VictorJuiz/thesis huggingface dataset:
Dynamics of the subpolar North Atlantic ocean circulation—the role of surface forcing and topography

The ocean is a fundamental component of the global climate system, acting as a colossal sink of heat and carbon dioxide. Its effectiveness as a sink is enhanced by the transport of these tracers into the deep ocean by the Atlantic Meridional Overturning Circulation (AMOC). Hence, due to its location near the northern terminus of the AMOC, the subpolar North Atlantic plays a crucial role within the global climate system. Unfortunately, this is a fiendishly difficult region to model. As such, a better understanding of the physical mechanisms setting the large-scale flow at these latitudes is required.
In this thesis, the roles played by wind stress, surface buoyancy forcing, and topography in determining the mean barotropic and overturning circulations in the subpolar North Atlantic Ocean are explored. An idealised model of the region is introduced, and the response of the mean circulation to different combinations of wind, buoyancy forcing and bathymetry is presented. The overturning circulations in both depth, and density, space are split into shear, Ekman, and external mode components.
A novel diagnostic is then derived allowing for the isolation of the force balances controlling the large-scale flow. This diagnostic is based on the previously proposed rotational momentum framework, whereby the rotational component of an applied force is extracted in the form of a set of force func- tions. An error in the original derivation of this framework is highlighted which limits its utility to domains without topography. A new derivation generalising the approach to apply to domains with arbitrary topography is presented, and the derived force functions are related to the barotropic and overturning circulations.
This diagnostic is then applied to the aforementioned experiments, allowing the dominant force balances in each to be identified. A key result emerging from this analysis is that the presence of sloping sidewalls drastically alters the dominant force balance in the mean barotropic circulation.

Keywords: streamfunction
North Atlantic
ocean modelling
barotropic
vorticity
large-scale ocean circulation
Advisor: Marshall, D
Johnson, H
The enantioselective total synthesis of Sealutomicin C

This thesis is divided into six chapters and concerns the successful total synthesis of the natural product sealutomicin C. Chapter 1 provides an overview of anthraquinone-fused enediyne natural products, the sealutomicin natural products, and other related cycloaromatised natural products. Chapter 1 also discusses prior work carried out in the Burton group by previous group member Dr Sean Guggiari towards the synthesis of the natural product unciaphenol, which bears structural similarities to sealutomicin C.
Chapter 2 details work undertaken to prepare lactone-fused chiral dihydroquinolines, using methodology developed by Dr Guggiari to construct the chiral dihydroquinoline scaffold. Chapter 3 discusses the use of these lactone-fused dihydroquinolines as substrates in a key organolithium mediated cyclisation to construct the core of enantiomeric sealutomicin C. Chapter 3 also discusses efforts to elaborate this core, resulting in the synthesis of tris-benzyl protected enantiomeric sealutomicin C.
Chapter 4 concerns the application of the chemistry developed in Chapters 2 and 3 to the synthesis of the correct enantiomer of sealutomicin C, culminating in a successful first-generation synthesis of the target natural product. Chapter 5 presents a shorter and more streamlined second-generation synthesis of sealutomicin C, improving on the work described in Chapters 2 – 4 by employing a more efficient protecting group strategy. Finally, Chapter 6 summarises our achievements and suggests potential strategies to apply the chemistry developed here to the synthesis of the structurally related natural products sealutomicins B and D.

Keywords: sealutomicin
natural product synthesis
total synthesis
Advisor: Burton, J
Big data in viral hepatitis

Chronic infection with hepatitis B virus is one of the leading global causes of chronicliver disease, specifically primary liver cancer. The population is not well characterisedin the United Kingdom, with evidence gaps including lack of characterisation of theinfected population, the burden of comorbid disease and risk factors for progressionto liver cancer. Antiviral treatment eligibility and coverage across the diseasepopulation is unclear, as are impacts of COVID-19 and health policy on viralsurveillance and vaccination. This thesis presents results from analyses undertakenacross multiple electronic health record databases in the United Kingdom to addressthese gaps.
Systematic literature review and meta-analysis were undertaken to appraise previousstudies describing epidemiology and investigating primary liver cancer risk factors.Subsequently the largest cohort of chronically infected individuals to date wascharacterised in the QResearch database. The chronic hepatitis B virus population inthe United Kingdom has been characterised as a young, ethnically diverse andsocioeconomically deprived population of individuals. Risk factors for primary livercancer included male sex, increasing age and comorbidities. A protective associationof statin use with risk of primary liver cancer was observed.
In the NIHR HIC database, antiviral treatment coverage across individuals with chronichepatitis B virus was quantified, reporting treatment initiation practices in line withclinical recommendations. The impact of COVID-19 on surveillance was quantified,reporting a decrease in surveillance as compared to the pre-COVID-19 era.Surveillance has not recovered to pre-COVID coverage. In the Clinical PracticeResearch Datalink database, it was demonstrated hepatitis B virus vaccinationcoverage has both increased since the compounds introduction as a universalcomponent in 2017 and has remained high despite the COVID-19 pandemic.
These results have clinical relevance to both care pathways and researchinvestigations. They may facilitate improvements in clinical management, resourceallocation and future investigations.

