VictorJuiz/thesis huggingface dataset:
Development of strains and procedures for genetic control of Aedes aegypti (Diptera: Culicidae)
Keywords: genetic sexing system
transgenics
fecundity
fertility
sterile insect technique
Aedes aegypti

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.
Thin film flows in curved tubes
Keywords: applied mathematics

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.
Developing clinical measures of lung function in COPD patients using medical imaging and computational modelling
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

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.
Precise verification of C programs
Keywords: program synthesis
Software verification
software engineering

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.
Anteromedial osteoarthritis - a surgical perspective of incidence, progression and risk factors
Keywords: knee
arthritis
surgery
anteromedial

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.
The normativity of rationality: a defense
Keywords: coherence
reason
normativity
rationality
reasoning
consistency
action
intention

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.
The International Criminal Court and the end of impunity in Kenya
Keywords: International Criminal Court
accountability
Impunity
Transitional Justice
International Criminal Law
crimes against humanity
prosecutions
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.
The construction of the South: developing countries, coalition formation and  the UN climate change negotiations, 1988-2012
Keywords: United Nations
climate change
developing countries

The North-South divide is one of the central political characteristics of the UN climate change negotiations. But while the Group of 77 coalition has been the main negotiating group for the South, developing countries have often faced challenges to their unity, magnified by the recent establishment of smaller negotiating groups. How has 'the South' hung together? This thesis investigates how developing countries have formed negotiating groups over the two decades of the UN climate negotiating process. It explains the origins of the different negotiating groups that have formed over this time, as well as the timing of their emergence and the scope of their membership. In particular, while scholarly attention has focused on the G77, Alliance of Small Island States (AOSIS) and most recently the Brazil-South Africa- India-China (BASIC) coalition, this thesis corrects the relative neglect in understanding the many other negotiating groups that have formed.
While conventional explanations highlights the shared material interests that underpin group formation, this thesis advances a constructivist argument that emphasises instead the importance of collective identities in shaping norms of 'appropriate association' – the social bases of whose one's friends and allies are. It highlights the regional basis for many of these negotiating groups that cut across shared material circumstances, and draws upon historical institutionalist insights on critical junctures and path dependence to place this larger pattern of Southern coalition formation in the appropriate historical and institutional context of the UN system. It demonstrates the continuing persistence of countries identifying as the 'South', where despite changing material circumstances and disagreements among developing countries, the salience of the G77 as the constitutive institution of this identity remains. Above all, in investigating the processes of coalition formation among developing countries in the climate context, this thesis deepens scholarly understanding about the contemporary meaning of the 'South'.
Link-directionalities in carrier sense wireless networks
Keywords: MAC protocol
wireless LAN
Link-directionalities
capacity
wireless ad-hoc networks
carrier sensing
multi-channel

In this thesis, research is described which leads to the proposal of a link-directionality-based dual channel MAC (Medium Access Control) protocol (DCP) for carrier sense wireless ad hoc networks. It attempts to double the capacities of such networks using an industrial standard (the single-channel IEEE 802.11 protocol) as a benchmark. Simulations show that the proposed scheme can increase the capacities to more than 1.7 times of the single-channel IEEE 802.11 protocol in large-scale random network topologies. The algorithm, however, requires extra radio spectrum resource which could be costly.
In addition to DCP, a signal-to-interference ratio comparison algorithm (SCA) is proposed to further release the protocol constraints imposed by the virtual carrier-sensing mechanism. Interestingly, while the capacity of the pure DCP decreases when link lengths are short, the capacity of the pure SCA increases when link lengths are short. The two algorithms compensate for the downside of each other to bring about a more uniform capacity improvement. Simulations show that the integrated scheme can further increase the network throughputs to more than 2.13 times in random topologies.
This thesis also clarifies inter-link interference in wireless ad-hoc networks by using link-directional interference graphs (l-graph). By colouring the l-graphs, independent data streams obtained by Multi-Carrier Code Division Multiple Access (MC-CDMA) are assigned for transmitting up-link and down-link traffic separately in order to eliminate the hidden-node and exposed-node problems in wireless local area networks (WLAN).
Finally, a generic approach for capacity analysis is proposed to show that the concept of link-directionality can also be adopted with other network models, protocols and parameter settings. However, in certain scenarios where links are densely packed together, the advantage of using link-directionality could be diminished. Therefore, the proposed generic approach for capacity analysis allows one to determine whether channel allocations according to link-directionalities should be applied to a given network.
Accounting for sustainability in Bengal: examining arsenic mitigation technologies using Process Analysis Method
Keywords: Water
Groundwater
Process Analysis Method
Mitigation
India
User-Centered
Design
Metrics
Sustainability
Filters
arsenic
West Bengal

This thesis shows how the Process Analysis Method (PAM) can be applied to assess technologies used to mitigate arsenic from drinking water in rural India, using a set of sustainability indicators. Stakeholder perspectives, gathered from a fieldwork survey of 933 households in West Bengal in 2012, played a significant role in this assessment. This research found that the ‘Most Important’ issues as specified by the technology users are cost, trust, distance from their home to the clean water source (an indicator of convenience), and understanding the health effects of arsenic. It was also found that none of the ten technologies evaluated are economically viable, as many do not charge user-fees, which creates reliance upon donations to meet recurring costs. Utilisation of a technology is strongly related to sociocultural capital, but in many cases, features that contribute to sociocultural value, like regular testing of the treated water, are not included in the financial budget. It is suggested that increased awareness might change attitudes to arsenic-rich waste and its disposal protocols. This waste is often currently discarded in an uncontrolled manner in the local environment, giving rise to the possibility of point-source recontamination. All technologies proved to have difficulties in dealing with waste, except the Tipot and Dug wells which produce no waste. Of the methods considered, the BESU technology scored highest, but still only with 47-62% of the maximum scores achievable within each domain. This explains the widespread failure of mitigation projects across the region. The indicators and metrics show where improvements can be made. A model scheme based on these findings is outlined which could be applied with the objective of increasing utilisation and improving sustainability. It can be concluded that a product stewardship approach should be taken in regard to design, implementation and operation of the technologies, including the creation of a regulated toxic waste collection and disposal industry.