VictorJuiz/thesis huggingface dataset:
Methods of classification of the cardiotocogram

This Thesis compares CTG classification techniques proposed in the literature and their potential extensions. A comparison between four classifiers previously assessed - Adaboost, Artificial Neural Networks (ANN), Random Forest (RF), Support Vector Machine (SVM) - and two proposed classifiers - Bayesian ANN (BANN), Relevance Vector Machine - was conducted using a database of 7,568 cases and two open source databases. The Random Forest (RF) achieved the highest average result and was proposed as a benchmark classifier. The proposal to use model certainty to introduce a third, unclassified, class was investigated using the BANN. An increase in the classification accuracy was demonstrated, however the proportion of cases in the unclassified class was too great to be of practical value.
The information content of time series was explored using a Hidden Markov Model (HMM). The average performance of the HMM was comparable with the performance of the benchmark with a smaller distribution across validation folds, demonstrating that time-series information provides more stable estimates of class than stationary methods.
Finally a method of system identification was implemented. Significant differences between feature trends and histograms in low pH (&LT; 7.1) and healthy pH (≥ 7.1) cases were observed. These features were used as classifier inputs, and achieved performance similar to existing feature sets. When these features were aligned according the onset of stage 2 labour three unique trend patterns were discovered.

Keywords: Systems Identification
Intrapartum Labour
Classification
Fetal heart rate monitoring
Advisor: Payne, S
A new approach to investigating neural transposition challenges current insertion mapping strategies and provides an alternative explanation for differential transposon expression

Prior work has suggested the provocative, and somewhat controversial idea, that transposable element mobilization introduces genomic heterogeneity in certain regions of the mammalian brain. Findings in the fruit fly suggested that this might be a conserved phenomenon. Perrat et al. (2013) reported that transposons are overexpressed in the αβ-Kenyon Cells (αβ-KCs) of the Drosophila mushroom bodies and whole genome sequencing suggested that de-novo insertions map to neural genes within these cells.
In this study I revisited these topics and investigated what impact elevated transposon expression has on the heterogeneity of the genomes of αβ-KCs. Since post-mitotic transposon insertions occur in single DNA molecules, they are rare and difficult to detect, and are particularly hard to distinguish from experimental artefacts. I developed a new protocol to analyse transposon insertions in individual flies, instead of groups. This approach significantly increased the theoretical power to detect rare somatic insertion events, and it also enabled comparison to somatic genomes from cells isolated from the same animal. This advance allowed me to distinguish true somatic events from rare germline polymorphism in the fly population. Furthermore, the new analysis pipeline utilises longer overlapping sequencing reads, which permits the identification of the precise break points of transposon insertion events.
I confirmed that some transposons are more highly expressed in αβ-KCs, but I did not find evidence that this increase correlates with an increased number of transposon insertions. In addition, I did not detect an increase in the number of transposon insertions with age, challenging the idea that damage accumulates with age. A set of in-silico simulation experiments revealed that the rate of putative somatic insertion events is comparable to the rate of presently unavoidable experimental artefacts. Lastly, my analyses suggest that elevated and cell-restricted expression of the LINE-like retrotransposon Ivk in αβ-KCs might result from its co-expression with the αβ-KC specific gene CG17684, within which a germline insertion of Ivk resides.

Advisor: Waddell, S
The association between hip morphology parameters and 19-year risk of end-stage osteoarthritis of the hip in caucasian females: a case-control study

