VictorJuiz/thesis huggingface dataset:
Enhancement of temperature diagnostics with application to dynamically compressed materials

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.

Keywords: dynamic emissivity
shock
temperature
pyrometry
plate impact
lead
tin
Advisor: Eakins, D
Chapman, D
Agency and confidence: on the function of metacognition in action

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.

Keywords: Confidence
Sense of agency
Decision making
Metacognition
Associative learning
Advisor: Murphy, R
Yeung, N
Structure-based inhibitor design for substrate reduction therapy towards primary hyperoxaluria and 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.

Keywords: fragment screening
protein crystallography
structural biology
primary hyperoxaluria
classic galactosaemia
Advisor: Brennan, P
Yue, W
Soldiering for Christ: the role of the Miles Christi in four Old English Saints’ lives

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.

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
Advisor: Orchard, A
Investigation of the cis-regulation of vaso-intestinal peptide receptor 2 in zebrafish epicardial development

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.

Keywords: Transcription Factors
Heart Regeneration
Transcription Enhancers
Zebrafish transgenesis
Epicardial development
Epicardium
vaso-intestinal peptide receptor 2
Vipr2
Chromatin accessibility
Advisor: Riley, P
Obedient rebellion: nuclear-weapon-free zones and global nuclear order, 1967–2017

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.

Keywords: Nuclear weapons
NWFZ
Nuclear-weapon-free zones
Nuclear politics
Advisor: Nicolaidis, K
Manners cost nothing?  Civility on Twitter and political engagement, trust, and affective polarisation in Britain

The precise mechanisms through which social media affects democratic political discourse are academically underexplored, but pertinent given evidence that the online information environment is characterised by increasing polarisation, factual relativity, incivility, and disengagement. This thesis contributes to scholarly understanding of the implications of social media as a forum for public debate in advanced democracies, and tests the mediating role of issue salience on these effects. To do this, it employs two identically-structured experiments on issues of contrasting current salience in Britain (Brexit and poverty) using Twitter, a prominent social media platform for public debate. The experiments seek to measure the attitudinal effects of exposure to civil and uncivil debate on Twitter for political engagement and trust, focussing on the contrasting reactions of partisans and passive observers. Results indicate that civility in online political debate can significantly improve levels of trust and engagement, particularly for those with low political interest who are unsure of their political orientation. Interestingly, these findings are most consistent in the poverty-related condition and corresponding negative impacts of incivility are not as prominent in either experiment. Concerningly, this implies that incivility is becoming normalised on Twitter and that polarised issue contexts inhibit the ameliorating value of civility. Implications of these findings are discussed with reference to existing literature, and the thesis concludes that attempts to diffuse polarised topics offline while cultivating norms of civility online could help to recast social media as platforms for the inclusion of currently disengaged voices and a force for democratic stability.

Keywords: Misinformation
Polarisation
Online incivility
Democratic stability
Social media
Advisor: Kosmidis, S
Territory and state formation in the Archaic Peloponnese

During the Archaic period (C800-500), a key foundational era of Greek history, several paradigm shifts within society resulted in the ‘Rise of the Polis’, the development of this key institution of Greek life and culture. The last thirty years have seen dramatic changes in our understanding of the emergence of complex societies, new and more critical approaches to textual sources, and a broadening of archaeological research in Greece, particularly in the countryside, alongside the ever-increasing body of excavated material from early poleis. However, the nature and origins of the polis remains one of the most discussed and debated issues in the study of ancient Greece. This on-going lack of consensus stems partly from the under-utilisation of many of these advances. My research presented here aims to remedy this by focussing on data gathered from numerous surface survey projects and combining it with text and excavated material, in the context of new critical approaches to the past. Through synthesising and analysing this survey material, a resource currently under-used and largely overlooked in the study of Archaic Greece, this study casts new light on the vital changes in the chora, the territory of the polis; on the border areas between poleis, and on broad trends in social change and social organisation in the Archaic period. My research shows that the closer incorporation of survey material into the study and understanding of Archaic history is not only possible, it is vitally important for advancing the relationship between text, material culture and historical archaeology, thus opening up broad, innovative and exciting possibilities for future research.

