VictorJuiz/thesis huggingface dataset:
Genetic and environmental factors influencing susceptibility to the complex disease multiple sclerosis

Multiple sclerosis is a complex immune mediated condition of the central nervous system characterized by myelin loss and progressive neurodegeneration. The risk of developing MS is influenced by both genetic and environmental agents and, among them, several lines of evidence support a role for vitamin D deficiency, Epstein-Barr virus (EBV) infection and smoking in the aetiology of this disease. The aim of this work was to further elucidate how nature and nurture act in the causal cascade leading to MS. In chapter 1, I show that the main genetic factor in adult MS (the HLA-DRB1*1501 allele) plays an equally important role in paediatric cases of MS (PMS) and that EBV negative PMS patients represent a separate entity characterized by lower age at disease onset, lower female to male ratio and a trend towards a lower frequency of the HLA-DRB1*1501 allele. In chapter 2, I provide evidence in support of month of birth having a role on MS risk and T cell production and that vitamin D may underlie this effect. In chapter 3 I demonstrate the presence of a link between vitamin D deficiency and the immune response against EBV, whereby the proportion of EBV seropositive MS patients and controls increases with increasing latitude and high dose vitamin D supplementation appears to reduce the level of antibodies against this virus. In chapter 4, I show that MS associated genetic variants are located in genomic regions that exert a regulatory function and are active in immune cell types. In chapter 5, I illustrate how vitamin D receptor binding is also located within active regulatory regions in immune cells and that this is particularly evident near MS associated genes. Finally, in chapter 6, I use chromatin data on more than 100 different cell types and conclude that MS associated genetic variants are particularly active in T helper, T cytotoxic and B cells. Further work is needed to elucidate how genetic and environmental agents play a role in the cause of MS and to develop effective strategies for disease treatment and prevention.

Keywords: Multiple sclerosis
Epstein-Barr virus
genetics
vitamin D
risk factors
Advisor: Ebers, G
Ramagopalan, S
What factors assist clinicians to determine dying in an acute setting?

Background: The End of Life Care Strategy stated that there should be a reduction of expected deaths in the acute setting. In order to achieve this goal, when it has been identified that where the patient's preferred place of care is home, clinicians need to be able to recognise when a patient is dying in order to achieve their preferred place of death. The aims of this study were to identify any factors that help or hinder a clinician when they are determining when irreversible dying begins and to seek consensus on which of these topics would be useful to include in an education programme.
Method: A 3 stage mixed methods study was developed. Phase 1was a Systematic Review of current primary research in order to provide an evidence base for the study. Phase 2 involved unstructured interviews with clinicians in the acute setting utilising the Grounded Theory approach to the analysis identify potential factors. Phase 3 was a Delphi study used to identify which of these factors would be useful in an education programme.
Conclusions: The Systematic Review identified four themes "Patient Observation", "Knowledge of the Patient", "Communication" and "Attitudes of the Clinician". These were confirmed by the interviews and a further theme "Experience" identified. The over-arching theme emerging from the findings of the interviews was that clinicians have a fear of getting the timing of the recognition of irreversible dying wrong because the decision making process is so complex and this is exacerbated by fear of missing the treatable. Many factors identified in the interviews were acknowledged as factors that could be included in an education package. It was also identified that there is the need for a culture shift in society regarding death and dying and a change in the philosophy of care for health care professionals.

Keywords: end of life
dying
terminal
fultility
palliative
Advisor: Wee, B
Endacott, R
Stochasticity in foraging theory: risk and information

