VictorJuiz/thesis huggingface dataset:
Human-carnivore conflict in Tanzania: modelling the spatial distribution of lions (Panthera leo), leopards (Panthera pardus) and spotted hyaenas (Crocuta crocuta), and their attacks upon livestock, in Tanzania’s Ruaha landscape
Keywords: human-carnivore conflict
Support vector machines
ENFA
modelling
Maxent
Large carnivores

Tanzania’s Ruaha landscape is an international priority area for large carnivore conservation, harbouring roughly 10% of the world’s lions, and important populations of leopards and spotted hyaenas. However, these large carnivore populations are threatened by intense retaliatory killing due to human-carnivore conflict on village land around Ruaha National Park (RNP), mostly as a result of livestock predation by lions, leopards and spotted hyaenas. Moreover, a current lack of ecological data on the distribution of these carnivores hinders the development of effective strategies for conservation and targeted conflict mitigation in this landscape. This study aimed to identify the most significant ecogeographical variables (EGVs) influencing the distribution of lions, leopards and spotted hyaenas across the Ruaha landscape, and to map areas of conservation importance for these species. In addition, the study assessed the influence of EGVs on livestock predation risk by these carnivores in the village land around RNP, and generated a predictive map of predation risk. The relative importance of livestock husbandry practices and EGVs in terms of influencing predation risk within enclosures was also investigated. Proximity to rivers was the most important variable influencing the distribution of large carnivores in Ruaha, and contributed to predation risk of grazing livestock. The traditional livestock husbandry adopted in bomas appeared insufficient to alleviate the inherent risk of predation by large carnivores. The study produced the first detailed maps of lion, leopard and spotted hyaena distribution in the critically important Ruaha landscape, and identified likely livestock depredation hotspots. These results will target conflict mitigation approaches around Ruaha, by identifying particularly high-risk areas for livestock enclosures and grazing stock. Improving husbandry in these areas could help reduce livestock depredation and retaliatory carnivore killing, therefore reducing one of the most significant conservation threats in this critically important landscape.
The centrality of the state in the governing of higher education in South Korea: A critical discourse analysis
Keywords: higher education governance

This thesis takes the critical incident of the suicide of a part-time lecturer in South Korea in 2010 and the subsequent policy response as paradigmatic of the problems of governing higher education. In terms of theoretical resources, it draws on state theories, especially a cultural approach to the state, in order to understand the multiple relations and the interplay of different layers of governing practices in the governing of higher education in South Korea. This thesis argues that mainstream theories of the state are often culturally 'blind' and that the specificities of the Korean state need to be understood with reference to its particular culture, history and context. The thesis also draws on literature on higher education governance, from which three governing principles are identified as topics for investigation, along with a process-oriented approach to professionalism. The research question emerging from this is 'how does the centrality of the Korean state play out in the governing of higher education in South Korea?' Methodologically, the enquiry is shaped by critical discourse analysis (CDA). This approach explores the ways in which higher education governing discourses are related to other social elements. By analysing policy texts and institutional characteristics, the first phase of the enquiry explores how the governing discourses have been indigenised, constructing particular state-academy relations in South Korea. The second phase scrutinises the case of part-time lecturer policy in order to illuminate the distinctive governing dynamics, by which the centrality of the Korean state is assumed to be practised.
Molecular dissection of ionotropic glutamate receptor delta-family interactions with trans-synaptic proteins
Keywords: membrane proteins
trans-synaptic protein complexes
X-ray crystallography

Correct functioning of the brain relies upon the precise connectivity between the billions of neurons that make up this crucial organ. Aberrations in the formation of these elaborate neural networks lead to neurodegenerative and neuropsychiatric disorders. A synapse-spanning molecular triad, involving members of the Neurexin, Cbln and ionotropic glutamate receptor delta families of proteins, is crucial for the accurate formation and proper function of synapses in the cerebellum. This trans-synaptic complex has been implicated in the molecular mechanisms behind motor control and motor learning, and furthermore individual members have been linked to diseases such as Alzheimer’s, autism spectrum disorders and schizophrenia.
The major findings presented in this thesis include: crystal structures of the amino-terminal domains (ATD) of the two members of the ionotropic glutamate receptor delta (iGluR-Delta) family, functional characterisation of the effects of disrupting the ATD interface in one member of the iGluR-Delta family, a crystal structure of the C1q domain of Cbln1, biophysical analysis of the molecular interactions within the Neurexin-Cbln1-GluD2 trans-synaptic complex, as well as evidence for the domain arrangement of the ecto-domain of the iGluR-Delta proteins. Together, these data enhance our knowledge of the molecular details of this macro-molecular complex and provide evidence to support models for the mechanisms of their involvement in synapse formation and function, thereby making a contribution to the vast and medically relevant field of molecular neurobiology.
Hydrodynamics of ducted and open-centre tidal turbines
Keywords: hydrodynamics
yawed flow
tidal turbine
ducted turbine
flow separation
marine energy
hydrokinetic turbine
open-centre turbine

