VictorJuiz/thesis huggingface dataset:
Computerised analysis of fetal heart rate

This thesis presents a comprehensive work on computerised analysis of fetal heart rate (FHR) features, including feature extraction, feature selection, analysis of influencing factors and setting up/validation of a computerised decision support system.
Firstly, a novel feature – pattern readjustment – was extracted and tested. Clinical data were used to train a Support Vector Machine (SVM) to detect pattern readjustment. Then, the association of pattern readjustment and adverse labour outcome was investigated. The validation results with clinical experts show that the pattern readjustment can be accurately detected, while the study on labour outcome shows that the feature is related to fetal acidemia at birth.
Secondly, Genetic Algorithms were employed as a feature selection method to select a best subset of FHR features and to use them to predict fetal acidemia with linear and nonlinear SVM. The diagnostic power of the classifier output using selected features was tested on the total set of 7,568 cases. As the classifier output increases, there is a consistent increase of the risk of fetal acidemia.
Thirdly, an important influencing factor on FHR features - signal loss – was investigated. A bivariate model was built to estimate error based on signal loss. Validation results show that the bivariate model can accurately predict the error generated by signal loss. The influence of signal loss on labour outcome classification was also investigated.
Finally, a computerised decision support system to estimate the risk of fetal acidemia was set up based on the above studies. The system was validated using new retrospective data. Validation results show that the system is capable of predicting adverse labour outcome and providing timely decision support. It is the first time an intrapartum computerised FHR decision support system has been built and validated on this size of dataset. With further improvements, such a system could be implemented clinically in the long term.

Keywords: genetic algorithms
Fetal heart rate
decision support system
signal loss
Advisor: Georgieva, A
Payne, S
An edition with commentary of the Batrachomyomachia

The thesis consists of three main sections: the Introduction, the text (with apparatus), and the Commentary.
The Introduction begins with a survey of the available evidence for the poem’s date and authorship, before moving on to consider its generic affiliations and influences, focusing on two particular areas: its links with the ill-defined genre of παρῳδία, and its relationship to animal-narratives elsewhere in ancient literature (particularly fable) and visual art. This is followed by a detailed analysis of the poem’s style and metre, a brief tour of its Nachleben up to the 13th century, and a summary of the notoriously tangled manuscript tradition.
The text is new, and differs substantially from both that of Allen (in the OCT) and of West (the most recent English edition). The apparatus, as explained in more detail on p. 117, is somewhere between the two: it takes into account the readings of only nine MSS from the 80-100 extant, and does not attempt to represent every single textual variation even among these nine, but it is much fuller than the minimalist apparatus of the Loeb. It aims to provide a useful source for scholars interested in the poem’s many and serious textual cruces, while remaining more succinct and user-friendly than the dense and sometimes baffling apparatus of Ludwich’s monumental 1896 edition. The text is followed by an English prose translation: this makes no claims to beauty, and is simply intended as a relatively literal guide to the sense of the Greek.
The Commentary, finally, is twofold. Any commentary on the Batrachomyomachia will inevitably spend much space and ink on purely textual issues, and on the fundamental task of unearthing meaning from the dizzying range of wild and nonsensical variants available. Interspersed with these textual points, however, this commentary includes considerations of the poem not as a mechanics problem but as a sophisticated Hellenistic work of art – exploring its intertextualities, its characterisation, its dramatic effects, its dry sense of humour, and subjecting it to the serious literary analysis it has often been denied.

Keywords: Batrachomyomachia
Hellenistic
textual criticism
parody
Ancient Greek
mice
Homer
frogs
Advisor: Kelly, A
Modelling of equatorial wave motions in the middle atmosphere

A three-dimensional mechanistic model of the middle atmosphere is used to model various classes of equatorial wave motions that are observed in the atmosphere. These waves are thought to be largely responsible for the forcing of the quasi-biennial oscillation (QBO) in the tropical lower stratosphere. By generating a combination of different classes of equatorial waves in the model, an oscillation which has many similarities to the observed QBO is produced in the model.
The numerical model used is run in a variety of configurations, including running it at different vertical resolutions and with two different radiation parameterisation schemes. It is found that model used in the project must be modified to allow the accurate modelling of equatorial waves. Several modelling problems are encountered while applying the modifications necessary in the model; the steps necessary to rectify these problems are detailed in this thesis.
Equatorial waves are then forced in this modified model under a range of conditions and their interaction with the mean flow is observed. Their dissipation mechanisms and the influence of changes in model conditions on these waves are investigated. The model is found to be generally very successful in modelling these equatorial waves.
Modelling of the QBO is one of the principle aims of this project and a QBO is successfully generated in a variety of model configurations. The modelled QBO is found to be sensitive to changes in the temperature structure of the model (brought about by changes in the model's radiation scheme) and several experiments are performed in order to learn what processes affect this sensitivity. A QBO is then generated in series of model runs where the state of the model is varied from very idealised (where temperatures in the model are relaxed towards an isothermal state by the radiation scheme) to a state that is far more realistic (a perpetual January run with realistic boundary information). A fairly realistic QBO is generated throughout many of the experiments. The properties of this QBO are investigated and compared to the observed QBO.
The model is then run with planetary waves forced in addition to the QBO. The interaction between the planetary waves and the QBO is investigated. It is found that the planetary waves have little effect on the QBO propagation. The QBO however has a fairly strong modulating effect on the planetary waves in certain regions.
Role of the NMB0342-NMB0348 locus in meningococcal pathogenesis and investigation of NMB0345 as a vaccine candidate

