VictorJuiz/thesis huggingface dataset:
Mathematical modelling of subglacial drainage and erosion

The classical theory of channelized subglacial drainage,due orginally to Röthlisberger (1972) and Nye (1976), considers water flow in an ice channel overlying a rigid, impermeable bed. At steady flow, creep closure of the channel walls is counteracted by melt-back due to heat dissipation, and this leads to an equilibrium relation between channel water pressure and discharge. More generally, such a balance exhibits an instability that can be used to describe the mechanics of catastrophic flood events known as `jökulhlaups'. In this thesis, we substantiate these developments by exploring a detailed model where the channel is underlain by subglacial till and the flow supports a sediment load. Attention is given to the physics of bed processes and its effect on channel morphology. In particular, we propose a theory in which the channel need not be semi-circular, but has independently evolving depth and width determined by a local balance between melting and closure, and in which sediment erosion and deposition is taken into account. The corresponding equilibrium relation indicates a reverse dependence to that in the classical model, justifying the possibility of the subglacial canals envisaged by Walder and Fowler (1994). Theoretical predictions for sediment discharge are also derived. Regarding time-dependent flood drainage, we demonstrate how rapid channel widening caused by bank erosion can explain the abrupt recession observed in the flood hydrographs. This allows us to produce an improved simulation of the 1972 jökulhlaup from Grímsvötn, Iceland, and self-consistently, a plausible estimate for the total sediment yield. We also propose a mechanism for the observed flood initiation lake-level at Grímsvötn. These investigations expose the intimate interactions between drainage and sediment transport, which have profound implications on the hydrology, sedimentology and dynamics of ice masses, but which have received little attention.
The role of RAD51-like genes in the repair of DNA damage in mammalian cells

Homologous recombination (HR) is essential for the repair of severe forms of DNA damage such as double strand breaks and interstrand cross-links. The highly conserved RAD51 protein is central to this process and forms nucleoprotein filaments on ssDNA that catalyse strand exchange. In mammalian cells, five genes that share sequence homology with RAD51 have been identified; XRCC2, XRCC3, RAD5JL1, RAD51L2 and RAD51L3. Interactions amongst the RAD51-like proteins have been demonstrated but at present little is known about their functions in HR. Progress has been hampered in the cases of RAD5lLl, -L2 and
-L3, which were identified through database homology searches, because of a lack of suitable mutant cell lines in which to study them.
Cultured mammalian cell lines, selected for sensitivity to DNA-damaging agents, have been used to clone and characterise the function of genes from several DNA repair pathways. The irs3 cell line was isolated from the Chinese hamster line V79-4 in a screen for radiosensitive mutants and has a unique genetic defect. irs3 cells are sensitive to X-rays (2-fold), ethyl methanesulphonate (2.5-fold) and especially mitomycin-C (MMC) (7-fold), as well as showing chromosomal instability. In this study, the sensitivity of irs3 to DNA-damaging agents was found to be substantially complemented by expression of the human RAD51L2 gene, but not other RAD51-like genes or RAD51 itself. An increased level of spontaneous chromosome aberrations was also complemented by RAD51L2 cDNA expression. irs3 cells were found to have little or no RAD51L2 cDNA and RAD51L2 protein. This is likely due to a G → T base substitution at the first nucleotide of exon 6 in the hamster RAD51L2 gene, which encodes an amino acid change of Val to Phe and disrupts the exon 6 3' acceptor splice site.
In collaboration with Dr. Jean-Yves Masson and Dr. Steve West (Cancer Research UK, Clare Hall Laboratories, London), two RAD51 -like protein complexes were shown to exist in hamster cells as they do in human cells. Strikingly, neither complex is formed in irs3. Site-directed mutagenesis of the invariant lysine in the RAD51L2 Walker A box ATP-binding domain showed that this residue is required for MMC resistance. Consistent with a role in HR, -the RAD51L2 protein was found to localise to the nucleus. This localisation was dependent on the eleven amino acids at the C-terminus of the protein.
irs3 cells showed a reduced number of MMC-induced sister chromatid exchanges compared to wild type cells. irs3 cells were also found to be defective in damage-dependent RAD51 focus formation, providing the first evidence that RAD51L2 is involved in repair via RAD51-dependent HR. Using the I-Scel endonuclease to generate a double strand break, it was found that gene conversion is decreased 7-fold in irs3 compared to wild type cells. In summary, this study provides data which identify irs3 as a RAD51L2-deficient cell line and demonstrate that RAD51L2 plays a key role in RAD51-dependent HR processes.

