VictorJuiz/thesis huggingface dataset:
Machine learning for the detection of clinical deterioration on hospital wards
Keywords: early warning scores
data science
electronic health records
deep learning
predictive analytics
machine learning

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.
“Follow the noise so far as we have quarter”: sound and the early modern stage
Keywords: sensory studies
Jonson
acoustic
soundbite
noise
listening
early modern drama
Shakespeare
Sound effects

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.
Pastoral support for UK higher education students in the context of Covid19 – A case study
Keywords: students views
students' voice
Covid19
Personal tutoring
pastoral support
lockdown experiences
online learning
uk higher education
student support services

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.
Rule-based stream reasoning
Keywords: query answering
stream processing
datalog
stream reasoning
temporal logic
automated reasoning
query evaluation
knowledge representation
sliding window
computational complexity
temporal datalog
data stream

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.
Enhancement of temperature diagnostics with application to dynamically compressed materials
Keywords: dynamic emissivity
shock
temperature
pyrometry
plate impact
lead
tin

The behaviour of materials at high pressure is relevant for a number of fields, including defence, aerospace and Earth and planetary science where understanding of material behaviour under high strain-rate conditions such as impacts is required. State variables such as pressure and density are readily accessible in shock experiments but determination of temperature remains challenging.
Temperature affects material behaviour substantially, thus the determination of temperature in materials at high pressure (giga-Pascal range) enables progress in the fields noted above. This thesis outlines improvements to the technique of pyrometry which is a widely used diagnostic for determining temperature in shock experiments. Despite the popularity of pyrometry, concerns remain regarding the significance of different uncertainties and equivalence of independently-developed systems.
The primary goal of this research has been to improve the technique of pyrometry; this has been accomplished in a number of areas. First, an extensive review of potential components and their impact on pyrometer operation has been completed which more clearly defines the sources of uncertainty in pyrometry systems. Second, collaborative experiments have allayed concerns about the validity of comparisons of measurements from differing pyrometry systems. Finally, an integrated reflectivity diagnostic has been developed and demonstrated which enables simultaneous measurement of radiance and reflectivity, removing reliance on assumptions to determine temperature.
In addition to diagnostic development, equation of state (EoS) measurements on tin and lead have been made. Measurements of shock speed, particle velocity and radiance (converted to temperature) have been made during plate impact experiments. Results obtained from tin have validated existing EoS models however small but significant differences were identified. The measurements of lead temperature have been inconsistent, the results could indicate a phase transition.
In summary, the work presented here provides a clear framework for understanding uncertainties in pyrometry and has demonstrated multiple practical improvements to the technique.
Agency and confidence: on the function of metacognition in action
Keywords: Confidence
Sense of agency
Decision making
Metacognition
Associative learning

Throughout the history of psychology, a lively debate has surrounded people’s ability—known as metacognition—to represent, reflect upon, and control their own thoughts. This debate has taken many forms, from questioning whether it is even possible to be both subject and object of observation in the first place, to discussing whether, if so, subjective experience is worth studying experimentally. The cognitive revolution and the associated resurgence in focus on the workings of the so-called black box has brought with it an increased interest in metacognition, its origins and its functions. The research in the present thesis follows in those footsteps and consists of an investigation into the role that metacognition serves during action, analysing two related types of judgments: the feeling of controlling one’s actions and their outcomes, known as sense of agency, and decision confidence.
The first half of my research evaluates whether sense of agency impacts performance monitoring and learning. Two experiments failed to identify a role for perceived control in modulating the extent to which people monitor the accuracy of their decisions. However, a second series of experiments found some evidence that being able to choose which action to perform might improve memory, so that both the outcomes and the actions that generated those outcomes are remembered better when choosing to act than when following an instruction.
In the second half of the thesis, I report studies using a combination of behavioural, electrophysiological, and computational methods to determine how confidence in the accuracy of one’s actions affects the way feedback is treated during learning. I present data indicating a role for confidence in modulating learning by regulating resource allocation to obtaining and processing feedback. This characteristic of confidence is reflected both in a negative relationship between prior confidence and the amplitude of neural signals associated with attention to feedback, and between confidence and deciding when to invest resources into obtaining further information about the accuracy of one’s actions. Overall, my results suggest that metacognition is not just an epiphenomenon accompanying our actions; rather, it shapes how we make decisions and learn about our environment.
Structure-based inhibitor design for substrate reduction therapy towards primary hyperoxaluria and galactosaemia
Keywords: fragment screening
protein crystallography
structural biology
primary hyperoxaluria
classic galactosaemia

