VictorJuiz/thesis huggingface dataset:
e-Research in the life sciences: from invisible to virtual colleges

e-Research in the Life Sciences examines the use of online tools in the life sciences and finds that their use has significant impact, namely the formation of a Scientific/Intellectual Movement (SIM) (Frickel & Gross, 2005) complemented by a Computerisation Movement (CM) (Kling & Iacono, 1994) which is mobilising global electronic resources to form visible colleges of life science researchers, who are enrolling others and successfully promoting their open science goals via mainstream scientific literature. Those within this movement are also using these online tools to change their work practices, producing scientific knowledge in a highly networked and distributed group which has less regard for traditional institutional and disciplinary boundaries. This thesis, by combining ideas about SIMs and CMs, fills a gap in research that is typically confined to treating new tools as a part of scientific communication or in specialist areas like distributed collaboration but not in terms of broader changes in science.
Case studies have been conducted for three types of online tools: the scientific social networking tool FriendFeed, open laboratory notebooks, and science blogs. Data have been collected from semi-structured interviews, and the online writings of research participants. The case studies of exemplary use by scientists of the web form a baseline for future studies in the area.
Boundaries between formal and informal scholarly communication are now blurred. At the formal level, which peer-reviewed print journals continue, many academic publishers now also have online open access, frequently in advance of print publication. At the informal level, what used to be confined to water-cooler chat and the conference circuit is now also discussed on mailing lists, forums and blogs (Borgman, 2007). As these online tools generate new practices they have potential to affect future academic assessment and dissemination practices.

Keywords: sociology of science
internet
social media
Advisor: Schroeder, R
Meyer, ET
Efficient numerical modelling of wave-structure interaction

Offshore structures are required to survive in extreme wave environments. Historically, the design of these offshore structures and vessels has relied on wave-tank experiments and linear theory. Today, with advances in computing power, it is becoming feasible to supplement these methods of analysis with fully nonlinear numerical simulation.
This thesis is concerned with the development of an efficient method to perform this numerical modelling, in the context of potential flow theory. The interaction of a steep ocean wave with a floating body involves a moving free surface and a wide range of length scales. Attempts to reduce the size of the simulation domain cause problems with wave reflection from the domain edge and with the accurate creation of incident waves.
A method of controlling the wave field around a structure is presented. The ability to effectively damp an outgoing wave in a very short distance is demonstrated. Steep incident waves are generated without the requirement for the wave to evolve over a large time or distance before interaction with the body. This enables a general wave-structure interaction problem to be modelled in a small tank, and behave as if it were surrounded by a large expanse of water.
The suitability of the boundary element method for performing this modelling is analysed. Potential improvements are presented with respect to accuracy, robustness, and computational complexity. Evidence of third order diffraction is found for an FPSO model.

Keywords: ocean waves
BEM
fluid mechanics
Advisor: Taylor, P
Eatock Taylor, R
An exploration of sight, and its relationship with reality, in literature from both world wars

Writers from both world wars, concerned with the representation of war, wrestled with the predicament of partial sight. Their work reveals the problematic dichotomy that exists between the individual’s selective range of vision and the immense scale of conflict. Central to this authorial dilemma is the question of the visual frame: how do you contain – within the written word – sight that resists containment and expression? The scale of the two world wars accentuated the representative problem of warfare. This thesis, by examining a wide range of World War One and World War Two literature, explores the varied literary responses to the topical relationship between sight and reality in wartime. It examines the war poetry of Wilfred Owen, Ford Madox Ford’s tetralogy Parade’s End, The Return of the Soldier by Rebecca West, Elizabeth Bowen’s The Heat of the Day, and Virginia Woolf’s novels Mrs Dalloway and Between the Acts alongside less well-known works such as David Jones’s prose-poem In Parenthesis, the two short stories ‘The Soldier Looks for His Family’ by John Prebble and ‘The Blind Man’ by D.H. Lawrence, as well as William Sansom’s collection of short stories Fireman Flower, and Louis Simpson’s war poetry. This thesis, by focussing on the inherent difficulties of reconciling perception and representation in war, interrogates the boundaries of sight and the limits of representation. The changing place of sight in writing from the two world wars is examined and the extent to which discourses of vision were shaped and developed, in the early decades of the twentieth century, by war experience is explored. The critical containment and categorisation of sight that often dominates readings of sight in texts from both world wars is questioned suggesting the need for a more flexible understanding of, and approach towards, sight.

