VictorJuiz/thesis huggingface dataset:
From fig leaves to skinny jeans: how clothes shape our experience of God, ourselves, and everything else

In the history of sartorial reflection, the usual offerings for human motivations to dress are: protection (i.e. from the elements), modesty, decoration, and socio-political self-expression. The literature on clothing rarely attends, however, to the question of garments' impact on wearers' self-experience. There is some social science research, for example, suggesting that when we wear clothing we associate with individuals who have a high degree of mental focus and attention to detail, it causes us—probably, in most cases, pre-reflectively—to experience ourselves as such and therefore to perform better on tests that measure these qualities. Apart from this research, exploration into the matter, regardless of field, is scant, but it is especially thin in philosophy and theology.
This thesis seeks to address the shortfall in these fields by providing at least one model of the human relationship to clothes that, unlike what is currently on offer, accounts for findings like the above. To do so, it draws on the sartorial reflection of the British artist and essayist Eric Gill, who understands clothes as architectural spaces of sorts, as encasements that house our being, and the German philosopher Martin Heidegger, whose philosophy of being and 'thinking about building' can do similar work less explicitly but more robustly.
After outlining this new way of looking at humanity's relationship to clothes, the thesis will conclude by discussing some theological implications. In particular, it discusses how the overlap between Gill's sacramental perspective and Heidegger's similar understanding of an inherently meaning-infused 'world' can yield an account of clothes as facilitators (or hinderers) of the attunement or comportment of openness and/or proximity to God through their potential to bear theological resonances.

Advisor: Pattison, G
Ward, G
Electron microscopy and multi-scale modelling of radiation damage recovery in tungsten

The thesis is concerned with understanding the recovery mechanisms of radiation damage in tungsten. Tungsten is a key material in next-generation fusion reactors such as ITER, which will be exposed to intense neutron radiation, plasma and high temperatures, and its durability will determine the reactor’s competitiveness versus other energy sources.
The thesis makes a comprehensive, quantitative study of recovery and its depen- dence on temperature, time, and material purity. It employs both experiments (ion-beam irradiation with ex and in situ analysis via transmission electron mi- croscopy) and multi-scale deterministic and stochastic modelling techniques such as molecular dynamics and dislocation dynamics.
Annealing experiments on ultra-pure tungsten reveal the presence of several re- covery stages, and an acceleration of dislocation defect recovery and loop coarsening above &Tilde;900°C. They also reveal discrepancies with dislocation climb models in the literature, suggesting the presence of additional recovery pathways leading to coars- ening, most notably conservative self-climb.
Presence of helium is found to cause an increase in the equilibrium concentration of defects at a given temperature. Also, very high doses cause morphological changes to the radiation damage structure, from relatively homogeneous defect concentra- tions of dislocations in a narrow size range, to complex dislocations networks with voids.
Finally, modelling techniques are able to successfully predict dislocation motion phenomena observed in experiments at high temperature (including quantitatively accurate defect densities), but only after extensive modification of publicly available dislocation dynamics codes to include boundary conditions and stochastic behaviour of crystal defects.

Keywords: Dislocation dynamics
Transmission electron microscopy
Multi scale materials modelling
Molecular dynamics
Langevin dynamics
Advisor: Roberts, S
Fitzgerald, S
Tarleton, E
Comprehension strategies when listening to the teacher in the ESL classroom

Listening comprehension strategies have been explored almost exclusively in uni-directional listening when learners are listening to audio recording. The lack of research on students' strategy use in understanding the teacher in the classroom is surprising, given how pervasive it is for students to listen to the teacher. In order to fill this research gap, this study explored the listening strategies adopted by learners in comprehending the teacher’s input in the English as a Second Language (ESL) classroom in Hong Kong (HK). A Likert-scale questionnaire was developed and administered to 867 HK Secondary 3 students, 646 of whom also completed two tests of linguistic knowledge (LK) – a receptive Vocabulary Levels Test (VLT) and a grammaticality judgement task (GJT). A sub-sample of 59 students then took part in an innovative computer tracking programme which simulated classroom learning and incorporated different types of teacher input while eliciting learners' strategy use targeted at these inputs. Lesson observation and stimulated recall interviews were also conducted to give insight into learners’ strategy use in an authentic lesson from a more qualitative point of view.
Findings suggested that there were some strategies which were specific to the context of listening to the teacher in the ESL classroom. Furthermore, while learners with low and high LK demonstrated some differences in their strategy use, there existed a sub-group of learners with low LK who were at least comparably strategic with learners with higher LK, providing some evidence that strategy use is not wholly dependent on levels of LK. Finally, findings also pointed to the importance of the type and difficulty of teacher input on learners’ strategy use. Implications for further research and pedagogy are discussed.