Neisseria meningitidis is the most common cause of bacterial meningitis in the Western world and the second leading cause of mortality in 1-5 year-olds in the United Kingdom. A signature-tagged mutagenesis screen of approximately 3,000 insertional mutants of a serogroup B isolate of N. meningitidis, C311⁺, identified 73 genes required for pathogenesis in an infant rat model of meningococcal septicaemia. Homology-based searches indicate that two of the genes identified, NMB0342 and NMB0345, have homologues in other pathogenic bacteria and exist within a potential operon of seven genes (NMB0342-NMB0348). NBM0342 is a homologue of ispA (intracellular septation protein) of Shigella flexneri, required for effective intercellular spread and plaque formation in epithelial cells. NMB0345 is a homologue of cbf, a Campylobacter jejuni gene that encodes a 29 kDa protein which is a major antigenic peptide. PCR and Southern analyses of genes in the NMB0342-NMB0348 locus show that they are conserved across a wide range of pathogenic isolates and serogroups of N. meningitidis. However, these genes are present only in a subset of commensal strains. N. meningitidis mutants with transpoon insertions in NMB0342 and NMB0345 are highly attenuated when directly competed with the wild-type bacterium in the infant rat model of infection. Mutations have been introduced into other genes within the locus and the resulting mutants analyzed for their ability to cause systemic disease. Mutants with transpoon insertions in the NMB0343 and NMB0344 genes are significantly attenuated, while mutants with insertions in NMB0347 and NMB0348 are attenuated to a lesser degree. Complementation of the NMB0342 mutation by ectopic chromosomal integration of a wild-type copy of NMB0342 almost completely restores the virulence of the bacterium. In vitro cell-culture analyses and microscopic analysis of mutants in association with host cells demonstrate that a mutant with a transpoon insertion in NMB0345 is significantly reduced in its adherence to Chang epithelial cells compared to the wild-type bacterium. Whole blood and serum-sensitivity assays show that the NMB0342 and NMB0345 mutants are highly serum-sensitive compared to the wild-type bacterium. Preliminary experiments have demonstrated that immunization of mice with recombinant NMB0345 protein confers protection against challenge with the serogroup B isolate MC58. In vitro assays demonstrate that recombinant NMB0345 is an active peptidyl polyl cistrans isomerase (PPIase). Together, the results from these investigations support a role for genes of the NMB0342-NMB0348 locus in the pathogenesis of N. meningitidis infections. Further investigation is needed to assess the potential of NMB0345 as a vaccine candidate.

Keywords: bacterial meningitis
Advisor: Tang, C
Hood, D
Credit networks and agent games

This thesis is divided into three parts; an intensity based network model of firm default, an agent based network model of firm default, and an agent based model of feedback effects from dynamic hedging. The common theme among all three parts is the application of ideas from both physics and mathematics to the solution of problems motivated by the financial markets. Less broadly, in the first two parts, the common themes are credit markets, networks, and dependent defaults. Part one tackles the problem of default dependence from a probabilistic perspective, modeling the default of companies as generalised Poisson processes, with the default dependence structure given by a network. We present a mathematical framework to solve a generalised version of the Jarrow Yu model of looping defaults [27] and study the relationship between network structure and the resilience of a network of firms to default events. Using this model we then show how to price simple multi-name credit products such as kth to default baskets. Part two again considers dependent defaults, but here the network is dynamic and firms are modelled as simple agents, defined by strategies, whose interactions determine a network of trading links. Using our agent based network model of firm default we study network structure and their degree distributions, firm lifetimes, and look for evidence of agent learning and default clustering. We then study the effect of default on a network of firms and the response of remaining firms to that default event. Part three considers a relatively more established agent based framework, called the Minority Game. We first describe in detail the Minority Game and discuss its suitability as a market model. We then show how it may be applied to modelling the actions of traders delta hedging a short option position. We show that for a variety of option positions, in a sufficiently illiquid market feedback effects arise from the actions of the traders as their trades impact upon the underlying market.
The role of ubiquitylation in regulating apurinic/apyrimidinic endonuclease 1

