VictorJuiz/thesis huggingface dataset:
Mapping the global distribution of zoonoses of public health importance

Medical cartography can provide valuable insights into the epidemiology and ecology of infectious diseases, providing a quantitative representation of the distribution of these pathogens. Such methods therefore provide a key step in informing public health policy decisions ranging from prioritising sites for further investigation to identifying targets for interventions. By increasing the resolution at which risk is defined, policymakers are provided with an increasingly informed approach for considering next steps as well as evaluating past progress. In spite of their benefits however, global maps of infectious disease are lacking in both quality and comprehensiveness.
This thesis sets out to investigate the next steps for medical cartography and details the use of species distribution models in evaluating global distributions of a variety of zoonotic diseases of public health importance.
Chapter 2 defines a methodology by which global targets for infectious disease mapping can be quantitatively assessed by comparing the global burden of each disease with the demand from national policymakers, non-governmental organisations and academic communities for global assessments of disease distribution. Chapter 3 introduces the use of boosted regression trees for mapping the distribution of a group of vector-borne diseases identified as being a high priority target, the leishmaniases. Chapter 4 adapts these approaches to consider Ebola virus disease. This technique shows that the West African outbreak was ecologically consistent with past infections and suggests a much wider area of risk than previously considered. Chapter 5 investigates Marburg virus disease and considers the variety of different factors relating to all aspects of the transmission cycle that must be considered in these analyses. Chapters 6 and 7 complete the mapping of the suite of viral haemorrhagic fevers by assessing the distribution of Crimean-Congo haemorrhagic fever and Lassa fever. Finally, Chapter 8 considers the risk that these viral haemorrhagic fevers present to the wider African continent, quantifying potential risk of spillover infections, local outbreaks and more widespread infection.
This thesis addresses important information gaps in global knowledge of a number of pathogens of public health importance. In doing so, this work provides a template for considering the global distribution of a number of other zoonotic diseases.

Advisor: Hay, S
Understanding the psychological health and experiences of dementia care staff

Care work is emotionally and physically demanding and is coupled with organisational challenges. As such, care work has been associated with emotional exhaustion which not only negatively impacts staff but also the care that they provide. Greater understanding of the psychological health of dementia care staff and their perceptions of their work will provide insights into how this group may be better supported.
The first paper provides a review of the literature relating to psychological outcomes in dementia care staff. The literature identified was viewed in terms of an existing model of psychological health, the BASIC Ph, with the aim of evaluating the evidence and enhancing understanding of psychological health in this group. The utility of this model was also evaluated. The model highlighted areas for potential intervention as well as those for future research. Clinical implications for Clinical Psychologists were also discussed.
The second paper aimed to increase understanding of the experiences of dementia care assistants who perceived themselves to be competent in their role. Eight care assistants who had high levels of self-efficacy were interviewed. Interpretative Phenomenological Analysis (IPA) revealed four superordinate themes. Accounts of experiencing dilemmas provided important contextual information and constituted the first superordinate theme. The second theme 'togetherness and connection' described participants' experience of the need for support, closeness and the value of engaging with older people with dementia. The third theme encompassed the attunement between care assistants and the older people for whom they cared and described empathy, personal perspective-taking and circularity of emotion as guides to care. The final theme 'caring as part of life' described the link between caring and identity as well as a genuine interest in people, an accepting attitude and motivation to care. These themes provide fruitful areas for further research and have implications for care staff training.

Keywords: psychological health
self-efficacy
dementia
care staff
Advisor: Murphy, D
Investigating cell type specific metabolism using GFP as a reporter protein

Metabolic flux analysis (MFA) is a powerful technique for quantifying the intracellular fluxes in central carbon metabolism. It relies on detection of stable isotope labelling from metabolites such as amino acids derived from protein. Current standard techniques are, however, unable to distinguish between different cell types in heterogeneous tissue. The aim of the thesis was to address this problem by developing and validating a strategy using green fluorescent protein (GFP) with cell type specific expression as a reporter protein for investigating the fluxes in specific cell types in the Arabidopsis thaliana root. The fundamental difficulty in applying a reporter protein strategy in a multicellular organism arises from the limited amount of recombinant protein expressed by the cells.
The main novel contributions of the work in this thesis are threefold. First, a robust protocol for purification of GFP from the roots of Arabidopsis seedlings and for detection of reliable mass isotopomer distributions from the amino acids derived from GFP are described. Secondly, the reporter protein strategy is validated in this biological system with a focus on showing the data obtained by the use of the reporter protein is equal to that normally obtained from the total protein fraction. To expand on this, stable isotope labelling in isolated root hair cells is explored. These cells are easily isolated and show potential as a model system for cell type specific metabolism. Finally, the experimental data provide evidence for the feasibility of measuring data from specific cell types with appropriate mass spectrometric techniques. Analysis of cell type specific gene expression in this system suggests differences in the primary metabolism of different cell types cannot be ruled out without further investigation. Based on small scale in silico modelling described in this thesis, new solutions capable of providing data on sub-populations of cells are required, if central metabolism of the cell types differs significantly.
The nature of configurationality in LFG