Inborn errors of metabolism are a group of more than 1000 inherited single gene disorders for which few effective treatments are available. In almost all of these disorders, mutations cause a loss of function in the encoded protein that is essential to normal metabolism, resulting in accumulation of metabolites upstream of the variant and/or deficiency of downstream metabolites. Where the disease pathogenesis results from toxicity of accumulated metabolites, inhibition of proteins preceding the metabolic block has been shown to be an effective therapeutic strategy. For example, proof-of-concept, genetic knockdown studies support the inhibition of galactokinase 1 (hGALK1), which precedes the defective variant in galactose metabolism, to treat classic galactosaemia; and inhibition of hydroxyacid oxidase 1 (hHAO1), which precedes the defect in glycolate metabolism, to treat primary hyperoxaluria. However, existing inhibitors for these two targets have limited scaffold diversity and their poor pharmacokinetic and toxicity profiles preclude therapeutic use. In this work, fragment screening by X-ray crystallography was combined with solution binding and activity assays to generate novel chemical starting points for the development of hGALK1 and hHAO1 inhibitors. Two fragments weakly inhibited hGALK1 upon binding to novel allosteric pockets away from the active site. Merging of fragments in one such pocket yielded two inhibitor hits of good potency and efficacy with potential for future drug development. For hHAO1, analogues of fragments binding to the active site, a nearby novel pocket and at the subunit-subunit interface yielded a total of 9 high efficacy inhibitors, spanning all three sites and diverse scaffolds. Altogether, the compounds described in this work hold promise for addressing the unmet therapeutic need in classic galactosaemia and primary hyperoxaluria, and the methodology developed suggests a broader application to the field of inborn errors of metabolism.
Soldiering for Christ: the role of the Miles Christi in four Old English Saints’ lives
Keywords: Anglo-Latin literature
Old English Literature
Martin of Tours
Soldier of Christ
Anglo-Saxon England
Ælfric
saints lives
Saint Eustace
medieval Christianity
Andreas
Guthlac of Crowland
Vita Eustachii
Old English philology
militant Christianity
hagiography
miles Christ

This dissertation studies the diverse approaches to ‘soldiering for Christ’ in Anglo-Saxon hagiographical narratives of warrior-saints. The investigation selects a group of four saints — Martin of Tours, Guthlac of Crowland, the Apostle Andrew, and Placidas–Eustace — as case studies of non-royal warrior-saints who are celebrated in anonymous Old English prose and poetic Lives that engaged diverse audiences. Medieval hagiographers associated each of these saints with literal as well as spiritual warfare and appear to have used the saint’s association with warrior culture to define Christianity’s relationship to a martial ethos. The Old English narratives concerning these four saints are analysed by comparing the vernacular texts to their sources and intertextual parallels while also placing the compositions, transmissions, and audiences of the Old English accounts in their historical contexts. In doing so, the analyses find that there was a range of perspectives surrounding Christian warrior culture which were produced and copied in tandem, from peaceful and nonviolent portrayals in the ninth-century Martinmas-homily and various Anglo-Saxon narratives on Guthlac, to the apparent advocacy of Christian violence for converting or subduing pagans reflected in the ninth-century poem Andreas, the tenth-century prose Life of Andrew, and the late tenth- or early eleventh-century Life of Eustace. Texts presenting conflicting attitudes towards Christian warrior culture are transmitted in similar contexts and time periods, sometimes within the same manuscript, suggesting that no cohesive ideology concerning milites Christi developed throughout the Anglo-Saxon period. Moreover, the works on Martin, Guthlac, Andrew, and Eustace illustrate that Old English depictions of spiritual warfare were heavily indebted to models inherited from Scripture and early Christian texts, indicating that Christian militancy was not the result of a ‘Germanisation’ of the faith. Rather this dissertation argues that Anglo-Saxon hagiographers were individually responding to their historical context, source material, and intended audiences to define what it meant to soldier for Christ.
Investigation of the cis-regulation of vaso-intestinal peptide receptor 2 in zebrafish epicardial development
Keywords: Transcription Factors
Heart Regeneration
Transcription Enhancers
Zebrafish transgenesis
Epicardial development
Epicardium
vaso-intestinal peptide receptor 2
Vipr2
Chromatin accessibility

