VictorJuiz/thesis huggingface dataset:
Ethical issues in the bioprediction of brain-based disorder

The development of predictive biomarkers in neuroscience is increasingly enabling bioprediction of adverse behavioural events, from psychosis to impulsive violent reaction. Because many brain-based disorders can be thought of as end-states of a long development, bioprediction carries immense therapeutic potential.
In this thesis, I analyse issues raised by the development of bioprediction of brain-based disorder. I argue that ethical analysis of probabilities and risk information bioprediction provides is confounded by philosophical and social structures that have, until recently, functioned nominally well by assuming categorical (binary) concepts of disorder, especially regarding brain-disorder. Through an analysis of the philosophical concept of disorder, I argue that we can and ought to reorient disorder around probability of future harm and stratify disorder based on the magnitude of risk. Rejection of binary concepts in favour of this non-binary (probability-based) one enables synergy with bioprediction and circumnavigation of ethical concerns raised about proposed disorders of risk in psychiatry and neurology; I specifically consider psychosis and dementia risk.
I then show how probabilistic thinking enables consideration of the implications of bioprediction for two areas salient in mental health: moral responsibility and justice. Using the example of epilepsy and driving as a model of obligations to protect others against risk of harm, I discuss how the development of bioprediction is poised to enhance moral responsibility. I then engage with legal cases and science surrounding a predictive biomarker of impulsive violent reaction to propose that bioprediction can sometimes rightly diminish responsibility.
Finally, I show the relevance of bioprediction to theories of distributive justice that assign priority to the worse off. Because bioprediction enables the identification of those who are worse off in a way of which we have previously been ignorant, a commitment to assign priority to the worse off requires development of and equal access to biopredictive technologies.

Keywords: Biomarkers
neuroscience
epilepsy
omics
ethics
psychosis
bioprediction
psychiatry
neuroethics
predictive biomarkers
DSM
distributive justice
MAOA
disorder
neurology
risk
applied philosophy
public health
alzheimers disease
Advisor: Savulescu, J
Sheehan, M
Adjoint methods for computing sensitivities in local volatility surfaces

In this paper we present the adjoint method of computing sensitivities of option prices with respect to nodes in the local volatility surface. We first introduce the concept of algorithmic differentiation and how it relates to path-wise sensitivity computations within a Monte Carlo framework. We explain the two approaches available: forward mode and adjoint mode. We illustrate these concepts on the simple example of a model with a geometric Brownian motion driving the underlying price process, for which we compute the Delta and Vega in forward and adjoint mode. We then go on to explain in full detail how to apply these ideas to a model where the underlying has a volatility term defined by a local volatility surface. We provide source codes for both the simple and the more complex case and analyze numerical results to show the strengths of the adjoint approach.
Bank credit and legal status in Moroccan manufacturing

Moroccan manufacturing firms generally choose to incorporate under one of two legal forms: ‘Société Anonyme’ (SA) and ‘Société À Responsibilité Limitée’ (SARL). This thesis is about that choice and its consequence for firms’ access to bank overdraft facilities. In 2001, Morocco made a radical change to its company law regime: it replaced a company law dating from 19th-century France with modern standards of corporate governance and accountability. In Chapter One, I use the two-period FACS/ICA panel to analyse that reform and to evaluate its impact upon manufacturing firms’ access to bank credit. I find that the reform induced a substantial share of SA firms to switch to SARL, and that — relative to firms remaining in the SA status — this caused a significant and substantial withdrawal of bank overdraft facilities. In Chapter Two, I develop a theoretical model in which an agent signals its continuous type by using a variable that may take one of only two values (a ‘binary signal’); this is intended to represent a firm’s choice of legal status. I show that this binary signal provides only ‘coarse information’, and I consider the consequences of this coarseness; I solve for equilibrium conditions and I consider both the role of a principal’s risk aversion and the role of other observable agent characteristics (‘indices’). Chapter Three uses the results of Chapter Two to develop a new structural methodology for the separate identification of information and incentive effects. I apply the method to the data used in Chapter One, on the subset of firms having an overdraft facility in both survey periods (approximately two-thirds of the total sample). I find that, among that limited sample, there is no relevant information asymmetry. I estimate the potential welfare loss and conclude that, in the 95% confidence region of potential information effects and incentive effects, the maximum median welfare loss from information asymmetry is equivalent to approximately only 3% of the median bank overdraft limit. For the sample of firms having an overdraft facility in both survey periods, this challenges the common narrative that information asymmetry is an important reason for bank credit market failure.