Keywords: learner strategies
Advisor: Macaro, E
Applications of probabilistic programming

This thesis describes work on two applications of probabilistic programming: the learning of probabilistic program code given specifications, in particular program code of one-dimensional samplers; and the facilitation of sequential Monte Carlo inference with help of data-driven proposals. The latter is presented with experimental results on a linear Gaussian model and a non-parametric dependent Dirichlet process mixture of objects model for object recognition and tracking.
We begin this work by providing a brief introduction to probabilistic programming.
In the second Chapter we present an approach to automatic discovery of samplers in the form of probabilistic programs. Specifically, we learn the procedure code of samplers for one-dimensional distributions. We formulate a Bayesian approach to this problem by specifying a grammar-based prior over probabilistic program code. We use an approximate Bayesian computation method to learn the programs, whose executions generate samples that statistically match observed data or analytical characteristics of distributions of interest. In our experiments we leverage different probabilistic programming systems, including Anglican and Probabilistic C, to perform Markov chain Monte Carlo sampling over the space of programs. Experimental results have demonstrated that, using the proposed methodology, we can learn approximate and even some exact samplers. Finally, we show that our results are competive with regard to genetic programming methods.
In Chapter 3, we describe a way to facilitate sequential Monte Carlo inference in probabilistic programming using data-driven proposals. In particular, we develop a distance-based proposal for the non-parametric dependant Dirichlet process mixture of objects model. We implement this approach in the probabilitic programming system Anglican, and show that for that model data-driven proposals provide significant perfomance improvements. We also explore the possibility of using neural networks to improve data-driven proposals.

Keywords: model induction
program induction
probabilistic inference
automatic programming
Markov chain Monte Carlo
generative models
data-driven proposals
automatic modelling
probabilistic programming
Advisor: Wood, F
Fabrication and characterisation of ultrafast direct laser written waveguides

A novel ultrafast direct laser writing (DLW) system using adaptive optics is proposed and demonstrated. This system has the potential to generate high-quality three-dimensional (3D) optical waveguides and components. The experimental setup and procedures for the DLW process are studied, after which various optical waveguides are fabricated in different transparent materials. The resulting waveguides are characterised by the measurement of the near-field laser coupling profiles in combination with optical microscopy techniques. Quantum random number generation (QRNG) and the potential application of the DLW technique in quantum information is also discussed.
To completely understand the fabrication procedures for the DLW system, the experimental equipment and effects of different fabrication parameters are studied and analysed. With the use of a liquid-crystal spatial light modulator (SLM) in the DLW system, dynamic control of phase modulation can be provided to correct aberrations adaptively. An SLM can also make the cross-sectional profile of the written waveguides more circular and facilitate the fabrication of more complex 3D structures. Experiments reveal that the shape of the focal spot can be improved dramatically with adaptive optics, resulting in higher-quality optical waveguides.
The refractive-index information of the written waveguides and their optical properties are measured using the propagation-mode near-field method (PMNFM). Simulation results and experimental measurements of a commercial single-mode fiber and a waveguide sample are demonstrated and compared. Quantitative phase measurement is also applied via the transport of intensity equation (TIE) to monitor the refractive-index change during fabrication. The propagation losses of the waveguides are measured and discussed.
Different optical waveguides are fabricated using DLW in fused silica, potassium dihydrogen phosphate (KDP), and lithium niobate (LiNbO3) crystals. Different materials have different characteristics and properties, requiring different fabrication parameters and resulting in waveguides exhibiting different properties. Waveguides at various depths are demonstrated both with and without effects of adaptive optics. Experimental results indicate great improvements in the quality of the written waveguides after aberration correction. With an understanding of the optical properties of the straight waveguides using the characterisation methods, modelling and fabrication of bend waveguides and y-splitters are presented and studied.
A high-speed QRNG system is also demonstrated in this thesis, with potential implementation using the DLW technique for a more compact and stable system. Finally, the possibility of the DLW fabrication of complex 3D optical components and their applications are discussed for future work.

