VictorJuiz/thesis huggingface dataset:
Aspects of beyond the Standard Model string phenomenology

String theory is currently the best-known candidate for a theory of quantum gravity, having the necessary ingredients to describe all known elementary particles and interactions. It also includes several novel features, arising, for instance, from the additional six compact dimensions required for its internal consistency, making it the natural arena to construct extensions of the Standard Model. In this thesis, we analyze some of the new phenomenological aspects introduced by string theory within the framework of low energy effective theories, focusing on their applications to cosmology, astrophysics and collider experiments. We first consider a particular realization of the brane-world scenario in branonium bound states, showing that the orbital motion of a probe antibrane about a central brane stack leads to a resonant amplification of its world-volume scalar modes. We analyze the cosmological development of this process and also its potential relevance for either dark or baryonic matter generation in the early universe. We then focus on the spectrum of quark and lepton string excitations in warped compactifications, modeled by an effective 5-dimensional Randall- Sundrum throat. Motivated by the observed fermion mass hierarchy, we show that the spin-3/2 Regge excitation of the right-handed top quark is the lightest of such resonances in a significant region of parameter space, possibly lying below the TeV scale, and discuss its potential signatures at the Tevatron and at the LHC. Finally, we study the emission of sub-eV scalar particles by maximally rotating Kerr black holes, motivated by the recent string axiverse proposal. We focus on the spectrum of unstable scalar bound states in the superradiant regime, leading to an exponentially large axion cloud around astrophysical black holes, and analyze two semi-analytical methods for computing the growth rate of this instability, comparing the obtained results with previous analytical and numerical analyses.

Keywords: branonium
black hole superradiance
string excitations
string phenomenology
Advisor: March-Russell, J
A study of the cone-pressuremeter test in sand

The cone-pressuremeter is a new site investigation device which incorporates a pressuremeter behind a standard cone penetrometer tip. This dissertation is concerned with an understanding of the new device, and in particular the establishment of a detailed procedure to allow the test to be used to determine the engineering properties of cohesionless soils. A series of 34 calibration tests was performed, in which three cone-pressuremeter prototypes with cross-sectional areas corresponding to 15cm², 10cm² and 5cm² were used. The tests were carried out on cylindrical samples, enclosed in a chamber 1.0 m in diameter and 1.5 m in height. Stress controlled boundaries allowed independent control of vertical and horizontal stress in the range of 50 kPa to 300 kPa. A raining deposition technique was used to produce three sand densities, corresponding to loose, medium and dense samples. A programme of calibration was designed to provide an examination of the influence of relative density, stress level and stress ratio on cone-pressuremeter test data. Soil properties were related to the values of the limit pressure obtained from the pressuremeter test and the cone resistance values from the cone test. Empirical relationships were proposed for deriving density, friction angle and horizontal stress. Cone-pressuremeter tests were used for assessing directly the shear stiffness of the soil. A series of calibrations was needed to obtain the best possible estimation of the unload-reload shear modulus. Interpretation of the measured modulus was made by examining appropriate methods of calculating the modulus from unload-reload loops. Strain arm measurements and volume change measurements were compared. A method has been presented that allows the shear modulus values to be correlated to the relevant stress level acting around the pressuremeter during the test. The values of shear modulus obtained with the cone- pressuremeter were compatible with those obtained from the self-boring pressuremeter. An assessment of chamber size effects yielded useful information regarding the applicability of test correlations derived from calibration chambers to field problems. An additional study identified experimentally the influence of length to diameter ratio on the pressuremeter pressure-expansion curve.

Keywords: cone pressuremeter
sand
Advisor: Houlsby, G
High frequency dynamics of order flow

In this paper, we focus on the high frequency dynamics of limit order flow and market order flow. We compared the fitting performance of different models for the inter-arrival time of the order flow, including exponential distribution, gamma distribution and power law. We then studied the dependence of the placement of these two order flows, which can be captured by the self-excitation effect and mutual-excitation effect of Hawkes process. We also introduced a new model which combines the Hawkes features with the gamma distribution. Key words: High frequency dynamics; order flow; market microstructure; maximum likelihood estimation; Hawkes process; Hawkes-Gamma distribution.
Consequence-based reasoning for ontology classification

