VictorJuiz/thesis huggingface dataset:
Behavioural adjustments of lion (Panthera Leo) in response to risk of human-caused mortality

Fear of predation can have a major impact on the behaviour of prey species. Despite recent codifying of the concept of the ecology of fear, there has been relatively little focus on how these ideas apply to large carnivore species which, although not prey sensu stricto, may experience fear as a result of threats from humans. This thesis argues that large mammalian carnivores are subject to a Landscape of Fear similar to that described for prey species, and will respond behaviourally to fear of human-caused mortality.
The idea of a "Landscape of Coexistence" is introduced to denote the perceived risk from humans and associated behavioural responses that can be overlain on spatio-temporally heterogeneous landscapes. Literature on the ecology of fear for large mammalian carnivores and, as there is a dearth of such literature, the current theory on the ecology of fear for other guilds is reviewed, and how this might inform large carnivore behaviour in a Landscape of Coexistence is explored. Behavioural effects of human-caused mortality risk are revealed for lions living in a human dominated landscape (Laikipia County, Kenya), specifically how lions adjust their movement patterns, habitat use and foraging tactics when in proximity to humans. It is argued that these behavioural adjustments represent a trade-off between maximising fitness enhancing activities and minimising the risk of human-caused mortality, thus need to be taken into consideration along with the lethal effects of humans when explaining the density, distribution and behaviour of lions throughout much of their remaining range.
Although fear is generic, 'human-caused mortality risk' represents a distinct and very important sub-set of the ecology of fear for the carnivore guild. The existence of a Landscape of Coexistence has implications for understanding their foraging ecology, and ultimately their population dynamics and role in the ecosystem, and is therefore, important for the conservation of large carnivores throughout large parts of their remaining ranges.

Keywords: Lion behavioural ecology
Landscape of coexistence
Human carnivore conflict
Ecology of fear
Advisor: Macdonald, D
Tense networks: exploring medical professionalization, career making and practice in an age of global empire, through the lives and careers of Irish surgeons in the Indian Medical Service, c. 1850-1920

This thesis explores the historical relationships between the professionalization of medicine and Britain's Empire across the Indian subcontinent between c. 1850-1920. That relationship is focused on through the lives and careers of Irish surgeons who, over the course of the period, enlisted in the IMS, the GoI's paramilitary medical service.
As a result of tracking the networks these men occupied between Ireland and India, professional status emerges as a series of negotiations between the State and the profession, negotiations that were in turn a result of cultural values, social relations and institutional politics. Such a view of professionalization stands in distinction to the predominant narrative authored to date about our period. Within that narrative, occupations that became and maintained professional status did so through cordoning off areas of knowledge in the pursuit of financial gain and socio-political prestige. That approach has fostered assumptions about the ease of relations between States and professions. Furthermore, little has been written about how those relations were shaped, and disrupted, by the dominant polity of the time: global empires.
Britain's Empire undoubtedly aided the professionalization of medicine. Our first two chapters highlight how the subjects of this thesis were drawn from a variety of social, cultural and economic backgrounds, whose differences were, to an extent, ameliorated by a growing professionalism in medicine. That professionalism was incubated by the material needs of Britain's Empire, especially in India, which triggered administrative reforms to rationalise entrance requirements to the IMS, and provide potential applicants with a seemingly sure-footed career path. However, life in India for these medical men was not as well administered. Although the GoI required their professional services, politicians and administrators were not as keen to acknowledge their professional status, except for when absolutely necessary to uphold the moral order of imperial rule.

Advisor: Harrison, M
A molecular dynamics study of the vascular endothelial glycocalyx layer

The luminal surface of endothelial cells which line the vasculature is coated with a layer of membrane-bound macromolecules of a mixed carbohydrate and protein nature, collectively described as a glycocalyx, from the greek meaning "sweethusk/covering". Experiments have consistently revealed the pivotal role of the endothelial glycocalyx layer in vasoregulation and the layer's contribution to mechanotransduction pathways. However, the exact mechanism by which the glycocalyx mediates and interprets fluid shear stress remains elusive. This study employsatomic-scale molecular simulation with the aim of investigating the conformational and orientation properties of the highly flexible components of the glycocalyx and their suitability as transduction molecules under hydrodynamic loading. To this aim, two molecular dynamics systems were constructed. The first system focused on the impact of flow on a tethered, branched, oligosaccharide. Fluid flow was shown to only moderately affect the conformation populations explored by the oligosaccharide, in comparison to static conditions. On the other hand, the glycan exhibited a significant orientation change, when compared to simple diffusion, aligning itself with the flow direction. The tethered end of the glycan, an asparagine amino-acid, experienced conformational changes as a result of this flow-induced bias. Results of the "glycan in flow" model suggest that shear flow through the layer can have an impact on the conformational properties of saccharide-decorated transmembrane proteins, thus probably acting as a mechano-transducer. The second system consisted of charged and non-charged heparan sulfate, a component found in large quantities in the endothelial glycocalyx layer. Systems of paired heparan sulfate strands were investigated under conditions of increasing proximity, which is the expected effect of compression of the layer under the effect of flow; a process explored formally using the adaptive biasing force method. This approach warranted the implementation of enhanced sampling for the high energy states of heparan sulfate in close proximity. Results of the heparan sulfate model suggest that areas of locally high charge density within the glycocalyx, generally areas of high sulfation, are characteristically more resistant to compression than non-sulfated areas. The sulfation mix therefore emerges as an important determinant of glycocalyx mechanical properties.

