VictorJuiz/thesis huggingface dataset:
The space-times of post-capitalist transformation: More-than-human affects in French and Catalan eco-communities 

This thesis aims to understand how post-capitalist life is made possible in eco-communities and how it might travel beyond them. I do so with a view of uncovering attempts at thinking and doing differently in ways that may guide us in the Anthropocene (Clark, 2011: 162, see Gibson- Graham and Roelvink, 2009; Haraway, 2008; Povinelli, 2011; Tsing, 2015), whilst simultaneously responding to calls to study such sites in further depth as potential ‘niches’ with lessons to help address the excesses of capitalism and the associated climate crises (Litfin, 2014; Pickerill, 2017). I have conducted an ethnographic study of three eco-communities in Southwestern France and Catalonia in a broadly comparative vein and have drawn on the disparate body of literature around post-capitalist transformations and eco-communities on one hand, and more-than-human and non-representational geographies on the other. I have worked to address five gaps in the literature on eco-communities, namely, a lack of attention to embodiment and affect and to everyday material practices, their more-than-human constitution, their contribution to economic transformations, and finally, their endurance over time. I argue that repetitive, more-than-human affective relations along with moral-political convictions are crucial to understanding how post-capitalist transformations come about, especially when examining how affective relations and moral-political convictions emerge as motivations, how they are cultivated and passed onto to others, and how difficulties in doing so might arise over time. I have laid out this central argument in four space-times of transformation, that is, the variegated space-times of motivational experiences to move to an eco-community, the building of post-capitalist commons on site, the transformative potential of economic practices in and beyond the sites and finally, the endurance of post-capitalist practices over prolonged periods of time.

Keywords: diverse economies
more-than-human
affect
eco-communities
post-capitalist transformation
Advisor: Greenhough, B
Schwanen, T
Optimisation through innovation: judicial exercise of discretionary remedial power to enforce the state's positive human rights duties

This thesis bridges remedial theory and practice to explore how the judicial exercise of discretionary remedial power can be optimised to enforce the state’s positive human rights duties. Recognising both the difficulty and the importance of remedying breaches of the state’s positive duties, this thesis advances a constructive project that illuminates not just the risks but also the potential rewards of discretionary remedial power.
Part I develops a theoretical account of the optimal exercise of discretionary remedial power that is attentive to both the challenges and the responsive nature of the judicial task in remedying breaches of the state’s positive duties. I argue for a principled exercise of discretionary remedial power that involves the contextualised prioritisation and optimisation of four remedial principles: (1) Effective Relief, (2) Systemic Compliance, (3) Institutional Responsiveness, and (4) Institutional Complementarity. Remedial decision-making should not only assign a conditional order of preference to the remedial principles when they are in tension, but also optimise all four principles as far as possible in any particular case.
Part II uses a case study method to illuminate how this imperative of optimisation can be achieved through remedial innovation. Using the evaluative framework developed in Part I of the thesis, I trace the trajectory of remedial development in two case studies: the litigation on education financing run by the Campaign for Fiscal Equity in New York State, and the education litigation on school infrastructure, furniture and teachers run by the Legal Resources Centre in South Africa. In drawing out the potential of the featured remedial innovations for addressing the distinctive remedial challenges posed by positive duties, my thesis demonstrates how the exercise of discretionary remedial power can be optimised through innovation.

Keywords: judicial discretion
remedies
positive duties
constitutional remedies
human rights
right to education
courts
Advisor: Fredman, S
Modelling multimodal population brain imaging data

Neuroimaging allows for the non-invasive study of the brain in rich detail. Data-driven discovery of patterns of population variability in the brain has the potential to be extremely valuable for early disease diagnosis and understanding the brain. The resulting patterns can be used as imaging-derived phenotypes (IDPs), and may complement existing expert-curated IDPs. However, population datasets, comprising many different structural and functional imaging modalities from thousands of subjects, provide a computational challenge not previously addressed. Here, we proposed two approaches, termed BigFLICA and SuperBigFLICA, that are scalable for data fusion of voxel-level neuroimaging data in the UK Biobank (UKB) dataset, that will soon reach 100,000 imaged subjects. The BigFLICA is an unsupervised multimodal independent component analysis approach, and the SuperBigFLICA improves BigFLICA by using the information from non-imaging phenotypes in a semi-supervised fashion. Both of them can estimate modes of population variability that enhance the ability to predict thousands of phenotypic and behavioural variables compared to previous approaches. Many interpretable associations with non-imaging phenotypes were identified, including multimodal spatial maps related to fluid intelligence, handedness and disease.
For the longitudinal prediction of brain imaging data, it remains largely unknown whether we can predict individualised longitudinal changes of brain imaging features based only on the baseline brain images, which would be of great value for longitudinal brain studies and early design of personalised treatments. We explore this possibility of using longitudinal data of 50 modalities in UK Biobank brain imaging studies with around 3500 subjects. We designed a deep U-Net based model for predicting longitudinal changes in multimodal brain images, and proposed a new mathematical framework for evaluating the longitudinal prediction results, including detecting the existence of changes in data, deriving baseline prediction performance and distinguishing change prediction from data denoising. Our results show that the proposed model can predict to a modest degree individualised longitudinal changes in almost all 50 modalities, and outperforms other popular models. Further, the predicted longitudinal changes have a similar or even improved accuracy of predicting subjects’ non-imaging phenotypes, and have a high between-subject discriminability. Our results show the potentials of our model for longitudinal data imputation, and show several caveats when performing longitudinal data analysis.