This thesis considers the importance of adding stochasticity to models of optimal foraging behaviour. The problem is divided into two elements, risk and information, which are treated separately.
Part One: Risk. The theoretical and empirical results concerning animal preferences in risky situations are reviewed. Animals are known to show both risk-averse and risk-prone preferences over food reward. It is shown, theoretically, that a simple optimality model mimimizing the probability of death due to starvation accounts for at least some of the observed patterns of preference. The model is generalized to consider preference from arbitrary combinations of mean and variance. Three limitations of the model are treated in detail, that is the importance of starvation by "ruin", mind-changing about risk preferences, and energetic carry-over are discussed. The implications and limitations of these models are outlined.
Part Two: Information. The theoretical literature is reviewed, and the problem of information is divided into three elements.
A simple model of environmental tracking is studied. The model suggests that there is a trade-off between sensitivity to change and the costs of sampling. The model is tested using great tits (Parus major) foraging in an aviary. The trend in sampling was as predicted, but the birds were less sensitive to change than predicted.
The problem of patch sampling is critically discussed. The value of sampling is defined, and this definition is used to compare the assumptions of previous models. Three such problems are treated: the importance of variance in the mixing distribution of patch sub-types; the importance of alternative and unambiguous patch types; and the importance of patch depression. It is concluded that previous models have often over-valued sampling. A simple and natural model of partial patch recognition is considered, and is shown to have empirical support. Implications and limitations of these models of information are discussed.

Keywords: stochasticity
optimal foraging behaviour
environmental tracking
Advisor: Krebs, J
Houston, A
The Arnoldian element in Yeats's A Vision

In this study of the influence of Matthew Arnold on W.B. Yeats, I describe a tendency in the critical field to overlook the placement of Arnold at Phase 18, and the implications of his presence beside Yeats at Phase 17, in Yeats’s key philosophical treatise A Vision (1926, 1937). The central contribution of my thesis is to address this crucial blind spot but also the concomitant failure by critics to consider Arnold’s overall bearing on the ‘System’ itself. Chiefly through analysis of the gyres, two types of man, and lunar phases of the Great Wheel, I trace five main, interrelated aspects comprising ‘the Arnoldian element’ in A Vision: 1) Romanticism; 2) morbidity; 3) Celticism; 4) culture; and 5) the over-arching ideal of ancient Greek genius. My thesis that Arnold is paramount to Yeats’s poetical and political concerns in the treatise demonstrates how the Arnoldian element – including a covert extension of Yeats’s dialogue with Arnold in “The Celtic Element in Literature” (1897) – within its abstruse occult discourse partly but powerfully shapes: 1) the projection of Irish self-rule and unity, principally in the figure of the Daimonic Man of the ideal Phase 17 (Yeats) subversively juxtaposed with the fragmenting Emotional Man of Phase 18 (Arnold and Goethe), in a time of anarchy; and 2) the representation of a range of phasal examples (named and unnamed, encompassing both literature and sexual love). I argue that Yeats’s considerable indebtedness to Arnold 1) both spurs and troubles readings of Yeats as a poet of decolonization; 2) merits attention in the long-running ‘Orwellian’ debate over Yeats’s alleged fascism, coinciding with Yeats’s eugenics; 3) illuminates A Vision as an ‘anxiety of influence’ text in which Yeats ‘kills’ his critical fathers Arnold and J.B. Yeats; and 4) warrants Arnold’s routine inclusion among Yeats’s foremost influences like Nietzsche, Blake, Dante, and Shelley whose portrayals in A Vision are partly bound up, as I show, with Yeats’s engagement with Arnold.

Keywords: Arnold
A Vision
Yeats
Advisor: O'Donoghue, J
Consumed yet quickened by the glance of God: John Henry Newman's Theology of Purgatory

This thesis outlines the development of the doctrine of Purgatory in the theology of the nineteenth century theologian John Henry Newman (1801-1890). I trace the beginning of this development from 1816-1828 by identifying key theological themes from Newman’s early Evangelical writings on holiness, purification and conversion. After rejecting the Evangelicalism of his youth, Newman moved progressively towards High-Church Anglicanism from 1828 onward, and adopted the Anglican teaching of the 'intermediate state'. From 1830 he began to preach on this teaching by presenting it as an alternative to the 'depressing prospect' to the 'Romish' doctrine of Purgatory. However from 1837-1845 his views on Purgatory shifted considerably after studying the Tridentine decrees. In 1841 he claimed in Tract XC of Tracts for the Times that significant changes in the formulation of Article XXII of the XXXIX Articles meant that the Church of England did not reject the doctrine of Purgatory in its primitive form, but rather only the 'Romish' extremes of mediaeval theology which had corrupted her teaching. His claim that there was no disparity between what Trent taught on Purgatory and what the Church of England held in Article XXII caused widespread controversy among his contemporaries.
In his early Roman Catholic years, from 1845-1853, he initially adopted the commonly held punitive model of Purgatory, but leaned increasingly towards an ameliorative understanding of the doctrine. By 1865 Newman had adumbrated a theology of Purgatory in The Dream of Gerontius, in which he showed how rather than being purged by material fire, the soul was purified by a singular and instantaneous experience of the holiness of God. I demonstrate how his theology of Purgatory in the Dream represents a significant contribution to a renewed understanding of the doctrine in Roman Catholic theology.