Keywords: electronic health records
Hepatitis B virus
epidemiology
real world data
Advisor: Philippa , M
Eleanor, B
Iain, G
Translational profiling of motor neurons with C9orf72 mutations under acute oxidative stress


Amyotrophic lateral sclerosis (ALS) is the most common adult-onset motor neuron disease (MND) with a median survival of 30 months from disease onset and no cure available. Mutations in the gene C9orf72-SMCR8 complex subunit (C9orf72) are the most common cause of ALS in populations of European genetic heritage. Previous studies suggest that RNA processing, global translation and stress granule (SG) dynamics are dysregulated in C9orf72-ALS, which might alter the profile of translating mRNAs (translatome) in motor neurons. To test this hypothesis, I employed translating ribosome affinity purification (TRAP) to obtain the parallel transcriptome and translatome of human induced pluripotent stem cell-derived motor neurons (iPSC-MNs) from patients with C9orf72 mutations and healthy controls. I examined their expression profiles both at baseline and after transient oxidative stress. While minimal differences were present in the transcriptome and translatome at baseline and immediately after stress, 68 differentially expressed genes (DEGs) were identified in the translatome 2 h after stress removal. Functional over-representation analysis showed that they were enriched in synaptic transmission, small GTPase-mediated signalling transduction, and neuron projection. Two of the downregulated DEGs, unc-13 homolog A (UNC13A) and purine rich element binding protein A (PURA), have been previously associated with ALS. Further characterisation of the acute stress response in iPSC-MNs revealed that transient oxidative stress exacerbated or induced some key molecular phenotypes related to C9orf72-ALS. Additionally, the mutant iPSC-MNs exhibited a gradual and persistent decrease in the signal of a cell viability assay, in contrast to the control group. No differences were found between the two groups in global translational activity or SG dynamics. Preliminary investigation into the subcellular distribution of UNC13A and PURA transcripts suggested potential dysregulation in nucleocytoplasmic redistribution and sequestration by SGs in C9orf72-ALS iPSC-MNs, although further experimentation is needed to reach a definitive conclusion.

Keywords: amyotrophic lateral sclerosis
stem cell model
cellular stress
C9orf72
translating ribosome affinity purification (trap)
motor neuron disease
translatome
Advisor: Scaber, J
Talbot, K
Tofaris, G
Everyday betrayal, relentless hope: political life in a Lebanese city 

This work is an exploration of the limits of resistance within oppressive contexts. It is based on an ethnography of the Lebanese city of Tripoli, which is associated with Islamism, soaring poverty rates, and an extractive clientelist political system that has remained unchanged for decades. Tripolitans who are actively resisting oppression use repertoires of action that inadvertently entrench the oppressive status quo. The first is that Tripolitans cultivate intimacy and conviviality with the ruling class, which the latter then use to exploit the former in the name of friendliness and familiarity. The second is the hustler mentality of Tripolitans, which promotes a dream of quick, easy transformation, but in reality contributes to overwhelming exhaustion and further reliance on clientelist networks. The third is the constant possibility that Tripolitans will engage in violence against structures of oppression, which in the end is contained and resolved by these structures themselves.
The thesis explores Tripolitan aspirations and their aftereffects during three key political ruptures in Tripoli’s recent past: a sectarian civil conflict (2008-2014), a Salafi-jihadist wave of radicalisation (2013-2015), and a secular uprising (2019), during which Tripolitans took radical action to change their political conditions but were unable to realise a political transformation. I view this outcome as nourishment of an ever-present, well recognised, and domesticated state of deadlock that, at the same time, Tripolitans continue to vehemently oppose. In discussion with literature on hope and resistance, I argue that resistance and complicity with oppressive political states are not contradictory processes, but are rather nestled closely together. This situation creates an anxious sense of stagnation where subjects constantly navigate the tension between hope and acquiescence. The thesis focuses on what is lost and gained by living in such anxious and unforgiving state of being.

Keywords: uprising
clientelism
political anthropology
Tripoli
Islamism
Lebanon
Advisor: Clarke, M
Powerline communication and demand side management for microgrids

Motivation: The greatest challenge for microgrid deployment is making energy affordable, especially in remote low-income communities. This thesis answers the following research question:

Can digital communication reduce the price of electricity for an islanded low voltage microgrid and if so, can broadband powerline communications meet microgrid control requirements?