Advisor: Thacker, J
A study of calcium carbonate formation in biological systems

This thesis has studied aspects of biomineralisation, covering the inorganic mineral, the organic matrix, the possible use of phospholipid bilayer vesicles to control mineralisation, calcium and other metal binding to an antibiotic ionophore, Lasalocid-A and a study of a known inhibitor of biomineralisation, the glycopeptide antifreeze found in the plasma of fish which live under polar conditions. The mineral systems studied have been calcium carbonate formations in otoconia and otoliths, crystals which form part of the balance organs of the inner ear, and coccoliths, the earliest eukariotic formation of calcium carbonate, from an alga. Both these systems have been studied by ultra-high resolution electron microscopy with the observation that both types of structures grow in a unique manner, quite distinct from their geological counterparts; indeed the coccolith system involves two distinct mechanisms of growth for different parts of its structure, which is only 2 μm in diameter. Mechanisms of growth of both biominerals are proposed. The study of the organic matrix was less successful in that it was not possible to fully characterise an acidic matrix protein, but it has been shown that the soluble matrix consists of many polypeptide chains cross-linked together, which undergo a conformational change on dissolution from the insoluble matrix on which they lie in vivo and consequently give in vitro results which do not mimic the in vivo condition. Equally, the use of vesicles to control the formation of calcium carbonate was shown to be possible on occasion, but lipids are very unstable in the presence of calcium and no means of stabilising the system to produce consistent results was determined.
Two studies were made by 1H-nmr, the metal-ion complexes of the ionophore Lasalocid-A and the antifreeze glycopeptide of polar fish, in order to demonstrate principles of the handing of isolated ions and of crystallisation inhibition. In both cases, the biological action of the system was mimicked and followed by nmr and a mechanism for their function proposed.

Advisor: Williams, R
A study of regulatory T cells in allogeneic haematopoietic stem cell transplantation

Allogeneic haematopoietic stem cell transplantation (alloHSCT) is an established therapy for many haematological disorders. Unfortunately, the new donor-derived immune system may damage host cells (graft-versus-host disease (GvHD)), causing significant morbidity and mortality. Since regulatory T cells (Tregs) can modulate immune responses, it was hypothesised that Treg numbers in the haematopoietic stem cell grafts and/or peripheral blood may influence the development of GvHD and other transplant-related complications.
In this project, a prospective observational clinical study of putative Tregs in human alloHSCT was performed in Oxford. Flow cytometry and methylation-specific qPCR assays were developed to quantify putative Tregs and lymphocyte populations within the grafts and post-transplant blood samples. Although low CD4(+)CD25(+)FOXP3(+)CD127(-/dim) T-cell numbers were not associated with increased incidence of GvHD, low proportions of CD25(+)FOXP3(+)CD127(-/dim) cells in the graft (as a percentage of total CD4(+) T cells) were independently associated with poor engraftment, increased non-relapse mortality and inferior overall survival. Similarly, falling CD4(+)CD25(+)FOXP3(+)CD127(-/dim) T-cell counts over the first three months post-transplant were associated with higher non-relapse mortality and inferior overall survival. In view of these novel findings, strategies that increase CD4(+)CD25(+)FOXP3(+)CD127(-/dim) T cells in alloHSCT may improve clinical outcomes.
One possible route for increasing Tregs is through cellular therapy. This project therefore tested the hypothesis that CD4(+)CD25(+)FOXP3(+) Tregs can be produced in vitro from conventional CD4(+) T cells. In the presence of TGFβ and Azacitidine, FOXP3 was expressed in the majority of activated CD4(+) T cells. These cells also had a demethylated FOXP3 TSDR enhancer which is specific to natural Tregs. However, most of these cells produced pro-inflammatory cytokines, for example, TNFα. Therefore, under these conditions, FOXP3 expression was not sufficient to produce a Treg phenotype. It is proposed that current focus for generating Tregs for human clinical trials should be directed towards improving isolation and expansion of ex vivo isolated Tregs.