Keywords: sight
world war one literature
eye sight
world war two literature
Advisor: Whitworth, M
Psychological agency in a neighbourhood on the urban fringe of Bamako

This thesis is about psychological constructions underpinning intentional action to improve well-being by people in a neighbourhood on the urban fringe of Bamako, Mali. There is a large deficit in the theorisation of psychological elements of agency and empowerment in the development literature. Instead empowerment is generally defined as a favourable opportunity structure, as choice or as the distribution of power. Further still, the examination of the psychological literature reveals a lack of empirical research related to non-Western contexts and development policy. In view of this, I present the results of an empirical study using the inductive mixed methods to examine the central factors contributing to initiatives people undertake to improve personal and collective well-being. Informants articulated that the psychological concepts of dusu (internal motivation) and ka da I yèrè la (self-efficacy) were most important to their purposeful agency. The empirical analysis is divided into three parts and based primarily on qualitative data, enriched by quantitative analysis. Firstly I will examine the concepts of dusu and ka da I yèrè la, which are characterised as having an instrumental and intrinsic significance to people’s purposeful agency. They were also characterised as important factors in supporting local social development initiatives. Secondly, I will show how these psychological concepts were not related to the agent’s socio-economic characteristics or decision making ability, rendering both variables weak proxies for measuring psychological agency. Instead I found that measures of intrinsic motivation and self-efficacy are more viable for evaluating psychological agency. Thirdly, however, whilst dusu and ka da I yèrè la are important to people’s agency and the social development of the neighbourhood, they cannot be viewed as a silver bullet to social development in Kalabankoro Nerekoro. Specifically, in the examination of collective purposeful agency in group work (associations), the functioning of groups is impacted by the internal dynamics within the group, causing sometimes breakdown of the group. Further still, gender and age norms as well as capability deprivation and conflicting world views all thwart the ability of associations to achieve their goals. I underline that agents cannot always succeed in the pursuit of their well-being goals, even though they demonstrate high levels of psychological agency unless structural inequality at the micro, meso and macro levels of Malian society are addressed. Through this empirical study, this thesis will contribute the closing of the gap between psychological and development literatures as well as work towards developing measures of psychological agency.

Keywords: Empowerment
Agency
Mali
Social Change
Advisor: Alkire, S
Giuffrida, A
Aspects of the glaciation and superficial deposits of Pembrokeshire

"Since the publication of the work of Jehu and Charlesworth the distribution and significance of the glacial deposits of the Irish Sea have remained in a somewhat confused condition." So said Professor w.D. Evans in 1964. This thesis represents an attempt to remove the confusion from one small corner of the Irish Sea basin; it is concentrated largely in North Pembrokeshire, and aims to resolve some of the stratigraphic and chronological problems concerned with the Pleistocene deposits of the region.
There is a long history of research into the glaciation of North Pembrokeshire. Most of the early work was undertaken in Dewisland (the St. David's Peninsula), but in the major contributions of Jehu (1904) ond Charlesworth (1929) something was revealed of the Pleistocene history of North Pembrokeshire as a whole. Subsequent work has been greatly influenced by these two authors, and there has been no detailed field study of the area since Charlesworth. As a result, many controversies have arisen in recent years; these range from the purely stratigraphic problems of the classic tripartite drift succession and the nature of the Upper Boulder-clay to the absolute age of the Pembrokeshire drifts. Again, there is doubt concerning the number of glaciations represented in North Pembrokeshire; about the existence of the South Wales End-moraine, the pro-glacial lakes, and the so-called overflow channels of Charlesworth; and about the age and origins of the coastal features of the county. These are among the problems that this thesis attempts to answer.
[Please see pdf. for full abstract]

