VictorJuiz/thesis huggingface dataset:
Looking and perception in nineteenth century poetry

The thesis examines a series of nineteenth century poets whose poems are concerned with complex relations of looking and perception, and concentrates on Shelley and the poets he influenced: Browning, Rossetti, Swinburne, and Hardy. It focusses on poems dealing with the visual arts and aesthetic modes of perception, and concludes with a study of Walter Pater - an unrecognised follower of Shelley - and his notions of artistic character. An emphasis on the way face and bodily form are scrutinised, in poems concerning painting, sculpture and portraiture, leads to the hypothesis that the way the poet pictures essence or character through corporeal form is correlative to the essence or character of his own poetry. The particular spatial relations and visual representations of the poetry provide an index to specific patterns of reading. At the heart of this examination is a Shelleyan conception of the "unsculptured image", the characterising force and pre-given perspective of a poet's poem, which has a primary shaping effect on his language and representations, and continues to exert itself in the poem's reading. As this "image" is an imaginative rather than purely linguistic force, the analyses of selected poems avoid reduction to considerations of language and rhetoric alone, seeking rather to engage with the question of what constitutes a writer's own essence or particularity and what gives a strong poem its compulsive power.
The thesis draws on the work of the French literary critic Maurice Blanchot to inform its ideas of poetic space and depth, and to produce an understanding of the poetic text very different from that given by a classical reading; and so alter the way one perceives the poem as literary object. In addition to this, certain nineteenth century and earlier aesthetic writings, and the prose works of the poets themselves, establish the critical basis of the arguments advanced. The thesis also endeavours to follow through the arguments of traditional scholarship in order to provide critique on distinctions or departures made.
Chapter I examines Shelley's 'On the Medusa of Leonardo da Vinci in the Florentine Gallery'; Chapter II deals with portraiture in Browning's 'My Last Duchess' and Rossetti's The Portrait'; Chapter III turns to the sculpture of the hermaphrodite in Swinburne's early lyric 'Hermaphroditus'; Chapter IV looks at Thomas Hardy's poems about sketches and shades; Chapter V is an epilogue in which the work of Walter Pater draws together the ideas developed in the rest of the thesis.
Simulations of shock-induced phase transitions in silicon

An understanding of the fundamental mechanism behind the relief of shear stress in single-crystal silicon subject to loading by shock-waves has to this day remained elusive. What is known is that this material undergoes a first-order pressure-induced polymorphic phase transition from its ambient pressure cubic-diamond (cd) crystal structure to its first stable high-pressure phase, known as β-Sn, at a pressure of about 120 kbar under hydrostatic compression. By investigating the evolution of the transition parameters for this phase transition as a function of increasing uniaxial shear stress representative of the effects of shock-compression via ab-initio Density Functional Theory computational techniques, we predict a significant lowering of the stress at which the phase transition occurs. This raises the question as to whether the onset of plastic response at the material's Hugoniot Elastic Limit (HEL) reported in experiments corresponds in fact to the phase transition itself, a very plausible possibility which has never been considered before. Furthermore, we present molecular dynamics simulations using a Tersoff-like potential of shock-compressed single crystals of silicon. We find an elastic response up to a critical stress, above which the shear stress is relieved by an inelastic response associated with a partial transformation to a new high-pressure phase, where both the new phase (Imma) and the original cubic diamond phase are under close to hydrostatic conditions. We note that these simulations are also consistent with shear stress relief provided directly by the shock-induced phase transition itself, without an intermediate state of plastic deformation of the cubic diamond phase.

Keywords: pressure
physics
SIlicon
material
laser
Phase Transition
shock
density functional theory
molecular dynamics
Crystal
Advisor: Wark, J
Multilocus approaches to the detection of disease susceptibility regions: methods and applications

This thesis focuses on multilocus methods designed to detect single nucleotide polymorphisms (SNPs) that are associated with disease using case-control data. I study multilocus methods that allow for interaction in the regression model because epistasis is thought to be pervasive in the etiology of common human diseases. In contrast, the single-SNP models widely used in genome wide association studies (GWAS) are thought to oversimplify the underlying biology. I consider both pairwise interactions between individual SNPs and modular interactions between sets of biologically similar SNPs. Modular epistasis may be more representative of disease processes and its incorporation into regression analyses yields more parsimonious models. My methodological work focuses on strategies to increase power to detect susceptibility SNPs in the presence of genetic interaction. I emphasize the effect of gene-gene independence constraints and explore methods to relax them. I review several existing methods for interaction analyses and present their first empirical evaluation in a GWAS setting. I introduce the innovative retrospective Tukey score test (RTS) that investigates modular epistasis. Simulation studies suggest it offers a more powerful alternative to existing methods. I present diverse applications of these methods, using data from a multi-stage GWAS on prostate cancer (PRCA). My applied work is designed to generate hypotheses about the functionality of established susceptibility regions for PRCA by identifying SNPs that affect disease risk through interactions with them. Comparison of results across methods illustrates the impact of incorporating different forms of epistasis on inference about disease association. The top findings from these analyses are well supported by molecular studies. The results unite several susceptibility regions through overlapping biological pathways known to be disrupted in PRCA, motivating replication study.

