VictorJuiz/thesis huggingface dataset:
Developing translational tools for measuring pain in neonates

Despite the high burden of pain experienced by hospitalised neonates, there are few analgesics with proven efficacy. In part, this is due to the lack of a gold standard to measure pain in neonates. Assessing a complex experience like pain is challenging and, in the absence of self-report, all indicators of pain are surrogate measures. Clinicians often rely on behavioural and autonomic physiological responses which can be subjective and have limited sensitivity and specificity to detect pain. The pain experience requires the nociceptive signal to be processed in the brain. From a very young age, infants have the basic neural functional connectivity for pain perception. Thus, brain activity may provide a quantitative and objective measure of nociceptive processing in the infant brain.
Noxious-evoked brain activity using electroencephalography (EEG) has been previously characterised following experimental noxious stimuli and heel lances. In this thesis, I assessed the generalisability of a brain-derived surrogate measure of pain across various body locations and stimulus modalities. The morphology and latency of the evoked potentials were characterised following clinically-required injections applied to the thigh, and the efficacy of paracetamol during routine immunisations was evaluated in a pilot study.
The magnitude of the brain activity response to the same stimulus intensity can be highly variable between infants. As a result, large sample sizes are often required in studies of analgesic efficacy to account for inter-individual variability. In the second study, I developed an EEG-based paradigm that can be used to determine the baseline sensitivity of individual infants to noxious stimuli and I demonstrated that this paradigm can help to reduce sample sizes in analgesic clinical trials in infants. The normal development of the nervous system is vulnerable to alterations by multiple factors, with the potential for long-term structural and functional detrimental outcomes. Immune function and sensitivity to pain are closely related, but the impact of early life inflammation on sensory nervous system development is poorly understood. In the final study, I used electrophysiological measures to investigate this relationship. I demonstrated in a cohort of term neonates that inflammation is associated with increased spinal cord excitability and hyperalgesia.
In summary, this thesis advances our understanding of the processing of nociceptive information in the infant brain and demonstrates how the use of brain-derived measures of pain can improve the evaluation of analgesic interventions.

Keywords: EEG
neonatal
clinical trials
neuroimaging
analgesic interventions
pain
Advisor: Slater, R
Bhatt, A
Adams, E
'Wisdom's the noblest ware that Travel brings': English clerics and experiences of travel within the Mughal and Ottoman Empires, 1616-1724

This thesis centres on a small group of clerics within the Church of England, all of whom travelled throughout either Mughal India or the Ottoman Empire during the seventeenth century. It examines their understandings and perceptions of the myriad religious traditions that populated those states, most notably Eastern Christianity and Islam. In so doing, this thesis explores the impact of travel to the Mughal and Ottoman empires, and of first-hand exposure to their religious diversity specifically, on how English travellers thought about religious theory, ceremony and practice within the Church of England. In short, it considers how experiences of travel within the East shaped English travellers’ views of the right and wrong ways of worshipping God, and how they sought to apply this knowledge in their service of the English Church.
Within this broader framework, this thesis makes several interlocking arguments. Firstly, that our travellers used their experiences overseas to reflect on the role of Church-led education and learning in the cultivation and consolidation of right worship. Secondly, that there exists a uniquely English, as opposed to Western, or European, experience of the Mughal and Ottoman empires in the early modern period, insofar as that experience was shaped by uniquely domestic frames of reference, regarding, say, the Church of England. And finally, that our travellers, as a result of their experiences abroad, frequently thought and wrote about religious issues in ways that distinguished them from their non-travelling contemporaries, and that paved the way for new, and even controversial, intellectual and practical approaches to the established Church. In making these arguments, this thesis seeks to open up new avenues for the study of early modern English travel, on the one hand, and of the early modern Church of England, on the other.

Keywords: Anglican-Orthodox Relations
travel
superstition
Church of England
Edward Terry
travelling clerics
Islam
Anglican
Greek Church
sign of the cross
early modern England
paganism
Ottoman Empire
Eastern Christianity
religious diversity
Mughal Empire
Sir George Wheler
John Covel
travel literature
travelogues
Sir Thomas Roe
religion
Advisor: Ghobrial, J
Mortimer, S
Bayesian online learning for online portfolio selection

We propose a novel family of Bayesian learning algorithms for online portfolio selection that overcome many of the shortcomings of traditional techniques, including selection bias (the failure to cover a broad universe of assets), data-snooping bias (the risk that a trading strategy's performance on past data is inflated due to hyperparameter overfitting) and a lack of robustness to transaction costs.
As the basis for this novel family, we develop a Bayesian treatment of the online passive-aggressive and gradient descent algorithms, some of the most popular algorithms in the literature. Our approach starts from a probabilistic interpretation of the underlying objective functions and enables uncertainty modelling, probabilistic predictions as well as automatic, data-dependent hyperparameter tuning.
We conclude by testing our proposals on real-world financial data. We further benchmark our framework on a wide range of canonical test problems, over which it achieves a significant improvement on its competitors. Beyond online portfolio selection, our algorithms contribute to the theory of adaptive gradient methods by equipping these with uncertainty estimates and a self-tuning mechanism for the learning rate parameter, which constitutes a major milestone in the area of Bayesian inference for neural networks.