Keywords: Moroccan manufacturing
information asymmetry
company law
development economics
Advisor: Fafchamps, M
Mechanistic studies on 2-oxoglutarate dependent oxygenases

The first identfied 2-oxoglutarate (2OG) dependent oxygenase was a collagen modifying enzyme in the work by Hutton et al. in 1967. Subsequent work has revealed that 2OG dependent oxygenases are a large family with diverse biological roles. With small molecule substrates, these enzymes catalyse a wide range of oxidative reactions, including those that form part of antibiotic biosynthetic pathways. The currently accepted consensus mechanism for catalysis by 2OG-dependent oxygenases is based on crystallographic data, kinetics and on quantum chemical calculations. The consensus mechanism involves oxidative decarboxylation of 2OG by reaction with an oxygen molecule producing CO2, succinate and a reactive oxidising species that reacts with the `prime' substrate.
Deacetoxycephalosporin C synthase (DAOCS) is a 2OG-dependent oxygenase involved in cephalosporin biosynthesis. The mechanism of DAOCS is of particular interest because it has recently been proposed to be different from the consensus mechanism. The new mechanism proposal from Valeg ard et al. is primarily based on high-resolution crystallographic data with support from steady-state kinetic experiments and quantum-chemical calculations.
The work in discussed in this thesis aimed to test the proposal of Valegård et al. by using a combination of spectroscopic and spectrometric methods analysing enzyme-substrate interactions. Substrate binding was investigated using both protein-observe (Chapter 3) and ligand-observe (Chapter 4.1 and 4.2) methods. Preliminary UV-visible data on enzyme-substrates complex formation was also obtained. The strength of substrate and cosubstrate binding was characterised through dissociation constant measurement. An activity assay (Chapter 2) that allows for direct and simultaneous monitoring of 2OG decarboxylation and penicillin ring expansion was optimised.
Both the ligand-observe and protein-observe binding experiments as well as the preliminary UV-visible data indicate that the formation of a ternary complex between DAOCS, 2OG and the penicillin substrate is viable. The activity assay conclusively showed that in the presence of unnatural substrates, such as penicillin G, 2OG oxidation is significantly uncoupled from penicillin oxidation. Uncoupled turnover does not occur in the presence of the natural substrate, penicillin N, which is an aspect that should be considered in the analysis of the steady-state kinetic data.
Overall, the results provide evidence that, the consensus mechanism for 2OG-dependent oxygenases is viable for DAOCS, at least in the presence of the natural substrate, penicillin N. It is possible that in the presence of an unnatural substrate, the catalytic process undergoes a more complex mechanism, possibly with the direct involvement of reducing agents in the system.

Keywords: DAOCS
NMR
uncoupled turnover
enzyme mechanism
2OG oxygenases
mass spectrometry
Advisor: Schofield, C
From Jew to Gentile: Jewish converts and conversion to Christianity in medieval England, 1066-1290

The subject of this thesis is Jewish conversion to Christianity in medieval England. The majority of the material covered dates between 1066 and c.1290. The overall argument of the thesis contends that converts to Christianity in England remained essentially Jews. Following a discussion of the relevant secondary literature, which examines the existing discussion of converts and conversion, the principal arguments contained in the chapters of the thesis include the assertion that the increasing restrictiveness of the laws and rules regulating the Jewish community in England created a push factor towards conversion, and that converts to Christianity inhabited a legal grey area, neither under the jurisdiction of the Exchequer of the Jews, nor completely outside of it. Numerous questions are asked (and answered) about the variety of convert experience, in order to argue that there was a distinction between leaving Judaism and joining Christianity. Two convert biographies are presented. The first shows how the liminality that was a part of the conversion process affected the post-conversion life of a convert, and the second shows how a convert might successfully integrate into Christian society.
The analysis of converts and conversion focusses on answering a number of questions. These relate to, among other things, pre-conversion relationships with royal family members, the reaction to corrody requests for converts, motives for conversion, forced or coerced conversions, the idea that a convert could be neither Christian nor Jew, converts re-joining Judaism, converts who carried the names of royal functionaries, the domus conversorum, convert instruction, and converting minors. The appendix to the thesis contains a complete catalogue of Jewish converts in medieval England. Among other things noted therein are inter-convert relationships, and extant source material. Each convert also has a biography.