Description logics (DLs) are knowledge representation languages that provide the theoretical underpinning for modern ontology languages such as OWL and serve as the basis for the development of ontology reasoners and tools.
Most modern ontology reasoners are based on optimized tableau algorithms, which perform reasoning by trying to build counter-models. More recently, another kind of reasoning algorithms has been introduced that, instead of building counter-models, directly derive logical consequences of axioms in the ontology using inference rules. Such consequence-based algorithms were first introduced for the EL family of DLs, and later extended to more expressive Horn DLs. However, up until now, consequence-based algorithms could not handle non-Horn features such as disjunctions.
We consider several complementary aspects of consequence-based reasoning in this thesis. Firstly, we describe the parallelized consequence-based reasoner ELK, which is currently the fastest reasoner for EL ontologies. Secondly, we demonstrate how consequence-based algorithms can be extended to handle disjunctions using inference rules reminiscent of ordered resolution. Finally, we combine our consequence-based framework with methods based on tree decompositions, and thus obtain what we believe are the first fixed-parameter tractability results for subsumption reasoning in DLs.

Keywords: description logics
classification
algorithms and optimization
Advisor: Horrocks, I
Kazakov, Y
A model-independent theory of computational complexity: from patience to precision and beyond

The field of computational complexity theory--which chiefly aims to quantify the difficulty encountered when performing calculations--is, in the case of conventional computers, correctly practised and well understood (some important and fundamental open questions notwithstanding); however, such understanding is, we argue, lacking when unconventional paradigms are considered. As an illustration, we present here an analogue computer that performs the task of natural-number factorization using only polynomial time and space; the system's true, exponential complexity, which arises from requirements concerning precision, is overlooked by a traditional, `time-and-space' approach to complexity theory. Hence, we formulate the thesis that unconventional computers warrant unconventional complexity analysis; the crucial omission from traditional analysis, we suggest, is consideration of relevant resources, these being not only time and space, but also precision, energy, etc.
In the presence of this multitude of resources, however, the task of comparing computers' efficiency (formerly a case merely of comparing time complexity) becomes difficult. We resolve this by introducing a notion of overall complexity, though this transpires to be incompatible with an unrestricted formulation of resource; accordingly, we define normality of resource, and stipulate that considered resources be normal, so as to rectify certain undesirable complexity behaviour. Our concept of overall complexity induces corresponding complexity classes, and we prove theorems concerning, for example, the inclusions therebetween.
Our notions of resource, overall complexity, normality, etc. form a model-independent framework of computational complexity theory, which allows: insightful complexity analysis of unconventional computers; comparison of large, model-heterogeneous sets of computers, and correspondingly improved bounds upon the complexity of problems; assessment of novel, unconventional systems against existing, Turing-machine benchmarks; increased confidence in the difficulty of problems; etc. We apply notions of the framework to existing disputes in the literature, and consider in the context of the framework various fundamental questions concerning the nature of computation.

Keywords: theoretical computer science
computational complexity
unconventional computing
Advisor: Coecke, B
Ouaknine, J
Studies on HIF hydroxylases

Hypoxia-inducible factor (HIF) is the master regulator of genes involved in adaptation to hypoxia. The stability and transcriptional activity of HIF are regulated by post-translational hydroxylations: prolyl hydroxylation by the prolyl hydroxylase domain-containing enzymes PHD1 – 3 earmarks HIF for proteasomal degradation, whilst asparaginyl hydroxylation by factor inhibiting HIF (FIH) blocks the interaction of HIF with the transcriptional coactivators p300/CBP. The PHDs and FIH hydroxylate HIF directly from molecular oxygen and are therefore oxygen sensors.
Recent literature shows that FIH also hydroxylates a number of proteins containing an ankyrin-repeat domain (ARD). Together with reports suggesting that the PHDs are involved in HIF-independent pathways, this suggests that the HIF hydroxylases may have a wide range of non-HIF targets. This thesis describes my investigations into novel substrates of the HIF hydroxylases.
This work has characterized the FIH-dependent hydroxylation of the ARD-containing protein Notch1, and defined a consensus sequence for hydroxylation that corresponds to the ankyrin-repeat consensus. Using this consensus potential sites of hydroxylation in a novel ARD FIH substrate, myosin phosphatase targeting subunit 1 (MYPT1), were identified then subsequently confirmed and characterized.
Notch1 competes with HIF for FIH hydroxylation. My experiments show that this occurs because Notch1 is a more efficient substrate than HIF, whilst studies on MYPT1 and other proteins indicate that competitive inhibition of FIH may be a general property of ARDs.
There are more than 300 ARD proteins in the human genome, and this thesis demonstrates that FIH may hydroxylate a significant percentage of these. In addition to the analysis of ARD hydroxylation a proteomic investigation into novel PHD3 substrates has identified two candidate proteins, suggesting that the PHDs may also have multiple targets. These results have important implications for oxygen sensing, and indicate that post-translational hydroxylation is likely to be a widespread modification in cell biology.

