VictorJuiz/thesis huggingface dataset:
Static pile-soil-pile interaction in offshore pile groups

This thesis is a theoretical study, using both finite element and boundary element methods, of the behaviour of single-piles and pile groups under vertical and lateral loading. It offers an improved understanding of the soil-structure interaction that occurs in pile groups, particularly closely spaced piles subjected to lateral loads. The potential of a two- dimensional idealisation of what is a three-dimensional problem is demonstrated by achieving real insight into the complex nature of pile-soil and pile-soil-pile interaction in pile groups. A new load transfer mechanism is presented for a rigid, axially loaded vertical pile. From this an improvement is then derived to the analytical solution for pile head settlement given by Randolph and Wroth (1978). The improved mechanism has the further merit that it can be applied also to solutions for flexible piles and pile groups. The improved analytical solution is further adapted in the development of two correcting layers specifically for vertically loaded piles to model infinite boundaries in the finite element model. The correcting layers help in establishing superiority of the finite element method over the boundary element method. To model pile-soil interaction, a purely cohesive interface element is developed and then validated by performing various two-dimensional test problems, including stability analysis of flat surface footings. Footing-soil interface tension is successfully modelled in this way - an outcome that entails a significant modification to the Hansen (1970) bearing capacity solution. Stability analysis is also carried out of conical footings using a three-dimensional finite element model: the results help to explain the applicability of the existing bearing capacity theories to conical footings. The ultimate lateral soil reaction is determined and various pile loading stages are investigated through parametric studies. Study of the stage immediately following pile installation (i.e. the consolidation stage) highlights the need to develop an effective stress analysis for laterally loaded piles. Pile-soil interaction is studied using the cohesive interface element presented earlier, which proves to be quite successful in smoothing out the stress discontinuities around the pile. A new material model for frictional soils is presented, and validated by using it to model an extension test: it captures well post-peak behaviour and takes care of the effects of dilation on the response of laterally loaded piles. Finally, mechanisms of interaction in closely spaced pile groups are studied. Simple analytical expressions are derived which quantify the effects of interaction. A new method of analysis is presented for single-piles and pile groups which offers a considerable degree of reliability without having to do either impossibly expensive full scale field tests or prohibitively expensive full three-dimensional analysis using the currently available computers.

Keywords: foundations
piles
offshore
Advisor: Burd, H
Williams, M
Seamus Heaney and society, 1964 - 1994

The contexts of Seamus Heaney's writing have been routinely noted but their critical interrogation has, to date, been limited. This thesis resituates Heaney's work to reassert the significance of his writing in its varied times and places. Its aim is to revive the web of connections within which Heaney's work was written, published, and received, and this accounts for the "society" of the title. While the idea of society as entity remains important, the word is employed primarily as a capacious guiding principle. Society's adjective, social, is always connected: to be "social" in any sense is always to be implicated in a wider context or contexts.
A central ambition has been to reappraise Heaney's work in relation to the situation in Northern Ireland during the three decades under consideration. A trend in criticism has been to offer reductive contextual accounts which risk depreciating the value of a historicist approach. This thesis demonstrates instead how Heaney's work is implicated in textual, cultural, and institutional networks which were themselves conditioned by the unique circumstances in Northern Ireland. It considers: the London publishing scene on which his work emerged; his relationship to Belfast mediated through television documentary; his radio work for the BBC Northern Ireland Schools Service; his relationship to Derry mediated through photography; and ideas of audience, address, and redress in his Oxford lectures. Participating in the increasingly interdisciplinary treatment of literature within and beyond Irish Studies, the literary analysis at the heart of this project is undertaken within a broader framework of cultural criticism.
The significance of this contribution lies not solely in its acts of historical recovery, but in the critical reorientation these permit. By locating Heaney as a respondent in varied public arenas we can understand the genesis not only of his work but of the international establishment literary figure he became.

Keywords: Northern Ireland
Heaney
society
poetry
Advisor: O'Donoghue, B
Analysis of SMN function in development and Nedd4, a putative modifier of Parkinson's disease, in Drosophila melanogaster

Neurological diseases are devastating illnesses that affect over one billion people worldwide. Drosophila melanogaster provides a genetically tractable system in which to study gene function and the mechanisms of pathogenesis of neurological diseases. In this study I have investigated the function of survival motor neuron (SMN), the causative gene in the neuromuscular disease spinal muscular atrophy (SMA), in growth and differentiation in Drosophila. In addition, I have used the fruit fly to investigate a putative modifier of a previously characterised Drosophila model of Parkinson's disease.
Spinal muscular atrophy is an autosomal recessive neurological disease that is characterised by motor neuron loss resulting in muscle weakness. The disease is caused by the deletion or mutation of the survival motor neuron (SMN) gene. In Drosophila, SMN was found to be highly expressed in dividing tissues and a reduction in SMN levels resulted in growth defects, stem cell defects and developmental delay. SMN was also shown to regulate chromosome morphology of the endocycling nurse cells of the female germline. Therefore it appears that SMN has a role in growth control and development in Drosophila.
Parkinson's disease is a common disorder that results in widespread neurodegeneration with a predilection for dopaminergic neuron loss resulting in movement defects. A defining neuropathological feature of the disease is the presence of alpha-synuclein containing inclusions. Using a Drosophila model of PD, I have shown that specific alpha-synuclein-induced phenotypes in the fly can be suppressed by the overexpression of the E3 ubiquitin ligase, Nedd4.