Keywords: Eschatology
Oxford Movement
John Henry Newman
Doctrine
Dream of Gerontius
Purgatory
Advisor: Ker, I
Vision-based demonstratives

How should we account for our ability to entertain simple, vision-based demonstrative thoughts about particular objects (that is, our ability to entertain thoughts about particular objects simply on the basis of seeing them)? In this thesis I propose an account of this ability that accords with the common-sense view that seeing an object puts one in a position to single it out by visually attending to it, and that this provides one with the ability to entertain demonstrative thoughts about it.
An account of this type requires that we account for what it is to see a particular object and to visually attend to it without appealing to particular demonstrative abilities. However, it has been argued that a notion of seeing an object, and similarly a notion of attending to an object, which is accounted for in this way is unsuitable for accounting for demonstrative abilities.
I argue that there is no real problem: what we need is a notion of experiential content which is concept-dependent only in a general manner. That is, the account of the relevant notion of experiential content requires appeal to the subject's conceptual abilities, but the account is not given in terms of specific conceptual abilities (especially, not specific demonstrative abilities). I then characterize a notion of attention to a seen object which can be accounted for without appeal to particular demonstrative abilities, and explain how attending to an object in the relevant sense provides the subject with the ability to think about the object demonstratively.
It is widely agreed that spatial location plays a central role in an account of demonstratives. I explain this role in terms of the role played by location in visual attention to the object and the subject's grasp of the fact that he attends to the object.

Advisor: Professor John Campbell, N
Ultrafast and continuous-wave spectroscopy of multiferroic oxide thin films

Thin film multiferroic oxides with co-existing ferroelectric and ferromagnetic ordering have attracted much interest in recent years, partly as a result of the enhancements achieved through the adoption of strained thin film geometries. This thesis presents work on two such thin film oxides; lanthanide substituted BiFeO3 and Fe substituted PbTiO3.
Coherent magnons and acoustic phonons were impulsively excited and probed in thin films of the room temperature multiferroic Bi1-x-yDyxLayFeO3 using femtosecond laser pulses. The elastic moduli of rhombohedral, tetragonal and rare-earth doped BiFeO3 were determined from acoustic mode frequencies in conjunction with spectroscopic ellipsometry. A weak ferromagnetic order, induced alternately by magnetization in the growth direction or by tetragonality, created a magnon oscillation at 75 GHz, indicative of a Dzyaloshinskii-Moriya interaction energy of 0.31 meV.
Bulk crystals and thin films of PbTi1-xFexO3 (PTFO) are multiferroic, exhibiting ferroelectricity and ferromagnetism at room temperature. Here we report that the Ruddlesden-Popper phase Pbn+1(Ti1-xFex)nO3n+1 forms spontaneously during pulsed laser deposition of PTFO on LaAlO3 substrates. High-resolution transmission electron microscopy, x-ray difraction and x-ray photoemission spectroscopy were utilised to perform a structural and ompositional analysis, demonstrating that n&sime;8 and x&sime;0.33. The complex dielectric function of the films was determined from far-infrared to ultraviolet energies using a combination of terahertz time-domain spectroscopy, Fourier transform spectroscopy, and spectroscopic ellipsometry. The simultaneous Raman and infrared activity of phonon modes, and the observation of second harmonic generation, establishes a non-centrosymmetric point group for Pbn+1(Ti0.67Fe0.33)nO3n+1-δ consistent with ferroelectricity. No evidence of macroscopic ferromagnetism was found in SQUID magnetometry. The ultrafast optical response exhibited coherent magnon oscillations compatible with local magnetic order, and additionally was used to study photocarrier cooling on picosecond timescales. An optical gap smaller than that of BiFeO3 and long photocarrier lifetimes may make this system interesting as a ferroelectric photovoltaic.