Keywords: Oxygen sensing
Factor Inhibiting HIF
MYPT1
2OG-dependent dioxygenases
Prolyl Hydroxylase Domain-containing 3
FIH
Hypoxia
Myosin phosphatase
HIF
Ankyrin repeat proteins
Proteomics
Mass spectrometry
Notch
PHD3
Hydroxylation
Advisor: Pugh, C
Foragers on the frontiers: the |Xam Bushmen of the Northern Cape, South Africa, in the nineteenth century

This thesis constructs an ethnography for the nineteenth century ǀXam Bushmen of the Northern Cape Province of South Africa, known primarily through a nineteenth century manuscript collection of oral narrative (the Bleek-Lloyd archive), which has, over the past twenty-five years, increasingly become the focus of scholarly attention, mined for insights about the cultural world of southern Bushman societies. It draws on the Bleek-Lloyd archive to produce a detailed ethnographic case study, focusing on the ideological and ontological concepts that underpinned the differentiation of ǀXam society. Firstly, the thesis situates the archive and ǀXam society within their particular environmental and historical contexts, providing valuable supplementary information that informs readings of the narratives. By producing a fully searchable transcription of the entirety of the archive, paying close attention to emic terminology, and examining the recurrence of thematic associations of this phraseology throughout the narratives, the analysis explores the constitution of ǀXam ‘personhood’ and examines the extent to which the ‘hunter-gatherer’ category forms a useful heuristic for understanding ǀXam society, with a particular focus on models of the ‘animic ontology’. The ǀXam deployed a series of positively and negatively evaluated traits in the creation of dimensions of authority, obligation, and social responsibility, embedded in particular social identities; central to these constructions and to the differentiation of these identities were the techniques and resources of ǀXam subsistence practices, salient in the production of admirable (socially-responsible hunters), reprehensible (antagonistic ‘beasts of prey’), and more ambiguous (ǃgi:tǝn ritual specialists) identities. Recognising this internal differentiation, the thesis outlines ǀXam ‘subsistence strategies’ and suggests they should be defined broadly to include their contacts and interactions with non-ǀXam groups, with domesticated animals, and with the novel material culture of the colonial period; these interactions were a consequence of their ‘hunter-gatherer’ strategies rather than a negation of them. Such strategies generated experiences that reinforced and reconstituted ǀXam ideological frameworks, incorporating the dynamics of the nineteenth century ‘frontier’ scenario and provided avenues for social change that ultimately led to the collapse of independent hunter-gatherer lifeways, and to the adoption of strategies that incorporated ǀXam individuals within rural and urban ‘Coloured’ populations of the Northern Cape; placing the ǀXam in a comparative colonial context, the thesis stresses the wider relevance of this particular ethnography for understanding hunter-gatherer engagements with food-producing, state-level societies.

Keywords: hunter-gatherer
animism
colonial history
shamanism
San
Bushmen
Khoisan
Advisor: Mitchell, P
In vivo brain changes in late-life depression

Late-life depression (LLD) is common illness, frequently associated with neuropsychological impairment. Disruption of frontal-subcortical and limbic networks may play a key role in LLD and can be examined using magnetic resonance imaging (MRI). Grey matter (GM) can be examined using T1-weighted MRI, white matter (WM) using diffusion tensor imaging (DTI), and functional connectivity using resting-state functional MRI (fMRI).
To clarify the roles of GM, WM and functional connectivity in LLD, systematic reviews and meta-analyses of T1-weighted MRI, DTI and resting-state fMRI studies of depression were performed. The literature provided evidence for GM and WM abnormalities within frontal-subcortical and limbic networks, and increased functional connectivity within the default-mode network, in depression. To examine whether results gained from different techniques are complementary, multi-modal MRI was used to compare GM, WM and functional connectivity between thirty-six participants with LLD and twenty-five control participants. WM integrity was widely reduced in LLD, without significant group differences in GM or functional connectivity.
To investigate whether neuropsychological deficits represent independent processes with specific neural correlates, or whether they can be explained by a core deficit, the relationships between neuropsychological and MRI measures were explored. Executive function and processing speed were found to represent core deficits that contribute to impairment in other domains; and impaired performance was correlated with reduced frontal WM integrity. Episodic memory deficits were dependent on executive function and processing speed; and associated with reduced frontal and hippocampal WM integrity.
The relationships between age at onset, severity and MRI measures of GM, WM and functional connectivity were also investigated. Later onset was associated with reduced WM integrity, in line with the vascular hypothesis. Earlier onset was associated with greater duration of illness and reduced hippocampal volume, consistent with the glucocorticoid cascade hypothesis. Severity was not associated with any MRI measure.
This thesis strongly supports the hypothesis that WM abnormalities in frontal-subcortical and limbic networks play a key role in LLD, with abnormalities related to neuropsychological impairment and compatible with the vascular hypothesis.

