VictorJuiz/thesis huggingface dataset:
Multicomponent fractional quantum Hall effects

This thesis scrutinizes the condensed matter physics phenomenon known as the fractional quantum Hall effect (FQHE), in particular fractional quantum Hall effects occurring in multicomponent systems. Broadly speaking, the FQHE can be defined as a many-electron quantum phenomenon, driven by strong interactions, that occurs in two-dimensional electron gasses in the presence of a perpendicular external magnetic field (and it is also predicted to occur for any two-dimensional particles, such as confined cold atoms, in an external gauge field). Multicomponent systems are systems where the constituent particles (such as electrons or cold atoms) possess internal degrees of freedom, for instance a spin or valley index. These internal degrees of freedom are often overlooked when modeling the FQHE.
Taking into account the multicomponent degree of freedom yields an abundance of possibilities for the intellection of new types of so-called “topological phases of matter”, which are ubiquitously associated with the FQHE. In this thesis several different cases are considered. The first topic discussed herein is a study of phase transitions that can take place between FQHE phases with different net values of their multicomponent degrees of freedom. Examples are phase transitions between phases of different uniform net spin polarization, tunable as a function of certain system parameters. Some significant technical refinements are made to a previous model and comparisons are made with a variety of different experiments. The results are relevant for multicomponent FQHEs occurring in GaAs,AlAs and SiGe semiconductor systems where the electronic structure is confined to two dimensions, as well as in two-dimensional materials such as graphene.
The second topic discussed herein is the introduction of the multiparticle multicomponent pseudopotential formalism. This methodology is oriented towards considerably expanding an existing framework for the construction of exactly solvable FQHE models by parameterizing multicomponent interactions. The final topic is the first example application of this new formalism to the construction of an exactly solvable FQHE model.

Keywords: Fractional quantum Hall effect
Advisor: Simon, S
Qadizadeli Revivalism reconsidered in light of Ahmad al-Rumi al-Aqhisari's Majalis al-abrar

Shaykh Aḥmad al-R­ūmī al-Āqḥiṣārī (d. 1041/1632), Ḥanafi jurist, theologian and Sufi, is largely an unknown figure to scholars of Ottoman religious history. Progress towards disclosing key aspects of al-Āqḥiṣārī’s thought has been made in recent times thanks to the important contributions of Y. Michot, who has, in particular, demonstrated the association of al-Āqḥiṣārī with the Ottoman puritanical movement, the Qaḍīzādelis. Building upon Michot’s work, this study delves further into the works of al-Āqḥiṣārī especially his seminal contribution, the Majālis al-abrār. The study sets out its main themes and the authorities on which it is based; it then moves to show the degree of overlap between al-Āqḥiṣārī’s understandings and Naqshbandī Sufism, as well as the extent to which his thought converges with that of better-known Ottoman puritans such as Birgivī Efendī (d. 981/1573) and Qaḍīzāde (d. 1044/1635). It is suggested that the impact of the Majālis al-abrār on the Qāḍīzādelis had the outcome in the second half of the seventeenth century of increasing the violence of their activists, a development which ultimately led to their downfall.
A key aspect of this study is the re-examination of the view that the Qāḍīzādelis were a proto-Wahhābī or proto-Salafī movement, which is typical in the existing literature. Whilst demonstrating the influence of Ibn Qayyim al-Jawziyya (d. 751/1350) and his teacher, Aḥmad b. Taymiyya (d. 728/1328), upon al-Āqḥiṣārī’s thought, the limits of this influence are clearly demonstrated by bringing to light al-Āqḥiṣārī’s distinct doctrinal and legal positions, which were very much embedded within the Ottoman Islam of his times. Ultimately, by studying the relationship between al-Āqḥiṣārī’s masterpiece, the Majālis al-abrār and Qāḍīzādeli and Naqshbandī beliefs, the study aims to place the movement in its own Ottoman, Ḥanafī, and Sufi milieu, thereby challenging the dominant approach which reads the movement through modern paradigms.

Keywords: Turkey
Ahmad al-Rumi al-Aqhisari
Ottoman Islam
history
Qadizadelis
Advisor: Al-Akiti, M
Development of models and methods to assess the efficacy of anti-cancer drugs targeted to the mitochondria

