VictorJuiz/thesis huggingface dataset:
Nonlinear diffusion filtering on surfaces

Nonlinear diffusion filtering is a PDE-based method to remove noise from images that has found much success. This dissertation looks at whether nonlinear diffusion filtering can be combined with the closest point method, a relatively new and novel method for solving partial differential equations on surfaces. The closest point method is an embedding method that uses a simple representation of surfaces. The theory and implementation of for the closest point method is presented. We perform convergence studies that show good agreement with theory. We discuss the use of linear and nonlinear diffusion for image processing, in particular the Perona{Malik and Gaussian schemes. We show that they can be combined with the closest point method to produce impressive results, visualised beautifully using an OpenGL raytracer designed for use with the closest point method. Some surprising and unexpected eects were discovered when moving from a plane to a three-dimensional surface. These effects are described and investigated.
The impact of implied constitutional principles on fundamental rights adjudication in common law jurisdictions

This thesis explores the roles played by implied constitutional principles in fundamental rights cases in the common law jurisdictions of Canada, Australia, the Commonwealth Caribbean, and the United Kingdom. The two principles selected for this research are the separation of powers and the rule of law, both of which are relied upon in courts in common law states. The thesis examines the types of cases in which such principles are used, the possible reasons for the appeal of these principles, and the functions that they play in fundamental rights adjudication.
The thesis begins with a brief discussion of the applications of the rule of law and the separation of powers, outlining the content of these principles as applied by the courts. However, the bulk of the analysis throughout the thesis is concerned with a thematic study of the functions played by the principles. It is argued that the principles are used as interpretative aids, as independent grounds for invalidating legislation, and as gateways to comparative legal analysis. The thesis ends by showing the necessary preliminary work that must be undertaken in order to engage in a thorough normative analysis of the use of implied principles in rights adjudication.
Throughout the thesis, several themes are identified as key to our understanding of the functions played by implied principles in the cases discussed. One such theme is legitimization, specifically the role the principles play in the attempt to legitimize arguments, state institutions (particularly the courts), and the state itself. The theme of institutional self-protection also arises; it is evident in the use of principles to protect the jurisdictional sphere of the courts. The analysis of the operation of implied constitutional principles also highlights the legacy of Empire and the deployment of traditional principles to signal the maintenance of democratic traditions and institutions.

Keywords: common law
constitutional principles
human rights
implied principles
constitutional law
Advisor: McCrudden, C
Background rejection for the neutrinoless double beta decay experiment SNO+

The SNO+ experiment will use a liquid scintillator based detector to study solar, geo, and reactor neutrinos and double beta decay. This thesis discusses the effect of backgrounds on the measurement of neutrinoless double beta decay and describes analysis techniques developed to reduce their impact.
Details of the modeling of the photomultiplier tubes in the SNO+ Monte Carlo RAT are first described and comparisons are made with the SNO Monte Carlo SNOMAN. SNOMAN has been extensively verified with calibration sources and RAT is shown to be in good agreement. The event reconstruction techniques are then presented and predict an achievable 15cm position and 7% energy resolution.
The backgrounds are discussed and pileup backgrounds identified, including many previous unknown pileup backgrounds. Techniques to reject the pileup background are presented and shown to give over 99% rejection in the region of the double beta decay end point (3-4MeV), below the irreducible background from solar neutrinos. Finally the resulting limit on the effective Majorana neutrino mass SNO+ could achieve in 2015 is predicted to be 270meV and this is compared with other experiments that are underway.

Keywords: SNO+ Neutrino
Advisor: Jelley, NA
Pliocene and Quaternary environmental change in Kashmir, north-west Himalaya