Over the past decade, measures of hip morphology have been recognised as biomechanical risk factors for the development of osteoarthritis (OA) in the hip. Few studies have examined the relationship between pelvic morphology and OA in a cohort of healthy volunteers with prolonged follow-up. The present study validates a new method for quantifying morphological parameters of the hip and pelvis and looks for relationships between these parameters and 19-year risk of total hip arthroplasty (THA) due to OA.
In order to conduct this investigation, we developed and validated a new software program specifically designed for measuring 23 selected morphological parameters in the pelvis, acetabulum and proximal femur. We tested inter-user reproducibility using 6 investigators, each of whom measured the same group of 10 blinded radiographs. Intra-user reproducibility was measured by the primary investigator measuring 10 blinded radiographs on three separate occasions.
Following validation of the new software, a nested case-control study was used with individuals from a well-described cohort of 1003 caucasian women who were recruited in 1989 and followed up for 20 years. A group of 157 individuals (31 THAs & 126 randomly-selected controls) were selected for morphological analysis. Pelvis radiographs taken at study-year two were analyzed for variations in hip morphology using the software. Morphological measurements were then compared between the THA case group and the control group in search of significant associations. THA was used as the clinical outcome measure for severe OA.
Most morphological measures were reproducible, with the exception of horizontal toit externe (HTE) and joint space width. The alpha-angle was significantly greater in the THA cases than in the controls (60.7 degrees vs 48.1 degrees; p &LT; 0.001). The lateral centre edge angle (LCE) was significantly smaller in the cases than the controls (30.0 degrees vs 33.4 degrees; p = 0.002). The Extrusion Index (Ext Ind) was significantly greater in the THA cases than in the controls (30% vs 20%; p &LT; 0.001). Significant morphological measures were then adjusted for epidemiological covariates (baseline age, height, weight & radiographic osteoarthritis) using a multivariate logistic regression analysis. Alpha angle (Odds ratio 1.040, degrees; p = 0.01), LCE (Odds ratio 0.871, degrees: p &LT; 0.001) and Ext Ind (Odds ratio 1.079, percent; p &LT; 0.001) each remained significantly associated with THA.
This investigation demonstrates measurements that provide a useful tool in predicting a woman's risk of THA before she develops radiographic hip OA. These measurements can be made on an AP pelvis radiograph which is cheap, accessible and commonly used as a clinical investigation tool.

Advisor: Carr, A
The right to be killed: reassessing the case for the moral right to voluntary active euthanasia

This thesis defends an individual's moral right to be aided in dying by a physician (that is, voluntary active euthanasia, or VAE), but departs significantly from the view in its favor generally accepted in the bioethics literature. The prevailing view appeals to both respect for an individual's autonomy and promotion of an individual's well-being as necessary conditions for a right to VAE, so as to justify the right only for those suffering grave illnesses and/or disabilities. The author argues that such a view is logically untenable; one or another aspect must be given up. Since invoking the premise that certain individuals would be better off dead necessarily relies on controversial assumptions about both the value of life and the nature and value of death, about which reasonable people disagree, it is the justification from an individual's best interest which must be excluded in a liberal society. The author endorses a self-determination justification for the right to VAE, but rejects understanding this in terms of respecting personal autonomy, instead making the case for a right to VAE grounded in self-ownership. The author’s main conclusion is that the right to VAE is a general right applying to all competent adults, not only those suffering grave illnesses or disabilities, or those whose choice for VAE is an exercise of autonomy. Moreover, by analyzing the basis of physician authority over prescription medicine and how this can be justified to a society of self-owners, she maintains that individuals have not only the right to choose VAE without state interference, but also the right to be provided VAE by doctors. Nevertheless, both rights are compatible with reasonable limitations to protect both the interests of VAE seekers and the rights of others.

Keywords: Physician-assisted suicide
Moral philosophy
Autonomy
Medical ethics
Bioethics
End of life
Moral rights
Professional ethics
Right to die
Self-determination
Euthanasia
Paternalism
Voluntary active euthanasia
Death
Self-ownership
Dying
Advisor: Caney, S
Effect of reward on visual perceptual decision-making in humans and non-human primates

When primates make decisions about sensory signals, their choices are biased by the costs and benefits associated with different possible outcomes. However, much remains unknown about the neuronal mechanisms by which reward information is integrated into the perceptual decision-making process. I used electrophysiological, psychophysical and imaging techniques to explore the effect of reward on sensory representations, whilst humans and monkeys made perceptual judgements about structure-from-motion (SFM) stimuli.
Electrical microstimulation of visual area V5/MT in the macaque monkey was used to bias perceptual judgements, under different available reward sizes for correct choices. The behavioural effect of microstimulation interacted with available reward, and, in the context of a drift diffusion model of decision-making, the results demonstrated that reward must influence sensory processing before visual signals and microstimulation signals are accumulated in sensorimotor areas. In a parallel human psychophysics experiment, viewers made decisions about SFM stimuli whilst their choices were biased towards one outcome or the other by unequal pay-offs. A full drift-diffusion model was fitted to human choice and reaction time data. There was a significant effect of reward on model drift rate, a parameter known to be dependent upon evidence represented in sensory brain regions.
A second set of experiments used magnetoencephalography (MEG) to explore activity in visual areas in human cortex and the effects of reward. Brain responses to retinotopic visual stimuli were localized with three different MEG source analysis methods, and localization accuracy was evaluated by comparison with fMRI maps obtained in the same individuals. The results demonstrated that the beamformer and minimum norm estimate (MNE) methods were most suitable for investigating early visual activity with MEG. Human brain activity was then recorded with MEG whilst viewers made perceptual judgements about SFM stimuli, under unequal pay-offs. The results revealed an effect of reward size on early MEG responses in the region of the occipital cortex and visual precuneus.
Taken together, the experiments presented in this thesis provide consistent evidence that information about reward can influence the processing of sensory information during perceptual decisions.