Keywords: spectroscopy
think film
multiferroic
oxide
THz
pump probe
Advisor: Lloyed-Hughes, J
Radaelli, P
Gender, space and empowerment in rural Hausaland, northern Nigeria

Reducing gender inequalities by enabling women's empowerment is a major focus of the literature and practices of gender and development. The work of this thesis contributes to debates about female empowerment, especially for peasant women in peripheral capitalist economies. The central themes of enquiry are power relations of gender and space in the socio-economic processes in which peasant households and their members are embedded. The focus of investigation is the extent to which commodity exchange outside the household reinforces, or reduces, women's position of power/disempowerment.
The central question taken for analysis is whether income earning via trading empowers women, thus reducing their subordination. This hypothesis is widely accepted. Many NGOs (non-governmental organisations) and other development institutions base efforts around the notion that income earning is liberating for women. This hypothesis is investigated for rural Hausa women in Northern Nigeria who are secluded within their homes by the religio-cultural practice of purdah, but who engage in trade, often through the agency of children. The major empirical part of the study develops and applies an original framework for analysis of empowerment that identifies and maps gender divisions of labour and space in the spheres of production, reproduction and circulation in which rural Hausa men and women are embedded.
The overall conclusion reached is that gender divisions of work, both inside and outside rural Hausa households, and especially in trade, reflect and sustain the subordination of women and their inferior position relative to men, especially through the control of space. The notion of income earning as universally empowering for women does not hold because rural Hausa women engaged in the market are not significantly empowered by their income earning because of the complex realities of patriarchy whereby women have weak bargaining powers.

Advisor: Harriss-White, B
A novel approach to the synthesis of the FG fragment of pectenotoxin-4

The cobalt-catalysed oxidative cyclisation of 5-hydroxy alkenes has been demonstrated to be a powerful synthetic tool for the formation of trans-THFs with excellent diastereoselectivity. This thesis describes the utilisation of this methodology in the synthesis of the FG fragment of pectenotoxin-4, allowing the scope of the reaction to be further explored.
Introduction: This section introduces the pectenotoxins, a family of structurally complex closed-chain polyether macrolides with promising biological activities. The isolation, structural elucidation, and biological properties of the pectenotoxins are reviewed, along with a summary of previous syntheses towards the FG fragment of pectenotoxin-4. In addition, the cobalt-catalysed oxidative cyclisation of 5-hydroxy alkenes and its application in synthesis is discussed.
Results and Discussion: An outline of the synthetic strategy employed in this project and details of the novel retrosynthesis of the C31-C40 fragment of pectenotoxin-4 is described. The synthetic studies carried out towards the synthesis of the FG fragment of pectenotoxin-4 are discussed in detail, with the exploitation of a cobalt-catalysed oxidative cyclisation as the key step to form the trans-THF F-ring. Overall, the FG fragment, which contains six stereogenic centres, was achieved in 18 total synthetic steps (13 longest linear sequence).

Keywords: cobalt
trans-Tetrahyrofuran
FG fragment
pectenotoxin
trans-THF
synthesis
Oxidative cyclisation
Advisor: Donohoe, TJ
Giovanni Puzzi