Advisor: Payne, F
The reception and transformation of homeopathy in Japan

This thesis examines from a medical anthropological viewpoint how the practice of the newly imported complementary and alternative medicine (CAM) has been transplanted, received and transformed in Japan. More specifically, I focus on homeopathy, which was introduced into Japan in the late 1990s.
To address the research question, I focus on the practice of homeopathy from the anthropological viewpoint. The adoption of any new form of medicine is influenced by the prevailing medical, social and cultural context. So, how and why was homeopathy introduced into Japan the late 1990s? I explore this question by focusing on three aspects of the reception of homeopathy in Japan: (1) the institutionalisation of the homeopathy, including the formation of associations of practitioners and homeopathic colleges; (2) the translation of the theory and practice of homeopathy by the practitioners into a culturally acceptable form; (3) the utilisation and consumption of homeopathy by the patients, their families and self-prescribers. Over eighteen months of fieldwork in Japan led me to focus on these three elements of homeopathic practice.
Regarding the theoretical framework, this mainly explores medical pluralism and the health care system in Japan from an anthropological perspective, and the globalisation and transmission of medicine.
I argue that the success of homeopathy in Japan was largely thanks to the transmission strategies set by the founders of the colleges for lay homeopaths. Mothers in particular, concerned by worries over family health care, were drawn by this approach. Furthermore I also argue that this group not only became consistent users of homeopathy but also propagated the therapy through mothers’ self-help groups, creating thereby a strong tie with the lay homeopaths. I argue that mothers gained a sense of the empowerment through homeopathy. Within the Japanese health care system it was the popular sector that received and developed homeopathy.

Keywords: homeopathy
illness narratives
Japan
complementary medicine
medical pluralism
Advisor: Hsu, E
Takehiko, K
Effect of multiple-antibiotic treatments on the evolution of antibiotic resistance in Pseudomonas aeruginosa

To combat the ever-growing clinical burden imposed by antibiotic-resistant pathogens, multiple-antibiotic treatments are increasingly being considered as promising treatment options. The impact of multiple-antibiotic treatments on the evolution of resistance is not well understood however, and debate is ongoing about the effectiveness of various multiple-antibiotic treatments. In this thesis, I investigate how aspects of multiple-antibiotic treatments impact the rate of evolution of antibiotic resistance in the opportunistic human pathogen Pseudomonas aeruginosa. In particular, I look at the impact of interactions between antibiotics in combination on the evolution of resistance, and how creating heterogeneity in the antibiotic environment by rotating the antibiotics used may change the rate of evolution of resistance.
I characterise the interactions present in 120 combinations of antibiotics and find that the type of interaction can be predicted by the mechanism of action of the antibiotics involved. I investigate the effect of a subset of these combinations on the evolution of antibiotic resistance. My results refute the influential but poorly-evidenced hypothesis that synergistic combinations accelerate the evolution of resistance, even when synergistic combinations have the same inhibitory effect on sensitive bacteria as additive or antagonistic antibiotic combinations. I focus on a combination of the antibiotics ceftriaxone and sulfamethoxazole and test whether it is more effective in preventing the evolution of resistance than predicted by the inhibitory effect of the combination on sensitive bacteria. I do not find the combination to be more effective than predicted.
Finally, I create heterogeneous antibiotic environments by rotating the antibiotic present at different rates. For the first time in a laboratory setting, I test how varying the rate of fluctuation in the antibiotics present in a heterogeneous antibiotic environment impacts the rate of evolution of resistance. Unexpectedly, I find the rate of evolution of resistance increases with increasing levels of antibiotic heterogeneity.

Keywords: drug resistance
evolution
multiple antibiotic resistance
multi-drug resistance
antibiotic resistance
Pseudomonas aeruginosa
environmental heterogeneity
drug interactions
Advisor: Maclean, C
Maiden, M
McLean, A
Optical sub-pixel matching and active tectonics

In this thesis I use sub-pixel optical matching, Interferometric Synthetic Aperture Radar (InSAR), and Light Detection and Ranging (lidar) spatial geodetic observations to produce reliable 3D displacement fields caused by co-seismic events and reliable earthquake source models with slip distribution on fault planes.
I produce horizontal displacement maps for the 2005 Dabbahu segment, Afar using SPOT4 satellite images. By combining InSAR descending data and range offsets with optical sub-pixel I produced a vertical displacement map of the event. I attempted to perform the inversion of the dataset obtained by sub-pixel matching but I found that datasets are not well suited for the typical numerical inversion, and I fit data with direct dislocation modelling instead.
I identify biases and errors that arise from optical sub-pixel matching of satellite images using many horizontal datasets constructed using SPOT5 images for the El Mayor-Cucapah earthquake. I develop algorithms for removal of some of these biases from horizontal displacement maps. Using sub-pixel matching I asses the quality of several DEMs available to me for study of the El Mayor-Cucapah earthquake.
I developed a novel technique for producing vertical displacement maps caused by an earthquake by combining archived pre-event satellite images with post event acquired lidar. I use this technique to produce a vertical displacement map of the El Mayor-Cucapah earthquake.
I produce a source model of the El Mayor-Cucapah earthquake by inverting InSAR datasets using the method. After attempts to do joint inversion of InSAR and optical sub-pixel matching I developed the code to use Bayesian inversion instead, because its advantages when it comes to joint modelling of datasets. I sucessfully invert four InSAR datasets on seven fault planes using the Bayesian approach. I found that the results of the Bayesian inversion are very similar to the results of the optimization inversion.