Advisor: Sweeting, M
The forms of combination of CU, NI and ZN in anaerobic sewage sludge

As a first step in understanding the chemistry of toxic elements in sludged soil, this thesis presents a comprehensive model of their chemistry in the digester. A review of the literature had shown that heavy metals were likely to be held in 3 pools: as precipitated and detrital mineral phases 'Particulate'; as complexes with the flocculated biomass 'Biofloc'; and as complexes in solution 'Soluble'.
A simple pragmatic fractionation procedure has been offered to separate these 3 pools based on their physical properties in water. A mass-balance between the pools showed that the 'Particulate' fraction held only 5-16% of the heavy metals but contained them in the highest concentration. The 'Biofloc' held 82-94% of the heavy metals.
The 'Particulate' material was subdivided by density separation and examined by a combination of analytical SEM and XRD. Thirty-four minerals were identified by XRD, many of which were detrital. Secondary precipitates on the surface of detrital minerals were revealed by the SEM; of these only the sulphides were found to contain detectable levels of heavy metals. Eleven minerals were identified in the 'Biofloc', of which most were clays.
The fractionation scheme defined 2 fractions that could hold heavy metals by complexation. The 'Soluble' had a CEC of 8.8 meq/gm and the 'Biofloc' 4 meq/gm. Complexation by the heavy metals and a few other important cations was measured.
A thermodynamic model was built which describes the possible solution species, mineral phases and complexation by the biomass in terms of a set of 33 primary components. This model was solved by computer for an 'average' sludge based on published analyses, and considered 313 solution species, 42 exchange reactions and 129 possible minerals. The predicted speciation was broadly in line with observations and suggested that the majority of the heavy metals separating with the 'Biofloc' would have been held as fine enmeshed sulphide precipitates.
The model may be used with existing programs such as MINEQL and GEOCHEM. Preliminary studies have shown that with a few additions the model may be used to describe the heavy metals in sludged soil.

Advisor: Beckett, P
Dr, P
Identification of immunological targets for HIV-1 vaccine and cure strategies 

HIV-1 chronically infected individuals represent a large disease burden, making the development of a therapeutic vaccine for use in chronic infection a priority. However, therapeutic vaccination has not been successful to date. Most approaches have employed viral vectored vaccines encoding full length viral proteins, which aimed to boost pre-existing CD8&plus; T cell responses by mimicking natural HIV-1 infection. Simply boosting these pre-existing CD8&plus; T cell responses which have previously failed to control the virus may be insufficient. Although HIV-1 has a huge capacity to diversify, certain regions are less tolerant of mutations due to structural and functional constraints. We therefore hypothesised that it would be necessary to redirect the immune response to more vulnerable regions of the proteome, such as conserved regions.
HIVconsv is a rationally designed conserved region vaccine. Vaccination of 19 chronically HIV-1 infected HAART treated patients with MVA.HIVconsv was safe and well tolerated. There was a significant increase in the magnitude of HIVconsv-specific T cell response following vaccination (p = 0.001), as measured by IFN-γ Elispot assay, but changes observed in vaccinees did not reach statistical significance when compared with placebo recipients (p = 0.48).
The capacity of CD8&plus; T cells to inhibit HIV-1 replication in vitro is highly predictive of virus control in vivo and is thus a possible surrogate of vaccine efficacy. There was a trend towards increased CD8&plus; T cell mediated inhibition following vaccination with 2x108pfu MVA.HIVconsv (17% inhibition pre- vs 54% inhibition post-vaccination, p = 0.06). However, measurement of the latent HIV-1 reservoir by quantification of total HIV-1 DNA in circulating CD4&plus; T cells by droplet digital PCR showed no reduction in size upon vaccination, indicating CD8&plus; T cells induced by vaccination with MVA.HIVconsv were not of sufficient potency to impact the reservoir.
In a second cohort of HIV-1 infected individuals, antiviral inhibitory activity was measured in 36 HIV-1-infected STEP and Phambili trial participants. Sustained potent CD8&plus; T cell antiviral inhibitory responses were rare but were strongly correlated with IFN-γ responses to so-called ‘beneficial’ low entropy regions in HIV-1 Gag and Pol, that had been reported previously to be associated with HIV-1 control, (r = 0.69, p = 0.0001). This correlation was still significant after controlling for protective HLA alleles, whereas responses to conserved elements were only weakly correlated with viral inhibition (r = 0.41, p = 0.04).
These data indicate that immunogens that are based on the selection of regions within the viral proteome by conservation score alone may not induce the most effective HIV-1-specific T cell responses and they highlight the importance of systematically selecting specific regions associated with HIV-1 control, together with exclusion of immunodominant decoy epitopes.