Keywords: perception
reward
cortex
neuroscience
vision
decision-making
Advisor: Krug, K
Parker, A
Implementation of aid initiatives in post-conflict reconstruction and development: Afghanistan 2002-2008

This study examines what drives success in the implementation of international reconstruction and development aid projects in a post-conflict environment. It poses three key questions: 1) How important is the national government's support for project success in post-conflict reconstruction and development? 2) What role does donor coordination on the ground play for project success? and 3) What other factors explain project success?
To address these questions, I design and test a novel explanatory model of effective project implementation in post-conflict reconstruction and development, using an original data set of 124 projects undertaken by six major multilateral and bilateral aid agencies in Afghanistan during 2002-2008.
Study results highlight two factors that appear to consistently influence project success: the national government’s support, and the quality of project leadership (i.e project manager or project coordinator) on the international project implementation side. Most interestingly, the combination of national government’s support and strong project leadership considerably increases the likelihood of project success, as well as the level of success achieved. Donor coordination arrangements made at the stage of project implementation appear to be a generally weak predictor of project success.
The qualitative findings of the study illustrate in what way various project success factors in the model impact on project success. Notably, they identify and add to the conventional 'instrumental' qualities of leadership the qualities of 'moral' leadership, such as ability to build trust and respect with national counterparts based on the record of competence, dedication, and delivery.

Advisor: Bermeo, N
Agreement through opposition: political ideology and legislative constraint in the 'special relationships' of the United States

Since 1945 the United States (US) has constructed a global web of 'special relationships' with states that share its political values, economic philosophy, or security predicament. Whether we understand these countries as 'clients', 'tributaries', 'friends', 'allies' or 'subordinates', what sets these relationships apart is the remarkably high level of cooperation and the extent to which this has endured over the decades. One question rarely asked, however, is how we can explain variation in the level of cooperation in these relations over time. Each of the 'special relationships' of the US has waxed-and-waned over the years, but the sources of this variation have not been fully uncovered. In this thesis I argue that changes in domestic political variables within each of the allied states are responsible for the varying degrees of cooperation witnessed over time. Utilising the example of Anglo-American relations in the postwar period, supplemented by a large-n statistical study, I demonstrate how a focus on political parties as the optimal actors in studying international cooperation helps us to understand the effects of political ideology and legislative constraint in foreign affairs.

Keywords: United States foreign policy
British foreign policy
Political ideology
International relations theory
Legislative constraint
Advisor: Snidal, D
Modelling drug taking in sport

This thesis considers optimal policies in response to doping in sport. Doping is an area of increasing public concern as growing numbers of athletes, and the organisations responsible for testing them, are implicated in doping scandals. These scandals affect not only those interested in sport, but also society as a whole since athletes are role models. Consequently it is important to consider optimal responses to doping.
The second chapter considers the optimal ban for a welfare maximising anti-doping agency (ADA) to impose on an athlete who tests positive for performance enhancing drugs. Previous authors have assumed that maximal deterrence is optimal, but this chapter shows that when the form of the punishment is a ban from competition, maximal deterrence may no longer be optimal. The optimal punishment is found to depend on factors such as the prevalence of doping and the variance of earnings.
The third chapter examines situations in which ADAs may not wish to uncover doping. In this case, if consumers cannot observe the frequency with which athletes are tested, a no-cheating equilibrium does not exist. I find two mechanisms which can lead to a nocheating equilibrium: consumers who can observe the frequency of testing and an external testing agency, such as WADA, which can retest athletes and punish the ADA if it failed to detect doping.
The final chapter examines whether increasing the frequency of testing deters athletes from doping. Since data is not available to analyse this problem directly, I use the relationship between testing and Olympic performance to infer the relationship between testing and doping. The results suggest that while in some sports, such as athletics, carrying out more tests does deter athletes from taking drugs, in others, such as cycling, there is no evidence of a negative relationship between testing and doping.