This study presents a numerical investigation of ducted tidal turbines, employing three-dimensional Reynolds-averaged Navier-Stokes simulations. Bidirectional ducted turbines are modelled with and without aperture, referred to as ducted and open- centre turbines respectively.
The work consists of two investigations. In the first, the turbine rotors are represented by actuator discs, a simplification which captures changes in linear momentum and thus the primary interaction of the turbine with the flow through and around the duct, while greatly reducing computational complexity. In the second investigation, the turbine rotors are represented through a CFD-integrated blade element momentum model, employing realistic rotor data, capturing swirl and blade drag in addition to the extraction of linear momentum.
Both modelling techniques were employed to investigate the performances of bare, ducted, and open-centre turbines, relating these to the flow fields exhibited. For axial flow, substantial decreases in power generated by the ducted and open-centre turbines were found, relative to a bare turbine of equal total device diameter. For open-centre turbines, an increase in aperture size leads to a further reduction in power generated. Increased blockage was shown to positively affect the performance of all devices.
Two further measures of performance were employed: power density, normalising the power by the rotor area, and basin efficiency, relating the power generated to the overall power removed from the flow. Moderate increases in power density can be achieved for the ducted and open-centre devices, while their basin efficiencies are of similar value to that of the bare turbine.
For yawed inflow, the performance of the bare turbine decreases, whilst that of the ducted and open-centre turbines increases. This is due to an increased flow velocity following flow acceleration around the inlet lip of the duct and also an increase in effective blockage as ducts present greater projected frontal area when approached non-axially.
Partisan politics and the British fiscal-military state, 1689-1713
Keywords: corruption
state formation
finance
administration

The rapid expansion in the size and effectiveness of the British fiscal-military state between 1689 and 1713 has been analysed by historians such as John Brewer and Michael Braddick as the outcome of increasingly impartial, rational and professional bureaucratic administration. Yet recent work on state formation in Britain and Europe has emphasised that effectiveness often arose from practices usually dismissed as inefficient or corrupt. This thesis provides a new paradigm by comparing fiscal-military structures to contemporary commercial enterprises, which functioned by coordinating the efforts of suppliers and buyers. Coordination was achieved in turn through mutual trust, which overcame principal-agent problems and reduced transaction costs. This thesis suggests that by analogy, those polities that could encourage cooperation and mutual trust between autonomous officials, agencies and private contractors enjoyed the greatest success as fiscal-military states.
In the mercantile or financial world trust was created through kinship and friendship, as well as common religious, ethnic or national identities, which contained inbuilt informal mechanisms for policing behaviour. This thesis examines the financing and supply of the British army in Ireland and Europe between 1689 and 1713 to conclude that these elements also served to create trust within state structures, and that even political partisanship – normally dismissed as a disruptive, even destructive, influence – generated a community of shared political interests that encouraged trust and improved coordination. It also demonstrates that officials, politicians and financiers constructed politicised networks that interlocked efficiently with each other, permitting the improved coordination of public and private credit, and even informal financial intermediation intended to maintain the liquidity of the army’s fiscal structures. It therefore concludes that the success of the British fiscal-military state during this period was the product of improved informal coordination rather than institutional change and bureaucratic reform, and that political partisanship was integral to this process.
DifFUZZY: a novel clustering algorithm for systems biology
Keywords: malaria
genetic expression data clustering
fuzzy clustering
diffusion distance
clustering algorithm

Current studies of the highly complex pathobiology and molecular signatures of human disease require the analysis of large sets of high-throughput data, from clinical to genetic expression experiments, containing a wide range of information types. A number of computational techniques are used to analyse such high-dimensional bioinformatics data.
In this thesis we focus on the development of a novel soft clustering technique, DifFUZZY, a fuzzy clustering algorithm applicable to a larger class of problems than other soft clustering approaches. This method is better at handling datasets that contain clusters that are curved, elongated or are of different dispersion. We show how DifFUZZY outperforms a number of frequently used clustering algorithms using a number of examples of synthetic and real datasets. Furthermore, a quality measure based on the diffusion distance developed for DifFUZZY is presented, which is employed to automate the choice of its main parameter.
We later apply DifFUZZY and other techniques to data from a clinical study of children from The Gambia with different types of severe malaria. The first step was to identify the most informative features in the dataset which allowed us to separate the different groups of patients. This led to us reproducing the World Health Organisation classification for severe malaria syndromes and obtaining a reduced dataset for further analysis. In order to validate these features as relevant for malaria across the continent and not only in The Gambia, we used a larger dataset for children from different sites in Sub-Saharan Africa. With the use of a novel network visualisation algorithm, we identified pathobiological clusters from which we made and subsequently verified clinical hypotheses.
We finish by presenting conclusions and future directions, including image segmentation and clustering time-series data. We also suggest how we could bridge data modelling with bioinformatics by embedding microarray data into cell models. Towards this end we take as a case study a multiscale model of the intestinal crypt using a cell-vertex model.
Hired to be daughters: domestic service among ordinary Moroccans
Keywords: kinship
women workers
servants
labour
rural-urban migration
gender
Morocco
Domestic service
domestic workers