Background: Malignant transformation of cells is typically characterised by aerobic glycolysis, resulting in supressed mitochondrial function, a state that helps resistance to apoptosis. This characteristic has been widely accepted as a hallmark of cancer and has been shown to be of critical importance in tumour development. The bioenergetic differences between normal and malignant cells are being exploited to identify potential cancer specific therapeutics. Improved in-vitro models are required to aid the identification and assessment of candidate drugs. In this project, we investigated the bioenergetic phenotypes of a panel of adult and paediatric cancer cell lines and evaluated the potential of 3D models as a platform for testing drugs that target cancer metabolism. We also investigated a novel method to assess mitochondrial function that enables the quantification of the level of oxygenation within the cell.
Results: The results presented in this thesis show that not all cancers display this aerobic glycolytic phenotype. We found that while some cell lines displayed the Warburg phenotype others displayed high levels of oxidative metabolism. These bioenergetic profiles need to be considered when deciding which anti-cancer drugs to use in a chemotherapeutic regime. If a bioenergetic pattern can be identified it may one day form the basis of a screening strategy for tumours. Dichloroacetate (DCA) is a small molecule PDK inhibitor that was investigated in this study. It was found to be relatively non-toxic to cells cultured in 2D but had improved toxicity when the cells were cultured in a 3D environment. Lastly, we evaluated a new oxygen sensing nanoprobe, Mito-Xpress Intra, and the results demonstrate its potential as a non-invasive means of measuring oxygen concentrations within the cell in real time as well as highlighting some striking differences between applied ambient and measured intracellular oxygen concentrations.
Conclusion: The findings suggest that not all cancers display the characteristic glycolytic phenotype. They also highlight the importance of controlling oxygen and glucose levels when evaluating metabolism and when drug testing.

Keywords: oxidative phosphorylation
glucose
cancer metabolism
Warburg effect
Advisor: Morten, K
An integrative approach to understanding the fitness cost of rifampicin resistance in Pseudomonas aeruginosa

Antibiotic resistance in bacteria is acquired through spontaneous chromosomal mutations or horizontal gene transfer. In the absence of antibiotics, resistant mutants generally show reduced fitness due to compromised growth rate, competitive ability and virulence compared to their antibiotic-sensitive ancestors. The focus of my research is to dissect the molecular underpinnings of the variations in the fitness cost of chromosomal antibiotic resistance using a systems-level approach. From an evolutionary perspective, my research aims are to understand how the fitness cost influences adaptation in resistant populations in an antibiotic-free environment. Using rifampicin resistance in Pseudomonas aeruginosa as a model, my work shows that most of the variation in the fitness cost of rifampicin resistance can be attributed to the direct effect of rifampicin resistance mutations on transcriptional efficiency. Through RNA-Seq transcriptome profiling, I demonstrate that global changes in gene expression levels associated with resistance mutations are surprisingly subtle, suggesting that the transcriptional regulatory network of P. aeruginosa is robust against compromised transcriptional efficiency. Using experimental evolution and whole-genome sequencing, my work reveals a systematic difference in the genetic basis of adaptation in mutants that were propagated in the absence of antibiotics. During compensatory adaptation, resistant mutants can recover the fitness cost of resistance by fixing second-site mutations that directly offset the deleterious effects of resistance mutations. Amongst resistant mutant populations with low fitness costs, general adaptation limits compensatory adaptation, which is most likely to be due to the rarity of compensatory mutations and clonal interference. Far from being the most ubiquitous mechanism in the evolution of resistance, compensatory adaptation is the exception that is more likely to be observed in resistant mutants with high fitness costs. In addition, I applied key elements of the integrative experimental approach developed in this work to dissect the molecular basis of the fitness cost associated with carriage of the pNUK73 small plasmid in P. aeruginosa, which carries the rep gene encoding a plasmid replication protein. My results confirmed that rep expression generates a significant fitness cost in P. aeruginosa and demonstrate how the molecular origins of the fitness cost of resistance can be dissected in a different biological context.

Keywords: experimental evolution
rifampicin resistance
pleiotropy
systems biology
fitness cost of antibiotic resistance mutations
transcriptome profiling
compensatory mutations
Advisor: MacLean, R
Preston, G
The political ecology of human-elephant relationships in India: encounters, spaces, politics

This thesis presents an examination of the political ecology of human-elephant relationships in India. Its overall aim is to revitalize the ecology that has been sifted out from the discipline. The thesis draws upon, and consequently develops, more-than-human geography through a sustained engagement of nature-society relations in a non-Western context.
The thesis has three broad objectives. First, to examine what more-than-human geography’s emphasis on non-dualistic forms of agency, could contribute to understandings of policy, planning and politics in conservation. Second, to examine the spatial dimensions of human-elephant relations and the social orderings of space which influence these relationships. The third objective of the thesis is to interrogate the politics of elephant conservation through a sustained engagement with diverse modes of human-elephant encounters and the socio-political assemblages with which they are entangled.
The thesis first deploys and develops the concept of ‘encounter value’ to account for the different forms of human-elephant encounters and how they contribute to the political economies of biodiversity conservation. The thesis then draws from a multi-sited ethnography examining both encounters and spaces of elephant conservation. It shows how elephants help forge connections across difference and the ways their geographies are reconfigured by global networks of conservation. The third empirical section has an implicit spatial dimension. It is concerned with writing a ‘more-than-human’ geography of landscapes, examining how humans and elephants cohabit with and against the grain of political design. Finally, the thesis examines politics as an ecology of relations, showing how human-elephant relations as well as social and political outcomes may be mediated by materials.
Modes of enquiry between these papers overlap. They offer critical insights into three themes that interface between political ecology and more-than-human geography. First, the thesis contributes to conceptualizing modes of human-animal encounters in a symmetrical fashion. It explicates the role of nonhuman agency as an organizing force in political economies of conservation. Second, it posits new understandings of the spaces of animals. This is developed in two ways: landscapes as dwelt, political achievements and as fluid spaces emerging through international networks of environmental governance. Third, the thesis ecologizes politics and goes beyond the humanist frameworks of political ecology. It fosters novel conversations between more-than-human geography and the postcolonial critique of political ecology in the context of human-elephant relationships. Taken together, the thesis offers up a concerted, symmetrical and novel approach to the study people’s relations with animals.