Keywords: Haematopoietic stem cell transplantation
immune reconstitution
regulatory T cells
FOXP3
graft-versus-host disease
Advisor: Roberts, D
Peniket, A
Waldmann, H
Porphyrin arrays for FET devices

Field effect transistors (FETs) are a key component of modern electronic devices. They require a semiconducting material that is traditionally made from doped silicon. Recently however it has been shown that porphyrin systems can be used in the same capacity.
This thesis therefore describes the investigation of new methods of porphyrin functionalization to synthesise 1,4,5,8-tetraazaanthracene-bridged porphyrin arrays, and their application to the synthesis of extended arrays for use in FETs. The 1,4,5,8- tetraazaanthracene bridge is synthesised through the condensation of a porphyrin alpha-dione with 1,2,4,5-tetraaminobenzene. Accordingly, the synthesis of an extended array requires a porphyrin tetra-one monomer unit.
Two methods for the synthesis of porphyrin tetra-ones have been investigated. The first approach attempts to adapt Knudsen's hydroxylation of an aryl halide by sodium benzaldoximate to a porphyrin system. Initial regiospecific halogenation of a porphyrin has been successfully achieved. However when hydroxylation was attempted, partial dehalogenation of the substrate was observed; and when applied to the synthesis of the porphyrin tetra-one the methodology failed.
The second approach involves the allylic oxidation of a chlorin (a reduced porphyrin) on silica. The transformation's mechanism has been thoroughly investigated and it has been successfully applied to the synthesis of a porphyrin tetra-one. This methodology has then been applied to the synthesis of extended porphyrin arrays. A sample incorporating 12 porphyrin units has been successfully constructed. It has been characterised by NMR, MALDI, GPC and UV-VIS spectroscopy. By comparison with previous results it has been concluded that the aromatic system- which spans 181 Ǻngstroms from end to end- can be described as a series of weakly interacting chromophores, in agreement with theoretical predictions made by Hush.
In addition a medium-scale synthesis of an array incorporating four porphyrins has been achieved so that it may now be tested as the semiconducting material in a FET.
Preventing forced marriage: a comparative analysis of France and Great Britain

This study aims at ascertaining via a cross-country/cross-city comparison why different national contexts characterized by allegedly opposite ideologies concerning the incorporation of immigrants (namely, the British Race Relations/multicultural model and French republicanism) have led to the adoption of similar policy tools in the prevention of forced unions amongst young people of ethnic minority background. In order to do so, the study will examine French republican and British multicultural rhetoric and policies aimed at the prevention of forced marriage at different institutional levels, with a focus on the preventive role played by the educational sector and within a historical institutionalist theoretical framework. The comparison begins with a consideration of French and British national rhetoric and policies against forced marriage from 1997 to 2008 to develop an adequate framework for the analysis of the preventive role attributed to educational policies in four major localities (the capital cities, Paris and London, and the second two largest cities per population size, Lyon and Birmingham). Despite differences in the policies and rhetoric adopted by multicultural Britain and republican France to tackle forced unions, the study hypothesizes a common trend in the ways French and British public authorities conceptualize the practice of forced marriage - intended mainly as the product of cultural difference. Similarities in the conceptualization of the practice, in turn, have contributed to the identification of similar policy tools despite dissimilar institutional contexts. Such a hypothesis contrasts with one of the key claims of historical institutionalism, according to which dissimilar institutions lead to different policy outcomes across different countries. The study will introduce the role of ideas – in the form of frames (Bleich 2003) – as a tool to explain the reasons why French and British policies aimed at the prevention of forced unions have led to similar policy outcomes despite dissimilar institutional contexts.