Apurinic/apyrimidinic endonuclease 1 (APE1) is a key DNA repair factor involved in the DNA base excision repair (BER) pathway that is required for the maintenance of genome stability. In this pathway, APE1 cleaves DNA at an abasic site to generate a DNA single strand break, allowing for repair completion by a DNA polymerase and a DNA ligase. High levels of APE1 have been observed in multiple cancer types however it is not understood if this contributes to cancer onset and development. What is known is that these cancers tend to display increased resistance to DNA damaging treatments and APE1 is therefore considered a key target for inhibition in the treatment of APE1-overexpressing cancers. Considering the relevance of modulating APE1 levels in disease and cancer treatment, very little is known about how cellular APE1 levels are regulated. Our lab has previously shown that the levels of the BER factors Pol β, XRCC1 and DNA Lig IIIα are regulated by ubiquitylation-mediated proteasomal degradation. The aim of this doctoral thesis was therefore to determine if ubiquitylation also regulates APE1 stability in cells. I present evidence that APE1 is ubiquitylated in cells and have identified the UBR3 E3 ligase that is responsible for this activity. Using mouse embryonic fibroblasts generated from Ubr3 knockout mice, I demonstrate that UBR3 regulates APE1 cellular levels. I furthermore show that a loss of cellular UBR3 leads to the formation of DNA double strand breaks and genome instability.

Keywords: Genome Stability
APE1
UBR3
Ubiquitylation
Apurinic/Apyrimidinic Endonuclease 1
Base Excision Repair
DNA damage repair
Advisor: Dianov, G
Parsons, J
Studies on the mode of action of cardioactive drugs in animals and man

Part.l of this thesis deals with the characterization, by electrophysiological and other means (in vivo and in vitro), of a putative steroidal antiarrhythmic agent CCI 22277. This compound is shown to act predominantly by reducing fast inward sodium current and is thus classified as Vaughan Williams Class I.
In Part 2, the rate- and voltage-dependence of depression of ̇vmax by seven class 1 antiarrhythmic agents Cincluding CCI 22277) is studied in guinea-pig ventricle, using standard microelectrode techniques. All drugs were shown to produce enhanced depression of ̇vmax at increased driving rates and/or reduced resting potentials. The rates of onset and offset of the rate-dependent effects varied greatly from drug to drug and in general, fast onset and offset kinetics were associated with low molecular weight and high lipophilicity. It is concluded (in Part 4) that these findings are consistent with the "modulated receptor" model of the interaction of the sodium channel with class I drugs, although molecular weight appears to be of more importance and lipophilicity of less importance, to these interactions than previously thought.
In Part 3 the hypothesis that drugs with faster rates of onset of rate-dependent depression of ̇vmax will produce greater prolongation of refractoriness than "slower" drugs, was tested experimentally using 11 class I drugs. The results were consistent with this hypothesis. Taken together with the relative effects of the various drugs on action potential duration, they provide a theoretical basis for the proposed subclassification of class I drugs into groups IA, IB and 1C.

Advisor: Vaughan Williams, E
Williams, E
Quantum simulation using ultracold atoms in two-dimensional optical lattices

Ultracold atoms in optical lattices can be used to model condensed matter systems. They provide a clean, tuneable system which can be engineered to reach parameter regimes that are not accessible in condensed matter systems. Furthermore, they provide different techniques for probing the properties of these systems.
This thesis presents an experimental and theoretical study of ultracold atoms in optical lattices for quantum simulation of two-dimensional systems.The first part of this thesis describes an experiment with a Bose-Einstein condensate of 87Rb loaded into a two-dimensional optical lattice. The beams that generate the optical lattice are controlled by acousto-optic deflection to provide a flexible optical lattice potential. The use of a dynamic ‘accordion’ lattice with ultracold atoms, where the spacing of the lattice is increased in both directions from 2.2 to 5.5 μm, is described. This technique allows an experiment such as quantum simulations to be performed with a lattice spacing smaller than the resolution limit of the imaging system, while allowing imaging of the atoms at individual lattice sites by subsequent expansion of the optical lattice. The optical lattice can also be rotated, generating an artificial magnetic field. Previous experiments with the rotating optical lattice are summarised, and steps to reaching the strongly correlated regime are discussed.
The second part of this thesis details numerical techniques that can be used to describe strongly correlated two-dimensional systems. These systems are challenging to simulate numerically, as the exponential growth in the size of the Hilbert space with the number of particles means that they can only be solved exactly for very small systems. Recently proposed correlator product states [Phys. Rev. B 80, 245116 (2009)] provide a numerically efficient description which can be used to simulate large two-dimensional systems. In this thesis we apply this method to the two-dimensional quantum Ising model, and the Bose-Hubbard model subject to an artificial magnetic field in the regime where fractional quantum Hall states are predicted to occur.