This thesis explores why shaʿbī (roughly, ‘ordinary’) Moroccans so often talk about their domestic workers as daughters, what this means for workers and employers, and how this is changing as community gives way to market. It brings together ethnographic study of urban shaʿbī society, of unmarried rural women who work as domestics, and of the communities from which the latter migrate.
Drawing on anthropological discussions of kinship and fosterage, the thesis examines the fading tradition of ‘bringing up’ in which, according to a moral economy, a ‘known’ rural girl could properly be placed in the homes of wealthier Moroccans until marriage. This is giving way to new arrangements in which ‘unknown’ workers are paid a wage and may not stay long, but in which the ethics of charity, religious reward and gratitude still inform expectations from both sides. Geared to play out among neighbours, or at least well-known clients, over a lifetime, these ethics are being disrupted by the easy-come-easy-go of strangers.
The thesis contributes to some fundamental concerns of economic anthropology: the atomisation of market exchange, the growing importance of physical marketplaces, and the meanings encoded in a monetary wage versus payment in kind. By putting together perspectives from domestics’ leisure time and life back home, it also questions the relationship between the commodification of labour and individualism. Finally, the thesis discusses a draft law which, if enforced, would mean employing domestics no longer made sense for shaʿbī Moroccans, state intervention respresenting a move away from local forms of empowerment and community.
At a broader level, the thesis is concerned with households as internally hierarchical units linked together through exchange to make up society and explores the gendered dimension of household economy in a wider world. This, of course, reaches beyond Morocco, and parallels are suggested with English domestic service.
Nucleophosmin and p14ARF mediated regulation of p53
Keywords: acute myeloid leukemia
nucleophosmin
AKT
p53
therapeutic resistance
p14ARF

Tumour initiation and progression occur due to oncogenic mutations that also contribute to therapeutic resistance in many human tumours. Mutations activating the "PI3K/AKT" signalling pathway and inactivating the "TP53" tumour suppressor gene are common mechanisms that cancer cells require to proliferate and escape pre-programmed cell death. p53 mutant (p53mut) tumours not only fail to respond to DNA damaging therapy, but are also described to promote therapeutic resistance by dominant negative suppression of p53 dependent promoter activity. Our work identifies the crucial interaction between the PI3K/AKT pathway and p53 mutations that regulate treatment sensitivity in tumours.
Using a combination of in vitro and in vivo techniques we demonstrate that AKT inhibition promotes reduced cellular levels of p53mut via a novel Nucleophosmin 1 (NPM) mediated regulation of the tumour suppressor p14ARF and promotes re-engagement of cell cycle arrest, senescence and increased sensitivity to ionising radiation in both in vivo and in vitro systems. We show that the PI3K/AKT pathway plays an important role in the regulation of p53mut and inhibitors of this pathway can re-sensitise treatment resistant tumours. This has helped us to simultaneously highlight the cohort of patients where the greatest efficacy may be achieved in clinical practise.
We further show that the AKT mediated regulation of NPM that we describe in solid tumours is relevant in Acute Myeloid Leukaemia (AML) with mutated NPM, albeit showing physiologically different effects. This further highlights the necessity for rational treatment planning with the newer targeted agents that inhibit specific signalling pathways in AML patients.
Constructing a conservative: the reception of Edmund Burke in British politics and culture, c. 1830-1914
Keywords: Conservative Party
Nineteenth-Century Political History
Conservatism
British Intellectual History
Edmund Burke
Victorian Political Thought