Keywords: Parkinson's disease
Drosophila
SMN
Advisor: Liu, J
Spectral data for G-Higgs bundles

We develop a new geometric method of understanding principal G-Higgs bundles through their spectral data, for G a real form of a complex Lie group. In particular, we consider the case of G a split real form, as well as G = SL(2,R), U(p,p), SU(p,p), and Sp(2p,2p). Further, we give some applications of our results, and discuss open questions.

Keywords: Hitchin fibration
spectral data
Higgs bundles
Advisor: Hitchin, NJ
Oriya literature and the Jagannath cult, 1866-1936

This work on 'Oriya Literature and the Jagannath Cult, 1866- 1936: Quest for Identity' studies the question of Oriya identity in cultural and religious terms. As the title suggests, the Oriya literature and the Jagannath cult during the period, 1866-1936, have been studied and analysed in order to demonstrate how Oriya identity has been progressively constituted and reflected in them. My work departs from earlier works in a number of ways. The most important departure is the study of Oriya identity from the religio-cultural perspective instead of studying political identity-formations which have already been dealt with at great length in some earlier works. One more important feature of my work is the study of the Jagannath cult in the light of Oriya identity- a question of interrelation hitherto neglected by scholars. Thus, my thesis is exclusively focused on Oriya identity- how it manifested itself in the Oriya literature and the Jagannath cult.
For the purpose, I have first shown in my second chapter how a consciousness about Orissa and Oriya, however rudimentary it might have been, was present in the early Oriya literature and in the Jagannath cult at its earlier stage of evolution. This rudimentary consciousness took the form of identity towards the second part of the 19th century under the compulsion of some historical forces that arose out of British colonialism-imperialism.
In my chapters on the Oriya literature, I have shown from the writings of selected, representative authors how Orissan history, tradition, legend, nature, the Indian link and even externalised 'Other' have been used and constructed in definition of Oriya identity. A major finding of my thesis is the gradual shift in the treatment of Oriya identity from the inward-looking, reactionary approach to a broadbased, expansive perspective due to changes in the political scenario of Orissa and the development of new, liberal ideas. In my discussion on the Jagannath cult, I have established that Oriya religious identity came to be Jagannath-centred during the period of our study. In order to prove it, while discussing various dynamic aspects of the cult and their particular significance in transforming it to a distinct Oriya faith, I have also studied how Lord Jagannath and His cult were constructed and construed in Oriya literary traditions and historiographical writings and narratives.
Finally, I have tried to establish a causal connection between Oriya identity and the political process of Orissa during the period of study.
Pushing the boundaries: molecular dynamics simulations of complex biological membranes

A range of simulations have been conducted to investigate the behaviour of a diverse set of complex biological membrane systems. The processes of interest have required simulations over extended time and length scales, but without sacrifice of molecular detail. For this reason, the primary technique used has been coarse-grained molecular dynamics (CG MD) simulations, in which small groups of atoms are combined into lower-resolution CG particles. The increased computational efficiency of this technique has allowed simulations with time scales of microseconds, and length scales of hundreds of nm.
The membrane-permeabilizing action of the antimicrobial peptide maculatin 1.1 was investigated. This short α-helical peptide is thought to kill bacteria by permeabilizing the plasma membrane, but the exact mechanism has not been confirmed. Multiscale (CG and atomistic) simulations show that maculatin can insert into membranes to form disordered, water-permeable aggregates, while CG simulations of large numbers of peptides resulted in substantial deformation of lipid vesicles. The simulations imply that both pore-forming and lytic mechanisms are available to maculatin 1.1, and that the predominance of either depends on conditions such as peptide concentration and membrane composition.
A generalized study of membrane protein aggregation was conducted via CG simulations of lipid bilayers containing multiple copies of model transmembrane proteins: either α-helical bundles or β-barrels. By varying the lipid tail length and the membrane type (planar bilayer or spherical vesicle), the simulations display protein aggregation ranging from negligible to extensive; they show how this biologically important process is modulated by hydrophobic mismatch, membrane curvature, and the structural class or orientation of the protein.
The association of influenza hemagglutinin (HA) with putative lipid rafts was investigated by simulating aggregates of HA in a domain-forming membrane. The CG MD study addressed an important limitation of model membrane experiments by investigating the influence of high local protein concentration on membrane phase behaviour. The simulations showed attenuated diffusion of unsaturated lipids within HA aggregates, leading to spontaneous accumulation of raft-type lipids (saturated lipids and cholesterol).
A CG model of the entire influenza viral envelope was constructed in realistic dimensions, comprising the three types of viral envelope protein (HA, neuraminidase and M2) inserted into a large lipid vesicle. The study represents one of the largest near-atomistic simulations of a biological membrane to date. It shows how the high concentration of proteins found in the viral envelope can attenuate formation of lipid domains, which may help to explain why lipid rafts do not form on large scales in vivo.

