VictorJuiz/thesis huggingface dataset:
Development of strains and procedures for genetic control of Aedes aegypti (Diptera: Culicidae)

The mosquito Aedes aegypti is responsible for 50 million dengue fever infections in humans each year. A novel control strategy, named RIDL (Release of Insects carrying a Dominant Lethal) relies on releasing large numbers of genetically sterile male insects in order to control pest populations. This thesis describes the development of new tools to improve the efficiency of RIDL against Ae. aegypti and assessment of candidate strains for field release. Chapter 3 describes a new selection system for Ae. aegypti based on ethanol susceptibility conferred by the alcohol dehydrogenase gene (Adh) from Drosophila melanogaster. I observed that the susceptibility of Ae. aegypti larvae to ethanol can be triggered by expression of Adh in larvae. Chapters 4 and 5 focus on RIDL strains with a genetic sexing mechanism, for easy and stringent selection for males before mass-releases, eliminating disease- transmitting females. In Chapter 4, I describe the creation of a late-acting sexing strain of Ae. aegypti based on the Ae. aegypti doublesex (Aedsx) alternative splicing system. In Chapter 5, I describe an attempt to create an early-acting sexing system. Killing the females of the release generation early would free space and resources for the production of males. This was done by combining the Adh gene and the Aedsx alternative splicing system described in Chapters 3 and 4. Chapter 6 reports the results of a comparison, in terms of quality and productivity, between an existing Ae. aegypti RIDL strain and a wild-type control. Results showed equivalent female quality and productivity between the two strains, while RIDL males were less fertile in comparison with wild-type males. RIDL eggs also seemed more susceptible to long- term storage. The results of this work show promise for development of novel RIDL strains that may be used in the field to control disease-transmitting mosquitoes.

Keywords: genetic sexing system
transgenics
fecundity
fertility
sterile insect technique
Aedes aegypti
Advisor: Alphey, L
Shimeld, S
Thin film flows in curved tubes

The main motivation of this thesis comes from a desire to understand the behaviours of blood flow in the vicinity of atheroma. The initiation and development of atherosclerosis in arteries are normally observed in the areas of low or oscillating wall shear stress, such as on the outer wall of a bifurcation and the inside of the bends.
We start by building on the background to the areas related to our models. We focus on the models of fluid flow travelling through a curved tube of uniform curvature because most arteries are tapered and curved. The flow of an incompressible Newtonian fluid in a curved tube is modelled. The derivation of the corresponding equations of the motion is presented. The equations are then solved for a steady and oscillatory driving axial pressure gradient. In each case, the flow is governed by different dimensionless parameters. The problem is solved for a variety of parameter regimes by using asymptotic technique as well as numerical method.
Some aspects of thin-film flows are studied. The well-known thin film equation is derived using lubrication theory. The stability of a thin film in a straight tube and the effects of a surfactant droplet on a liquid film are presented. The moving contact line problem, one of the controversial topics in fluid dynamics, is also discussed.
The leading-order equations governing thin-film flow over a stationary curved substrate is derived. Various approaches and the application of flow on particular substrates are shown.
Finally, we model two-layer viscous fluids using lubrication approximation. By assuming the thickness of a lower liquid layer is much thinner than that of the upper liquid layer, the equation governing the liquid-liquid interface is derived. The steady-state and trasient solutions of the evolution equation is computed both analytically and computationally.

Keywords: applied mathematics
Advisor: Waters, S
Developing clinical measures of lung function in COPD patients using medical imaging and computational modelling

Chronic obstructive pulmonary disease (COPD) describes a range of lung conditions including emphysema, chronic bronchitis and small airways disease. While COPD is a major cause of death and debilitating illness, current clinical assessment methods are inadequate: they are a poor predictor of patient outcome and insensitive to mild disease. A new imaging technology, hyperpolarised xenon MRI, offers the hope of improved diagnostic techniques, based on regional measurements using functional imaging. There is a need for quantitative analysis techniques to assist in the interpretation of these images. The aim of this work is to develop these techniques as part of a clinical trial into hyperpolarised xenon MRI.
In this thesis we develop a fully automated pipeline for deriving regional measurements of lung function, making use of the multiple imaging modalities available from the trial. The core of our pipeline is a novel method for automatically segmenting the pulmonary lobes from CT data. This method combines a Hessian-based filter for detecting pulmonary fissures with anatomical cues from segmented lungs, airways and pulmonary vessels. The pipeline also includes methods for segmenting the lungs from CT and MRI data, and the airways from CT data. We apply this lobar map to the xenon MRI data using a multi-modal image registration technique based on automatically segmented lung boundaries, using proton MRI as an intermediate stage. We demonstrate our pipeline by deriving lobar measurements of ventilated volumes and diffusion from hyperpolarised xenon MRI data.
In future work, we will use the trial data to further validate the pipeline and investigate the potential of xenon MRI in the clinical assessment of COPD. We also demonstrate how our work can be extended to build personalised computational models of the lung, which can be used to gain insights into the mechanisms of lung disease.

