VictorJuiz/thesis huggingface dataset:
Social evolution in class-structured populations
Keywords: reproductive value
individual quality
dispersal
inclusive fitness
kin selection
social value

Inclusive fitness theory concerns the study of social traits. Often, individuals differ in their phenotype (e.g. size, weight, nutritional state) independently of their genetic make up, that is, individuals differ in their quality. Individuals can then be classified into different “classes” according to their quality, which enable us to understand social evolution in class-structured populations. This is important because individuals in natural populations often differ in quality, either because of intrinsic factors (e.g. size), or extrinsic factors (e.g. resource availability). My thesis concerns the evolution of social traits in class-structured populations. In chapter 1, I make a brief introduction to my thesis, providing the abstract of each chapter. In chapter 2, I outline a general theory of individual quality, where I show how individual quality impacts social evolution in two fundamental ways. In chapter 3, I show that resource heterogeneity greatly influences the evolution of conditional social behaviour. In chapter 4, I show that temporal group-size heterogeneity promotes the evolution of both conditional helping and harming. In chapter 5, I analyse the effect of individual quality on kin selection. I find that individual quality has an important impact in kin selection, which can lead to extreme forms of social behaviour. In chapter 6, I show that stable environments promote the evolution of negative density-dependent dispersal, while unstable environments promote the evolution of positive density-dependent dispersal. In chapter 7, I show that budding and low local quality promote the evolution of dispersal and cooperation.
Computational electrochemistry
Keywords: computational electrochemistry
chronoamperometry
migration
cyclic voltammetry
finite difference
diffusion

Electrochemistry is the science of electron transfer. The subject is of great importance and appeal because detailed information can be obtained using relatively simple experimental techniques. In general, the raw data is sufficiently complicated to preclude direct interpretation, yet is readily rationalised using numerical procedures. Computational analysis is therefore central to electrochemistry and is the main topic of this thesis.
Chapters 1 and 2 provide an introductory account to electrochemistry and numerical analysis respectively. Chapter 1 explains the origin of the potential difference and describes its relevance to the thermodynamic and kinetic properties of a redox process. Voltammetry is introduced as an experimental means of studying electrode dynamics. Chapter 2 explains the numerical methods used in later chapters.
Chapter 3 presents a review of the use of nanoparticles in electrochemistry.
Chapter 4 presents the simulation of a random array of spherical nanoparticles. Conclusions obtained theoretically are experimentally confirmed using the Cr3+/Cr2+ redox couple on a random array of silver nanoparticles.
Chapter 5 presents an investigation into the concentration of supporting electrolyte required to make a voltammetric experiment quantitatively diffusional. This study looks at a wide range of experimental conditions.
Chapter 6 presents an investigation into the deliberate addition of insufficient supporting electrolyte to an electrochemical experiment. It is shown that this technique can be used to fully study a stepwise two electron transfer. Conclusions obtained theoretically are experimentally confirmed using the reduction of anthracene in acetonitrile.
Chapter 7 presents a new method for simulating voltammetry at disc shaped electrodes in the presence of insufficient supporting electrolyte. It is shown that, under certain conditions, the results obtained from this complicated simulation can be quantitatively obtained by means of a much simpler ‘hemispherical approximation’. Conclusions obtained theoretically are experimentally confirmed using the hexammineruthenium ([Ru(NH3)6]3+/[Ru(NH3)6]2+) and hexachloroiridate ([IrCl6]2−/[IrCl6]3−) redox couples.
Chapter 8 presents an investigation into the voltammetry of stepwise two electron processes using ionic liquids as solvents. It is shown that these solvents can be used to fully study a stepwise two electron transfer. Conclusions obtained theoretically are experimentally confirmed using the oxidation of N,N-dimethyl-p-phenylenediamine in the ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate ([C4 mim][BF4]).
The work presented in this thesis has been published as 7 scientific papers.
Biochemical studies of the cohesin complex
Keywords: biology chromosome cell biochemistry