Keywords: Greek archaeology
surface survey
Archaic Greece
Polis and Chora
The Polis
interdisciplinarity
state formation
Advisor: Lemos, I
Widening participation post-16: who participates? A case study of the Aim for Oxford programme

Widening participation programmes at highly selective universities select their participants according to a variety of individual, area-level, and school-based indicators. Academic selection criteria also play a key role in selection at high tariff institutions, especially in post- 16 widening participation work. When contextual indicators are used ineffectively, there is a significant chance that only the most advantaged of ‘disadvantaged’ young people will have the opportunity to participate in widening participation schemes. The purpose of this study is to understand the life experiences associated with commonly used contextual indicators and explore what young people who have applied to the Aim for Oxford widening participation programme believe to have advantaged and disadvantaged them in their education. Twenty-seven young people completed a questionnaire delving into more detail about their contextual background and ten participated in semi-structured interviews to consider how they believe highly selective universities should select students onto their widening participation programmes. The study found that young people valued being selected onto widening participation programmes for their own merits as opposed to their adverse circumstances, feeling patronised by the idea of selection to meet “quotas.” Yet, the young people also recognised the role that their contextual background has played in their ambitions towards and expectations of accessing higher education. Synthesising the young people’s views, this study concludes with five recommendations for widening participation practice when selecting students, including: the use of multiple contextual indicators; prioritisation of students who might have ‘isolated knowledge’ through concurrent familial and school-based circumstances; avoidance of area-based metrics; more explicit consideration of individual circumstances not captured by indicators; and consideration of academic attainment in the context of the young person’s school.

Keywords: IMD
Widening participation
Free School Meals
HE access
Russell Group
Local Authority Care
POLAR
first-generation student
educational disadvantage
outreach
IDACI
Oxbridge
Advisor: Elliott, V
Malware detection in security operation centres

Malware has evolved from viruses attacking single victims to more sophisticated malware with disruptive purposes. For example, WannaCry ransomware attacks led to hundreds of disruption to NHS care in 2017. Although organizations might have invested in security technologies, their susceptibility to WannaCry hints that the problem goes beyond technology. Security Operations Centres (SOCs) are the first-line of defence in an organisation, providing 24/7 monitoring, detection, and response to security attacks. This thesis aims to explore the challenges in malware detection in Security Operation Centres (SOCs) providing recommendations for possible technological solutions.
We first start by investigating the workflow SOC practitioners follow. Through semi-structured interviews, we recognise the analysts' role in the SOC and their interactions with the technological solutions for malware monitoring, detection, investigation and response. Our results highlight the overwhelming reliance on analysts throughout the SOC operations, which might benefit from automation. We elicit the analysts analytical thinking when making decisions, identifying the influential factors that might impact their decision making.
Moreover, we investigate security practitioners' perspectives of the security monitoring tools deployed in SOCs and their perception of the high false-positive rates. By identifying the weaknesses and strengths in current SOC tools and challenges in deploying network-monitoring tools, we derive recommendations for future SOC tools development.
Understanding the type of malware is an essential step in determining the best response. Sometimes getting access to the infected host is not possible and analysts refer to the network traffic for analysis. Hence, we propose a system that classifies network flow sequences to a malware family. The proposed system is privacy-preserving and effective in classifying a binary to a malware family based on its network traffic, not requiring access to the malware binary itself.
Behavioural malware detection approaches are found to be the most reliable by analysts. We propose a behaviour-based malware detection system that improves over state-of-the-art by detecting new or unseen malware. The system uses behavioural high-level network features preserving the privacy of the monitored hosts. Using this system, malware's network activities are captured and modelled as a Markov Chain. Due to the modeling of general bot network behavior by the Markov Chains, the system can detect new malware that has not been seen before making it robust against malware evolution.
The novelty of this research is to provide a systematic study on SOCs processes, people, and technology; providing researchers with an understanding of the challenges and opportunities within; bridging that knowledge gap and thereby setting a better foundation for future research in the field.

Keywords: Detection
SOC
Malware
Network Security
Security Operation Centres
Advisor: Martinovic, I