VictorJuiz/thesis huggingface dataset:
Modelling of extremes

This work focuses on statistical methods to understand how frequently rare events occur and what the magnitude of extreme values such as large losses is. It lies in a field called extreme value analysis whose scope is to provide support for scientific decision making when extreme observations are of particular importance such as in environmental applications, insurance and finance.
In the univariate case, I propose new techniques to model tails of discrete distributions and illustrate them in an application on word frequency and multiple birth data. Suitably rescaled, the limiting tails of some discrete distributions are shown to converge to a discrete generalized Pareto distribution and generalized Zipf distribution respectively.
In the multivariate high-dimensional case, I suggest modeling tail dependence between random variables by a graph such that its nodes correspond to the variables and shocks propagate through the edges. Relying on the ideas of graphical models, I prove that if the variables satisfy a new notion called asymptotic conditional independence, then the density of the joint distribution can be simplified and expressed in terms of lower dimensional functions. This generalizes the Hammersley– Clifford theorem and enables us to infer tail distributions from observations in reduced dimension. As an illustration, extreme river flows are modeled by a tree graphical model whose structure appears to recover almost exactly the actual river network.
A fundamental concept when studying limiting tail distributions is regular variation. I propose a new notion in the multivariate case called one-component regular variation, of which Karamata’s and the representation theorem, two important results in the univariate case, are generalizations.
Eventually, I turn my attention to website visit data and fit a censored copula Gaussian graphical model allowing the visualization of users’ behavior by a graph.

Keywords: Generalized Zipf Distribution
Student Graphical Models
Asymptotic Conditional Independence
Censored Copula
Tree Graphical Models
Gaussian Graphical Models
Discrete Pareto IV Distribution
Multivariate Regular Variation
Discrete Generalized Pareto Distribution
Advisor: Evans, R
Those swans, remember: Graeco-Celtic relations in the work of J.M. Synge

The Celts, as a distinct and culturally-unified people, are a social construction as much as an historical reality, endowing Celtic antiquity with a certain availability of outline, and a certain scope. When the Celtic world began to be scrutinised in the eighteenth century, its borders could, therefore, be filled with concepts drawn from other antiquities. Classical antiquity, and particularly its Greek variety, was a vital coordinate in this navigation of the past. This thesis explores the history of these Graeco-Celtic negotiations. Using Reinhart Koselleck’s theory of asymmetric counterconcepts, it calculates the precise angles of the relation between Greek and Celt in antiquarianism, comparative mythology and folklore, Classics and Celtic Studies, from the early eighteenth and to the late nineteenth centuries.
The thesis then puts forward one particular writer as an original and unique interpreter of the tradition of Graeco-Celtic relations, the Irish playwright J.M. Synge. Through archival research, it demonstrates quite how deeply Synge was immersed in this scholarly tradition; in the last years of the nineteenth century and the first years of the twentieth, he followed a deliberate path of reading in antiquarianism, Classics, Celtic Studies, comparative linguistics, mythology and folklore. It then argues that Synge transformed such Graeco-Celtic scholarship into a formidable authorial strategy, in his prose account of his travels on the Aran Islands and his famous, controversial plays. By identifying this strategy, it reveals how Synge’s work exploits the continued presence and power of antiquity.
Most studies of the reception of Greek antiquity in Irish literature in the twentieth and twenty-first centuries assume a straightforward, inherent connection between Ireland and Greece. This thesis complicates that connection by identifying the powerful history of Graeco-Celtic relations and, particularly, its transformation at the hands of J.M. Synge. This will allow for scrutiny of what actually happens at the crux between Greece and Ireland in literary texts.

Advisor: Macintosh, F
Adiponectin as a regulator of vascular redox state in human atherosclerosis

Atherosclerotic cardiovascular disease is a leading cause of death worldwide. Dysregulation of vascular redox state plays a crucial role in the atherosclerotic process. Increased production of vascular superoxide (O2·-) and other reactive oxygen species (ROS) leads to endothelial dysfunction, a key early step in atherogenesis. Adipose tissue is a source of vasoactive, hormone-like molecules which are termed adipokines. One of the most important adipokines is adiponectin. Adiponectin has been shown to have antioxidant, anti-atherosclerotic effects in cell culture studies and animal models. However, its role in human cardiovascular disease has not been extensively investigated. More specifically, its effects on the human vascular wall and the mechanisms regulating its synthesis in adipose tissue have not been studied before in humans. The aim of my thesis is to explore the role of adiponectin in human atherosclerosis. This was achieved through use of the Oxford CABG Bioresource: a well-phenotyped cohort and tissue bank of patients undergoing cardiac surgery. By employing a range of in vivo and ex vivo techniques, I demonstrate for the first time in humans that adiponectin has direct antioxidant effects in the vascular wall, by directly suppressing pro-oxidant vascular enzymes and restoring redox balance. These effects persist in type 2 diabetes, presence of which is linked to reduced circulating adiponectin levels. Indeed, a variety of stimuli affect adiponectin synthesis in human adipose tissue, with brain natriuretic peptide being a major driver of adiponectin synthesis. However, different adipose tissue depots demonstrate diverse responses to stimuli affecting adiponectin synthesis, owing to their functional and morphological differences. Of particular interest is the fact that synthesis of adiponectin in perivascular adipose tissue is driven by the oxidative stress status of the underlying vessel. This observation led me to document for the first time in humans the existence of a reciprocal, two-way interaction between perivascular adipose tissue and the vascular wall: high vascular oxidative stress leads to release of factors with the ability to up-regulate adiponectin expression in perivascular adipose tissue, acting as a local paracrine defence mechanism attempting to restore vascular redox state. My thesis provides proof-of-concept for this novel cross-talk between adipose tissue and the vascular wall. This can have significant impact in designing new therapeutic strategies against atherosclerosis.