Approach: This study conducts a cost-benefit analysis of the addition of a field area network to a microgrid. Broadband powerline communication is selected as a candidate technology and tested on various microgrid networks to determine its suitability.
Results: The main contributions of this study are:

A demand-side management strategy and unsubsidised cost reflective tariff structure for rural microgrids in the developing world.

A cost-benefit analysis that shows the addition of a low bit rate, medium latency communication system (1 kbps per customer, 100 ms) may reduce the levelized cost of energy by 32%.

A performance evaluation of broadband HomePlug powerline communications for microgrids which shows the Homeplug AV2 has a range of 600 m and functions well on complex radial distribution networks.

Conclusion: Investment in a minimally capable communication system has significant economic benefit to both customer and utility by enabling smart grid services such as automatic meter reading and demand side management. Since communication technologies share similar bit rate and latency capabilities and are similarly priced, the technology choice is driven more by microgrid geography, complexity, availability and reliability. Powerline communications require no additional cable, but boast reliability similar to dedicated cable solutions. The HomePlug AV meets bit rate and latency requirements, is affordable, reliable, simple and widely available around the world. This study concludes it is a solid candidate for low voltage islanded microgrids.

The material presented in this thesis has been published or submitted for publication in an abbreviated format in the following publications:
D. Neal et al, "Demand side energy management and customer behavioral response in a rural islanded microgrid," in IEEE PES/IAS PowerAfrica, 2020.
D. Neal, D. Rogers and M. McCulloch, "A Techno-Economic Analysis of Communication in Islanded Microgrids," unpublished. Submitted Oct 2023 to Elsevier Renewable and Sustainable Energy Reviews.
D. Neal, D. Rogers and M. McCulloch, "Broadband Powerline Communication for Low-Voltage Microgrids," unpublished. Submitted Oct 2023 to IEEE Transactions on Power Delivery.

Keywords: demand-side management
microgrid
smart grid
powerline communications
Advisor: Rogers, D
Proud humility: paradoxes of self-representation in Huguenot memoir

This thesis makes a contribution to early modern trauma theory and life-writing studies. I use memoirs written by French Protestants after the 1685 Revocation of the Edict of Nantes to explore the emotional impact of migration in the late seventeenth and early eighteenth centuries. In the past, some Huguenot historians have taken such ‘ego-documents’ as entirely veridical and factual accounts, whereas I engage with the metaphors and intertextual references employed by the writers. The present work can thus be situated within the growing field of Huguenot memoir scholarship. The central argument of this thesis is that memoir-writing offered refugees a space in which they could explore challenging moments in their pasts. In order to address the variety of post-Revocation experiences encountered by early modern Huguenots, each chapter of this thesis deals with a distinct ‘case study’ of sorts. I first look at writing by women who were imprisoned following initial unsuccessful attempts to escape France. I then focus on how galley slavery was depicted by Protestants who had close contact with its horrors. Finally, I explore memoirs whose contents concentrate on the difficulties of adapting to new cultures. Each of the authors whose works are examined in this thesis had their own personal concerns, but across the range of writings, some common strategies emerge for dealing with common issues. I engage with archival material and contemporary publications from the Grand Siècle to develop as full as possible an understanding of the authors’ worldviews, arguing that religious doctrine could be a source of both solace and stress. Throughout, I highlight what life-writing can reveal about inner, emotional worlds. I thus establish narrative as an important tool for Huguenots dealing with trauma in the early modern period.

Keywords: Louis XIV
early modern
life-writing
Huguenots
Advisor: Seth, C
Exploring probabilistic models for semi-supervised learning