Advisor: Ventikos, Y
Payne, S
Lung cancer assistant: a hybrid clinical decision support application in lung cancer treatment selection

We describe an online clinical decision support (CDS) system, Lung Cancer Assistant (LCA), which we have developed to aid the clinicians in arriving at informed treatment decisions for lung cancer patients at multidisciplinary team (MDT) meetings. LCA integrates rule-based and probabilistic decision support within a single platform. To our knowledge, this is the first time this has been achieved in the context of CDS in cancer care.
Rule-based decision support is achieved by an original ontological guideline rule inference framework that operates on a domain-specific module of Systematized Nomenclature of Medicine-Clinical Terms (SNOMED-CT), containing clinical concepts and guideline rule knowledge elicited from the major national and international guideline publishers. It adopts a conventional argumentation-based decision model, whereby the decision options are listed along with arguments derived by matching the patient records to the guideline rule base. As an additional feature of this framework, when a new patient is entered, LCA displays the most similar patients to the one being viewed.
Probabilistic inference is provided by a Bayesian Network (BN) whose structure and parameters have been learned based on the English Lung Cancer Database (LUCADA). This allows LCA to predict the probability of patient survival and lay out how the selection of different treatment plans would affect it.
Based on a retrospective patient subset from LUCADA, we present empirical results on the treatment recommendations provided by both functionalities of LCA and discuss their strengths and weaknesses. Finally, we present preliminary work, which may allow utilising the BN to calculate survival odd ratios that could be translated into quantitative degrees of support for the guideline rule-based arguments. An online version of LCA is accessible on http://lca.eng.ox.ac.uk.

Keywords: Bayesian Networks
Ontologies
Advisor: Bañares-Alcántara, R
Brady, M
The regulation of mobile money

This thesis examines the regulation of 'mobile money'. This is an electronic payment and storage service provided by phone companies ('mobile money firms' or 'MM firms'). The first mobile money service, M-Pesa, was launched in Kenya in 2007. Since then, mobile money has spread rapidly throughout the developing world, particularly across Africa. A novel feature of mobile money is its ability to serve large numbers of people who do not have bank accounts, commonly labelled 'the unbanked'.
The thesis offers a framework, based on a functional approach, to analyse the key regulatory and policy issues that arise when customers’ funds are stored and transferred within mobile money platforms. The objectives of this framework are drawn from traditional financial regulation, such as financial stability and consumer protection, and 'financial inclusion', which involves connecting the unbanked to formal, electronic payment and storage functions.
The thesis makes three main claims. First, mobile money operates as a shadow retail deposit system. Mobile money is 'shadow' because a customer contracts with a non-banking firm. It is 'retail' because the system meets the payment needs of individuals for ordinary transactions. And the service is a 'deposit' system because a mobile money account provides payment and storage functions which are functionally equivalent to a bank deposit.
Second, mobile money provides these payment and storage functions, functionally equivalent to a bank deposit, through a different legal structure to that used by a bank to provide deposit account services. This structure, which is established through private ordering, comprises a set of mechanisms by which the MM firm (the 'agent' in the service) and its associates credibly commit to safeguard the funds of the mobile money customers (the 'principals') for the purposes of providing payment and storage functions.
Collectively, these commitments require the MM firm to maintain a 1:1 relationship between cash received from customers, which is stored within the system as highly liquid assets, and 'e-money' which customers use in the mobile money service. As a result, mobile money customers face primarily operational risks, usually without the credit and liquidity risks associated with banking.
Third, public ordering can increase the efficiency of MM firms' commitments in addressing risks in mobile money platforms through adopting an 'active' approach to regulation. In this approach, the policymaker monitors a greater range of risks and more closely than what might be expected in other comparable principal-agent relationships, such as retail investors and financial intermediaries, and depositors and banks. This approach is appropriate because unbanked customers are likely to face significant information asymmetries with MM firms and coordination problems amongst themselves. This means they are unlikely to effectively monitor a range of risks to the service caused by the MM firm and its associates.