Keywords: HIV
CD8 T cells
Advisor: Dorrell, L
In the name of oil

Traditional historiographies of the Cold War Middle East read into Britain's postwar economic decline a corresponding demise of British regional influence. According to these accounts, the Suez Crisis served to teach Britain new limits to its military capabilities, occasioning a break from independent endeavours to project power in the region. However, the case studies presented in this thesis demonstrate that the Suez Crisis did not mark a precipitous turning point in Britain's political influence in the Middle East in the short- to medium-term. Britain's power in the region rested upon not only its material assets, but other less tangible bases as well. Most importantly, Britain's power in the Middle East during the period examined increasingly included its ability to influence the policies of United States – a country with great resources and an emerging presence in the region.

Keywords: Anglo-American relations
decolonisation
oil
Middle East
Cold War
Advisor: Piscatori, J
Bayesian methods for fine mapping in genetic association studies

Over the past several years genetic variation has been the centre of attention for different branches of genetics. The use of genome wide association studies (GWAS) has facilitated the discovery of a plethora of genetic variants which are associated with a vast range of diseases. These GWAS primarily examine a single variant, mostly a Single Nucleotide Polymorphism (SNP), at a time based on genotype data. Although this practice has proven to be powerful, low percentages of heritability prompt a call for the exploration of more complex structures of association.
As diseases are more likely to be caused by several variants, multi-SNP analyses are used to refine the signal leading to the development of fine mapping methodologies. Further biological information is accounted for by studying the diploid nature of the human genome which identifies phenomena, such as compound heterozygosity. We propose a flexible Bayesian fine mapping model for quantitative traits allowing for the analysis of haplotype data under a variety of genotype and haplotype models. A Metropolis-Hastings algorithm is employed to search the model space efficiently. Simulations show competitive performance over existing methods when compound heterozygous effects are present in the data.
An extension of a single cohort framework is meta-analysis where a collection of studies is used to increase confidence and boost power in noticeable associations. Traditional approaches include the fixed effects model where the assumption is that genetic effects are homogeneous amongst cohorts while the random effects model accounts for heterogeneity. We propose a Bayesian meta-analysis approach which implements both fixed and random effects with the addition of a parameter measuring the existence of effect in each cohort. Simulations and application to real samples explore the performance of the method under different conditions and show comparable evidence over established methodologies.