Deep neural networks are increasingly harnessed for computer vision tasks, thanks to their robust performance. However, their training demands large-scale labeled datasets, which are labor-intensive to prepare. Semi-supervised learning (SSL) offers a solution by learning from a mix of labeled and unlabeled data.
While most state-of-the-art SSL methods follow a deterministic approach, the exploration of their probabilistic counterparts remains limited. This research area is important because probabilistic models can provide uncertainty estimates critical for real-world applications. For instance, SSL-trained models may fall short of those trained with supervised learning due to potential pseudo-label errors in unlabeled data, and these models are more likely to make wrong predictions in practice. Especially in critical sectors like medical image analysis and autonomous driving, decision-makers must understand the model’s limitations and when incorrect predictions may occur, insights often provided by uncertainty estimates. Furthermore, uncertainty can also serve as a criterion for filtering out unreliable pseudo-labels when unlabeled samples are used for training, potentially improving deep model performance.
This thesis furthers the exploration of probabilistic models for SSL. Drawing on the widely-used Bayesian approximation tool, Monte Carlo (MC) dropout, I propose a new probabilistic framework, the Generative Bayesian Deep Learning (GBDL) architecture, for semi-supervised medical image segmentation. This approach not only mitigates potential overfitting found in previous methods but also achieves superior results across four evaluation metrics. Unlike its empirically designed predecessors, GBDL is underpinned by a full Bayesian formulation, providing a theoretical probabilistic foundation.
Acknowledging MC dropout’s limitations, I introduce NP-Match, a novel proba- bilistic approach for large-scale semi-supervised image classification. We evaluated NP-Match’s generalization capabilities through extensive experiments in different challenging settings such as standard, imbalanced, and multi-label semi-supervised image classification. According to the experimental results, NP-Match not only competes favorably with previous state-of-the-art methods but also estimates uncertainty more rapidly than MC-dropout-based models, thus enhancing both training and testing efficiency.
Lastly, I propose NP-SemiSeg, a new probabilistic model for semi-supervised se- mantic segmentation. This flexible model can be integrated with various existing segmentation frameworks to make predictions and estimate uncertainty. Experiments indicate that NP-SemiSeg surpasses MC dropout in accuracy, uncertainty quantification, and speed.

Advisor: Lukasiewicz, T
A diagrammatic approach to networks of spans and relations

In this thesis we exhibit nondeterministic semantics for various classes of circuits. Motivated initially by quantum circuits, we also give nondeterministic semantics for circuits for classical mechanical systems and Boolean algebra. More formally, we interpret these classes of circuits in terms of categories of spans or relations: in less categorical terms these are equivalent to matrices over the natural numbers or the Boolean semiring. In the relational picture, we characterize circuits in terms of which inputs and outputs are jointly possible; and in the spans picture, how often inputs and outputs are jointly possible. Specifically, we first show that the class of circuits generated by the Toffoli gate as well the states |0⟩, |1⟩, √2|+⟩ and their adjoints is characterized in terms of spans of finite sets. We also give a complete axiomatization for these circuits. With this semantics in mind, we discuss the connection to partial and reversible computation. Shifting to the phase-space picture we also characterize circuits in terms of how they relate abstract positions and momenta. We show how this gives a unifying relational semantics for certain classes circuits for classical mechanical systems, as well as for stabilizer quantum circuits

Keywords: classical mechanics
quantum mechanics
quantum computing
string diagrams
diagrammatic methods
Lagrangian relations
symplectic geometry
category theory
Advisor: Kissinger, A
Formation and collapse of non-wetting cavities in soft porous media

Various biological and chemical processes lead to the nucleation and growth of non-wetting fluid bubbles within the pore space of a soft porous medium, such as the formation of gas bubbles in liquid-saturated sea-bed sediments, or biomolecular condensates in the cellular matrix. The non-wetting nature of these bubbles makes it energetically costly for them to invade the narrow pore throats between solid. If the solid skeleton is sufficiently soft and/or the confining stress is sufficiently low, non-wetting bubbles can instead displace solid to form macroscopic (open) cavities. An increase in the confining stress can suppress the formation of cavities and even trigger the collapse of existing cavities, forcing the non-wetting fluid into the pore space. A quantitative understanding of the total volume of non-wetting cavities, their size distribution, and their formation and collapse are important for the macroscopic mechanics of this three-phase system, and its interactions with the surrounding environment. Here, we consider this process through the lens of phase separation, where thermomechanics govern the separation of the non-wetting phase from a fluid--fluid--solid mixture. We construct a novel phase-field model informed by large-deformation poromechanics, in which two immiscible fluids interact with a poroelastic solid skeleton. Our model captures the competing effects of elasticity and fluid--fluid--solid interactions (capillarity). We complement our theory with a series of simple experiments, using a packing of hydrogel beads as an example soft porous medium. As model problems, we consider the spontaneous formation of multiple cavities from an initial distribution of non-wetting fluid in the pore space, and the deformation-driven collapse of cavities due to the application of a fluid-permeable piston. We study our model in a 1D setting, via numerical simulation, linear stability analysis, and analytical solution of a reduced model. We identify the key parameters that control cavity formation, and the characteristic size of resulting cavities. We also investigate the confining stress required to trigger cavity collapse, and explore the reversibility of cavity formation and collapse under fluctuating confining stress. We complement our theory with a series of simple experiments, using a packing of hydrogel beads as an example soft porous medium.

Keywords: capillarity
phase separation
soft porous media
phase-field method
Advisor: MacMinn, C