The central issue in this thesis is configurationality, which has broadly been defined in terms of a division of the world's languages based on their core syntactic structure. Specifically, languages are traditionally divided into so-called configurational and non-configurational languages. Configurational languages are assumed to be languages with many restrictions on word order, and non-configurational languages are assumed to be languages with very few or no word order restrictions. Many linguists posit a strict division between the two different types of languages. In this thesis I propose a non-derivational approach to configurationality, and I discuss in detail three posited characteristics of non-configurational languages (in comparison to configurational languages): free word order, discontinuous expressions and subject-object asymmetries in binding. I propose a four-way classification of languages instead of a two-way one, based on constraints on annotations on phrase structure nodes, both for argument functions and for information structural roles (such as topic and focus). I propose that this four-way distinction is what underlies configurationality. I show that discontinuous expressions and potentially subject-object symmetries follow from the nature of languages that have traditionally been classified as non-configurational. For my analysis I employ Lexical Functional Grammar (LFG), a non-derivational framework which is particularly well-suited to account for languages in which grammatical functions are not tied to specific phrase structural positions, due to its parallel architecture. This characteristic of LFG enables me to provide a straightforward classification of languages, by the ability to separate the influence of grammatical functions and information structural roles on word order and phrase structural configuration.

Keywords: Configurational languages
Discontinuous expressions
Lexical-Functional Grammar
Non-configurational languages
Binding
Configurationality
Free word order
Advisor: Asudeh, A
Dalrymple, M
Clientelism, social policy and welfare state development: a case study on Thailand

This thesis consists of four independent chapters each of which addresses the relationship between clientelism and social policy in relation to welfare state development from different perspectives. The overarching research question examines whether the adoption of such policies leads to de-clientelisation, and, if so, to what extent. The research extensively draws upon both cross-national data and that from Thailand between 2000-2012 during which populist welfare policies have gained significant influence on political development. Chapter 1 employs a global dataset of developing countries to offer a comparative perspective on the subject and shows that political parties generally trade-off between social policy and their engagement in clientelism. The latter three chapters take Thailand as a case study empirically investigate clientelist mechanisms at different geographic levels. Focusing on the household level, Chapter 2 evaluates the role of patron–client relations in determining access to the Thailand Village Fund based on the Socio-Economic Household Surveys. The provincial level is examined in Chapter 3 which studies economic and political determinants of two types of provincial-level distributive transfers: social policy spending and discretionary spending. Chapter 4 examines the clientelist mechanism at the national level through an assessment of the electoral linkage dynamics by measuring changes in personal votes. The findings show some degree of resilience of clientelist relations as they intervene with social policy allocation, particularly at local level. The global trend contrasts with the case of Thailand where, as in-depth analyses of the latter three chapters have shown, clientelist relations often persist and convert into a new form, for example the southern model of welfare regimes.

Advisor: Bukodi, E
Detection and exploitation of expression QTL in drug discovery and development

Expression quantitative trait loci (eQTLs) are genetic markers associated with transcription of Ribonucleic Acid (RNA). eQTLs are detected using association analysis to detect correlations between RNA expression data (microarray or RNA-SEQ) and the genotypes of individuals within a study.
Trans-ethnic meta-analysis can increase power to detect genetic variants for eQTLs and improve fine-mapping resolution because of differential patterns of linkage disequilibrium (LD) between diverse populations. Lymphoblastoid cell lines (LCLs) from samples in the Phase II and III HapMap populations have been used to detect cis eQTLs using association analysis followed by meta-analysis. Phase III HapMap samples have also been imputed using the 1000 Genomes March 2012 "all ancestries" panel.
The goals of this thesis are to perform meta-analysis on multi-ethnic association summary statistics in order to: Increase the power to detect eQTLs, leverage differences in LD between ancestry groups to fine map eQTL variants and investigate and characterize heterogeneity in allelic effect sizes on expression between diverse populations.
In addition to this, eQTLs identified are used to perform integration with signals from genome-wide association studies (GWAS) of complex human traits. A pipeline has been developed where eSNPs from the eQTL datasets are integrated with disease SNPs (dSNPs) from the NHGRI GWAS catalog using reciprocal conditional analysis to determine whether eSNP and dSNP tag or are the same causal variant. Also, eQTLs which are also "absorption, distribution, metabolism, and excretion" (ADME) genes are studied in more detail, specifically looking for heterogeneity and enrichment in this dataset.
The analysis shows that combining association analysis summary statistics using meta-analysis leads to an increase in power to detect eQTLs. Differences in LD between ancestry groups can be used to improve fine mapping resolution, as measured by "credible sets" of variants most likely to drive the eQTL signal, when all ancestry groups are combined. Considerable heterogeneity between ancestry groups has been detected, much of which is due to differing LD between tag SNP and causal variants across ancestry groups.
Furthermore, the GWAS integration has led to the identification of several dSNP – eSNP pairs for disease such as Ulcerative Colitis, Inflammatory Bowel Disease, Bechet's Disease, Sarcoidosis, Crohn's Disease, Grave’s Disease and Primary Biliary Cirrhosis, and have provided potential novel insights of genes through which these disease association signals are mediated. Several eQTLs for genes within the ADME dataset have also been identified some of which have significant heterogeneity.