Keywords: Mobile money
Payments
Financial Regulation
Africa
Advisor: Armour, J
The relationship between theology and politics in the writings of John Lilburne, Richard Overton and William Walwyn

In assessing the relationship between theology and politics in the writings of the three major Leveller pamphleteers of the 17th century, scholars have tended to search for, and focus upon, individual aspects of one or other of the Levellers' respective theological positions which they consider to have had democratic implications - as, for example, the notion of congregational church government, or a universalist understanding of salvation - which are then deemed to have been foundational to their political theories.
But this approach is too abstract. The development of the Leveller platform can best be understood if it is seen as the attempt to answer a question posed by the Presbyterian opponents of religious liberty, and in particular, by William Prynne. In effect, the question was this: how can a society avoid anarchy and continue to exist in any civilised form if the social cement of established religion is removed? Prynne asked this of the Independents and sectaries in civil war England in the belief that there could be no satisfactory answer.
Lilburne, Overton and Walwyn sought to provide one by appealing to principles drawn from the law of nature. The major influence on the development of their political thinking was the revolutionary theory of natural rights which underpinned Parliament's struggle against the King Theology was but a secondary factor.
It was the fundamental secularity of the Levellers' approach which led to its rejection in 1649 by leading Independents and sectaries, whose own separatism was modified by millennialism and notions of 'godly rule'. Thus, while the Levellers' political platform developed as an attempt to translate into reality the separation of church and state that was at the heart of separatist ecclesiology, it failed because of the opposition of the very people whose ideas it was intended to reflect and embody.
The Life of S. Pancratius of Taormina

The Life of S. Pancratius of Taormina describes the mission and martyrdom of S. Pancratius, a disciple of the Apostle Peter sent to evangelize Taormina as its first bishop, and purports to have been written by S. Pancratius’ successor, Evagrius. It also records details concerning S. Marcian, who was dispatched to Syracuse at the same time. The text exists in three recensions. The editio princeps of the first recension is presented here, based on six manuscripts (Vat. Gr. 1591, Mess. S. Salv. 53, Crypt. BβV, Vat. Gr. 1985, Vind. Hist. Gr. 3 and Vat. Ottobon. Gr. 92), together with an introduction and commentary. External and internal evidence has been used to argue that it should be dated to the early eighth century and that it is of Sicilian provenance. The analysis of the sources of the text and its presentation of the apostolic era contributes to our understanding of the Byzantine attitude to the past and of the novelistic approach to hagiography. The Life is a product of an important, but obscure period of Sicilian history, and it provides some evidence from a local perspective concerning matters such as ecclesiastical arrangements and attitudes in Sicily, views about religious images, practices in church decoration, liturgical rites, book production, the development of legends concerning the apostles, especially S. Peter, civil and military administration, the Sicilian language question, the topography of Sicily and Calabria and contacts with Lombardy, as well as curious references to Slavs and Avars in Sicily. The Commentary is concerned with these questions and in general with the exegesis of the text. A summary of the use made of the Life of S. Pancratius by later writers contributes to our understanding of the iconoclastic controversy. An edition of the Encomium of S. Pancratius by Gregory the Pagurite, probably written in the early ninth century, has been included in an Appendix.

Keywords: Pancratius
Taormina
saints
The politics of counterinsurgency and statemaking in modern India

This thesis undertakes a study of the modern state in India in the context of counterinsurgency. Through a combination of ethnographic and historical methods, it explores the processes and practices of state formation and legitimacy-building in an erstwhile Maoist guerrilla zone of the eastern Indian state of West Bengal. The colonial and postcolonial histories of this forested region, known popularly as the Jungle Mahals, are punctuated by moments of violent conflict and regime-change. These moments of rupture have tended to periodically reorder the relationships between the modern state and its ordinary subjects. Accordingly, the thesis reconstructs a trajectory of state-society relations in the Jungle Mahals from the early colonial era, when East India Company officials created a modern state apparatus to deal with rural rebellions, to the present, when the Indian government has pursued a 'development' agenda to wean ordinary people away from Maoist rebels. I show that periods of insurgency and counterinsurgency ought to be recognised as critical junctures in the history of the modern state in frontier regions such as the Jungle Mahals.
The modern state is made and remade in the course of counterinsurgency as both state and rural society are reordered in tandem from above and below. Hence, I make a case for studying the state, understood as both an idea and a set of material practices, from 'within', that is, as emerging through the mediation of actors who represent the state and ordinary villagers in my fieldsites. Furthermore, through an exploration of ordinary villagers’ responses to counterinsurgency in the Jungle Mahals, this thesis argues that popular responses to counterinsurgency cannot be explained through the binaries of resistance and complicity. In other words, it is necessary to examine the complex textures of people's lives and subjectivities vis-à-vis the state during and after counterinsurgencies in order to appreciate how statemaking in such circumstances, far from being a top-down imposition on hapless subjects, emerges from below as well.