Keywords: comparative politics
harmful traditional practices
forced marriage
integration of immigrants
educational policies
Advisor: King, D
Structure and dynamics of metal clusters

This thesis is concerned with the development of ab-initio molecular dynamics (AIMD) using density functional theory, and its application to simple diatomics and small sodium clusters. The approach follows Car and Parrinello and the local spin density (LSD) approximation is taken as a starting point for the description of the electronic states in these systems. An improvement to LSD by correcting for the spurious self-interaction terms (SIC), as proposed by Perdew and Zunger, and the way in which this can be implemented is considered. The SIC corrected LSD is tested on simple diatomic molecules, and is shown, especially for the case of H2, to significantly improve on the LSD description of the potential energy curve and the spin pairing/unpairing transition. LSD and SIC are then compared for small sodium clusters, for which the geometries, binding energies, and polarizabilities are determined, as well as vibrational frequencies for two clusters. Conclusions are hampered by the lack of experimental data, and uncertainties due to the pseudopotential. However SIC gives a more accurate description of the binding energies, and the unique SIC orbitals allow a description of the bonding which accurately predicts the relative stabilities of the clusters and rationalises their geometries.
The problems of breakdown of the Car-Parrinello (CP) method due to "nonadiabatic" effects is considered and it is shown that the problems arising during bond formation and bond breaking, as illustrated by the case of Na2, can largely be overcome by applying an external thermostat to the fake degrees of freedom. This method is then tested using the dynamics of small sodium clusters. In particular the dynamics of the pseudorotation of Na3 is studied and it is shown that the mechanism and information about the kinetics can be determined.
Finally other methods for improving upon LSD are considered. It is shown that gradient corrections using a plane wave basis set have inherent problems in implementation. Implementation of the exact Hartree-Fock exchange is considered, and this in conjunction with a form of self-interaction correction on the correlation is shown give very accurate results for simple diatomics which are cheaper than using full configuration interaction methods.

Advisor: Madden, P
The etymological poetry of W. H. Auden, J. H. Prynne, and Paul Muldoon

This thesis investigates the roles played by etymology in the work of three late modernist poet-critics: W. H. Auden, J. H. Prynne, and Paul Muldoon. The relationship between poetry and etymology has a long history, but the advent of modern linguistics at the beginning of the twentieth century brought about a change in this relationship. Structuralism developed a more comprehensive condemnation of the etymological fallacy – the view that historical forms and meanings are relevant to current ones - that both isolated etymology as an abstract field of study and undermined its scientific validity. One reaction to this state of affairs has been to re-evaluate etymological discourse itself as poetic or rhetorical. But it is the tension created by what Paula Blank has called 'the quasi-disciplinarity of etymological desire' that motivates Auden, Prynne, and Muldoon's concerns with linguistic historicity.
Etymological poetry encourages, even necessitates, very close reading. While this thesis accepts the challenge to read arguably too closely, it also examines the limits of such an approach and its implications for the relationship between poetry and criticism. The first three chapters consider how Auden, Prynne, and Muldoon invoke etymologies in their own criticism, and how etymology affects the ways their poetry may be said to communicate. The second three develop these analyses into new interpretations of commonly debated aspects of their work: Auden's landscape poetry, Prynne's lyricism, and Muldoon's onomastics. It is argued that the fact of obsolescence is key to the etymological poetic; obsolete forms and meanings make poetry difficult, but in the process they intimate that a truer way of representing the world may be (re)discovered. All three poet-critics confront and absorb the consequences of etymological obscurity. Their preoccupation with the history of words is self-consciously and unavoidably pedantic, and it is this pedantry that plays the most significant role in the poetic power they accord to etymology.