Keywords: optical lattices
quantum simulation
ultracold atoms
strongly correlated systems
Advisor: Foot, C
Jaksch, D
Violent crime, public perceptions and citizen security strategies in Colombia during the 1990s

This research deals with the topic of violent crime in urban Colombia. Although many references are made to the conflict between the State, guerrilla groups and paramilitary organisations in rural areas, and to the problem of drug-cartels and illegal-drug production, the main aim of the thesis is to show recent trends in violent crime and discuss citizen security strategies followed during the decade of the 1990s.
Chapter 1 focuses on urban homicides. In Colombia, 40 percent of the 25,000 annual homicides are committed in the ten largest cities. The cities of Medellin, Bogota and Cali account for almost 30 percent of this total. Although the victims are mainly young men from the poorest socio-economic levels, homicides are not necessarily correlated to the areas where the poor live. The probability of getting involved in a homicide, either as a victim or as victimiser, is significantly higher in places where access to economic resources is greater.
Chapter 2 analyses the problem of kidnappings. The chapter looks at recent progresses in Colombian anti-kidnapping legislation and focuses on the authors, the victims and the riskzones where most cases take place. Although these crimes affect mainly the rich and the middle class, kidnappers have recently started to target victims from all social backgrounds. This strategy creates fear among citizens and permits kidnappers to extort more fees from people who could be at risk of being kidnapped.
Chapter 3 looks at the issue of perception and fear of crime. This question provides a better understanding of the concept of risk and the subjectivity of decision-making when facing insecurity. If citizen security strategies have had little impact during the last decade, it has been partly because of poor levels of co-operation and communication with the population. The consequence of this has been an increasing perception of insecurity and distrust among citizens.
Chapter 4 assesses citizen security strategies followed during the administrations of Presidents Gaviria (1990-1994), Samper (1994-1998) and Pastrana (1998-2002). The reforms implemented since the adoption of a new Constitution in 1991 have had important impacts on security strategies as they have given more discretionary powers to civilian authorities, especially at the municipal level. Larger cities like Bogotá, Cali and Medellin, implemented a series of successful programmes that have reduced the levels of violent crime, notably homicides. Other crimes, like kidnappings, have not decreased since the government has lacked a coherent strategy to combine its peace negotiations with insurgent organisations with its legitimate right to fight violent crime.

Advisor: Deas, M
Comparing the radiological anatomy, electrophysiology, and behavioral roles of the pedunculopontine and subthalamic nuclei in the normal and parkinsonian brain

Deep brain stimulation (DBS) of the subthalamic nucleus (STN) and DBS of the pedunculopontine nucleus (PPN) have been shown to be effective surgical therapies for Parkinson’s disease (PD). To better understand the PPN and STN as DBS targets for PD, this research compares the anatomy, electrophysiology, and motor control roles of these nuclei. PPN and STN connections were examined in vivo in human subjects and in the non-human primate using probabilistic diffusion tractography. Both the PPN and STN were connected with each other and with the motor cortex (M1) and basal ganglia. After studying these anatomical connections in primates, their functional significance was further explored in an anesthetized rat model of PD. Examination of the electrophysiological relationship between the PPN and basal ganglia in the presence of slow cortical oscillatory activity suggested that excitatory input from the STN may normally modulate PPN spike timing but that inhibitory oscillatory input from the basal ganglia output nuclei has a greater effect on PPN spike timing in the parkinsonian brain. To examine transmission and modulation of oscillatory activity between these structures at higher frequencies, LFP activity was recorded from the PPN and STN in PD patients performing simple voluntary movements. Movement-related modulation of oscillatory activity predominantly occurred in the α (8-12 Hz) and low β (12-20 Hz) frequencies in the STN but in the high β (20-35 Hz) frequencies in the PPN, supporting observations from rodent studies suggesting that oscillatory activity is not directly transmitted from the STN to the PPN in PD. Finally, to better understand the roles of the STN and PPN in large-scale movement, the effects of STN and PPN DBS on gait abnormalities in PD patients were studied. DBS of the STN appeared to improve gait by optimising executive gait control while DBS of the PPN appeared to restore autonomic gait control. These results have several implications for DBS patient selection, surgical targeting, and for understanding the mechanisms underlying DBS efficacy.

Keywords: deep brain stimulation
Parkinson's disease
pedunculopontine nucleus
gait analysis
diffusion tensor imaging
local field potential
oscillations
posture
basal ganglia
subthalamic nucleus
Advisor: Aziz, T
Stein, J
Bergstrom, D
Judie, W