The accurate inheritance of genetic material depends upon the establishment and maintenance of sister chromatid cohesion. Replicated chromosomes are topologically encircled by the large, tripartite protein complex cohesin, allowing bi-orientation in mitosis. To entrap and reversibly dissociate from DNA, the annular complex structure must be disrupted at either the hinge domain between Smc1 and Smc3, or the interfaces created by the kleisin subunit Scc1 bridging the two ABC-like ATPase domains. The aim of this work was to characterise the cohesin complex loading and releasing mechanisms by examining the biochemical requirements for these processes. Although the identity of a chromosomal cofactor could not be assigned, the loading reaction was found to necessitate engagement of ATPase domains in an ATP-dependent manner. Notions of allosteric modulation of ATP binding and NBD engagement by acetylation were discredited. Likewise, a direct and stable physical association of hinge domains with NBDs was shown to be an unlikely conformational intermediate in a reaction thought to promote hinge opening for loading of cohesin onto DNA. The Smc3-Scc1 kleisin interface might be exploited during the opposing process of release of cohesin from DNA. Therefore, a novel protein- protein cross-linking system was adapted for use in S. cerevisiae, with a view to (1) confirming the well-founded role of hinge dissociation in topological entrapment, and (2) validating the Smc3- Scc1 interface as the recently conjectured exit gate. Despite promising preliminary kinetics in vitro, the SpyTag-SpyCatcher system was considerably less efficient in vivo. It was thus deemed unsuitable in its current format for investigating the process of interface dissociation in live cells. Finally, the large, cohesin complex-associated HEAT repeat protein Pds5 has been either speculated or shown to participate in all of the aforementioned processes, potentially modulating the hinge and Smc-kleisin interfaces. Acting as a regulatory node in cohesin function, it was pursued as an informative target for structural studies. Although no diffractive material could be obtained, Pds5 was confirmed to bind a short, N-terminal sequence of Scc1 and was in turn bound at its N- terminus by Wapl. Together, these findings contribute to defining the structures and states of the cohesin complex.
Information as care: reconnecting internet use, HIV and health
Keywords: internet
performativity
HIV
care
health
ethics

Internet technologies are increasingly advocated as a means for transforming health care and improving people’s health. In the field of e-health questions on the health implications of internet use are typically approached through attempts at measuring the effect of internet use on health outcomes. In this, information is usually conceptualised as a form of knowledge/power and online information practices are enrolled in discourses on patient empowerment. Taking the different meanings ascribed to information in these approaches as my point of departure, in this thesis I rethink the implications of internet use on health through an empirical exploration of alternative conceptualisations of the relationship between information and health in the context of contemporary HIV treatment and care. I do this through two analytical moves. First, drawing on the concept of performativity, a concern with what effect internet use has on health is turned into one of how internet use enacts health. Second, rather than treating information as knowledge/power, through an analysis of how a specific group of women ‘living with HIV’ in the UK use the internet, I reconfigure the connections between internet use and health through a conceptualisation of information as care. Drawing on a range of empirical materials – including forty-seven in-depth interviews with patients and internet content providers, non-participant observations, document and website analysis – three areas of health-related internet use are analysed in detail: the seeking out of health-related and specifically biomedical information; the seeking out and sharing of experiential knowledge and narratives about living with HIV; meeting prospective partners and dating. However, rather than studying these areas of internet use in order to interrogate what they can tell us about the internet, I analyse them as part of the ethical regime of ‘living with HIV’, in which the virus, previously thought of as ‘terminal’, becomes, through info and bio technologies, normalised as ‘chronic’. From this perspective, enacting health not only entails working on and with one’s body, but also always invokes its distribution across bodies, to other areas and relations, including internet technologies and the networks of relations established via these technologies.
Examining the role of traditional health networks in the Karen self determination movement along the Thai-Burma border
Keywords: Traditional Medicine
Humanitarianism
Indigenous Medicine
Ayurveda
Refugee Studies
International Development
Burma

According to the United Nations High Commissioner for Refugees (UNHCR), by 2012 there were 15.4 million refugees and 28.8 million internally displaced persons (IDPs) forced to flee their homes due to war or violent conflict across the globe. Upon arrival in their host settings, forced migrants struggle with acute health and material needs, as well as issues related to identity, politics, power and place. The Karen ethnic minority of Burma (also known as Myanmar) has been involved in a prolonged civil conflict with the Burmese military government for nearly six decades. This fighting has resulted in massive internal displacement and refugee flight, and although a ceasefire was signed in 2012, continued violence has been reported. This study among the displaced Karen population along the Thai-Burma border examines the relationships between traditional – or indigenous – medicine, the population's health needs, and the broader social and political context. Research was conducted using an ethnographic case-study approach among 170 participants along the Thai-Burma border between 2003 and 2011.
Research findings document the rapid evolution and formalisation of the Karen traditional medical system. Findings show how the evolutionary process was influenced by social needs, an existing base medical knowledge among traditional health practitioners, and a dynamic social and political environment. Evidence suggests that that Karen traditional medicine practitioners, under the leadership of the Karen National Union (KNU) Department of Health and Welfare, are serving neglected and culturally-specific health needs among border populations. Moreover, this research also provides evidence that Karen authorities are revitalising their traditional medicine, as part of a larger effort to strengthen their social infrastructure including the Karen self-determination movement. In particular, these Karen authorities are focused on building a sustainable health infrastructure that can serve Karen State in the long term.
From the perspectives of both refugee health and development studies, the revival of Karen traditional medicine within a refugee and IDP setting represents an adaptive response by otherwise medically under-served populations. This case offers a model of healthcare self-sufficiency that breaks with the dependency relationships characteristic of most conventional refugee and IDP health services. And, through the mobilisation of tradition for contemporary needs, it offers a dimension of cultural continuity in a context where discontinuity and loss of culture are hallmarks of the forced migration experience.
Electronic properties of mesostructured metal oxides in dye-sensitized solar cells
Keywords: hybrid solar cells
photovoltaic

