VictorJuiz/thesis huggingface dataset:
Studies towards the synthesis of himbacine

The natural alkaloid himbacine 1, first isolated in 1955 from Galbulimina baccata Bail, has attracted attention as a potential therapetic agent for Alzheimer's disease. It is proposed that a late stage in the biosynthesis of this compound may proceed via an iminium ion mediated Diels-Alder reaction (Scheme 1), which would yield the related alkaloid himgravine 2, which can be reduced to himbacine 1.
Precident for the iminium ion mediated Diels-Alder reaction has been provided by a related oxonium ion mediated cycloaddition reaction (Scheme 2). Confirmation of the stereochemistry of the product of this reaction has been obtained by X-ray crystallography of the tricyclic alcohol.
Studies towards the synthesis of the iminium ion have been undertaken. Piperidine sulfone has been synthesised in a 17% yield over 16 linear steps, and a synthesis of dihydrofuran has been investigated involving an enyne metathesis reaction. Additionally, methodology has been developed for a Julia coupling to join piperidine sulfone to dihydrofuran, and a Polonovski reaction for generation of the required iminium ion.
An integrated genomic approach for the identification and analysis of single nucleotide polymorphisms that affect cancer in humans

The identification of genetic variants such as single nucleotide polymorphisms (SNPs), which affect cancer progression, survival and response to treatments could help in the design of better prevention and treatment strategies. Genome-wide association studies (GWAS) have provided the first step of identifying SNPs associating with cancer risk. However, identifying the causal SNPs responsible for the associations has proven challenging, and GWAS have not been successful for time-to-event phenotypes such as cancer progression, due to the insurmountable obstacle of the large sample size needed. The aim of this thesis is to design and implement strategies that combine the identification of SNPs significantly associated with cancer, focusing on time-to-event phenotypes, with detailed bioinformatics analysis to allow for further experimental validation and modelling, to better understand cancer-associated genomic loci and accelerate their incorporation into the clinic.
First, a methodology that utilises the Random Survival Forest is developed and combined with a bioinformatics analysis that ranks SNPs according to their potential to result in differential protein levels or activity, in order to identify SNPs that affect the progression of B-cell chronic lymphocytic leukaemia. Next, an analysis that aims to extend our understanding of the role of SNPs in mediating the cellular responses to chemotherapeutic agents is applied. SNPs that could associate with differential cellular growth responses in cancer cell line panels are identified, and their association with the differential survival of cancer patients is explored. Finally, the potential roles of SNPs in affecting the transcriptional regulation of key cancer genes resulting in differential cancer risk are assessed. First, by focusing on SNPs in an important transcription factor binding motif that has been shown to be extremely sensitive to single base pair changes (the E-box) and next, by exploring the possibility that polymorphic transcription factor binding sites could underlie the significant associations noted in cancer GWAS.

Keywords: Transcription Factor Binding Sites
Survival Analysis
SNP
Random Survival Forest
Cancer
Advisor: Bond, G
Meinshausen, N
Women's writing in exile

Despite the recent increase in scholarship on the subject of the female experience in exile, there is still much to be done. Exile scholars now have at their disposal an abundance of broad, general overviews of the circumstances and fates of displaced women writers, but a dearth of scholarship that considers specific literary works in an individualised fashion still exists. This is especially true of those female writers who have only recently been 'rediscovered', such as the three under discussion in this thesis.
This thesis explores in detail the exile writings of Veza Canetti, Anna Gmeyner, and Lili Korber, about which little scholarship exists, and uses them as case studies to illuminate the situation of exiled women writers in general The exile works of these three authors repay study both for their own literary merits and for what they can tell us about the individual experience of exile. In their broad similarities, these writers also provide us with case studies of the larger experience of authorial exile - particularly, but by no means exclusively, the gendered experience - that allow us to derive more general lessons about the influence of forced flight on literary art. By giving due consideration to work produced in exile, this thesis calls into question some of the generalisations commonly found in recent scholarship and demonstrates that, despite hardsrnps and setbacks and contrary to common scholarly contention, all three women continued to write well into their exile years and that in those years they took their writing in new, skilful, and creative directions.