Advisor: Smith, S
Beckmann, C
Matrix assisted room temperature and vacuum drying of functional proteins and applications

Proteins in aqueous solution are commonly unstable at room temperature and require a cold chain to maintain low temperatures during storage and transportation to minimise degradation. The need for the cold chain limits product distribution and increases the cost of goods. An alternative to prevent degradation and extend the shelf life is to remove water from protein solutions, drying with protective agents. The well-established freeze-drying has prolonged drying processing time and is energy-intensive, potentially increasing the cost of products.
In this work, a novel and cost-effective drying method, Matrix Assisted Room Temperature (MART) drying, was proposed and tested. The technique, initially developed from sugar film drying of vaccines at room temperature, was applied to dry functional proteins. A mathematical model to simulate the simplified MART drying was established to investigate the stabilisation mechanisms of sugar films on proteins. The simulation results showed that capillary bridges of trehalose solution formed on the fibre matrix would not rupture during the drying at a suitable concentration range. Proteins were immobilised in sugar glass to minimise degradation.
The feasibilities of drying proteins with MART drying were also experimentally studied. Two functional proteins, lactate dehydrogenase (LDH) and fibroblast growth factor 2 (FGF-2), were dried on a biocompatible and sterile cellulose fibre matrix at room temperature or even at elevated temperatures. Two sets of drying conditions, drying under low relative humidity conditions (RH<5%) at atmospheric pressure (MART drying) and drying under vacuum (MART-V drying), were investigated. The results showed that MART drying, with or without vacuum, can preserve proteins without any significant activity and functionality loss after drying and one-week storage at 40 °C. More than 80% of the initial activity was maintained for the MART dried LDH after six-month storage at 25 °C. Meanwhile, the activity of dried FGF-2 by both drying conditions was retained after one week of storage at 40 °C. The efficacy of dried FGF-2 after storage did not show a significant difference with FGF-2 solution stored at -80 °C on the proliferation assay of human Mesenchymal Stem Cells.
Another novel drying strategy, vacuum-spin drying, was developed to stabilise the enzymes and other reagents with the supplement of sugars in SARS-CoV-2 rapid detection kits, using the reverse transcription-loop mediated isothermal amplification (RT-LAMP) technique. In the clinical trial, the vacuum-spin dried detection kits demonstrated a sensitivity of 95% and specificity of 99%. As the first attempt of its kind, stabilising the RT-LAMP reagents at room temperature made the storage and transport of the COVID-19 rapid test kits much simpler and more economical, and contributed significantly to its commercial success.

Keywords: COVID-19 LAMP Test
Protein long-term storage
reverse transcription-loop mediated isothermal amplification
Protein stabilisation
Matrix Assisted Room Temperature Drying
Advisor: Cui, Z
Characters and characterisation in the epic cycle

The aim of this thesis is to use the various characters who play a part in the Epic Cycle as a tool with which to understand more about the Cycle and the pre-Homeric oral tradition. In Part 1, I use characters as a way to approach the different sources of information we have for the Epic Cycle, namely the Bibliotheca of Apollodorus and the various fragments from later writers and scholiasts. I take the view that these sources are, on the whole, less valuable than Proclus’ epitomes. By looking at the characters unique to these accounts, I assess the value and utility of Apollodorus and the fragments for our knowledge of the Epic Cycle. Nevertheless, the thesis also raises questions about the status of Proclus’ epitomes and the extent to which they give us access to the ‘authentic’ Epic Cycle.
Part 2 is dedicated to the individual characters who play a part in the narrative of Proclus’ epitomes. Using a mixture of methodological tools from the camps of both Neoanalysis and Oral Theory, I attempt to trace out a full account of how these different characters were depicted in the tradition of the Trojan War. By using the information given by both Proclus, the fragments, and the Homeric poems, the aim is to build as full a picture as possible of the position and characterisation of these characters in the pre-Homeric oral tradition of the Trojan War. The individuals discussed are both major (Achilles, Diomedes, Odysseus, and the Trojan Princes) and minor (Protesilaus, Philoctetes, Polypoites, Leonteus, and Palamedes).

