict is not important for the contribution preferences of players. Furthermore, the gender of participants and the decision making speed were not important factors for their relative contribution as well, neither under political, nor under economic hierarchy.

Keywords: hierarchy
egalitarianism
resistance
evolution
game theory
cooperation
public goods games
contest games
Advisor: Fortunato, L
Athenian power in the fifth century B.C.

The aim of this thesis is to provide a distinctive study of fifth-century BC Athenian power. I argue that Athenian power was composed of multi-directional and heterogenous interactions between the Athenians and allied communities, including assertions of allied agency and negotiation.
Studies of other ancient Mediterranean empires have benefitted from the fresh perspectives provided by awareness of scholarship on imperial and hegemonic powers of other periods and geographies. Approaches to the fifth century, however, are to a significant extent dominated by diachronic, narrative historiography, and hierarchical and centralised examinations of Athenian power, both rooted in close study of Thucydides. Understanding of the ancient economy has not been sufficiently integrated into analysis of political development. Some recent scholarly contributions have begun to break with these approaches, but there is scope for a new examination of Athenian power.
This thesis differs from previous contributions in three key ways: through engagement with a comparative framework; through new analysis of Athenian sources, inscribed documents and Old Comedy in particular; and through comparison of Athenian power in the context of regional dynamics. After demonstrating in the first half of the thesis that Athenian power, particularly its fiscal aspect, was flexible and negotiated - but that this negotiation was increasingly controlled in the final decades of the fifth century - I consider in the second half how local conditions determined the operation of Athenian power in three contested and peripheral Aegean regions, resulting in similar but opportunistically differentiated strategies.

Keywords: Greek history
Athens
Epigraphy
Empire
Advisor: Thonemann, P
Kallet, L
Exhibiting archaeology: constructing knowledge of Egypt at temporary exhibitions in London, 1884-1939

Between 1884 and 1939 the Egypt Exploration Fund (later Society) and the British School of Archaeology in Egypt held a series of annual exhibitions in London to showcase the finds of each archaeological season. Displaying artefacts excavated just weeks before, alongside new archaeological interpretations and interpretive devices, and in varying locations across the capital, these temporary exhibitions functioned as network hubs for the circulation of disciplinary objects and knowledge. Established at a time when archaeology was emerging as a new, professional scientific discipline and the British occupation of Egypt was altering political dynamics, the practice reflected a period of considerable change in the display and reception of ancient Egyptian collections. The aim of this thesis is to centre the exhibitions in the theoretical framework of archaeological representation, addressing how the practice contributed to the construction and communication of knowledge about ancient and contemporary Egypt in the imperial metropole. The following discussion will argue that the annual exhibitions utilised their temporary, transient, and transitional nature to experiment with new ways of displaying Egypt and of shaping the visual culture and material products of Egyptian archaeology.

Keywords: Egypt Exploration Fund
Egypt
Archaeological representation
Egypt Exploration Society
History of Archaeology
Temporary exhibition
Ancient Egypt
Annual exhibition
Museum
Reception
Exhibition
British School of Archaeology in Egypt
History of Egyptology
Advisor: Stevenson, A
Baines, J
Machine learning for the detection of clinical deterioration on hospital wards

Assessment of physiological instability preceding adverse events on hospital wards has been previously investigated through clinical early warning score (EWS) systems. Such systems often rely on routinely collected vital-sign data, such as the National Early Warning Score system that is currently deployed across the United Kingdom. In this thesis, we propose improved and generalisable risk assessment algorithms, that can continuously alert for deterioration preceding the composite outcome of unplanned intensive care unit admission, cardiac arrest, and mortality. We develop and validate three statistical and machine learning models using large-scale datasets from two independent centres: Oxford University Hospitals and Portsmouth NHS Hospitals within the HAVEN database. The retrieved datasets include patient demographics, vital signs, laboratory tests, and data of the occurrence of any adverse events. The first model is the Age- and Sex- specific Early Warning Score (ASEWS), which was derived from statistical distributions of vital signs. The work suggests that accounting for age-related vital-sign changes can more accurately detect deterioration in younger patients (16-45 years old). We also propose the Deep Early Warning Score (DEWS), which consists of an end-to-end attention-based deep learning architecture that processes vital-sign time-series data. The vital-sign data is initially modelled using Gaussian Process Regression. The results suggest that deep learning improves the detection of clinical outcomes by recognising complex patterns in the data. The final model is the information Fusion in a multi-modal Early Warning System (iFEWS), which incorporates additional information about the patient, such as results of laboratory tests or the first diagnosis assigned at admission. In this framework, representation learning and continued learning within a multi-modal system improved the performance of detecting deterioration. All of our proposed models achieved a better performance than the state-of-the-art clinical EWS systems across two independent testing sets. Given their high performance, clinical utility, and illustrated interpretability, our models can be easily deployed in clinical settings to supplement existing EWS systems since they use the same data streams.