Keywords: psychiatry
magnetic resonance imaging
depression
Advisor: Ebmeier, K
Mackay, C
Metacognition in decision making

Humans effortlessly and accurately judge their subjective probability of being correct in a given decision, leading to the view that metacognition is integral to decision making. This thesis reports a series of experiments assessing people’s confidence and error-detection judgements. These different types of metacognitive judgements are highly similar with regard to their methodology, but have been studied largely separately. I provide data indicating that these judgements are fundamentally linked and that they rely on shared cognitive and neural mechanisms. As a first step towards such a joint account of confidence and error detection, I present simulations from a computational model that is based on the notion these judgements are based on the same underlying processes.
I next focus on how metacognitive signals are utilised to enhance cognitive control by means of a modulation of information seeking. I report data from a study in which participants received performance feedback, testing the hypothesis that participants will focus more on feedback when they are uncertain whether they were correct in the current trial, whilst ignoring feedback when they are certain regarding their accuracy.
A final question addressed in this thesis asks which information contributes internally to the formation of metacognitive judgements, given that it remains a challenge for most models of confidence to explain the precise mechanisms by which confidence reflects accuracy, under which circumstances this correlation is reduced, and the role other influences might have, such as the inherent reliability of a source of evidence. The results reported here suggest that multiple variables – such as response time and reliability of evidence – play a role in the generation of metacognitive judgements. Inter-individual differences with regard to the utilisation of these cues to confidence are tested. Taken together, my results suggest that metacognition is crucially involved in decision making and cognitive control.

Keywords: cognitive control
uncertainty
metacognition
confidence
error detection
decision making
Advisor: Yeung, N
Chance and determinism in Ibn Sīnā and Ibn Rushd

This thesis analyses the concept of 'chance' as it is understood by two Muslim philosophers, Ibn Sīnā (Lat. Avicenna, CE 980-1037) and Ibn Rushd (Lat. Averroes, CE 1126-1198). On the philosophical plane, I seek to ascertain whether they are determinists, i.e., whether they hold that everything that happens is necessarily conditioned by its causes so that it could not have been otherwise. This analysis discusses chance from a physical and a metaphysical perspective. Physics is here understood in the Aristotelian sense as the study of nature and change, and metaphysics as the study of being qua being (ontology) and of the divine (theology). Hence a particular stress on natural causation and on divine providence and causation.
On the historical-philosophical plane I endeavour to determine the historical/philosophical sources of their views, namely the Graeco-Arabic philosophical tradition - Aristotelian and Neoplatonic on the one Band, and the tradition of Islamic theology (kalām) on the other. Particular emphasis is laid upon the original way in which Ibn Sīnā and Ibn Rushd combine these two traditions.

Advisor: Professor Yahya Michot, C
A responsible great power: the anatomy of China's proclaimed identity

There has been much interest and attention on the representation of China as a responsible great power. Indeed, Chinese leaders, policymakers and scholars have not been hesitant to declare China as one. Yet, relatively little is known about when, how and why this proclaimed self-identity emerged in Beijing. This thesis represents an initial attempt to unpack these questions. Mobilising the idea of international identity, I map the evolution of China’s declared identity as a responsible power, and examine its attributes and drivers.
My central contention is that since the early 1990s, China has been increasingly identifying—not only portraying—itself as a responsible great power. As this thesis shows, there is a vibrant epistemic terrain relating to the idea of global responsibility within China. For some time now, Chinese elites have been debating intensely the kind of responsible power that China should be. That these domestic identity debates take place frequently, away from the attention of most of the world, suggests the Chinese regard the idea of big power responsibility far more seriously than had it been purely a convenient propagandist tool. Examining how these elites think about the responsible power role, hence, may be crucial to a better understanding of the implications and trajectory of China's rise. Nevertheless, the development of this identity has not been solely a product of Chinese domestic narratives and perceptions. The role of the United States as a moral adjudicator and pressure source is also significant.

Keywords: great power
identity
China
Advisor: Foot, R