Keywords: India
Asian elephant
human geography
political ecology
biodiversity
posthumanism
postcolonialism
Advisor: Jepson, P
Illness and mental illness

The arguments in the literature for and against "mental illness", are shown to founder on the lack of a thorough analysis of the sense of "illness" itself. Such an analysis is developed in the present study in three main stages. STAGE ONE: The ordinary use of "dysfunction" is examined. The term is shown to imply a particular kind of value judgement, derived, in respect of objects, from the purposes of living things for them. STAGE TWO: The sense of "illness" is interpreted from examples of physical illness by comparing and contrasting it with "dysfunction". An important logical link with "action" is identified, which provides an interpretation of the particular kind of negative evaluation implied by "illness". The relationship between "illness" and "disease" is examined in terms of this negative evaluation. STAGE THREE: The results of stage two are generalised from "physical illness" to "mental illness" by way of the notion of "action". "Mental illness" is examined as illustrated by examples of four main kinds of condition - organic psychosis, neurosis, addiction and functional psychosis. In respect of the first of these, "mental illness" is shown to be similar in its logical properties to "physical illness"; in respect of the remaining three, it is shown to be different, but in three quite distinct ways. In each case, however, the properties of "mental illness" are derived consistently with the interpretation of "illness" developed from examples of physical illness in stage two. "Mental illness" and "physical illness" are thus shown to be logically equivalent. In a concluding section, the implications of this result for the debate about "mental illness" are examined.
Simplified fixed pattern noise correction and image display for high dynamic range CMOS logarithmic imagers

Biologically inspired logarithmic CMOS sensors offer high dynamic range imaging capabilities without the difficulties faced by linear imagers. By compressing dynamic range while encoding contrast information, they mimic the human visual system’s response to photo stimuli in fewer bits than those used in linear sensors. Despite this prospect, logarithmic sensors suffer poor image quality due to illumination dependent fixed pattern noise (FPN), making individual pixels appear up to 100 times brighter or darker. This thesis is primarily concerned with alleviating FPN in logarithmic imagers in a simple and convenient way while undertaking a system approach to its origin, distribution and effect on the quality of monochrome and colour images, after FPN correction. Using the properties of the Human visual system, I propose to characterise the errors arising from FPN in a perceptually significant manner by proposing an error measure, never used before. Logarithmic operation over a wide dynamic range is first characterised using a new model; yi j =aj +bj ln(exp sqrt(cj +djxi)−1), where yi j is the response of the sensor to a light stimulus xi and aj, bj, cj and dj are pixel dependent parameters. Using a proposed correction procedure, pixel data from a monochromatic sensor array is FPN corrected to approximately 4% error over 5 decades of illumination even after digitisation - accuracy equivalent to four times the human eyes ability to just notice an illumination difference against a uniform background. By evaluating how error affects colour, the possibility of indiscernible residual colour error after FPN correction, is analytically explored using a standard set of munsell colours. After simulating the simple FPN correction procedure, colour quality is analysed using a Delta E76 perceptual metric, to check for perceptual discrepancies in image colour. It is shown that, after quantisation, the FPN correction process yields 1−2 Delta E76 error units over approximately 5 decades of illumination; colour quality being imperceptibly uniform in this range. Finally, tone-mapping techniques, required to compress high dynamic range images onto the low range of standard screens, have a predominantly logarithmic operation during brightness compression. A new Logr'Gb' colour representation is presented in this thesis, significantly reducing computational complexity, while encoding contrast information. Using a well-known tone mapping technique, images represented in this new format are shown to maintain colour accuracy when the green colour channel is compressed to the standard display range, instead of the traditional luminance channel. The trade off between colour accuracy and computation in this tone mapping approach is also demonstrated, offering a low cost alternative for applications with low display specifications.