Keywords: early warning scores
data science
electronic health records
deep learning
predictive analytics
machine learning
Advisor: Clifton, DA
Zhu, T
“Follow the noise so far as we have quarter”: sound and the early modern stage

This thesis seeks to examine the use of sound on (and often, off-) the early modern stage. While its initial – and primary – focus is sound effects, it also explores the definition of sound itself, according to early modern understandings of the acoustic world to be found in medical manuals, sermons, and academic drama. It develops previous work on sound, such as that by Bruce Smith, Wes Folkerth, and Gina Bloom, while putting pressure on the methodologies used to understand so intangible an effect. Moreover, while existing critical studies favour Shakespeare, this thesis also hears the sounds of non-canonical plays.
Chapter One explores sound effects as “soundbites” (sonic memes) and shows that sound effects can act as an allusion or create nostalgia for older plays. Chapter Two examines Jacobean drama in the light of Schaeffer’s term, ‘acousmatic’ (as used and reconsidered by Brian Kane). It shows that Jacobean playwrights concealed the sources of sound effects in order to create a frightening and uncanny atmosphere on stage. Chapter Three explores the plays of Ben Jonson and their representation of sound and the body, moving between speech and noise, lungs and instruments. It concludes that Jonson’s attempts to define and control sound while making use of sound effects are contradictory. Chapter Four suggests that Shakespeare’s use of sound was often verbal, as “phonographic” (or narrated) sound. It offers readings of “ekphrastic” speeches which describe and conjure sound that is not performed.
This thesis concludes that not only are sound effects an integral unit of early modern play texts, but that attention to their use can offer fresh readings and new understandings of such plays. Blending theatre history and sensory studies, this thesis recaptures the sound of early modern drama and hears the early modern stage amidst its considerable noise.

Keywords: sensory studies
Jonson
acoustic
soundbite
noise
listening
early modern drama
Shakespeare
Sound effects
Advisor: Smith, EJ
Pastoral support for UK higher education students in the context of Covid19 – A case study

This study explores the provision of pastoral support for students in the context of a lockdown, due to Covid19. As institutions have been focusing their efforts on redirecting teaching provision and assessments to online fora, there is a risk that adapting personal tutoring and pastoral support is comparatively less systematic. The mental health and wellbeing of students and staff have been prevalent issues in Higher Education. For students, pastoral support from their tutors, and other members of staff, can make a massive difference to their wellbeing and academic success. In the current context of Covid19, the crisis of student mental health and wellbeing has worsened.
This exploratory study examines the views and experiences of 17 students, 6 academic staff and 4 professional services staff regarding the provision of pastoral support at Manchester Metropolitan University, at this time. The study aims to do the following:
• explore the nature of pastoral support offered to students in the context of a lockdown;
• identify issues and challenges experienced by staff providing the support and students experiencing it;
• offer potential solutions.
The study incorporated the most appropriate qualitative data collection method at this time, online interviews, to gather the most in-depth experiences, to inform the study. The findings revealed that the demand on pastoral support services had increased, students had experienced a diverse range of issues and concerns, many of which were worsened by the pandemic. The effective use of technology and the proactive role played by staff was key in making pastoral support accessible for students.
The data analysis adopted the Miles and Huberman framework (Miles, Huberman, & Saldaña, 2013). From the analysis, the research identifies the following inter-linked categories being important factors in student satisfaction and wellbeing in the current climate. These are: academic and social integration, a sense of community, flexible and informal mechanisms of support, support regarding academic progress and employability prospects. The research also emphasized the importance of effective referrals, appropriate advice, goal-setting, feedback, motivation and closing the loop. The study considered students’ experiences prior to lockdown and analysed their experiences thereafter, highlighting best practice regarding effective pastoral support. The research considers students’ concerns for the future and makes many useful suggestions for enhancing pastoral support systems in the context of this new reality.

Keywords: students views
students' voice
Covid19
Personal tutoring
pastoral support
lockdown experiences
online learning
uk higher education
student support services
Advisor: Robson, J
Rule-based stream reasoning

In recent years, there has been an increasing interest in extending stream processing engines with rule-based temporal reasoning capabilities. To ensure correctness, such systems must be able to output results over the partial data received so far as if the entire (infinite) stream had been available; furthermore, these results must be streamed out as soon as the relevant data is received, thus incurring the minimum possible latency; finally, due to memory limitations, systems can only keep a limited history of previous facts in memory to perform further computations. These requirements pose significant theoretical and practical challenges since temporal rules can derive new information and propagate it both towards past and future time points; as a result, streamed answers can depend on data that has not yet been received, as well as on data that arrived far in the past. Towards developing a solid foundation for practical rule-based stream reasoning, we propose and study in this thesis a suite of decision problems that can be exploited by stream reasoning algorithms to tackle the aforementioned challenges, and provide tight complexity bounds for a core temporal extension of Datalog. All of the problems we consider can be solved at design time (under reasonable assumptions), prior to the processing of any data. Solving these problems enables the use of reasoning algorithms that process the input streams incrementally using a sliding window, while at the same time supporting an expressive rule-based knowledge representation language and minimising both latency and memory consumption.

Keywords: query answering
stream processing
datalog
stream reasoning
temporal logic
automated reasoning
query evaluation
knowledge representation
sliding window
computational complexity
temporal datalog
data stream
Advisor: Kaminski, M
Cuenca Grau, B