Keywords: bayesian
genetics
random effects
mcmc
fine mapping
meta analysis
compound heterozygosity
statistics
Advisor: Marchini, J
Biochemical determinants of nitric oxide synthesis in severe malaria

Inhibition of nitric oxide (NO) signalling may contribute to the pathogenesis of severe malaria. This thesis examines the impact of Plasmodium infection on three key determinants of nitric oxide synthase (NOS) biochemistry: substrate availability, substrate/inhibitor homeostasis and cofactor availability. Arginine, the NOS substrate, is depleted in human patients with severe Plasmodium falciparum malaria and mice infected with P. berghei ANKA. Using heavy isotope tracer infusions to quantify arginine metabolism in infected mice, we found no evidence of increased catabolism by the enzyme arginase, widely assumed to be responsible for arginine depletion. Genetic knock-out of parasite arginase had no effect on arginine depletion in mice. Instead, our findings link arginine depletion to decreased rates of arginine and citrulline appearance in the plasma of infected mice. Asymmetric dimethylarginine (ADMA) competes with arginine for binding to the NOS catalytic site. We observed elevation of the ADMA/arginine ratio in Gambian children with severe malaria, favouring NOS inhibition. In mice infected with P. berghei ANKA, we found evidence of degradation of dimethylarginine dimethylaminohydrolase 1 (DDAH1), the enzyme primarily responsible for ADMA metabolism. We also observed reduced DDAH activity and accumulation of intracellular ADMA in hepatic tissue of infected mice, suggesting that DDAH dysfunction could contribute to disruption of ADMA/arginine homeostasis. Tetrahydrobiopterin (BH4) is an essential NOS cofactor. In P. berghei ANKA-infected mice, BH4 concentrations were decreased in plasma, erythrocytes and brain tissue, which could inhibit NO synthesis and promote NOS-dependent superoxide production. To reverse deficiencies of NOS substrate and cofactor availability, we infused P. berghei ANKA-infected mice with citrulline, an arginine precursor, and sepiapterin, a BH4 precursor. Restoration of systemic arginine and BH4 availability in infected mice improved whole blood nitrite concentrations, a biomarker of NO synthesis, but did not prevent onset of disease symptoms. These studies have identified biochemical disturbances that may contribute to severe malaria pathogenesis by inhibiting NO synthesis.

Keywords: Infectious Disease Pathogenesis
Vascular Homeostasis
Analytical Biochemsitry
Nitric Oxide
Tetrahydrobiopterin
Severe Malaria
Arginine Metabolism
Advisor: Roberts, D
Ackerman, H
Importance sampling on the coalescent with recombination

Performing inference on contemporary samples of homologous DNA sequence data is an important task. By assuming a stochastic model for ancestry, one can make full use of observed data by sampling from the distribution of genealogies conditional upon the sample configuration. A natural such model is Kingman's coalescent, with numerous extensions to account for additional biological phenomena. However, in this model the distribution of interest cannot be written down analytically, and so one solution is to utilize importance sampling.
In this context, importance sampling (IS) simulates genealogies from an artificial proposal distribution, and corrects for this by weighting each resulting genealogy. In this thesis I investigate in detail approaches for developing efficient proposal distributions on coalescent histories, with a particular focus on a two-locus model mutating under the infinite-sites assumption and in which the loci are separated by a region of recombination. This model was originally studied by Griffiths (1981), and is a useful simplification for considering the correlated ancestries of two linked loci. I show that my proposal distribution generally outperforms an existing IS method which could be recruited to this model.
Given today's sequencing technologies it is not difficult to find volumes of data for which even the most efficient proposal distributions might struggle. I therefore appropriate resampling mechanisms from the theory of sequential Monte Carlo in order to effect substantial improvements in IS applications. In particular, I propose a new resampling scheme and confirm that it ensures a significant gain in the accuracy of likelihood estimates. It outperforms an existing scheme which can actually diminish the quality of an IS simulation unless it is applied to coalescent models with care. Finally, I apply the methods developed here to an example dataset, and discuss a new measure for the way in which two gene trees are correlated.

Keywords: likelihood
infinite sites
probability
importance sampling
resampling
coalescent
Monte Carlo
two-locus
Advisor: Griffiths, R