Between 1830 and 1914 in Britain a dramatic modification of the reputation of Edmund Burke (1730-97) occurred. Burke, an Irishman and Whig politician, is now most commonly known as the 'founder of modern conservatism' – an intellectual tradition which is also deeply connected to the identity of the British Conservative party. Indeed, the idea of 'Burkean conservatism’ – a political philosophy which upholds ‘the authority of tradition', the organic, historic conception of society, and the necessity of order, religion, and property – has been incredibly influential both in international academic analysis and in the wider political world. This is an intellectual construct of high significance, but its origins have not hitherto been understood: insofar as it has been considered at all, it has been typically seen as the work of Cold War American conservatives. In contrast, this thesis demonstrates that the transformation of Burke into the 'founder of conservatism' was in fact part of wider developments in British political, intellectual, and cultural history in the nineteenth and early twentieth centuries.
Drawing from a wide range of sources, including political texts, parliamentary speeches, histories, biographies, and educational curricula, this thesis provides a properly contextual history of political thought. It shows how and why Burke's reputation was transformed over a formative period of British history. In doing so, it bridges the significant gap between the history of political thought as conventionally understood and the history of the making of political traditions. The result is to show that, by 1914, Burke had been firmly established as a 'conservative' political philosopher and was admired and utilised by political Conservatives in Britain who identified themselves as his intellectual heirs. This was one essential component of a conscious re-working of 'C/conservatism', especially from the mid-1880s, which is still at work today
A glycopore for bacterial sensing
Keywords: Alpha-hemolysin
glycopore
bacterial sensor
multivalency

Increasing antibiotic resistance has created a need to develop rapid and reliable methods to identify bacteria and provide pertinent information to ensure suitable antibiotics or sugar therapeutics can be chosen for treatment. Carbohydrate structures attached to proteins on host cell surfaces provide a binding point for many pathogens, including bacteria. These structures can be mimicked using single monosaccharides glycosylated to alpha-hemolysin (alpha-HL). Alpha-HL is a beta-barrel pore-forming toxin secreted by Staphylococcus aureus that forms an SDS stable heptamer, which can be expressed by coupled in vitro transcription and translation and purified by polyacrylamide gel electrophoresis. The purified heptamers can be reconstituted into planar lipid bilayers and studied at the single channel level. Through single channel recordings the effects of sugar-linker lengths, different glycans and the interaction between the ‘Glycopore’ and sugar binding molecules can be studied. The glycopore, therefore, acts as a scaffold for analysing protein-sugar interactions. Studies in this thesis have focused on the synthesis of carbohydrates for site-selective protein glycosylation; cloning and in vitro transcription translation of alpha-HL monomers; and glycosylation and oligomerisation of alpha-HL to form glycopores suitable for lectin-binding studies. Lectins DC-SIGN and FimH have been expressed in Escherichia coli and these lectins as well as others have been screened using alpha-HL glycopores. The glycopores have also been investigated with bacteria in serum in a controlled molecule-specific manner using single-channel electrical recording. In this work glycosylated alpha-HL-monomers have been found to form stable heptamers which can be formed by oligomerisation on red blood cell membranes. The purified glycopores were reconstituted into planar lipid bilayers and studied at the single-channel level. Through single-channel recordings an optimised glycopore has been shown to be effective in distinguishing lectins alone and in a mixture and has afforded qualitative and quantitative information about the binding interactions between carbohydrates and sugar binding proteins. Furthermore, the glycopore has been used to sense bacteria which may provide an insight into modes of bacterial infection. In addition, a multivalent glycopore has been formed which has proved preliminary information about the effects of multivalency in lectin binding. The design and synthesis of non-beta-lactam antibiotic candidates and their evaluation has also been carried out.
Investigating the role of memory on pain perception using FMRI
Keywords: pain
primary sensory cortex
FMRI
imagined pain
perception
short-term memory

It is now widely accepted that the experience of pain is subject to cognitive influences that may determine the severity of subjectively perceived pain. Many of these top-down factors rely on memory-based processes, which in turn are related to prior experience, learned beliefs and behaviours about pain. As such, memory for pain heavily contributes to the physical pain experience. We posit that pain memory is bidirectional in that following each painful event a trace is stored and that these traces in turn may modify future pain perception prospectively. The following body of work explores aspects of what we have termed a memory template for pain. The results of these chapters taken together, examine these bidirectional aspects of short-term memory for pain employing a recall pain task. Specifically, we explore how, after an acute pain event, a short-term mental representation of the initial event persists. We show that during this time, sensory re-experiencing of the painful event is possible. Furthermore, we investigate aspects of recalled pain, namely intensity and vividness. Data suggests that the intensity and the vividness of this mental representation are determined by the intensity of the initial stimulus, as well as the time-to-test delay. We identify regions that characterise short-term memory for pain. Following on from studies in motor and visual imagery, we explore how pain imagery in the form of recall may affect subsequent pain perception. Our results demonstrate that the inclusion of pain-related imagery preceding physical pain events reduces affective qualities of pain. Testing healthy, naïve subjects, we replicate the effect observed in studies using attention management and imagery strategies, which normally require extensive training. Finally, in a cohort of neuropathic pain patients we show significant reductions in white matter connectivity between areas responsible for working and prospective memory. Collectively, these studies emphasise and elucidate the role of short-term memory of pain in physical pain perception. Acting both retrospectively and prospectively, cognitive reinforcement can increase or decrease the subjective feeling of pain, and therefore manipulating how pain is recalled may have therapeutic potential.