Advisor: Parsons, B
Dowman, I
The Dirac-Higgs bundle

The Dirac–Higgs bundle is a vector bundle with a natural connection on the moduli space of stable Higgs bundles on a compact Riemann surface. It is a vector bundle of null-spaces of a Dirac-operator coupled to stable Higgs bundles. In this thesis, we study various aspects of this bundle and its natural connection.
The Dirac–Higgs bundle is hyperholomorphic on the smooth hyperkähler moduli space of stable Higgs bundles. This property is a generalisation of the four-dimensional anti- self-duality equations to hyperkähler manifolds. One use of the Dirac–Higgs bundle is the construction of a Nahm transform for Higgs bundles. This transform produces hyperholo- morphic bundles on the moduli space of rank one Higgs bundles.
The Higgs bundle moduli space is non-compact and we study the asymptotics of the connection in the Nahm transform of a Higgs bundle. We show that elements of the null- spaces concentrate at a finite number of points on the Riemann surface. This asymptotical behaviour naturally defines a frame for the Nahm transform, which is conjectured to be asymptotically unitary.
By considering only the holomorphic structure, the Nahm transform of a Higgs bundle extends to a holomorphic bundle on the natural compactification of the rank one Higgs bundle moduli space. We discuss various aspects of this extended holomorphic bundle. Most importantly, it is a sheaf extension in which the constituent sheaves and the extension class have natural interpretations in terms of the original Higgs bundle. Furthermore, the extended bundle is not fixed at the divisor at infinity; explicit examples show that it depends on the type of Riemann surface, for example.
The Dirac–Higgs bundle has a parabolic cousin. In the parabolic case the rank depends on the number of marked points and the total multiplicity of the zero weights in the parabolic structure. The moduli space of stable rank two parabolic Higgs bundles on the Riemann sphere with four marked points has complex dimension two. Furthermore, there is a combination of parabolic weights such that the Dirac–Higgs bundle is a line bundle with an instanton connection. We study the topology of this line bundle and find that the instanton does not have finite energy. As in the non-parabolic case we define a Nahm transform for parabolic Higgs bundles, and in the case of genus one Riemann surfaces use it to produce doubly-periodic instantons of finite energy.

Keywords: Dirac operators
instantons
Fourier-Mukai transform
self-duality equations
Nahm transform
Higgs bundles
Advisor: Hitchin, N
Galois groups and anabelian reconstruction

In this thesis we investigate the problem of recovering arithmetic structure on a field F from small quotients of its absolute Galois group. In particular, we are interested in recovering the p-adic valuation on a p-adic field from such quotients. After establishing several such results, we apply this to obtain strong versions of the Birational Section Conjecture for curves over p-adic fields. We also discuss the model-theoretic interpretation of these results, as well as begin investigating the foundations of a model-theory of schemes.

Keywords: Galois Theory
p-adic arithmetic
Anabelian Geometry
Valued Fields
Advisor: Koenigsmann, J
Non-reductive geometric invariant theory and compactifications of enveloped quotients

In this thesis we develop a framework for constructing quotients of varieties by actions of linear algebraic groups which is similar in spirit to that of Mumford's geometric invariant theory. This is done by extending the work of Doran and Kirwan in the unipotent setting to deal with more general non-reductive groups.
Given a linear algebraic group acting on an irreducible variety with a linearisation, an open subset of stable points is identified that admits a geometric quotient in the category of varieties. This lies within the enveloped quotient, which is a dense constructible subset of a scheme that is locally of finite type, called the enveloping quotient. Ways to compactify the enveloped quotient---and the quotient of the stable locus therein---are considered. In particular, the theory of reductive envelopes from Doran and Kirwan's work is extended to the more general non-reductive setting to give ways of constructing compactifications of the enveloped quotient by using the techniques of Mumford's geometric invariant theory for reductive groups.
We then look at two ways in which this non-reductive geometric invariant theory can be used in practice. Firstly, we consider a procedure for constructing quotients inductively, using the extra data of a choice of appropriate subnormal series of a group. Related to this is a method for constructing an approximation of the stable set. Secondly, we study the actions of certain extensions of unipotent groups by multiplicative groups on projective varieties with very ample linearisation. Here we identify an open subset of points that admits a geometric quotient by the action of the extended group and which is explicitly computable via Hilbert-Mumford-like criteria.

Keywords: Geometric Invariant Theory
non-reductive groups
Advisor: Kirwan, F