Keywords: Great Britain -- Church history -- 1066-1485
conversion
Christianity and other religions
Church history -- Middle Ages
Christianity
Christian converts from Judaism -- England -- History
Judaism -- History
Judaism -- Relations -- Christianity -- History
600-1500
Advisor: Brand, PA
Completely iterative monads in semantics of coinductive programs

Some programs are not merely sets of batch instructions performed in isolation. They interact, either directly with the user, or with other threads and resources. This dissertation tackles the problem of mathematical description (denotational semantics) of the observable behaviour of such programs.
In the tradition of denotational semantics and functional programming, one can distinguish between pure computations, which are regarded as mathematical functions, and effectful ones, like those generating behaviour. Both effects in general and behaviour of interactive systems have been thoroughly studied, and they both have elegant category-theoretic explanations: the frameworks of, respectively, monads and coalgebra. The point of this dissertation is to explore the area where the two meet.
The thesis of this dissertation is that the right kind of monads to describe the observable behaviour of programs are completely iterative monads (cims), introduced by Elgot and more recently studied by Adamek and others. They are monads equipped with a certain corecursion scheme that allows us to describe the computation in a coinductive, step-wise manner.
To support this, we introduce a formal coinductive semantics parametrised with a cim. We study its properties and show that it instantiates to a number of known approaches, based on metric spaces and final coalgebras.
Then, we focus on studying properties of cims, especially those important in semantics and programming, like composability. We show that a number of constructions used in denotational semantics to model different aspects of behaviour are instances of the constructions that we introduce. The most important structure that we study are coinductive resumptions, generalising previous results by Moggi or Hyland, Plotkin, and Power.
The language of our development is category-theoretic, and so are the properties that we investigate. We are interested in universal properties, distributive laws, algebras, and monadicity. Thus, the results apply not only to semantics and programming, but can be construed as a general investigation of algebraic structures with iteration.

Keywords: coinduction
coalgebra
monad
semantics
Advisor: Gibbons, J
Craftsmanship, teleology, and politics in Plato's 'Statesman'

In this thesis I attempt to bring out some interesting implications of Plato’s political thought as it is presented in the Politicus. In particular, I will show how this dialogue provides a new picture of the relation between ruler and ruled; a picture that stresses the importance and responsibility of every citizen, not just of the statesman himself. This is achieved by an analysis of the notion of political craftsmanship envisaged by the main speaker of the dialogue, the Eleatic Stranger. However, before I turn to consider the Politicus itself, I provide a brief presentation of another Platonic craftsman, the demiurge of the Timaeus. As will be clear, the teleological structure, and the accompanying terminology, of his craftsmanship will mirror that of the true statesman and thus help us understand the latter’s political rule. My choice to focus on this aspect of the Politicus is motivated by the text itself. For the question of the kind of craftsmanship involved in political rule is picturesquely, yet effectively, brought to the fore by the myth in the early parts of the dialogue, which distinguishes between two rival conceptions and associates the statesman with one of them.
I conclude by reflecting on the significance of my findings for Plato’s political thought as a whole.

Keywords: Plato
'Statesman' (dialogue)
Ancient philosophy
Advisor: Johansen, T
Computational studies of protein sequence and structure

This thesis explores aspects protein function, structure and sequence by computational approaches. A comparative study of definitions of protein secondary structures was performed. Disagreements in assignment resulting from three different algorithms were observed. The causes of inaccuracies in structure assignments were discussed and possibilities of projecting protein secondary structures by different structural descriptors were tested. The investigation of inconsistent assignments of protein secondary structure led to a study of a more specific issue concerning protein structure/function relationships, namely cis/trans isomerisation of a peptide bond. Surveys were carried out at the level of protein molecules to detect the occurrences of the cis peptide bond, and at the level of protein domains to explore the possible biological implications of the occurrences of the structural motif.
Research was then focussed on andalpha;-helical integral membrane proteins. A detailed analysis of sequences and putative transmembrane helical structures was conducted on the ABC transporters from different organisms. Interesting relationships between protein sequences, putative a-helical structures and transporter functions were identified. Applications of molecular dynamics simulations to the transmembrane helices of a specific human ABC transporter, cystic flbrosis transmembrane conductance regulator (CFTR), explored some of these relationships at the atomic resolution. Functional and structural implications of individual residues within membrane-spanning helices were revealed by these simulations studies.
Foreign military intervention in response to microstate security crises