Keywords: state-society relations
counterinsurgency
India
development
Maoism
the state
Advisor: Gooptu, N
Measurements of the K-shell Opacity in Solid-density Plasmas heated by an X-ray Free Electron Laser

The advances achieved using X-ray Free Electron Lasers such as the Linac Coherent Light Source (LCLS), have revolutionised the routine production of uniform solid-density plasmas. Pulses of X-rays above 1 keV and with durations shorter than 100 fs attaining intensities on target of around 1017 Wcm-2 are now routinely created. Through simple single-photon photoionization events with atoms in ambient solid conditions, it is possible to create uniform samples that are simultaneously hot, dense, and highly ionized which may be easily modelled.
This thesis describes measurements of the spectrally-resolved X-rays emitted from solid-density magnesium targets of varying sub-μm thicknesses isochorically heated by an X-ray laser. The data exhibit a thickness-independent source function, allowing the extraction of a measure of the opacity to K-shell X-rays within well-defined regimes of electron density and temperature, extremely close to Local Thermodynamic Equilibrium conditions by fitting to the simple 1D slab solution of the equation of radiative transfer. The deduced opacities at the peak of the K-α transitions of the ions are consistent with those predicted by detailed atomic-kinetics calculations.
The extracted opacities transpire to be robust to a plethora of variations in X-ray drive conditions, including the shape, pulse-length, and energy content. Furthermore the approximations in using the 1D slab solution are examined in detail and found to be good.
A full three-dimensional model of the plasma is advanced which includes attenuation, line-of-sight effects, full longitudinal and transverse gradients, and photon time-of-flight effects. The results from this model are found to also agree with the simpler 1D slab solution.
This novel method of elucidating opacities may complement other methods based on absorption and could be important for further benchmarking of opacities in solar-interior relevant conditions.

Keywords: Hot Dense Matter
Atomic Physics
Plasma Physics
X-ray spectroscopy
X-ray Free Electron Lasers
Advisor: Wark, J
Phase-change materials for photonic memories and optoelectronic applications

The content of this thesis encompasses the fundamentals, modelling, chip design, nanofabrication process, measurement setup, and experimental results of devices exploiting the optical properties of phase-change chalcogenide materials. Special attention is paid to integrated Si3N4 nanophotonic circuits for optical switching and memory applications, as well as to multilayer stacks for colour modulation.
Herein, the implementation of the first robust, non-volatile, phase-change photonic memory is presented. By utilising optical near-field effects for Read, Write and Erase operations, bit storage of up to eight transmission levels is demonstrated in a single device employing Ge2Sb2Te5 as the active material. These on-chip memory cells feature single-shot read-out of the transmission state and switching energies as low as 13.4pJ at speeds approaching 1GHz. The capability to readily switch between intermediate states is also demonstrated, a feature that requires complex iteration-based algorithms in electronic phase-change memories. This photonic memory is not only the first truly non-volatile memory---a long-term elusive goal in integrated photonics---but could also potentially represent the first multi-level memory, including electronic counterparts, that requires no computational post-processing or drift correction. These findings provide a pathway towards solving the throughput limitations of current computer architectures by eliminating the so-called von-Neumann bottleneck and portend a new paradigm in all-photonic memory, non-conventional computing, and tunable photonic devices.
Finally, novel capabilities in electro-optic colour modulation using phase-change materials are demonstrated. In particular, this thesis offers the first implementation of Ag3In4Sb76Te17-based optical cavities for colour modulation on low-dimensional multilayer stacks. Moreover, "gray-scale" image writing is demonstrated by establishing intermediate levels of crystallisation via voltage modulation. This finding, in turn, corresponds to the first demonstration of nonvolatile colour-depth modulation in the emerging phase-change materials nanodisplay technology, featuring resolutions down to 50nm. Furthermore, a comprehensive comparison is carried out for two types of materials: growth- (Ag3In4Sb76Te17) and nucleation-dominated (Ge2Sb2Te5) alloys in terms of colour, energy efficiency, and resolution. These results provide new tools for the new generation of bistable and ultra-high-resolution displays and smart glasses while allowing for other potential applications in photonics and optoelectronics.

Keywords: Phase-change photonics
Phase-change chalcogenide photonics
Non-volatile memories
Phase-change nanodisplay
Photonic memories
Advisor: Bhaskaran, H