Keywords: genetic interaction
statistical genetics
prostate cancer
multilocus analysis
Advisor: Holmes, C
Chatterjee, N
Generation of a novel endogenously StrepII/FLAG tagged system for the identification of the vertebrate FANCJ associated proteins

Fanconi Anaemia (FA) is a rare inherited chromosomal instability disorder characterized by developmental abnormalities, bone marrow failure, increased risk of developing cancer and an increased cellular sensitivity to DNA interstrand crosslinking compounds, including the anticancer drugs, cisplatin, nitrogen mustard and mitomycin C. From a therapeutic point of view, it is important to understand how cells respond to and repair DNA damage caused by crosslinking compounds, used to treat cancer. To date, fifteen different proteins involved in a common pathway, known as the FA pathway have been identified and are known to respond to, and influence repair of interstrand crosslinks (ICLs). So far, the role of these proteins in ICL repair remains elusive. To gain insights into the molecular basis of ICL repair, we chose to study the FA-associated helicase FANCJ, as it is known to bind and metabolize a variety of DNA substrates, implicating it in maintenance of genomic stability. Here, I report a novel genetic-proteomic approach to study FANCJ. This system uses epitope tagged FANCJ expressed from its chromosomal locus, in chicken DT40 cells, kept under the control of its endogenous promoter. Tandem affinity purification is employed to purify and isolate the tagged protein and identify interacting partners of interest. To date, I have generated, characterized and validated epitope tagged FANCJ cell lines. Pilot immunoprecipitations were carried out to establish the efficiency and reproducibility of the immunoprecipitations (IPs). Analysis by mass spectrometry revealed the presence of epitope tagged FANCJ in scaled-up immunoprecipitations. In the future, these cell lines will be used to identify and characterize the FANCJ interactome.

Keywords: Fanconi anaemia
StrepII/FLAG tag
FANCJ
interstrand crosslink
helicase
DNA damage
Advisor: McHugh, P
Niedzwiedz, W
The concept of community in the transformation of systems theory: Luhmann, Habermas and recent German writing

The concept of community is highly problematic in the German context. ‘Gemeinschaft’ plays only a minor role in post-1945 philosophical writing, arguably as a result of the abuse of the concept by the National Socialists (‘Volksgemeinschaft’). Two of the major contemporary social philosophies in the German language, those of Jürgen Habermas and Niklas Luhmann, are deeply critical of ‘community’. Habermas rejects ‘community’ that has not been purified by a rational filter (as opposed to what he conceives of as the ideal ‘Kommunikationsgemeinschaft’). Luhmann rejects the concept outright, arguing that it is simply ‘alteuropäisch’ (i.e. based on out-of-date philosophical assumptions), and that it has no place in the description of modern society. In contrast to these prominent dismissive positions, I argue that the concept of community is an underrated one. First, Habermas relies more heavily on the concept of community than his focus on the ‘Lebenswelt’ makes us believe. I characterise his conception as a ‘transformation’ of systems theory, because his social philosophy partly adopts systems theory, while complementing it with the aspect of ‘community’. Second, I argue that contemporary cultural theoreticians (for example, Peter Sloterdijk) take systems theory as a starting point for developing ultimately communitarian social philosophies. The concept of community proves crucial as supplementation and balancing of systems-theoretical elements in contemporary thinking. Once this transformative role is recognised, a purely historical treatment of the concept of community – one which, as in Luhmann’s systems theory, sees no place for it in present or future theory – begins to look premature.