Keywords: chronic obstructive pulmonary disease
computed tomography
computational modelling
hyperpolarised xenon MRI
hyperpolarised gas MRI
medical image analysis
respiratory disease
biomedical imaging
pulmonary imaging
respiratory imaging
magnetic resonance imaging
lung disease
medical imaging
Advisor: Gavaghan, DJ
Grau, V
Precise verification of C programs

Most current approaches to software verification are one-sided -- a safety prover will try to prove that a program is safe, while a bug-finding tool will try to find bugs. It is rare to find an analyser that is optimised for both tasks, which is problematic since it is hard to know in advance whether a program you wish to analyse is safe or not. The result of taking a one-sided approach to verification is false alarms: safety provers will often claim that safe programs have errors, while bug-finders will often be unable to find errors in unsafe programs.
Orthogonally, many software verifiers are designed for reasoning about idealised programming languages that may not have widespread use. A common assumption made by verification tools is that program variables can take arbitrary integer values, while programs in most common languages use fixed-width bitvectors for their variables. This can have a real impact on the verification, leading to incorrect claims by the verifier.
In this thesis we will show that it is possible to analyse C programs without generating false alarms, even if they contain unbounded loops, use non-linear arithmetic and have integer overflows. To do this, we will present two classes of analysis based on underapproximate loop acceleration and second-order satisfiability respectively.
Underapproximate loop acceleration addresses the problem of finding deep bugs. By finding closed forms for loops, we show that deep bugs can be detected without unwinding the program and that this can be done without introducing false positives or masking errors. We then show that programs accelerated in this way can be optimised by inlining trace automata to reduce their reachability diameter. This inlining allows acceleration to be used as a viable technique for proving safety, as well as finding bugs.
In the second part of the thesis, we focus on using second-order logic for program analysis. We begin by defining second-order SAT: an extension of propositional SAT that allows quantification over functions. We show that this problem is NEXPTIME-complete, and that it is polynomial time reducible to finite-state program synthesis. We then present a fully automatic, sound and complete algorithm for synthesising C programs from a specification written in C. Our approach uses a combination of bounded model checking, explicit-state model checking and genetic programming to achieve surprisingly good performance for a problem with such high complexity. We conclude by using second-order SAT to precisely and directly encode several program analysis problems including superoptimisation, de-obfuscation, safety and termination for programs using bitvector arithmetic and dynamically allocated lists.

Keywords: program synthesis
Software verification
software engineering
Advisor: Kroening, D
Mexican Catholic women's activism, 1929-1940

This dissertation examines Catholic lay women's roles in the Church-State conflict in Mexico during the 1930s. After the Cristero Rebellion (1926-1929), clergy and laymen who publicly supported the Catholic Church were threatened with legal sanctions and government reprisal. Thus, Church leaders called upon Catholic women to assume public roles and to work creatively in defence of their faith, albeit following strictly delineated, gendered norms of behaviour.
The Introduction discusses the lack of nuanced analysis of women's participation in the Catholic Church in Mexico. Chapter 1 traces the history of Catholic Social Action as envisioned in Europe and as adapted to Mexico from the end of the nineteenth century through the Cristero Rebellion, and includes a discussion of the roles envisaged for women in the Church hierarchy's strategy to concentrate and centralise lay people's efforts into the Acción Católica Mexicana (ACM). The first chapter also includes an overview of the Church-State conflict in nineteenth- and twentieth-century Mexico. Chapter 2 presents the reorganisation of various Catholic lay women's social and civic associations into the Union Femenina Católica Mexicana (UFCM). Chapters 3 and 4 form a case study of the UFCM in the Archdiocese of Guadalajara and the state of Jalisco. Chapter 3 concentrates on the Guadalajara Diocesan Chapter of the UFCM and on Catholic women's activism in the context of urban and regional issues. Chapter 4 compares the experiences of women in smaller towns and rural communities throughout the diocese and state, examining women's collective and independent responses to anticlerical legislation, the Mexican state's programs of socialist and sexual education and agrarian reform, the Church hierarchy's calls to action, and their own perceived need for religious and social organisation. The Conclusion evaluates Mexican Catholic women's responses to the social conflicts of the 1930s, their accomplishments, and the legacies of their mobilisation.
Anteromedial osteoarthritis - a surgical perspective of incidence, progression and risk factors