Late Cainozoic environmental changes in Kashmir (33°30' to 34°30' N: 74°10' to 75°30' E) have been reconstructed using a range of techniques. The sedimentary record in Kashmir consists of a thick (>1000m) basin-fill sequence known as the Karewa group, together with glacial and related sediments in the surrounding mountain flanks. The Karewa sediments are fluviolacustrine in origin and comprise alternations of conglomerates, sands and clayey silts.
Work on the lower Karewa formation, which has previously been dated palaeomagnetically to between 4 and 0.4 MaBP, involved the semi- quantitative analysis of clay-mineral assemblages by X-ray diffraction.The clay minerals in the lower Karewa mudstones are interpreted as detrital clays which reflect weathering within Kashmir basin. The analyses showed a change in clay mineralogy between about 2.5 and 2.3MaBP, from abundant kaolinite to abundant smectite.
Work on the upper Karewa formation involved field description and mapping of facies, sedimentological analysis, dating using thermoluminescence (TL) and amino-acid racemization, and analysis of ostracod assemblages from lacustrine sediments. Areal restriction of the lake in Kashmir occurred about 0.4MaBP with the rapid uplift of the Pir Panjal Range. Sedimentological data show that aeolian dust formed a major input into the lake. Ostracod assemblages show that the lake itself was cool, shallow, alkaline and had abundant plant macrophytes, The lake drained between 120 and SOkaBP. Stratigraphical, sedimentological and faunal evidence suggests that this was a result of tectonically-induced drainage rather than climatically-induced desiccation.
The glacial history of the surrounding mountain flanks was reconstructed by field mapping of glacial sediments and dated using TL and radiocarbon methods. Present and past patterns of glaciation wore assessed by the determination of equilibrium-line altitudes (ELAs), glaciation thresholds (GTs) and cirque aJtitudes. Glaciers extended to 2150 m a.s.l in the Great Himalayan flank and 2600 m a.s.l. in the Pir Panjal. There is evidence for only 2 pre-Holucene advances in Kashmir, the older of which predates 35kaBP. Present patterns of glacierization indicate a SW to NE rise in the height of ELAs and GTs suggesting topographic and precipitation control. An apparent reversal of trends during the past is explained by Quaternary uplift of the Pir Panjal Range.
Social evolution in class-structured populations

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.

Keywords: reproductive value
individual quality
dispersal
inclusive fitness
kin selection
social value
Advisor: Gardner, A
Brown, S
West, S
Computational electrochemistry

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.

Keywords: computational electrochemistry
chronoamperometry
migration
cyclic voltammetry
finite difference
diffusion
Advisor: Compton, RG
Biochemical studies of the cohesin complex

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.

Keywords: biology chromosome cell biochemistry
Advisor: Nasmyth, K
Information as care: reconnecting internet use, HIV and health

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.

Keywords: internet
performativity
HIV
care
health
ethics
Advisor: Brown, I
Marres, N
Examining the role of traditional health networks in the Karen self determination movement along the Thai-Burma border

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.

Keywords: Traditional Medicine
Humanitarianism
Indigenous Medicine
Ayurveda
Refugee Studies
International Development
Burma
Advisor: Chatty, D
Bodeker, G
Electronic properties of mesostructured metal oxides in dye-sensitized solar cells

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.

Keywords: hybrid solar cells
photovoltaic
Advisor: Snaith, H
Burial practice and aspects of social structure in the late Chalcolithic of north-east Bulgaria

The study considers archaeological evidence for burials and other mortuary practices from the Late Chalcolithic period in north-east Bulgaria. The Late Chalcolithic is defined (circa 4500-4000 B.C.) and around 900 burials are attributed to two cultural groups within the region in this period.
It is argued that previous studies of the evidence can be rejected for assuming a straightforward equivalence between burial forms and social structures. An alternative model of social organization is proposed based on the 'structuration' and 'habitus' models of Giddens and Bourdieu which emphasize the role of the individual in the reproduction of social institutions. This framework is used to examine the importance of (mortuary) rituals and the symbolic use of material culture in strategies intended to maintain or alter the distribution of power and resources.
The data is examined using quantitative measures of spatial and temporal variability and statistical measures of association between variables. It is argued that two basic patterns can be discerned and which correspond to the defined cultures. The inland cultural pattern is further divided into two 'types' based on the location and forms of burials.
Burial forms and grave goods are also examined qualitatively and the values attributed to artefacts, materials and the processes of burial are addressed. From this it is argued that meanings are fundamentally mediated through processes of reciprocation between kinship groups and with ancestors. Social structures based on gender and age, the settlement community and residence are proposed.
'Codes' of the use of material culture within mortuary rituals are described and evaluated through a consideration of assemblages and performance. Changes within and between cemeteries over time are used to reconstruct patterns of competition and emulation.
The interpretations of social interaction in burial practices are related to other forms of evidence from the Late Chalcolithic in north-east Bulgaria and suggestions made for a new understanding of social organization in both cultures.
The conclusions are placed in a wider spatial and temporal perspective and conclusions presented relating to both the data studied and the theoretical models adopted.