Advisor: Morris, A
Huxley-Jones, J
Whittaker, J
Cell replacement and ex vivo gene therapy for photoreceptor regeneration

Photoreceptor degeneration due to retinitis pigmentosa (RP) is a primary cause of inherited retinal blindness. Photoreceptor cell-replacement therapies may hold the potential for repair in a degenerate retina, by reinstating light sensitive cells to project and form connections with downstream retinal cells and finally the visual cortex. Patient-specific induced pluripotent stem cells (iPSc) could provide an autologous source of cells to replace lost tissue. However, the use of patient-derived iPSc would require that the disease-causing gene mutation be corrected in cells before transplantation.
Ex vivo gene therapy of mouse photoreceptor precursor (PhRP) cells and subretinal transplantation of treated cells are here studied in a disease-specific animal model of RP; rhodopsin was ectopically expressed ex vivo in rod precursor cells, sourced from a transgenic model lacking the rhodopsin gene. Treated rod precursors were here transplanted in mice of the same disease model and are shown to gain expression of rhodopsin and mature to regenerate the absent outer nuclear layer (ONL) of degenerate mice. Visual function, assayed in the same animals before and after transplantation, was restored in animals which had no rod function at baseline.
Delivery of the rhodopsin gene by both an adeno associated viral (AAV) vector and a non-viral minicircle DNA vector developed here for ex vivo gene delivery to rod photoreceptor precursors showed comparable efficiency and sustained expression. The non-viral minicircle method provides a novel system for efficient photoreceptor therapy and may offer a platform of genetic treatment of photoreceptor degenerations in which the gene in focus exceeds the size limit for packaging in AAV.
Human embryonic stem cell (ESC) and human iPSC-derived PhRPs were also transplanted in mice with complete ONL degeneration and were able to reform the lost photoreceptor layer and mature in the host retina. Human cells developed light-sensitive outer segments, and reconnect with host neurons downstream to improve vision in previously blind mice.
Efficient transplantation of ex vivo genetically treated rod precursors and human stem cell-derived PhRPs in animal models of progressive RP may provide a clinically-relevant model for the investigation of cell-replacement therapy for photoreceptor regeneration in retinal disease.

Advisor: MacLaren, R
Asphalt encounters: Chinese road building in Ethiopia

Over the past decade, road construction has come to represent Chinese engagement with Ethiopia. This study considers the lives of Chinese workers at the lower end of one such project in Tigray, northern Ethiopia. By examining the ways in which Chinese road workers tried to make sense of daily life on the construction site, I reveal the inherent contradictions of a state rhetoric that promoted 'win-win cooperation' ('huying huli hezuo') and 'friendly collaboration' ('youhao hezuo') between China and Africa, and demonstrate the local manifestations of the much-debated 'China Model'. Initial expectations coloured by state narratives, as well as the migrants' own experiences with domestic development, stood in sharp contrast to realities on the ground. Convinced of the goodwill nature of their activities, Chinese workers were puzzled by and resentful of the apparent ingratitude of local Ethiopians, their lack of cooperation, and, worse, repeated attempts to sabotage the construction work.
Chinese workers' struggles with development in Africa, I argue, should be understood in relation to their background as upwardly mobile rural migrants at the bottom of the corporate hierarchy, successors of engineers dispatched under Mao Zedong who had enjoyed a respectable reputation at home – a reputation current workers felt they were about to lose – and as citizens aware of their country’s status in the world as superior to Africa and inferior to the West. The workers sought to live up to Chinese ideals of development by demonstrating and promoting the virtues of self-development, simultaneous development, and entrepreneurialism. Ethiopians, however, did not concede to these ideas, and their lack of cooperation stirred resentment and expressions of self-pity on the part of the Chinese, who blamed the Ethiopian labourers, their suzhi (human quality), and wenhua (culture) for the limited success of the projects. What Chinese workers failed to realise was that the attitude of Ethiopians was in fact a response to asymmetrical and contested power relations that did not allow for win-win cooperation and friendly collaboration.