Advisor: Robertson, R
Elections and politics in Canada West under responsible government, 1847-1863

The aspects of mid-nineteenth-century Canadian history which have received the fullest examination are the Rebellions of 1837, the Union of Upper and Lower Canada in 1841, the winning of Responsible Government in 1847-48, and Confederation in 1864-67. To a large extent these have been studies in imperial relations and the character of internal politics has received less attention. The purpose of this thesis is to examine the political system which evolved in Upper Canada after 1848 from the vantage point of the six general elections between 1848 and 1863. (The Legislative Council was made elective in 1856, but there was little interest taken in it or its elections and this study is concerned only with elections to the Legislative Assembly.) The thesis attempts to discover the internal wordings of politics in Upper Canada: the issues which aroused the most interest in the elections, the parties and their organizations, the electorate and the system of representation, and the various forces, both legitimate and corrupt which were used to influence the voters. In some instances there has been an attempt to arrive at quantitative or definitive conclusions, but in most cases this was neither desirable or possible. Instead, specific examples hove been used to give e general picture of how the political and electoral systems operated.
[Please see pdf. for full abstract.]
Causes and consequences of maternal sepsis in the UK

Background: The rate of maternal death from sepsis has increased in several European countries, most notably the UK, where sepsis is now the leading cause of direct maternal death. An increase in maternal mortality also implies an increase in the number of women with severe, life-threatening morbidity. Key information gaps in the understanding of severe maternal sepsis in the UK are: the incidence, main causative organisms, infection sources, and risk factors for severe maternal sepsis.
Methods: Four population-based observational studies were conducted to address these evidence gaps.
Results: The incidence of severe maternal morbidity from sepsis is increasing in the UK, a trend also evident in the USA. The most common sources are respiratory tract, genital tract and urinary tract infection. The predominant organisms causing infection are E. coli, group A streptococcus, and strong circumstantial evidence of Streptococcus pneumonia. Sepsis progresses very rapidly particularly with group A streptococcal infection. Approximately 20% of women with severe sepsis progress to septic shock and 2% of women die.
Risk factors for severe maternal sepsis in the UK with a large effect size are: febrile illness or antibiotics in the 2 weeks prior to onset of severe sepsis (aOR=12.1, 95% CI 8.1-18.0), caesarean section after the onset of labour (aOR= 8.1, 95% CI 4.7-14.0), multiple pregnancy (aOR= 5.8, 95% CI 1.5-21.5), infection with group A streptococcus (aOR=4.8 for progression to septic shock, 95% CI 2.2-10.8), pre-labour caesarean section (aOR= 3.8, 95% CI 2.2-6.6), low socioeconomic status (aOR=2.6, 95% CI 1.03-6.7), and operative vaginal delivery (aOR=2.5, 95% CI 1.3-4.7). Risk factors are significantly cumulative.
Conclusions: Infection prior to or after delivery, even if the woman appears to be well, should be a marker for close clinical monitoring. Suspicion of group A streptococcus should be regarded as an obstetric emergency and treated ahead of laboratory confirmation.

Keywords: sepsis
epidemiology
maternal health
severe sepsis
Advisor: Knight, M
Kurinczuk, J
A measurement of the ratio of the W+1 jet and Z+1 jet cross sections using the ATLAS detector at the LHC.

The first measurement of the ratio of the W and Z cross sections in association with a single jet, known as the R_{Jets} measurement, is presented. The measurement was performed using 33pb^-1 of integrated luminosity, recorded during the year 2010 by the ATLAS detector at the LHC. At this time the LHC was operating at a center-of-mass energy of 7 TeV. The measurement is made as a function of the threshold on the jet transverse momentum, from 30 GeV up to a value of 200 GeV. The motivation for this measurement is outlined in terms of providing a stringent test of the Standard Model of particle physics, as well as a model independent tool for searching for new physics. Data driven tools are developed to perform the measurement and their performance is discussed. The result of the measurement is compared with the predictions of Next-to-Leading order perturbative QCD and found to be in good agreement over the entire range of transverse momenta considered.

Keywords: Standard Model
LHC
ATLAS
Advisor: Beauchemin, P
Viehhauser, G
Moral emotions as antecedents of political attitudes

The main objective of this thesis was to investigate the proposition that moral emotions act as antecedents of political attitudes. My approach (Chapter 1) stems from moral foundations theory, which proposes that liberals and conservatives have different moral values (Graham, Haidt, & Nosek, 2009). Chapter 2 presents Study 1, an experimental test of the hypothesis that induced disgust leads participants to adopt more left-wing economic attitudes in comparison to a control condition (sadness). Results supported this hypothesis. Chapter 3 reviews emotion-regulation theories, and presents Study 2, which investigated whether emotion-regulation strategies, disgust sensitivity (DS-R), and private body consciousness (PBC) moderate the effects found in Study 1. As predicted, disgust led to more left-wing economic attitudes, but this was only the case for high-PBC and high-DS-R participants. Chapter 4 presents Study 3, which replicated Study 2, and showed dissociations between the effects of disgust on economic and social attitudes. Chapter 5 presents a cross-sectional investigation (Study 4) that tested for associations between the predisposition to experience disgust and both social and economic attitudes. As predicted, core disgust and pathogen disgust were associated with left-wing economic attitudes and these effects applied only to British participants, and not non-British participants. Chapter 6 presents Study 5 – an experiment investigating the relationship between disgust and prejudiced attitudes towards outgroups. Induced disgust led to more prejudiced attitudes towards a novel group than both sadness and neutral emotion. Chapter 7 is focused on two self-conscious moral emotions: guilt and shame. Study 6, presented in this chapter, found a positive association between guilt proneness and left-wing economic attitudes, and a relationship between shame proneness and social-conservative attitudes. Study 7 failed to reveal causal relationships between incidental guilt and shame and political attitudes. Chapter 8 presents the general discussion addressing limitations, implications, and future research directions.