Keywords: Luhmann
systems theory
community
Advisor: Groiser, D
Undialectical conclusions

My thesis is a critique of Adorno's method that stays true to the dialectical spirit of his philosophy precisely by calling it in question. It opens, in Part I, with an account of Habermasian objections to negative dialectics. Habermas is concerned that Adorno's assault on rationality is so allembracing that it undermines the very standards it requires rationally to legitimate its critique. Adorno consciously embraces this self-undermining position. But Habermas believes its aporias, however self-conscious, to be misguided because a less paradoxical standard was close to hand. Language itself could have supplied negative dialectics with the norms it needed to criticize the abuses of instrumental reason. If Adorno is not logically forced to adopt an aporetic position, the question arises why a philosopher so gifted should manoeuvre himself into a theoretical dead-end. Habermas's answer to this, in the essay on Dialektik der Aufklärung included in Der philosophische Diskurs der Moderne, is that Adorno illicitly privileges one of the three distinct logics of modernity, inappropriately judging cognitive and moral discourses by aesthetic criteria. When compared to the subject's awe-struck contemplation of a work of art, any more practical intervention in the world is bound to appear crude and instrumental.
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Close together but a world apart: a comparative history of research practices during the formative years of Brazilian academic science (1934-1955)

This thesis compares the ways in which the nationalisation process impacted the research practices of academics from two universities, the University of Rio Grande do Sul and the University of Parana. Systematic comparisons of both institutions located in the South of Brazil has shown that the differences between them were, indeed, significant during pre-nationalisation years. In Brazilian terms, they are ‘close’ together since only seven hundred kilometres separate them. However, the necessity for regionalised studies on the development of academic science is demonstrated in this thesis through a focus on specific faculties that achieved remarkably different research results, despite their geographical proximity. The comparative analysis carried out in this thesis reveals that significant differences existed, such as institutional arrangements, disciplinary boundaries and networks, despite the fact that they were often found under similar academic arrangements. The nationalisation project carried out in 1950 did not alter these differences overnight, but introduced a new element in both settings that would shape their scientific capabilities to this day. Substantial new evidence presented here indicates that in the early 1950s President Dutra, perhaps inadvertently, forced research-minded academics in both universities to consider the possibility of adapting their research projects to their nationalised institutions. Because of the chain of events enabled by this initiative, in later years, these universities became some of the most prominent institutional settings for scientific research in Brazil. A comparative study of the differences and similarities between ongoing practices in these academic settings at the moment of nationalisation indicates that nationalisation did not occur in an historical vacuum; rather, it enhanced and legitimised deeply rooted academic traditions that came to shape local research cultures over the following decades. When this context is explored it becomes clear that an understanding of nationalisation actually lends greater coherence to traditional chronologies of Brazilian academic science.

Keywords: History of Science
Brazilian Studies
Comparative History
Advisor: Corsi, P
The globalisation of universal human rights and the Middle East

The goal of this study is to generate a more holistic picture of the diffusion and assimilation of universal human rights norms in diverse cultural and political settings such as the Middle East and North Africa (MENA). The overarching question to be investigated in this thesis is the relationship between the evolving international human rights regime and the emerging human rights normative and legal culture in the Middle East. This question will be investigated in detail with reference to regional human rights schemes such as the Arab Charter of Human Rights, as well as local human rights developments in three Middle Eastern states, Egypt, the United Arab Emirates, and the Islamic Republic of Iran. Having gauged the take-up of human rights norms on the ground at the local and regional levels, the thesis examines in full the extent of socialisation and internalisation of human rights norms across the Middle East region at large.

Keywords: Arab Charter of Human Rights
United Arab Emirates
MENA
Globalisation
Dubai
Islam
Gulf Cooperation Council
Transnational Activist Networks
Regionalism
UN Human Rights Council
Arab League
Middle East
North Africa
Egypt
Arab Awakening
Women's Rights
Human Rights
Arab Spring
Norm Diffusion
Iran
Cultural Relativism
Universalism
Advisor: Shlaim, A
Fawcett, L
Transcriptional brain networks and their key regulators across the human lifespan

The human brain’s transcriptome undergoes substantial changes over the lifespan and shows characteristic patterns that reflect anatomical regions and cellular compositions. In this thesis, I applied combinations of network algorithms and tools from computational biology to analyse transcriptional networks and their key regulators in the human brain across space (brain regions) and time (the human life course). First, I identified an age-dependent transcriptional network enriched for microglial markers. The microglia network recapitulated haematopoietic master regulators that are crucial for early microglia development using data from the ageing human brain only. In the second project, I demonstrated that gene clusters linked to neurogenesis during fetal life show moderate to strong preservation in the human adult brain. In addition to temporal development, I analysed transcriptional network dynamics across the spatial axis and detected a network of ion channel/transporter genes that express their longest 3’ untranslated regions (3’UTRs) exclusively in the brain. Enrichment for predicted miRNA response elements that are often shared among the ion channel/transporter genes, along with increased co-expression of this gene set, indicated that the extended 3’UTRs could serve as a hub for an endogenous competitive RNA network. I extended the analysis to differentiate between brain regions and additional regulatory RNA elements, namely long noncoding (lnc) RNAs. I found that genes in the hypothalamus express a region-specific network to which are also associated co-expressed lncRNAs. Finally, I added global metrics to the analysis of local networks. The dynamics of global network metrics indicated strong coordination of expression across the lifespan compared to similar variance within age groups. This work shows that the transcriptome of human post-mortem brains at least partially preserves the network structure of cell types and functionally related genes, and how it may be dissected using suitable combinations of bioinformatic algorithms.