Solid-state dye-sensitized solar cells (ssDSCs) offer the possibility of high power conversion efficiencies (PCEs) of over 20%. However, after more than a decade of research, devices still barely reach over 7% PCEs. In this thesis, limitations to device performance are studied in detail, and solutions for future advancement are put forward.
In the first part of the thesis, factors limiting charge generation are explored by studying the crystallization environment of mesoporous TiO2 self-assembled through block copolymers. It was found that the density and distribution of sub band gap states are a function of the synthesis conditions and critically affect the performance characteristics of the self-assembled titania used in ssDSCs. As a result, the self-assembled mesoporous oxide system presented in this thesis outperforms for the first time the conventional nanoparticle based electrodes fabricated and tested under the same conditions, with demonstrated PCEs of over 5%.
In chapters 6, 7, and 8, the factors limiting the diffusion length and hence, the thickness of the fabricated devices, are carefully examined. Previous literature points towards insufficient pore-filling of the hole transporting material (HTM) as the main limiting factor. In chapter 6, a pore-filling study is shown where a new technique to evaluate the pore-filling fraction of the HTM in the conventional mesoporous metal oxide electrode is also presented and conclude that sufficient pore-filling of thick films can easily be achieved. Another usual strategy to extend the electron lifetime in the devices and thus, the charge diffusion length, involving thin film coatings of insulating metal oxides is examined in chapter 7, with satisfactory results for SnO2-based ssDSCs. The diffusion length can also be extended if the factors limiting the diffusion of charges through the device are identified and removed, as presented in chapter 8.
Finally, a study on the stability of the ssDSC is presented in chapter 9. The developments achieved enable long term stability to be effectively targeted, and represent a key milestone towards commercial realization of ssDSCs.
Wildlife is our oil: conservation, livelihoods and NGOs in the Tarangire ecosystem, Tanzania
Keywords: International NGO
Tanzania
Tarangire
Conservation
Pastoralism

The Tarangire ecosystem of northern Tanzania is proclaimed a site of global biodiversity significance. The economic value of wildlife in Tarangire and Lake Manyara National Parks is substantial and growing. Maintaining the health of these parks is important to Tanzania’s overall tourism industry and macroeconomic health. A considerable proportion of Tarangire’s wildlife leaves the park for approximately six months a year, migrating onto village lands under the jurisdiction of local communities. Of particular importance are grazing and calving areas in the Simanjiro Plains. Conservation of the ecosystem’s migratory wildlife populations largely depends on maintaining these habitats on communally owned lands. However, populations of most large mammal species have declined by over fifty percent in the last decade. The progressive conversion of pastoral rangelands to agriculture is believed to be a major contributing factor to this decline. Community-based conservation (CBC) interventions in the Tarangire ecosystem aim to increase the combined economic returns from wildlife and pastoral livestock production in order to reduce incentives for non-wildlife compatible agricultural land-use change. Increased State investment in CBC, continued growth in photographic and hunting tourism revenues, and large infusions of funding from international conservation organisations suggest that substantial potential exists for CBC to play a significant role in poverty reduction and biodiversity conservation. This thesis examines the fortunes of CBC in the Tarangire ecosystem. It uses a household survey conducted in a village earning substantial wildlife tourism revenues to show that wildlife benefits are concentrated in the hands of the elite, and have limited livelihood or conservation impacts. By documenting the root causes of local resistance to conservation, this thesis explains the failures of new conservation strategies in Tanzania.
Molecular pathological investigation of the pathophysiology of fatal malaria
Keywords: microRNA
cloning
african
malaria
pathology
hypoxia
autopsy
microarray
cerebral malaria
cell culture
luciferase assay
tie-2
molecular pathology
tissue quality
acute kidney injury
malaria associated acute renal failure
angiopoietin
asian