Advisor: Roberts, S
Osborne, M
'With the vision they see': identity and aesthetic experience in Puerto Limón, Costa Rica

This thesis examines aesthetic experience as it relates to the formation of cultural identity in the urban environment of Puerto Limon, Costa Rica. Based on twelve months of fieldwork, the thesis presents an analysis of aesthetics as a cross-cultural process of value attachment which, like identity, is founded on the dialectical relationship between the discursive realm of conceptual meaning and the non-discursive realm of lived experience.
The first of two sections in the thesis shows how identity, as the dialectic between the ideal and the experiential, fits with the concept of a cultural aesthetic, where the discursive quality of art as a symbolic system is constantly negotiated by the non-discursiveness of aesthetic experience. The first section also introduces the city of Puerto Limon through a detailed history of its development, a presentation of the contemporary context, and an analysis of an emergent ideology of blackness.
The second section divides the aesthetic practices found in Limon into four principal forms: the built environment; canvas art and small crafts; music and performance; and literature. Chapter Four discusses the broad theme of the socialisation of space and place in both the national and local contexts. Chapter Five examines a community of canvas artists who participate in constructing an ideal notion of Limonense identity. Chapter Six focuses predominantly on street bands known as comparsas to demonstrate the power of embodied experience to transform idealised notions of identity. Chapter Seven examines the substantial body of literature to come out of the province of Limon, and the split between women as poets and men as novelists.
Finally, the thesis offers a narrative by way of conclusion to demonstrate the complexity of presenting an ethnography of aesthetics and encourage further research in this area.

Keywords: ethnicity
identity
Costa Rica
intellectual life
aesthetics
Puerto Limón
aesthetic experience
Cellular and molecular pharmacology of the lipid-sensitive channel TMEM16A/Anoctamin1

TMEM16A Ca2+-activated Cl- channels (CaCC) control vital functions including arterial smooth muscle tone and blood flow. The TMEM16A has a pore with regions surrounding plasmalemmal lipids, an arrangement where lipids can directly influence the ion permeation and gating of the channel. Here, it is hypothesised that TMEM16A channel may serve as a lipid sensor and couple changes in lipid metabolism to changes in cell electrical activity. It is also argued that TMEM16A channels may be indirectly modulated by the lysosome and in particular by the lysosomal lipid transporter Niemann-Pick type C 1 (NPC1) protein, given the key involvement of this organelle in the control of plasmalemmal lipid composition. Thus, it is suggested that changes in the plasmalemmal composition driven by lysosomes, can modulate the plasma membrane-residing TMEM16A channel, impacting vascular function. Indeed loss-of-function mutations in NPC1 leads to Niemann-Pick disease Type C (NPC), a neurodegenerative disorder with a range of systemic alterations, including vascular. Here, I explore the capacity of the NPC1 to control TMEM16A function, and examine the consequence of this modulation on the tone of isolated arteries, which abundantly express TMEM16A. Key results include: (i) TMEM16A currents were enhanced during NPC1 inhibition; (ii) depletion of plasmalemmal phosphatidylinositol 4,5-biphosphate (PIP2) prevented this activation; (iii) plasmalemmal PIP2 distribution was increased during NPC1 inhibition; (iv) aortic rings and cerebral capillaries obtained from Npc1 null mice showed enhanced contractility; (v) β-cyclodextrin, a drug currently studied for treating NPC disease, prevented TMEM16A activation and aortic contractility in samples obtained from Npc1 null mice. These results indicate that TMEM16A activity is modulated by NPC1. This regulation affects the tone of arteries. PIP2-dependent changes in TMEM16A activity may be the basis of vascular overactivity associated with NPC disease.