The focus of this dissertation is a comprehensive study of the life and work of Giovanni Puzzi, nineteenth-century Britain's most celebrated virtuoso of the horn. In his hands, the horn -- hitherto largely known to England's aristocracy as an obstreperous member of the orchestra or popular form of pleasure garden entertainment became a sought-after attraction at London's most fashionable and exclusive concerts. An examination of Puzzi's activities as an orchestral player and as a soloist in a wide variety of public and private concerts chronicles his rise to celebrity and establishes his position in London's concert life. Equally impressive was Puzzi's sustained prosperity in a notoriously difficult business. Key to this triumph was his multifaceted exploitation of the Italian opera. Through his activities as an agent, impresario and arranger he allied himself as a fixer and performer with his era's most lucrative musical commodity: the singers of the Italian opera.
In the large body of music that he arranged and composed to capitalise on audience fascination with virtuosity and opera, Puzzi has provided the only substantial record of horn playing in Britain during the nineteenth century. The majority of fhe manuscripts considered in this dissertation are drawn from a private collection and have not been previously studied or published. This material, in conjunction with Puzzi's surviving instruments and critical accounts of his playing, has been utilised to reconstruct and assess the main attributes of his virtuosity. This dissertation shows that Puzzi was responsible for establishing the preference for French style instruments and performance technique in England and that he was the first exponent of the British school of horn playing that reached its culmination in Dennis Brain.
While virtuoso string players, pianists and singers have attracted much attention from scholars and biographers, this dissertation is the first full length historical study of a nineteenth-century horn virtuoso to be written.

Advisor: Montagu, J
Post-Roman Britain to Anglo-Saxon England

This thesis is the result of a decision to extend the approach used by me when examining Irish burial practices, to a review of the archaeological and documentary record for burial practices and associated phenomena in the transitional period from late/post-Roman Britain to Anglo-Saxon England.
The study considers burial rites; the method of disposal of physical remains, the position and orientation of bodies, and burial structures and enclosures: grave-goods are only referred to when they are pertinent to a particular line of argument. My intention is to draw together the various aspects of burial of the Iron Age, Romano-British and Anglo-Saxon periods in order to look at the overall picture. Occasionally this may mean stating the obvious, but by noting and plotting distributions of various burial traits first in the Iron Age and Romano-British periods, and then comparing these traits with the Anglo-Saxon period some revealing results can be obtained. It was important to begin with the Iron Age since some minority practices current in the early Anglo-Saxon period had a continuous history from the pre-Roman period. They are of importance in demonstrating the continuities that existed alongside major changes.
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Spectroscopic applications of pulsed metal vapour lasers

The early part of this thesis reports time-resolved measurements of the transverse coherence of radiation from a copper vapour laser (CVL), and shows the influence of an unstable resonator. Experiments to measure the visibility of fringes from pairs of pinholes with a range of spacings are described, and their results are shown to be consistent with a simple theory based upon geometrical optics. With a high magnification laser cavity, high transverse coherence can be achieved before the laser pulse has reached appreciable power. The average coherence over a number of pulses is found to be limited, however, because of distortions introduced by currents of warm air in the beam path. Substantial improvements have now been made.
The importance of the transverse coherence upon second harmonic generation is then investigated. By improving the transverse coherence of the laser beam, second harmonic generation has been demonstrated at efficiencies close to those theoretically predicted for stable Gaussian laser beams, and 200mW of ultraviolet radiation at 255nm has been produced with 10% conversion efficiency using the nonlinear material beta-barium borate (BBO). High birefringence in BBO causes cylindrical symmetry in the geometry for harmonic generation to be lost, and it has been suggested that the use of astigmatic focussing into the crystal might be advantageous. A theoretical analysis has therefore been made, and improvements are indeed predicted. Elliptical focussing is predicted to increase the typical harmonic power only by a factor of 1.3, however, and no experimental verification has been attempted.
The remainder of this thesis considers the longitudinal coherence of the copper vapour laser, and describes the design and initial performance of a narrow bandwidth dye laser for use with a CVL. Careful construction of a grazing-incidence grating arrangement similar to that of Littman has resulted in a laser which is particularly simple to align and which promises ease of tuning over a wide range. Operation confined to a single longitudinal mode has been demonstrated, corresponding to single shot bandwidths below IGHz, but instabilities caused by vibration and uneven dye flow broaden the time-averaged width to around 3GHz. Suggested improvements have not yet been implemented.

Advisor: Corney, A