Advisor: Biao, X
Zeitlyn, D
Reformers, rulers, and British residents: political relations in Bahrain (1923-1956)

This thesis explores the modern historical lineage of absolutism in Bahrain, and the history of challenges to absolutist state authority during the peak of British influence in the Persian Gulf, the period between the First World War to the Suez crisis of 1956. It rewrites the history of Bahrain and British colonialism in the Persian Gulf through two distinct narrative threads. First, it presents a new history of the colonial-dynastic state in Bahrain and the longer tradition of indirect rule from which its architects drew, and second, it retrieves the history of the popular movements that came to challenge it. This entails an examination of not only how colonial and dynastic authority was jointly exercised, but the ideas that justified such authority over a population conceived of as a set of cultural, and more specifically religious communities governed by their own 'custom' – the conceptual centerpiece of indirect colonial rule.
Both these narrative strands constitute part of a broader history of the ideological clash between late colonial ideologies of rule and anticolonial nationalism in the twentieth-century Persian Gulf—a region that was never formally colonized, nor became the site of any successful popular nationalism. Yet both these forces exerted a profound influence on the nation-states that would emerge in the late twentieth century, especially on Bahrain. To chart that historical conjuncture, the thesis begins with the creation of the modern colonial-dynastic state in Bahrain in 1923. It ends in 1956 with the last and most important uprising in Bahrain's during the 20th century, one that was largely a revolt against the political and institutional structures that colonial reformers had established three decades earlier. At its broadest, the thesis argues that the process of state-building under indirect colonial rule in Bahrain derived from a body of colonial thought on native political life and behaviour, and particularly, on the prevention of rebellion that has its origins in mid nineteenth century North India. In Bahrain and the Persian Gulf, as elsewhere in the late colonial world, ideas about empire, the state, authority and rebellion are the intertwined threads that shaped political life and the prose of history.

Advisor: Armbrust, W
Rogan, E
The dwelling perspective

This interdisciplinary thesis is about dwelling, both as a method in archaeology and as a mode of existence. My thesis has two principal aims. Firstly, to explore the 'dwelling perspective' as this has been outlined in recent archaeological theory. This will involve discussion of phenomenological philosophy and the figure of Martin Heidegger. The term 'dwelling' is a technical one originating in Heidegger's philosophy of being. Phenomenology has been making inroads into archaeological theory as a consequence of the interpretive turn of the 1980s. The theoretical commitment of this thesis is that phenomenological inquiry is a useful project in archaeological research. Reflexive archaeological research in the present might articulate and confirm certain phenomenological dimensions of present experience so as to inform and enhance our understanding of the past. Secondly, I discuss the notion of dwelling in the existential sense as a mode of existence in terms that might allow us to deploy this concept in Palaeolithic archaeology, with specific reference to mortuary practice and "art". I propose two case studies in order to explore this. Firstly, mortuary practice and existential awareness of death will be explored with reference to the site of the Sima de los Huesos. Secondly, Heidegger's notion of artistic production as a world-opening event will be explored in relation to Upper Palaeolithic art in caves. The focus on mortuary practice and art is not arbitrary: both are central planks of Heidegger's account of dwelling and both are linked by 'heterotopic' space. Heidegger presented a novel account of human existence as 'Dasein'. Dasein is being-in-the-world and being-in-the-world is unified by what Heidegger called 'care' (Sorge). Heidegger's account of Dasein remains anthropocentric: I argue that we should move away from Heidegger's own anthropocentric view of being-in-the-world, dwelling or care toward a phenomenological archaeology that goes 'beyond the human'. I argue that care or dwelling is evidenced by the archaeological record of human becoming and that our ancestors 'cared for' or 'dwelled with' their dead. Care is evidenced by appropriating the world and by looking after compatriots within the world, and I argue that such an existential state had been reached before the advent of the Upper Palaeolithic. I argue that Upper Palaeolithic "art" opened up a hunter-gatherer world that enabled others, including animal others, and objects, to become meaningful to groups of Daseins, and so to become part of particular "dwelling places". Heidegger remains the key theorist of dwelling but his anthropocentrism should be abandoned. Suitably revised, Heidegger's account of dwelling will provoke us to look at Palaeolithic archaeology from a fresh perspective.

Keywords: Heidegger
Advisor: Lock, G
Gosden, C