Advisor: Tammaro, P
Platt, F
The immune system and inflammation in cardiac dysautonomia during hypertension

Essential hypertension, along with a number of other cardiovascular diseases, is characterised by a state of hyperactivity of the sympathetic nervous system. This pathological phenomenon may contribute to the aetiology of hypertension itself, and causes end-organ damage. Elucidating the underlying cause of this dysautonomic phenotype could therefore provide a more effective means of therapeutic intervention to improve outcomes. Essential hypertension also features a state of low-grade systemic inflammation, which is hypothesised to drive peripheral sympathetic hyperactivity. This thesis examined this potential link in the Spontaneously Hypertensive Rat (SHR). The resident immune cells of the sympathetic ganglia, blood and kidneys of the SHR were first, examined using flow cytometry, and compared to those of the Wistar rat. The main finding was a systemic reduction in the classical-to-non classical monocyte-macrophage ratio. However, preliminary data suggest this is not replicated in blood samples taken from a small number of essential hypertension patients and matched controls, which may reflect low statistical power. Using qPCR analysis, no differences were found in the expression levels of a range of inflammatory or anti-inflammatory cytokines, macrophage polarisation markers or oxidative stress markers between SHR and Wistar stellate ganglia, except for a significantly higher expression of the chemokine ccl2 in the SHR. Blood monocytes and bone-marrow derived macrophages (BMDMs) also did not show any inter-strain differences with regard to cytokines or polarisation markers. SHR stellate neurons were shown to exhibit greater [Ca2+]i transients than those of Wistar rats in response to either nicotinic stimulation or high [K+]o-evoked depolarisation. When co-cultured with blood leukocytes, Wistar stellate neurons showed increased responsiveness to these stimuli, while SHR neurons did not. Interestingly, Wistar neuron [Ca2+]i transients were enhanced by the presence of BMDMs, those from the SHR only increased in responsiveness with their own, and not Wistar, BMDMs. This BMDM-induced enhancement of Wistar neuron [Ca2+]i transients were not affected by combined blockade of IL-1β, TNF-α, and IL-6, nor did IL-1β or TNF-α affect stellate neurons in mono-culture, suggesting these classical inflammatory cytokines are not involved in this effect. The results of this thesis suggest that SHR macrophages may play a role in driving stellate neuron hyperactivity in this model. Further elucidation of the role of this immune-neuronal axis may help uncover new pathophysiological nodes for effective therapeutic intervention in essential hypertension and other dysautonomic conditions.

Keywords: calcium imaging
sympathetic nervous system
hypertension
neuroimmunocardiology
Spontaneously Hypertensive Rat
immunopathology
stellate ganglia
cardiovascular disease
sympathetic neurons
macrophages
monocytes
co-culture
dysautonomia
flow cytometry
Advisor: Paterson, D
Domingos Jansen, A
Existing otherwise: from Jean-Paul Sartre and Maurice Merleau-Ponty to a critical phenomenology of bodily otherness

With their existential phenomenologies, Jean-Paul Sartre and Maurice Merleau-Ponty insisted upon a radical new conception of consciousness as embodied, in the world, and among other subjects. Their L’Être et le néant and the Phénoménologie de la perception have made perhaps the most lasting impression of any modern intellectual tradition on theories of the body and the social world, in philosophy as in the human sciences, in France as elsewhere. They have proven uniquely valuable for critical theorists of race, gender, sexuality, disability, and illness looking to give accounts of the lived experience of ‘bodily otherness’. In their will to rework French existential phenomenology to take stock of othering, violence, and oppression, accounts of this kind point at once to its shortcomings and its promise as a framework for making sense of such experiences. This thesis seeks to explore the depth of those shortcomings, in the first place, and the scope of that promise, in the second. Opening with a discussion of ‘bodily otherness’ and a comparative appraisal of Sartre and Merleau-Ponty’s theories of the body and autrui, it moves through to critique their engagements with othering and oppression, positing that those engagements are circumscribed by a normativity that operates at the most basic level of their thought to foreclose the realisation of the very ideals that they themselves place at the heart of phenomenology. The thesis thus contends that existential phenomenology might yet illuminate the lived experiences of ‘others’, should it remain alive to, and refuse complicity with, its own normative biases. It closes by taking up that mantle, reading Sartre and Merleau-Ponty with and against one another to propose some elements of a critical phenomenology of ‘bodily otherness’, and to stress the imperative of empathy as a philosophical and political practice.

Keywords: queer theory
otherness
feminism
critical race theory
jean-paul sartre
bodily otherness
crip theory
existentialism
phenomenology
critical phenomenology
maurice merleau-ponty
Advisor: Howells, C
Kemp, S
Fast adaptation via meta reinforcement learning