Keywords: gene expression
transcriptional network
ageing
neuroscience
Advisor: Ponting, C
Bayesian and frequentist methods and analyses of genome-wide association studies

Recent technological advances and remarkable successes have led to genome-wide association studies (GWAS) becoming a tool of choice for investigating the genetic basis of common complex human diseases. These studies typically involve samples from thousands of individuals, scanning their DNA at up to a million loci along the genome to discover genetic variants that affect disease risk. Hundreds of such variants are now known for common diseases, nearly all discovered by GWAS over the last three years. As a result, many new studies are planned for the future or are already underway. In this thesis, I present analysis results from actual studies and some developments in theory and methodology. The Wellcome Trust Case Control Consortium (WTCCC) published one of the first large-scale GWAS in 2007. I describe my contribution to this study and present the results from some of my follow-up analyses. I also present results from a GWAS of a bipolar disorder sub-phenotype, and a recent and on-going fine mapping experiment. Building on methods developed as part of the WTCCC, I describe a Bayesian approach to GWAS analysis and compare it to widely used frequentist approaches. I do so both theoretically, by interpreting each approach from the perspective of the other, and empirically, by comparing their performance in the context of replicated GWAS findings. I discuss the implications of these comparisons on the interpretation and analysis of GWAS generally, highlighting the advantages of the Bayesian approach. Finally, I examine the effect of linkage disequilibrium on the detection and estimation of various types of genetic effects, particularly non-additive effects. I derive a theoretical result showing how the power to detect a departure from an additive model at a marker locus decays faster than the power to detect an association.

Keywords: case-control
GWAS
Bayes factor
Genome-wide association study
linkage disequilibrium
complex human diseases
g-prior
Bayesian
frequentist
Advisor: Donnelly, P
The role of glutamate in rotator cuff tendinopathy

Thesis questions:
Is the glutaminergic system altered in rotator cuff tendinopathy?
Is the glutaminergic system altered by common treatments?
Are glutaminergic changes related to pain symptoms?
What are the effects of glutamate and glutamate receptor modulation on tendon derived cells?
Summary answers:
The glutaminergic system is altered in rotator cuff tendinopathy
Changes within this system are seen after common treatments
Specific glutaminergic changes are associated with the resolution of pain following shoulder surgery but do not predict the severity of pain symptoms
Glutamate has significant effects on tendon derived cells
What is known: It is known that extracellular glutamate concentrations are increased in both Achilles and patellar tendinopathy. It has also been previously shown that the glutamate receptors NMDAR1 and mGluR5 are upregulated in patellar tendinopathy.
What this thesis adds: This thesis has shown for the first time that glutamate and NMDAR1 are increased in rotator cuff tendinopathy. Increases in cell proliferation, vascularity and HIF1α are seen after surgical rotator cuff repair and these features are not seen after glucocorticoid injection. There are significant differences between painful and pain-free rotator cuff tendons in terms of glutamate receptor expression (KA1, mGluR7 and mGluR2) and inflammatory cell numbers (CD45 and CD206). Exposure to 1.875mM glutamate for 72 hours results in reduced cell viability, decreased collagen (COL1A1 and COL3A1) and increased aggrecan gene expression; NMDAR antagonism with MK-801 attenuates the deleterious effect on cell viability but had no effect on the changes in matrix gene expression.
Bias, confounding and other reasons for caution: The observational histological work was limited by the control tissue. Some control tissue was not age matched, while some of the pain-free control tendons were post-surgical intervention. Confounding factors include tendon structure, length of symptoms and previous treatments. Caution must be applied when discussing the in vivo implications of the in vitro work.
Study funding/potential competing interests: This thesis was funded by the Jean Shanks Foundation and Orthopaedic Research UK.

Keywords: rotator cuff
shoulder
tendon
pain
tendinopathy
glutamate
Advisor: Carr, A
Kassim, J