Keywords: diction
close reading
modern poetry
difficulty
etymology
pedantry
dictionaries
Advisor: Reynolds, M
Complexity, innovation and the dynamics of OTC derivatives regulation

Conventional financial theory has played an important – and yet largely unexamined – role in shaping how we regulate modern financial markets. This thesis explores the influence of conventional financial theory on the regulation of over-the-counter (OTC) derivatives markets in the U.S. and U.K. prior to the global financial crisis. More specifically, it explores how conventional financial theory failed to adequately account for both the complexity of OTC derivatives markets and the nature and pace of financial innovation and, ultimately, how these blind spots became reflected in a ‘non-interventionist’ approach toward their regulation now widely viewed as suboptimal.
This thesis yields three important contributions to the scholarly and public policy debates surrounding the regulation of modern financial markets. First, it articulates a more robust theoretical framework for understanding complexity, financial innovation, and the relationship between these powerful market dynamics. This, in turn, facilitates an examination of the implications of complexity and financial innovation in terms of the ongoing debates respecting the optimal source, form and scope of financial regulation. It also facilitates an examination of both the shortcomings of the pre-crisis regulatory regimes governing OTC derivatives markets and, looking forward, the prospective strengths and weaknesses of embryonic post-crisis reforms. Finally, and more broadly, this thesis enhances our understanding of the relationship between the important insights of financial theory and how we conceptualize and pursue the objectives of financial regulation.

Keywords: financial regulation
derivatives
Advisor: Armour, J
Measurement of properties of the lunar surface using the Diviner Lunar Radiometer experiment on the NASA Lunar Reconnaissance Orbiter

The Diviner Lunar Radiometer is a nine-channel radiometer on board the Lunar Reconnaissance Orbiter, launched in June 2009 and currently orbiting the Moon. Diviner is the first orbiting multi-spectral instrument to observe the lunar surface in the mid- and far- infrared, therefore this thesis details the first steps towards utilising observations in this new spectral region.
The author, as part of the Diviner instrument team, contributed to the pre-launch testing and calibration of Diviner. Specifically, the transmission profiles of the B2 and B3 filters, which could not be measured after integration into the instrument due to their long wavelength passbands, were determined. Further investigations of the far-infrared mesh filters were also conducted, as the spectral responses of similar mesh filters were found to have broadened after integration into the Mars Climate Sounder instrument, the pre-cursor instrument to Diviner. To test if this would occur in Diviner also, a new setup was made to approximately re-create the instruments' optical layout. No such spectral broadening was measured in the B1, B2 or B3 filters. The linearities of Diviner's detectors were also confirmed through analysis of the pre-flight calibration data.
Laboratory emission spectra taken under ambient conditions differ from those taken in a lunar environment, which induces a temperature gradient in soil and mineral samples. Due to a lack of spectra measured under such conditions, which are directly comparable to Diviner‟s measurements, a new chamber for performing high-resolution emission measurements in a simulated lunar environment was built and calibrated. This setup induces a temperature gradient in each sample by heating it from below while it is surrounded by a cooled radiation shield, all enclosed in a very low pressure vacuum chamber. Lunar analogue minerals have been measured, first in reflectance, and then in simulated lunar conditions, forming the basis of a new lunar spectral library.
The uses of the mid- and far-infrared have been described herein, utilising calibrated Diviner observations to: [1] map the temperatures of the lunar poles; [2] investigate regions containing higher than average abundances of rocks; and [3] determine the composition of regions of the lunar surface by combining observations with the new spectral library made during this project.

Keywords: moon
spectroscopy
infrared
lunar
mineralogy
instrument calibration
Advisor: Bowles, N