Reinforcement Learning (RL) is a way to train artificial agents to autonomously interact with the world. In practice however, RL still has limitations that prohibit the deployment of RL agents in many real world settings. This is because RL takes long, typically requires human oversight, and produces specialised agents that can behave unexpected in unfamiliar situations. This thesis is motivated by the goal of making RL agents more flexible, robust, and safe to deploy in the real world. We develop agents capable of Fast Adaptation, i.e., agents that can learn new tasks efficiently.
To this end, we use Meta Reinforcement Learning (Meta-RL), where we teach agents not only to act autonomously, but to learn autonomously. We propose four novel Meta-RL methods based on the intuition that adapting fast can be divided into "task inference" (understanding the task) and "task solving" (solving the task). We hypothesise that this split can simplify optimisation and thus improve performance, and is more amenable to downstream tasks. To implement this, we propose a context-based approach, where the agent conditions on a context that represents its current knowledge about the task. The agent can then use this to decide whether to learn more about the task, or try and solve it.
In Chapter 5, we use a deterministic context and establish that this can indeed improve performance and adequately captures the task. In the subsequent chapters, we then introduce Bayesian reasoning over the context, to enable decision-making under task uncertainty. By combining Meta-RL, context-based learning, and approximate variational inference, we develop methods to compute approximately Bayes-optimal agents for single-agent settings (Chapter 6) and multi-agent settings (Chapter 7). Finally, Chapter 8 addresses the challenge of meta-learning with sparse rewards, which is an important setting for many real-world applications. We observe that existing Meta-RL methods can fail entirely if rewards are sparse, and propose a way to overcome this by encouraging the agent to explore during meta-training. We conclude the thesis with a reflection on the work presented in the context of current developments, and a discussion of open questions.
In summary, the contributions in this thesis significantly advance the field of Fast Adaptation via Meta-RL. The agents develop in this thesis can adapt faster than any previous methods across a variety of tasks, and we can compute approximately Bayes-optimal policies for much more complex task distributions than previously possible. We hope that this helps drive forward Meta-RL research and, in the long term, using RL to address important real world challenges.

Keywords: Bayes-adaptive
reinforcement learning
meta reinforcement learning
meta learning
Advisor: Whiteson, S
Hofmann, K
The royalist army in the first civil war

The army under discussion is that which was directly under Charles I's command, and was based at Oxford during the war, not the forces stationed permanently in the North or West. This army, the chief strength of the Royalists, was raised in the Midlands in the summer of 1642, by loyal nobility and gentry, who recruited volunteer regiments in the counties where their "interest" was greatest. Attempts to use the existing militia system were largely unsuccessful at this stage of rhe war. The prospect before the King at first seemed unhopeful, but improved as arms from the continent, private financial contributions and Welsh recruits reached him; the army at Edgehill was strong in infantry and was well-paid, but was short of personal weapons.
The Council of War became the chief executive and administrative committee for the organisation of the army. The King presided at its meetings, which dealt with a wide range of topics. The papers of the secretary-at-war, Edward Walker, help us to see it at work. Civilian and military elements were combined in the Council, and its mixed character allowed it to act successfully as a mediator in disputes between army units and the civilian population. Subcommittees of the Council were charged with specialist tasks.
Other committees were set up at Oxford. The defence of the city, in the absence of the King and the field army during the summer campaigns, was in the hands of a body known as the “Lords Commissioners". In 1644 the King summoned a counter-Parliament to Oxford, and this assembly, and the committee of its members it left behind when it was not in session, played some part in decision-taking.
Continued in thesis ...

Keywords: Great Britain
Wales
army
England and Wales
royalist army
royalists
sixteenth century
17th century
civil war
military history
Egyptian queens in the 18th dynasty up to the end of the reign of Amenhotpe III

Much of the available material for this thesis is monumental and mostly concerned with the official view of "queenship", rather than the individual queen. Documents which might tell us something about the lives, characters and influence of these women are almost entirely lacking. It is possible that anomalies in the material which we have might supply some hints about the latter, but before any satisfactory examination can be made along these lines, we must first establish what the official position of the queen was; otherwise we cannot hope to pick out any unusual traits of a particular queen.
The first step in this study must be to identify the women we can consider as queens. The material shows that not only the king's chief wife (ḥmt nsw wrt) but also the king's mother (mwt nsw) are queens, while secondary wives (ḥmt nsw) are not. The titles "king's daughter" (s3t nsw) and "king's sister" (snt nsw) are not restricted to queens, but the first is only used by queens of royal birth, and the second by sisters of kings (section 1). This is helpful for establishing the genealogy of the 18th dynasty royal family, which is reconstructed in section 2 to provide a framework for the material.
In sections 3 and 4, I have made a systematic study of the iconography and titles of queens, to see if there is any distinction made in their use by queens, which might suggest a varying status among queens. For this purpose, I have divided the queens into three major types, and four minor ones each consisting of an individual queen in unique circumstances, on the basis of their use of the titles ḥmt nsw wrt and mwt nsw.
Continued in thesis ...

Keywords: 18th dynasty
antiquities
Egypt
women
queens
Amenhotpe III
Egyptian queens
Advisor: Baines, JR