Anteromedial osteoarthritis of the knee (AMOA) has been defined anatomically, histologically and radiologically and yet little is known about the epidemiology of the disease or the risk factors involved in the development of the disease.
The broad aim of this thesis was to combine clinical insight with the utilisation of modern, large epidemiological datasets to provide information to inform better the clinical management of patients with AMOA. Specifically, the prevalence and incidence of AMOA, the time taken to progress from early disease to severe disease that may require surgical intervention, the radiological characterisation of disease and the assessment of mechanical risk factors implicit in the development of this pattern of disease are investigated.
A cross-sectional study of the radiological prevalence of AMOA in a symptomatic cohort in a specialist secondary care knee clinic showed that AMOA was the commonest pattern of knee OA, present in more than 60% of symptomatic subjects. Less than 25% of subjects with AMOA presented with advanced or 'bone-on-bone' disease, emphasising the clinical importance of understanding the progression from earlier stages of disease to this advanced stage.
A 20-year longitudinal radiographic study was performed on 1000 women to describe the prevalence, incidence and progression of AMOA. The prevalence of AMOA was 43% and the incidence over 20-years was 0.4. Life table analysis showed that the risk of developing advanced AMOA in a previously normal knee was 2.6%. Of those subjects with early radiological AMOA, 11% progressed to advanced 'bone-on-bone' disease within 10 years and 37% within 20 years.
The role of mechanical risk factors in the development of AMOA showed that both anatomical limb and proximal tibial alignment were significantly more varus aligned in those that developed AMOA at 20-years. Assessment of the shape of the medial tibial plateau in a longitudinal MRI study showed that the angle of the upslope at the anterior aspect of the plateau was significantly increased in the group that subsequently developed AMOA. To enable AMOA to be studies in future MRI studies, the MRI description of the disease was defined.
In summary, AMOA was shown to be the most common pattern of knee OA both in symptomatic surgical cohorts and in the community. The progression of the disease from an early stage to an advanced stage, which may require surgical intervention, was described for the first time. To enable better the recognition of AMOA in modern epidemiological studies, the MRI description of AMOA was defined and the clinical relevance of modern MRI was discussed. The anatomical alignment of the limb, the alignment of the proximal tibia and the morphology of the tibial plateau were all shown to have a role in the development of AMOA. Addressing these mechanical factors may provide a therapeutic surgical target for the management of patients with AMOA.

Keywords: knee
arthritis
surgery
anteromedial
Advisor: Price, A
Beard, D
Missionary education, knowledge and north Indian society, c. 1880-1915

This dissertation is a critical examination of education via what I have termed the 'educational enterprise' run by Anglican Christian missions in north India c.1880-1915. It will focus in particular on the Gangetic plain, parts of Bengal, the Punjab and Central Provinces. The example of the United Provinces will be used to give context to missionary- Government relations, but will engage with arguments in upper and eastern India (especially Bengal) which are relevant to this research. The network of schools, their aims, orientation, and the degrees to which they were dependent upon Indian agency will all be considered. The first chapter begins with a review of the literature on colonial knowledge and Christian missions, and gives a brief review of religious debate and discourse in pre-British India. It then establishes the Protestant Christian theological context of the early-mid nineteenth century and delineates its development from a pugnacious confrontational one into a positivist and universal theology towards the late nineteenth century. Chapter II establishes the moral and economic context of education in late nineteenth century UP, accounting for religious instruction, the economic rationale for subsidising mission schools, the relationship between the two. It will further define the relationship between missions and Government. Chapter III defines the means and ends of mission schools, considers the degree to which they were dependent upon Indian agency and the impact of religious dialogue upon 'representations' of India. The reception and contestation of both religious and secular knowledge are dealt with in Chapter IV. Indian contestations of Orientalist and Christocentric scholarship receive particular attention. The development of a secular and religiously-plural educational sphere, as a by-product of missionary education, will be investigated in Chapter V. It considers the devaluation of the curriculum, investigates student hostels, Indian nationalism and their contribution to constructive nationalism. The infrastructural shortcomings of education will be addressed in Chapter VI, and ascertain the degree to which the enterprise reproduced Indian, European, and Christian values. Chapter VII will conclude with a review and offer insights into the relationships between Orientalism, religion and colonial Indian society.