Keywords: conservative
moral emotions
political attitudes
liberal
disgust
Advisor: Parkinson, B
Allostasis of cerebral water: modelling the transport of cerebrospinal fluid

A validated model of water transport in the cerebral environment is both an ambitious and timely task; many brain diseases relate to imbalances in water regulation. From tumours to strokes, chronic or acute, transport of fluid in the brain plays a crucial role. The importance and complexity of the brain, together with the range of unmet clinical needs that are connected with this organ,make the current research a high-priority.
One of the most paradoxical cerebral conditions, hydrocephalus, serves as an excellent metric for judging the success of anymodel developed. In particular, normal pressure hydrocephalus (NPH) is a paradoxical condition with no known cure and existing treatments display unacceptably high failure rates. NPH is considered to be a disease of old age, and like many such diseases, it is related to a change in the transport of fluid in the cerebral environment. This complex system ranges from organ-level transport to cellular membrane channels such as aquaporins; through integrating it in a novel mathematical framework, we suggest that the underlying logic of treatment methods may be misleading.
By modelling the transport of cerebrospinal fluid (CSF) between the ventricular system, cerebral tissue and blood networks, we find that changes to the biophysical properties of the brain (rather than structural changes such as aqueduct obstruction) are capable of producing clinically relevant ventriculomegaly in the absence of any obstruction to CSF flowthrough the ventricular system. Specifically, the combination of increased leakiness and compliance of the capillary bed leads to the development of enlarged ventricles with a normal ventricular pressure, replicating clinical features of the presentation of NPH. These results, while needing experimental validation, imply that treatment methods like shunting, that are focussed on structural manipulation, may continue to fail at unacceptably high rates.

Keywords: poroelastic theory
fluid dynamics
normal pressure hydrocephalus
multiple network poroelastic theory
Advisor: Ventikos, Y
Sixth-century fortifications in Byzantine Africa

This thesis surveys and discusses the documentary and archaeological evidence for sixth-century fortifications in Byzantine Africa. Chapter I examines the sources of evidence, noting that over 80 years have passed since the last major study of the subject was undertaken, by Charles Diehl in 1896. Chapter II traces the military history of Byzantine Africa from 533 to 602, with introductory and concluding sections on the fifth and seventh centuries. Chapter III discusses the evidence for the military organization and defensive strategy of Byzantine Africa in the sixth century, looking in particular at the structure of military command, the composition of the Byzantine army, the garrison structure (including the evidence for the nature and size of local garrisons stationed in forts and towns), the administrative machanisms by which fortifications were built and the strategy to be discerned in their siting. The chapter ends with a general appraisal of the benefits that Roman Africa received from Justinian's reconquest. Chapter IV examines the architecture of Byzantine fortifications in Africa, comparing it with earlier and contemporary practice in the eastern and western empires. The tactical aspects of fortifications are also considered, in particular the question of how far their design was influenced by the use made of artillery and archery in the sixth-century Byzantine army. In a short final chapter, an assessment is made of the value that the study of sixth-century Byzantine fortifications in Africa has for understanding later developments in the military architecture of eastern and western Christendom and of Islam. The Gazetteer includes full descriptions (with plans and photographs) of all the Byzantine fortifications identified in Africa, and shorter notes on other structures of more doubtful Byzantine identification; an index to fortifications in Africa referred to by Procopius; and a corpus of sixth- and seventh century military inscriptions from Africa.
Pairing, paramagnetism and prethermalization in strongly correlated low-dimensional quantum systems