Keywords: Influenza virus
antimicrobial peptides
biological membrane
molecular dynamics
membrane proteins
coarse-grained
Advisor: Sansom, M
The effects of a novel substrate on exercise energetics in elite athletes

The physiological ketosis of starvation makes sound evolutionary sense, as ketone bodies have several thermodynamic advantages over other nutritional substrates, in addition to their actions to conserve protein and glucose stores. Utilising the body’s metabolic responses to ketosis by delivering a novel nutritional source of ketone bodies, the work in this thesis explored the metabolic effects of ketosis on physical performance in humans. First, the pharmacokinetics and dosing requirements for ketone containing drink preparations were characterised in a population of athletes and healthy controls (n = 45). Using endurance exercise as a model of physiologic stress, the functional impact of ketosis during sustained high intensity effort was investigated in high performance athletes (n = 22). It was shown that nutritional ketosis improved performance in 18/22 athletes, who set 14 new best performances during 30 min of rowing. Furthermore, when ketones and glucose were delivered together, cycling performance was improved by 2% (n = 8) following 1.5 hours of fatiguing effort, compared with optimal carbohydrate intake. Blood D-β-hydroxybutyrate reached 3-5 mM following ketone drinks, equivalent to several days of total fasting, but rapidly decreased during exercise. It was found that higher physical workloads correlated with larger decreases in plasma ketone concentration (n = 8), consistent with their oxidation as respiratory fuels. Nutritional ketosis significantly altered fuel metabolism during exercise in elite athletes (n = 10), decreasing peripheral lipolysis, skeletal muscle glycolytic intermediates, blood lactate, and branched chain amino acid release. In conclusion this work suggests a new hierarchy of substrate preference during physical stress, whereby mimicking the physiology of starvation, the energetic consequences of oxidising ketones may significantly enhance athletic performance. The extrapolation of these findings may have therapeutic implications for patient populations where energetic demands are high, and deleterious switches in substrate selection occur.

Keywords: ketones
exercise
nutrition
metabolism
Advisor: Neubauer, S
Clarke, K
Holloway, C
Aberration free extended depth of field microscopy

In recent years, the confocal and two photon microscopes have become ubiquitous tools in life science laboratories. The reason for this is that both these systems can acquire three dimensional image data from biological specimens. Specifically, this is done by acquiring a series of two-dimensional images from a set of equally spaced planes within the specimen. The resulting image stack can be manipulated and displayed on a computer to reveal a wealth of information. These systems can also be used in time lapse studies to monitor the dynamical behaviour of specimens by recording a number of image stacks at a sequence of time points. The time resolution in this situation is, however, limited by the maximum speed at which each constituent image stack can be acquired. Various techniques have emerged to speed up image acquisition and in most practical implementations a single, in-focus, image can be acquired very quickly. However, the real bottleneck in three dimensional imaging is the process of refocusing the system to image different planes. This is commonly done by physically changing the distance between the specimen and imaging lens, which is a relatively slow process. It is clear with the ever-increasing need to image biologically relevant specimens quickly that the speed limitation imposed by the refocusing process must be overcome.
This thesis concerns the acquisition of data from a range of specimen depths without requiring the specimen to be moved. A new technique is demonstrated for two photon microscopy that enables data from a whole range of specimen depths to be acquired simultaneously so that a single two dimensional scan records extended depth of field image data directly. This circumvents the need to acquire a full three dimensional image stack and hence leads to a significant improvement in the temporal resolution for acquiring such data by more than an order of magnitude.
In the remainder of this thesis, a new microscope architecture is presented that enables scanning to be carried out in three dimensions at high speed without moving the objective lens or specimen. Aberrations introduced by the objective lens are compensated by the introduction of an equal and opposite aberration with a second lens within the system enabling diffraction limited performance over a large range of specimen depths. Focusing is achieved by moving a very small mirror, allowing axial scan rates of several kHz; an improvement of some two orders of magnitude. This approach is extremely general and can be applied to any form of optical microscope with the very great advantage that the specimen is not disturbed. This technique is developed theoretically and experimental results are shown that demonstrate its potential application to a broad range of sectioning methods in microscopy.