Advisor: Washbrook, D
The normativity of rationality: a defense

Rationality is very widely regarded as a normative notion, which underwrites various everyday normative practices of evaluation, criticism, and advice. When some agent behaves irrationally, she is likely to be critically evaluated, and advised to change her ways. Such practices seem to presuppose that agents ought to behave as rationality requires. But some philosophers question this thought. They argue that at least some requirements of rationality cannot be ones that we ought to comply with. This thesis aims to dispel such sceptical doubts over the normativity of rationality; it defends the idea that the requirements of rationality are indeed normative, in the sense that if one is rationally required to F, one ought to F because rationality requires one to F.
The normativity of three requirements of practical rationality in particular is the main target for defense in the following pages. They are:
[ENKRASIA] Rationality requires of A that, if A believes she ought to F, then A intends to F.
[MEANS-ENDS] Rationality requires of A that, if A intends to E, and believes that she will not E unless she intends to M, then A intends to M.
[INTENTION CONSISTENCY] Rationality requires of A that, if A intends to F, and believes that she cannot both F and G, then A does not intend to G.
After presenting some of the grounds for scepticism about the normativity of these three requirements in chapter 1, the thesis goes on in chapters 2 & 3 to critically examine several different accounts of why rationality is normative, concluding that they are all unsuccessful; a novel account is called for. An account of this kind is offered over the course of the two following chapters, 4 & 5. Each requirement is shown to be constituted by a certain kind of ought, while at the same time corresponding to a rule of correct reasoning. Chapter 6 is devoted to answering an objection to that account, according to which the rules of reasoning are given by permissions rather than requirements. Chapter 7 offers a digression into a related issue in action theory: it unfavorably explores the idea that reasoning is a factor that can be used to analyse not only rational action, but also intentional action more broadly; the chapter suggests that treating intentional action as irreducible is the more fruitful approach. Finally, chapter 8 summarizes the main conclusions of the thesis and comments on some remaining questions.

Keywords: coherence
reason
normativity
rationality
reasoning
consistency
action
intention
Advisor: Broome, J
Wedgwood, R
Hyman, J
The biochemistry of antigen presentation

This thesis describes studies on the binding of peptides to the murine major histocompatibility complex (MHC) class I molecule H-2Db (Db). The expression of the recombinant soluble Db molecule in Chinese hamster ovary cells and its subsequent purification by nickel affinity chromatography, gel filtration, and preparative native isoelectric focusing are reported. The product is the correct molecule, homogeneous, a dimer of dimers, and free of endogenous peptide.
A novel binding assay based on the enhancement of natural tryptophan fluorescence by the binding of peptide is introduced. This assay is used to determine melting curves of the empty and peptide-loaded protein, and to measure association rate constants by stopped-flow fluorescence spectroscopy.
Radioligand binding measurements of equilibrium as well as association and dissociation rate constants and their temperature dependence are reported. In agreement with earlier observations, the ratio of association and dissociation rate constants is much larger than the equilibrium association constant.
Fluorescence anisotropy decay spectroscopy gives evidence for conformational alterations in the Db molecule upon peptide binding.
The data, possible errors and ways to avoid them, and mathematical models of binding are discussed to obtain an overall picture of the binding process.
The International Criminal Court and the end of impunity in Kenya

This thesis considers the extent to which the International Criminal Court's Office of the Prosecutor ('OTP') has been successful in realising its self-defined mandate of ending impunity in Kenya. In particular, it focuses on the OTP's attempts to encourage domestic investigations and prosecutions as part of its strategy of positive complementarity. This strategy has been hailed as being the best and perhaps the only way that the OTP may use its finite resources to make a significant contribution to ending impunity. Despite this, no empirical study has been published that evaluates the effectiveness of this strategy and the impact that it has on ending impunity in the targeted situation country. This thesis seeks to address this gap in the literature by conducting a case study on the OTP's implementation of its strategy of positive complementarity in Kenya following that country's post-election violence in 2007/08. In doing so, I also hope to make a modest contribution to existing debates over the effectiveness of the ICC as an institution as well as international criminal justice and transitional justice more generally.

Keywords: International Criminal Court
accountability
Impunity
Transitional Justice
International Criminal Law
crimes against humanity
prosecutions
Kenya
Advisor: Pirie, F