Quasi-one-dimensional quantum models are ideal for theoretically exploring the physical phenomena associated with strong correlations. In this thesis we study three examples where strong correlations play an important role in the static or dynamic properties of the system.
Firstly, we examine the behaviour of a doped fermionic two-leg ladder in which umklapp interactions are present. Such interactions arise at special band fillings and can be induced by the formation of charge density wave order in an array of two-leg ladders with long-range (three-dimensional) interactions. For the umklapp which arises from the half-filling of one of the bands, we show that the low-energy theory has a number of phases, including a strong coupling regime in which the dominant fluctuations are superconducting in nature. These superconducting fluctuations carry a finite wave vector – they are the one-dimensional analogue of Fulde-Ferrell-Larkin-Ovchinnikov superconductivity.
In a second example, we consider a quantum spin model which captures the essential one-dimensional physics of CoNb2O6, a quasi-one-dimensional Ising ferromagnet. Motivated by high-resolution inelastic neutron scattering experiments, we calculate the dynamical structure in the paramagnetic phase and show that a small misalignment of the transverse field can lead to quasi-particle breakdown – a surprising broadening in the single particle mode observed in experiment.
Finally, we study the out-of-equilibrium dynamics of a model with tuneable integrability breaking. When integrability is broken by the presence of weak interactions, we show that the system relaxes to a non-thermal state on intermediate time scales, the so-called “prethermalization plateau”. We describe the approximately stationary behaviour in this regime by constructing a generalised Gibbs ensemble with charges deformed to leading order in perturbation theory. Expectation values of these charges are time-independent, but interestingly the charges do not commute with the Hamiltonian to leading order in perturbation theory. Increasing the strength of the integrability breaking interactions leads to behaviour compatible with thermalisation.
In each case we use a combination of perturbative analytical calculations and non-perturbative numerical computations to study the problem at hand.

Keywords: Strongly Correlated Systems
Out-of-equilibrium quantum mechanics
paramagnetism
Quantum Quench
Condensed Matter Theory
superconductivity
Advisor: Essler, F
A study of Mark Pattison's religious experience, 1813-1850

This study is an account of Mark Pattison's religious experience up to the year 1850. It tells the story of Pattison's intellectual and personal development during the most crucial period of his life, of his close connection with Newman and the leaders of the Oxford Movement and, finally, of his rejection of religious orthodoxy and the growth in him of a religious agnosticism and intellectual scepticism.
Pattison attempted to tell this story himself in his Memoirs, published posthumously in 1885. But the story he tells is by no means complete. Besides, it is frequently inaccurate in matters of fact and often seriously misinterprets events. Further, he has great difficulty (as he readily admits) in understanding the exact state of his mind at important stages in his development, and his account is tinged not a little with anger and bitterness. Finally, the impression conveyed by the Memoirs (as John Sparrow remarks in the Clark Lectures of 1965) is that they are being dictated by a "disembodied intellect".
The present study attempts to reincarnate Mark Pattison. He is seen as a man of flesh and blood participating actively in the great movement of his day at Oxford. The inaccuracies and misinterpretations of the Memoirs are corrected. The story, based on the collections of Pattison manuscripts in the Bodleian Library and in other libraries and in private hands at Oxford, is filled out and given a perspective. It is told not from the point of view of a disappointed and frustrated man on his deathbed, but from the diaries, notebooks, and letters of the young Pattison, contemporaneous with the events. The most significant information and much of the rest is entirely new. It brings to light an unusual perspective on the personalities, events, and influence of the Oxford Movement. Finally it throws new light on Pattison himself. For, instead of an embittered old man, we discover a much younger Pattison, a man who is shy but, at the same time, eager, passionate, enthusiastic, and hopeful, and a complete and thorough idealist.
Segmentation and analysis of vascular networks

From a clinical perspective retinal vascular segmentation and analysis are important tasks in aiding quantification of vascular disease progression for such prevalent pathologies as diabetic retinopathy, arteriolosclerosis and hypertension. Combined with the emergence of inexpensive digital imaging, retinal fundus images are becoming increasingly available through public databases fuelling interest in retinal vessel research.
Vessel segmentation is a challenging task which needs to fulfil many requirements: the accurate segmentation of both normal and pathological vessels; the extraction of vessels of different sizes from large high contrast to small low contrast; minimal user interaction; low computational requirements; and the potential for application among different imaging modalities. We demonstrate a novel and significant improvement on an emerging stochastic vessel segmentation technique, particle filtering, in terms of improved performance at vascular bifurcations and extensibility. An alternative deterministic approach is also presented in the form of a framework utilising morphological Tramline filtering and non-parametric windows pdf estimation. Results of the deterministic algorithm on retinal images match those of state-of-art unsupervised methods in terms of pixel accuracy.
In analysing retinal vascular networks, an important initial step is to distinguish between arteries and veins in order to proceed with pathological metrics such as branching angle, diameter, length and arteriole to venule diameter ratio. Practical difficulties include the lack of intensity and textural differences between arteries and veins in all but the largest vessels and the obstruction of vessels and connectivity by low contrast or other vessels. To this end, an innovative Markov Chain Monte Carlo Metropolis-Hastings framework is formulated for the separation of vessel trees. It is subsequently applied to both synthetic and retinal image data with promising results.

Keywords: Markov Chain Monte Carlo
vascular segmentation
particle filter
vascular analysis
image segmentation
Advisor: Noble, J