Keywords: focusing
two photon microscopy
aberrations
microscopy
confocal microscopy
Advisor: Wilson, T
The economy of certain Piedmontese noble families in the reign of Victor Amadeus II

Despite the evident importance of the nobility a study of its economic and social position in Piedmont has so far never been attempted.
All previous studies of any value have been dedicated almost exclusively to the growth of the State. Such attention as has been paid to the aristocracy has consequently been limited to its relations to government policy. The importance of the nobility has always been neglected and perhaps under-estimated. The fundamental works of Einuadi and Prato on the finances and economy of Piedmont in the early 18th century forms clear examples; the nobility is above all discussed for its immunities, and the final conclusion is that these immunities were remarkably limited. Einaudi, examining the 18.03% of ecclesiastical and fuedal exemption in 1700, compares it to other countries: in the Kingdom of Naples in 1740 2/3 of all landed revenues were in the hands of the clergy and nobility, all virtually immune; in the France of 1780 at least half the land was in some way exempt. At the same time, the Piedmontese nobility is judged as a fairly poverty-stricken class.
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Heterogeneity in Ewing sarcoma

Ewing sarcoma, an aggressive primary bone and soft tissue tumour is characterised by the expression of the chimeric transcription factor EWS-FLI1 in 90% of patients. This alters expression of many genes including activation of the Insulin Growth Factor (IGF) pathway via IGFBP3 supression. Phase I/II trials with an IGF-1 inhibitor have demonstrated tumour regression in a modest number of Ewing sarcoma patients.
The aim of this thesis was to identify mechanisms contributing to the heterogeneity of resistance in Ewing sarcoma following inhibition with OSI-906, a dual kinase inhibitor of IGF-1 (IGF-1R) and Insulin (IR) receptors. The hypothesis was that mechanisms of resistance relate to heterogeneity of responses to signalling pathway activation and inhibition. Through selection, disruption of the pathway would identify subpopulations of cells both sensitive and resistant in their response allowing for interrogation of resistance mechanisms.
A genome wide approach was taken to model the resistance profile of cell lines. Through developing a method of unbiased quantification, a panel of validated Ewing sarcoma cell lines (EuroBoNet) were imaged and segmented to assess the responses of biomarkers on signalling pathway activation. Heterogeneity was confirmed between cell lines. The application to diagnostic biopsies led to the identification of prognostic classifiers and cellular subpopulations with clinical prognostic significance. The distribution of Ki67 was found to be predictive of survival and cells with lower levels of CD99 in the cytoplasm were most discriminative. Parallel sequencing strategies (RNA-seq, whole exome sequencing, and aCGH/ SNP array) for genome-wide screening was carried out for point mutations, copy number changes and rearrangements. Systematic detection was used to characterise genomic rearrangements and functional validation performed. Resistant clones, formed via ENU mutagenesis of cell lines, were sequenced in order to demonstrate the resistance profile of OSI-906.
In summary heterogeneity of Ewing sarcoma at the genomic and proteomic level can influence the signalling dependency of tumours and response to inhibitors. Genomic and proteomic profiling of tumour cells may be relevant to future developments of novel therapies.

Keywords: Resistance
Ewing sarcoma
next generation sequencing
Advisor: Hassan, A
From old socialists to new democrats

In 1996, a new left of centre party emerged in Japan called the Democratic Party of Japan (DPJ) and effectively replaced the Japan Socialist Party (JSP) as the main opposition party. This thesis asks what conditions caused this realignment and how the DPJ differs from the JSP.
An increasing distrust and disinterest of politics and politicians has meant that the non-aligned voter in Japan forms the largest group of the electorate. Every party has lost support, but the left faced the worst drop of support. With the end of the Cold War, and the intensifying call for Japan to reassess its role on the World stage, the traditional ideology of the Japanese left, which has become synonymous with peace and preservation of the Peace Constitution, has lost its stabilising effect on the party and on its supporters. The labour unions, which were once the key mobilisational force for the left-wing parties at election time, began to question their relationship with the JSP and found new links to government. Simultaneously, they were also losing members so mobilisation of voters for the left also declined. Finally, a new electoral system did not reward the opposition as much as the LDP.
Overall, the mobilisation of the electorate has become increasingly difficult for the Japanese left as a result of these factors. The DPJ has had to find ways of dealing with them and also has had to create its own identity. The way in which the party has dealt with this is by 'widening out' its types of candidate and using new methods to attract support. Furthermore, the DPJ has become more aware of its party coherence and has ensured that party unity is maintained even when ideological disputes occur.

Advisor: Stockwin, J