Advisor: Norman, T
Young, P
Great power politics in multipolar systems

My dissertation develops Georealism, a theory to explain how great powers behave in international relations. The dissertation has two main goals. One is that it aims to create a uniform theory of international relations, particularly balancing, bandwagoning, alliances, and war. The other is that it intends to explain the behaviour of individual great powers in detail, rather than just systemic outcomes. The basic premise of Georealism is that states face a threat both from their neighbours and from potential hegemons. In four chapters, I explore the implications of this insight on great power behaviour. First, I explain why continental states choose balancing or bandwagoning when faced with a potential hegemon. Second, I look at how offshore states behave towards the continental states to maximize their security. Third, I create a theory of the alliance choices of great power. Last, I explain which great powers go to war with each other and when. All the theoretical implications are well supported by quantitative and qualitative tests taken from various cases of European great power politics from 1683 to 1913. Georealism can indeed predict the behaviour and motivations of individual states with great accuracy on a variety of topics.

Advisor: Snidal, D
Moral hostages: refugee co-operation and burden sharing during the Indochinese refugee crisis (1975-1996)

Why were Southeast Asian states so successful in outsourcing the costs of refugee protection during the Indochinese refugee crisis (1975-1996)? By refusing to grant asylum unless other states guaranteed to resettle refugees, this dissertation argues that real and threatened mistreatment of refugees by the states of first asylum was decisive in explaining why other states agreed to resettle them.
Mistreatment of Indochinese refugees not only activated strategic concerns for the political stability of first asylum countries themselves but also affective concerns for refugee welfare. Concern about what would happen to refugees if they weren’t resettled helped sustain resettlement long after doubts arose as to whether those fleeing were truly refugees. And in the final resolution of the crisis, a concern for refugee welfare made the return of non-refugees extremely controversial. By looking at the private and public framing of the Indochinese refugees as a collective action problem for governments to solve, it demonstrates the salience of mistreatment in explaining burden-sharing.
The study principally focuses on the actions of two major resettlement countries: the United States (the biggest in absolute terms) and Australia (the biggest in relative terms). Utilising extensive archival research, contemporary accounts and interviews with key policymakers of the period, it explores several distinct and important episodes over the duration of the outflow that reveal what motivated international assistance. This is descriptively important in adding to our knowledge of how refugees are treated as a question of international politics. The textural account of governmental motivation that is offered can also help test existing theoretical accounts of why governments cooperate to help refugees. Crucially, it shows that a humanitarian concern for refugee welfare both enabled and constrained co-operation.
Structural characterisation of the interaction between Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) and their human ligands in severe malaria

Sequestration of infected erythrocytes during P. falciparum infection can lead to severe malaria. PfEMP1 proteins are central to this process. Multimodular PfEMP1 proteins can bind to a variety of human ligands due to the presence of CIDR and DBL domains. CIDR and DBL domains are classified to three and six families respectively, with each thought to bind to unique human ligands. The interaction between PfEMP1 proteins and human ligands protects the infected erythrocytes against spleen-mediated destruction. Additionally, these PfEMP1 proteins undergo antigenic variation to evade immune surveillance. They also elicit immune suppression by binding to immunoglobulins within the circulatory system.
The work described here focuses on two interactions between PfEMP1 on the infected erythrocytes and their human ligands, the first involving CD36 and CIDR1α domains and the second involving human IgM and DBL domains. I have expressed and purified recombinant proteins involved in both interactions.
In this thesis, I have confirmed using a variety of biophysical methods that CIDR1α domains are able to bind CD36 in a 1:1 binding stoichiometry, and this accounts for the binding affinity of the full length protein. This interaction was not disrupted after performing deglycosylation procedures on CD36, allowing me to obtain stable complexes of these interacting partners for structural characterisation by crystallography. I have also confirmed the interaction between DBL domains and human IgM Fc region using similar biophysical methods. These experiments are important for paving the way towards further structural characterisation of these interactions that leads to sequestration. .

Keywords: Malaria
Plasmodium Falciparum
CD36
PfEMP1
IgM
Advisor: Higgins, M