The thesis explores political-security aspects of a late twentieth century phenomenon: the existence of many diminutive and weak, yet ostensibly sovereign and independent, states. The thesis addresses two main questions concerning these "microstates" (with a population of less than one million). What are the principal sources of microstate vulnerability? How best can we conceptualize microstates' security dependence on larger powers? Foreign military intervention in response to microstate security crises throws these dual issues into sharp relief. The study covers all 55 independent microstates during the years 1960 to 1989, from the conventional beginning of decolonization to the end of the Cold War. Particular attention is paid to four representative case studies: Vanuatu (Papua New Guinea's 1980 intervention to quell a secessionist rebellion); The Gambia (Senegal's 1981 suppression of a coup attempt); Grenada (Cuba's role in respect of the 1983 American invasion); and the Maldives (India's thwarting of a 1988 mercenary attack).
The thesis draws on an original data base of microstate security crises, a wide range of academic literature covering International Relations theory and small states, and field work. It tests the propositions that certain typical political, geographical and economic characteristics of microstates played a key role in determining vulnerability to security threats, and that microstates' dependent relationships with larger powers are in keeping with the patron-client model of such unequal associations. The thesis concludes that a mix of typical microstate features heightened their vulnerability, notably disadvantageous colonial legacies; tendencies towards "exaggerated personalism", "leadership longevity", and unrestrained executive power; remote insularity; and extreme government resource constraints. The patron-client model was found to be a useful conceptualization of dependent security relationships with larger powers, in terms of the pervasiveness of the latter's engagement in the microstates, conformity in foreign policy and mutual benefit, but the criterion of informality was frequently not met.
Mixing in multiphase jet flow

A series of experiments has been conducted for comparison with the results of a computer code called CHYMES. It is intended to calculate the coarse mixing of molten metal with water by solving the equations of the Separated Flow Model. These are derived by volume averaging and the terms that relate them to the particular case of participate flow are discussed.
An experimental apparatus that is compatible with CHYMES and coarse mixing has been constructed which projects a jet of ball bearings into a thin tank of water. Experiments over a wide range of conditions were conducted at room temperature. Owing to practical difficulties only one, poorly controlled experiment with hot ball bearings was performed.
Under nearly all sets of conditions an arrow-shaped plume was obtained. The speed of penetration of the plume varied little with changes in experimental conditions. The width of the plume was most strongly influenced by the widths of the tank and the jet. The individual paths of some particles were followed; it appeared that their motion was mostly dependent on their position in the plume. A model of the plume is proposed, based upon its front being impermeable to water in the vertical direction.
Much of the detail of the experimental plumes was not present in the computational results and they responded differently to changes in conditions. It is proposed that this is a result of the different forms of the two sets of plumes. To rectify this an experimental plume was volume averaged. A method to determine a suitable averaging volume size is described. The process results in a plume similar to the computational ones. The length scales required for volume averaging to be successful are discussed and the possibility that this method is inappropriate for describing coarse mixing is admitted.

Advisor: Kenning, D
Measuring treatment effects in poverty alleviation programs: three essays using data from Turkish household surveys 

The dissertation is a compilation of three essays on Turkey's poverty alleviation programs. The first paper focuses on the welfare impact of the global financial Crisis on Turkish households. The second paper considers the protective impact of the Green Card non-contributory health insurance program in Turkey during the Crisis in 2008-2009. The third paper uses experimental data from the field in eastern Turkey, to look at patterns of agricultural technology diffusion in a rural development program implemented in a post-conflict setting.

Keywords: Turkey
health insurance for the poor
poverty
crisis
rural development
health policy
impact evaluation
social networks
social protection
Advisor: Fafchamps, M
Inclusion and exclusion: NGOs and politics in Zimbabwe

The thesis explores the changing relations between the Zimbabwean state and local nongovernmental organizations (NGOs) after independence. It focuses on debates over the role of NGOs in democratization in developing countries, using Zimbabwe as an example. The thesis argues that the study of democratization is best accomplished through detailed empirical case studies, relying on historical narratives and participant-observation research. Such research reinforces our understanding of democratization as a complex and dynamic process.
The thesis proposes a framework for understanding state and society relations in Zimbabwe, emphasizing the ruling party’s use of coercive and consent-generating mechanisms to establish hegemony over the new nation. It examines the changing relationship between NGOs and the state after independence, when the ruling party’s efforts to include most groups within its nationalist coalition extend to NGOs. Case studies of NGO coalitions show how activist NGOs fail to mobilize others owing to the unwillingness of many NGOs to challenge the ruling party’s control over policy-making.
The establishment of the National Constitutional Assembly by some NGOs, churches and trade unionists set the stage for an increasingly tense engagement between NGOs and the state after 1997. The constitutional debate opened up the public sphere in new ways. As the ruling party attempted to retain control over the political sphere and the constitutional debate, NGO politics became increasingly polarized. The emergence of the opposition Movement for Democratic Change, and the prominence of NGO activists within its leadership, led to further conflict. After losing the February 2000 constitutional referendum, the regime sanctioned violent attacks on white farmers, businesspeople, and NGOs. While the ruling party attempted to shore up its support through nationalist rhetoric and financial incentives, groups perceived to oppose the state were excluded and vilified.

Keywords: NGOs
elections
Zimbabwe
constitution
churches
Advisor: Williams, G