Malaria remains one of the world's major health problems, especially in developing countries. A better understanding of the pathology and pathophysiology of severe malaria is key to develop new treatments. Different approaches have been used in malaria research including the in vitro co-culture models with endothelial cells and both murine and simian animal models. However these are open to controversy due to disagreement on their representativeness of human disease. Using human post-mortem tissue in malaria research is another important approach but is practically challenging, limiting the availability of post mortem samples from malaria patients.
The work in this thesis had two main themes. First I examined the role of the endothelial signalling Angiopoetin-Tie-2 receptor pathway in malaria. Ang-2 has been shown to be a significant biomarker of severe and fatal malaria. I examined the tissue specific expression of proteins from this pathway in post-mortem brain tissues from fatal malaria cases, but found no difference between cerebral malaria and non-cerebral malaria cases. Ang-2 correlated with the severity of malaria in these patients. An attempt to examine the interaction of hypoxia and the Ang-Tie-2 pathway in vitro using a co-culture model of human brain endothelial cells was unsuccessful due to contamination of the cell line.
The second part of the thesis aimed to utilise molecular pathology techniques including miRNA and whole-genome microarrays. I have shown for the first time that these can be successfully applied to human post-mortem tissue in malaria. First I used archival tissues to examine the microRNA signature in the kidney of patients with malaria associated renal failure. Second I optimised a protocol to preserve post mortem tissue for molecular pathology, from an autopsy study in Mozambique. Using the subsequent total mRNA transcriptomic data and bioinformatics analysis this work has expanded our knowledge of differential gene expression and the families of genes which are dysregulated in the brain in response to malaria infection.
Voltaire à l'ouvrage: une étude de ses traces de lecture et de ses notes marginales
Keywords: Voltaire
books and reading
marginalia
history of the book

The aim of the present study is to paint an overall picture of how Voltaire interacted with the books that made up his personal library. Situated at the crossroads between history of the book, literary history and literary studies in the standard meaning of the term, it seeks to deepen our understanding of the ways in which Voltaire used his books and of the different types of notes that he left in them. These notes are of course texts in themselves – short ones, to be sure, but texts all the same – and their material, literary and polemical significance have never before been studied in depth. We begin by classifying the marginalia according to the function they seem to have played for Voltaire and, based on their material characteristics, by developing methodologies to analyse these short manuscripts, along with the non-verbal markings that accompany them. An analysis follows of the ways in which Voltaire used the white spaces in his books, then of the links that can be established between the signs of his reading and the genesis of his published works. Finally, we study the poetics of the marginal notes as well as the dynamics at work in the annotated library as a whole. Throughout, Voltaire’s notes and reading habits are placed in the context of the critical literature that has grown up around the subject of marginalia. Along the way, we compare his marginal notes to those of other literary figures of the period, for the subject of this study is clearly the marginalia of a writer, which are necessarily inextricably linked to his principal activity – writing. Indeed, one might speak of an interpenetration, of a blurring of boundaries between reading and writing. Beyond the marks of Voltaire's reading, the study of marginalia raises questions that are relevant for other non-canonical and paratextual materials. To place them in the spotlight transforms their status, and a note that was 'marginal' comes to be considered a text in its own right.
The optimal application of common control techniques to permanent magnet synchronous motors
Keywords: space vector modulation
vector control
permanent magnet synchronous motor

Permanent magnet synchronous motors are finding ever increasing use in hybrid and electric vehicles. This thesis develops a new control strategy for Permanent Magnet Synchronous Motors (PMSMs) to reduce the motor and inverter losses compared to conventional control techniques. The strategy utilises three common control modes for PMSMs; brushless DC with 120°E conduction, brushless DC with 180°E conduction, and brushless AC control.
The torque and power output for each control mode is determined for an example motor system using a three phase axial flux YASA motor and an IGBT inverter. The loss components for the motor and inverter are also estimated using a combination of analytical and simulation techniques and results are then validated against experimental measurements. Efficiency maps for each control mode have been used to determine an optimal mode utilisation strategy, which minimises the total system losses and maximises the available motor torque output.
The proposed control strategy switches between the three control modes without interruption of motor torque to maximise the system efficiency for the instantaneous operating speed and demanded torque output. The benefits of the new strategy are demonstrated using an example vehicle over a simulated drive cycle. This yields a 10% reduction in losses compared to conventional brushless AC control.