Keywords: Early Greek Hexameter Poetry
Oral poetry
Homer
The Odyssey
The Epic Cycle
The Iliad
Advisor: Metcalf, C
The communicative architecture of policing

Inspired in part by the findings of, and fallout from, the Leveson Inquiry, and the recommendations in the subsequent Filkin Report on the relationship between the Metropolitan Police and the media, my DPhil explores police-media relations and police communications in the local (extra-London) and contemporary context. It also assesses the impact of social media technologies on both journalists and police, and on their social and informational relationships. The project involved an in-depth ethnography of newsrooms in local print and broadcast media in England, and police communications departments. The principal methodological approach is observation. Fieldwork lasted over two years, with more than seven months each of continuous observation with both local journalists and police communication professionals.
This research is unique in the limited scholarship on police-media relations, combining observational data from both newsrooms and police communications departments. It provides insights on the revenue crisis and decline in local journalism, and how this has impacted reporting on crime and policing. It details the emergence of a professional police communicator identity in British policing: tasked with managing public/media trust and confidence in policing. Perhaps most importantly, the thesis offers an account of how strategies by journalists and police to enhance their communication power, structures their relationship with one another, and the production of crime and policing knowledge. Finally, the thesis explores the deeper mechanics of power relations between policing and media, by theoretically situating them within the context of their broader fields of power.

Keywords: criminology
media sociology
policing
police-media relations
police accountability
police governance
police legitimacy
police communications
Advisor: Loader, I
The interplay between hypoxia signalling and hepatitis B virus replication

Viral replication is influenced by the host cell microenvironment, and local oxygen tension is a major factor that shapes the intracellular landscape. Hepatitis B virus (HBV) replicates in the liver which harbours a naturally low oxygen environment. However, in vitro culture systems apply atmospheric oxygen conditions, and so our understanding of the role of oxygen sensitive factors in the viral life cycle is limited.
We uncover evidence of hypoxic signalling in the HBV infected liver that associates with the inflammatory status of this chronic disease. We develop simple PCR assays to determine the source of HBV RNAs and ascribe patterns of viral transcription. Investigating the interplay between the hepatic inflammasome and viral transcription identified 24 host factors that positively associate with HBV transcriptional activity. Culturing HBV infected hepatoma cells under low oxygen uncovered a new role for hypoxia inducible factors (HIFs) in the viral life cycle. Our studies demonstrate that HIFs bind an evolutionarily conserved hypoxic response element in the basal core promoter in vitro and in vivo, which drives the synthesis of pre-genomic RNA and potentiates particle genesis. HIFs are not the only regulators of the cellular response to low oxygen, and we expand our observation to show that hypoxic inhibition of histone lysine demethylase 4 (KDM4) also promotes transcription from episomal and integrated HBV genomes. We show that KDM4 is a major orchestrator of host gene expression and this defines host susceptibility to HBV infection.
Identifying roles for oxygen sensors in the HBV life cycle suggests that this pathogen has evolved to exploit the hypoxic signalling pathways in the liver. This study highlights the importance of understanding the pathways which are active in physiological oxygen tensions when considering virus-host interactions, and provides innovative routes to therapeutically target HBV.

Keywords: hypoxia
oxygen signalling
hepatitis B virus
Advisor: McKeating, J
Harris, A
Integrating local knowledge into wildlife population monitoring

Gathering species population data from local people is growing in popularity in conservation, as a cost-effective way to rapidly collect information over spatiotemporal scales that are not always feasible using conventional surveys. However, few studies exist that assess the bias when incorporating local ecological knowledge (LEK) into wildlife population monitoring. In this thesis, I use a mixed-method approach to gain a better understanding of the uncertainty that can affect observational data and explore how local ecological knowledge can be better incorporated into wildlife population monitoring, using two wild meat hunting villages adjacent to the Dja Faunal Reserve in Cameroon as a case study.
I explore patterns of hunting offtake and intensity within a socioecological system framework, to identify the drivers of hunting and threats to hunted species in both hunting systems. I find clear village level differences in species depletion, as a result of differing geographical characteristics and hunter-level methods and motivations to hunt. I then triangulate estimates of species occupancy obtained from daily hunter diaries, seasonal interviews and camera traps, to better understands the sources of uncertainty when using each monitoring method. Estimates from LEK-informed methods were broadly comparable with camera trap data at the village level, but with species level differences. I explore the use of modern expert elicitation methods as a tool to better understand uncertainty around estimates of species occupancy and density from local people. Gender plays an important predictive role in the type of knowledge held. Further, those predicted to be the most knowledgeable by their peers (i.e. local experts) do not always provide the most robust estimates. Finally, power analysis that account for species detectability reveal that the cost and effort required to ensure power to detect trends in species occupancy over time is often prohibitive.
The thesis highlights the value that LEK-informed methods have for providing monitoring data on species hunted for wild meat, and how an improved understanding of LEK-informed data and integration into wildlife population monitoring can result in more ethical and just conservation efforts. However, conservation actors must account for species detectability when designing monitoring programmes and consider whether they have the logistical and financial resources required for effective and sustainable monitoring of trends over time.