Keywords: fixed pattern noise
high dynamic range
image sensors
CIELAB
tone mapping
colour quality
imaging
CMOS sensors
FPN modelling
colour error
logarithmic sensors
contrast sensitivity
EKV
Advisor: Collins, S
Identifying Romanness

This thesis deals with the role of the concept of virtus in Roman historiography of the late Republic and early Empire. I shall argue throughout the study that analysing and tracing this concept in the works of the historians of this period take us to the very heart of the question of their appraisal both of political change and Roman identity. Understanding this moral appraisal does not mean just a better comprehension of their concept of virtus, but a new approach to their concept of history as magistra vitae.
In the first chapter, I shall introduce some characteristics of the nature of historical writing and the approaches of ancient and modern historians. I shall be challenging some currents views on the complexity of evaluating ancient history by rhetorical and moral standards.
In chapter II, I shall consider the concept of virtus in terms of its etymology and usage; I will then attempt to show the particular connection between virtus and Romanness. I will also develop and explain the concepts of virilis-virtus and humana-virtus and place them in their philosophical context.
Chapters III, IV, V and VI will form part of what I have called 'Virtus in History', and in these chapters I shall deal with four historians. The first section is dedicated to Sallust and his analysis of political decline in relation to virtus. I shall attempt to assess Sallust's influential creation of moral language in the writing of history. Then, I will consider the connection of virtus as a means to preserve libertas in Livy's work, especially considering the author's time. Chapter V is concerned with Velleius' history and his view that the principate has re-established virtus in Rome. I shall concentrate on Tiberius for my analysis of virtus and challenge some traditional approaches to this author and his prince. Finally, in chapter VI, I will examine Tacitus' perception of the nature of the political change that Rome has undergone. I will show how the transformations in politics have a deep influence on the very idea of Romanness and how the disturbance of this concept leads to a more profound and internal interpretation of it.

Advisor: Clarke, K
Microcompartmentation of aldolase in Arabidopsis

Understanding the internal organization of cells from the molecular up to organelle level is a current challenge for biology if we are to better comprehend the mechanisms by which cellular processes occur. A prevailing view of the cell interior is that biochemical reactions and molecular movements are dominated by random diffusion. However, in addition to being compartmented into organelles, cells may well be organized at a finer level. Proteins may localise to specific areas within sub-cellular compartments, by associating with each other, the cytoskeleton and organelle membranes. Thus giving rise to distinct microcompartments. Considerable in vitro evidence exists for such interactions between enzymes and larger cellular components. This strengthens the idea that cells may be microcompartmented. However, little in vivo evidence supports this hypothesis, especially in plants. As a test-case for the concept of microcompartmentation this project investigated the sub-cellular distribution of the glycolytic enzyme fructose-bisphosphate aldolase in Arabidopsis thaliana; the ultimate aim being to establish whether it is microcompartmented in vivo and, further, to test the potential function(s) of such microcompartmentation.

Keywords: intracellular organisation
aldolase
microcompartmentation
enzyme moonlighting
actin
metabolons
Advisor: Sweetlove, L
Moore, I
Developing a risk map of malaria transmission for East Africa

Background: The distribution of malaria in sub-Saharan Africa is determined largely by climatic influences on the development and survival of P. falciparum and its Anopheline vectors. This inter-relationship has been exploited in developing a limited number of predictive maps of malaria's distribution but these climate maps have limitations. Climate alone does not fully describe the complex dynamics of transmission and, in particular, human influences such as urbanization and the use of widespread anti-malarial interventions. The improved accuracy and validation of solely climatedriven maps relies on the availability of robust malariometric training data. To date, such data have been scarce. This study redresses several deficiencies of existing malaria maps for Africa through the collation of an extensive database of empirical P. falciparum prevalence data, the investigation of the relationship between prevalence and a widely-used climate-driven map, an assessment of the influence of urbanization on prevalence and finally, through the use of empirical training data to develop an improved malaria map for Kenya, Tanzania and Uganda.
Methods: An extensive published and grey-literature search was conducted between 1996 and 2004 and identified 2003 P. falciparum prevalence surveys conducted among childhood populations across East Africa between 1927 and 2003. Stringent criteria were applied to select the best sample data; only randomly sampled community-based surveys, surveys with samples >=50 children, surveys conducted between 1980-2004 and children aged 0-14 years, and surveys which were spatially and temporally unique. The selected data were used to investigate the association between P. falciparum prevalence and a fuzzy logic climatic suitability (PCS) map of malaria transmission, the effect of urbanization on prevalence and to train Fourier-processed multi-temporal climate surrogate data derived from meteorological satellites in order to predict prevalence for un-sampled areas. Using discriminant analysis, the top ten climatic predictor variables that distinguished best between 4 categories of malaria prevalence (0-<5, 5-<25%, 25-<75% and >=75%) were selected and these used to develop a predictive transmission map.
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Advisor: Snow, R
Hay, S
Rogers, D