The human heart is known to have limited regeneration capability, and myocardial infarction leads to irreparable cardiac damage and pathological remodelling. The epicardial cell layer has been identified as a viable resident tractable source of multipotent progenitors in the heart which may be harnessed for cardiac regeneration. During development, the epicardium is known to be an important source of cardiomyogenic paracrine factors as well as supportive cardiac progenitors and thereafter becoming quiescent in adulthood. Interestingly, embryonic epicardial genes are re-expressed following cardiac injury and have been shown to be an important part of the zebrafish cardiac regeneration process. However, little is known about the upstream elements which underlie both epicardial development and regeneration processes, which may be utilized to improve current treatment regimes. In this report, my primary focus is centred on elucidating the cis-regulatory and trans-regulatory elements acting on an epicardial gene locus of interest during development. Previously generated RNA sequencing results show that the G-protein coupled receptor, Vaso-intestinal peptide receptor 2 (vipr2) was expressed in epicardial cells at 5 days post fertilization (5dpf). Vipr2 is also differentially expressed during cardiac regeneration at 3 days post-injury (dpi) of cryoinjured zebrafish hearts. Here, I show with in situ techniques that vipr2 is expressed in both a rare subpopulation of epicardial cells as well as in most cardiomyocytes in the myocardium. Chromatin accessibility assays and in vivo validation revealed a functional enhancer within vipr2 intronic regions, enhancer 14, which was found to be active from the 21-somite stage and exhibiting heart-specific activity from 3dpf to 5dpf during development. Enhancer 14 was further shown to be active in vipr2-expressing epicardial cells, as well as the cardiomyocytes of the primordial layer of the heart. Through combined transcription factor 3 binding motif identification, site-directed mutagenesis and transient transgenesis, two transcription factors, myeloid ecotropic viral integration site 1 homolog (MEIS1) and helicase-like transcription factor (HLTF), were found to be critical for enhancer 14 activity. In the future, vipr2 and enhancer 14 knockout zebrafish lines could be generated to elucidate gene and enhancer function during epicardial and myocardial development and regeneration.
Obedient rebellion: nuclear-weapon-free zones and global nuclear order, 1967–2017
Keywords: Nuclear weapons
NWFZ
Nuclear-weapon-free zones
Nuclear politics

Nuclear-weapon-free zones (NWFZs) cover territories from Africa to Latin America, and from the South Pacific to Southeast Asia. Yet traditional and critical scholars alike under-value their importance to global nuclear order and International Relations theory. In a comparative case study of the African, Latin American, and South Pacific NWFZs, I draw on archival and oral historical evidence to analyse why these zones exist, and why they persist. All three zones were triggered, I assert, by external nuclear interventions into already-peaceful, postcolonial contexts. The zones exist and persist, I contend, by paradoxically symbolising both obedience to—and rebellion against— global nuclear order. To actors inside the zones, on one hand, they legitimise an institutionally unequal nuclear order; on the other, they echo a tradition of postcolonial anti-nuclear solidarity. To the nuclear-weapon states, NWFZs at once tokenise nuclear responsibility, and entrench nuclear hierarchy. Counterintuitively, these ambivalences consolidate these zones by accommodating multiple, conflicting domestic and international audiences simultaneously. NWFZs thus offer unique insight into the complex, contending forces that balance nuclear order.