Keywords: wildlife population monitoring
comparison studies
Cameroon
Bushmeat
socioecological systems
occupancy analysis
power analysis
Local ecological knowledge
expert knowledge elicitation
Advisor: Milner-Gulland, E
Using antibody next generation sequencing data to aid antibody engineering

Future successful exploitation of antibodies as diagnostic and therapeutic agents will greatly benefit from an increased understanding of natural B-cell receptor (BCR) repertoire diversities. The advent of next-generation sequencing of immunoglobulin genes (Ig-seq) has made it possible to sequence large snapshots of BCR repertoires in a single experiment.
In the results chapters of this thesis, we begin by describing a method (AntiBOdy Sequence Selector, “ABOSS”) for filtering BCR repertoire data, which considers the structural viability of each sequence and is orthogonal to all other current methods (Chapter 2). ABOSS leverages the presence/absence of a conserved disulphide bridge found in antibodies as a way of both identifying structurally viable BCR sequences and estimating the sequencing error rate. We show that this method is able to identify structurally impossible sequences missed by common error-correction methods.
Next, we describe the development of Observed Antibody Space (OAS), the first resource that curates BCR sequences from publicly available studies. As of October 2020, OAS contains more than 1.9 billion sequences from 85 studies. In OAS, all BCR repertoire sequences are annotated and profiled for structural viability.
We next describe the development of a novel method (SAAB+) to interrogate complete BCR repertoires at the structural level (Chapter 4). SAAB+ annotates large portions of BCR repertoires with three-dimensional information by mapping sequences to crystallographically solved antibody structures. By applying SAAB+ to BCR repertoires in OAS we, for the first time, document repertoire structural changes along the B-cell maturation axis in humans and mice.
In the final experimental chapter, we describe our work in COVID-19 research where we have compared the structural and sequence diversities of SARS-CoV-2 BCR repertoires to healthy repertoires deposited in OAS. We also outline the development of the first organised database (CoV-AbDab) that curates all publicly available anti-SARS-CoV-2 antibodies in a standardised format.
Finally, we discuss how recent developments in paired-chain Ig-seq platforms and deep learning algorithms could have a lasting impact on established Ig-seq analysis pipelines. We also outline how the tools described in this thesis can be combined with these field-disruptive technologies to advance our understanding of the immune system and improve computational antibody engineering.

Keywords: BCR
NGS
Advisor: Deane, C
Investigations on synaptic plasticity: new tools and perspectives

For decades, neuroscientists have sought to understand the neural basis of learning and memory. As yet no unified model has emerged, although it is widely agreed that synaptic plasticity plays a pivotal role. In consequence, a great deal of research has focused upon the characterisation of synaptic plasticity both in vitro and in vivo. While the advances have been impressive, substantial gaps remain that may be slowing the identification of the precise relationship between synaptic plasticity and learning and memory: (1) there is a paucity of research examining presynaptic plasticity mechanisms and presynaptic receptor functions; (2) synaptic dynamics are studied in behaving animals without consideration of the impact of endogenous factors, even though it looks to be clear that hormone signalling impacts upon synaptic processes: (3) An accurate assessment of synapse biology with respect to cognitive function can only arise from studies in living animals, an ambition that will require the development of new imaging tools. In this thesis I begin to address each of these points. First, using a combination of optical and electrophysiological tools I provide a functional framework for presynaptic NMDA receptor signalling that has been previously lacking. I show that the specific subunit expression at presynaptic terminals is important as it regulates Ca2+ dynamics. Second, I demonstrate that oestrogen, a neuromodulator, lowers the threshold of plasticity in several brain regions, emphasising how important it is to consider hormone status when studying synaptic dynamics. Finally, I implement several advances to a multimode fibre based minimally invasive system for high-resolution brain imaging, including the first examples of two-photon MMF imaging of biological tissue and successive imaging cycles through a multimode fibre.

Keywords: fibre optics
plasticity
structural plasticity
hippocampus
short-term plasticity
Ca2+ imaging
oestrogen
presynaptic terminal
spines
NMDA receptor
Advisor: Emptage, N