Keywords: Adiponectin
Adipokines
Oxidative stress
Atherosclerosis
Advisor: Antoniades, C
Casadei, B
Channon, K
Between the conquests and the court: a critical analysis of the Kitāb Futūḥ al-Buldān of al-Balādhurī

When considering the available sources for Islamic history between the seventh and eighth centuries CE, there are few which have greater importance than al-Balādhurī’s (d. ca. 892 CE/279 AH) Kitāb Futūḥ al-buldān (The Book of the Conquest of Lands). While the text and its author are recognized for their importance as a historical source for the early Islamic period, there has previously been no in-depth study of either. This dissertation works to correct these gaps in knowledge of the author and his text by investigating the construction, form, content, and early reception history of al-Balādhurī’s book.
This research begins by providing a manuscript tradition of Futūḥ al-buldān, including a discussion of a previously unpublished manuscript. It thereafter illuminates the background of al-Balādhurī, bringing together much of the previous scholarship on the author while augmenting that information with an analysis of biographical sources and the text itself. It situates the author and his text in its ninth/third century milieu, a period of history where the early Arabic historical tradition was still in its infancy and only just being committed to writing. It suggests the text was likely completed at the end of the “anarchy at Sāmarrā’” in the late 860s CE, and highlights the author’s role at the court of several ‘Abbāsid Caliphs. After this, it discusses a number of al-Balādhurī’s most important (and, in some cases, previously understudied) sources of information, and argues that the author chose to differentiate when he was learning information directly from a teacher and when he had access to written sources. It then analyzes the content and themes of the text, placing special attention on the unique form of Futūḥ al-buldān and its importance in providing modern scholars with information on the conquest, settlement, and building projects of the early Islamic world. In considering these key themes, this research then argues that Futūḥ al-buldān defies traditional modern genre classification by borrowing form and content from several different Arabic genres including conquest literature (futūḥ), legal texts, and administrative geographies. It contends that both the text’s content and form suggest that it was written to be read by courtly administrators in the service of the state as both a site of memory (lieu de mémoire) and as an “administrator’s handbook” during a time of upheaval in the ‘Abbāsid realm. Finally, it considers the legacy of Futūḥ al-buldān and the popularity of al-Balādhurī’s book throughout the medieval period through an analysis of textual reuse.

Keywords: Futuh al-Buldan
Book of the Conquest of Lands
futuh
Kitab Futuh al-Buldan
al-Balādhurī
Arabic genre
Arabic Historiography
al-Baladhuri
futūḥ
Islamic historical writing
Advisor: Hoyland, R
The interaction between ketone bodies and carbohydrate in human metabolism

Thesis Abstract: The human brain cannot oxidise fat, so ketone bodies (KBs) are produced in the liver from fat to provide energy in starvation, the brain having a high capacity to oxidise KBs. KB levels rise as insulin falls, with reduced glucose availability, thereby providing a signal to conserve carbohydrate and to switch energy use to fat. Methods: Here, studies were conducted into the relationship between KB and carbohydrate metabolism using exercise and controlled diets to alter substrate availability. A ketone ester (KE) drink was used to raise D-β-hydroxybutyrate (βHB, ±13C-label) levels, at rest and during exercise. Glucose disposal, insulin and other markers of carbohydrate and fat metabolism, KB oxidation and glycogen synthesis rates were investigated by blood sampling, glucose clamp studies, 13C breath analysis and muscle biopsies. Results: βHB oxidation accounted for ≥ 28% of resting VO2, and increased 3-fold with exercise, but was 24% lower when exercising after a low-carb diet. After glycogen-depleting exercise, endogenous insulin levels rose two-fold, glucose disposal increased 32% and glycogen synthesis increased 50% during a 2-hour hyperglycaemic (10 mM glucose) clamp following the KE drink. In overnight fasted healthy controls and type-2 diabetic participants (T2DM), KE increased insulin and lowered glucose concentrations vs. control (zero calorie) drink. There was an increase in glucose disposal during euglycaemic (5 mM glucose) clamping in healthy controls, but no difference in T2DM patients. KE lowered circulating free fatty acids and peripheral lipolysis in T2DM patients. Conclusion: βHB can replace glucose as a fuel, increasing glucose disposal and glycogen synthesis, and increase insulin in health and disease. When carbohydrate is low, muscle βHB oxidation is downregulated to spare KBs for the brain, effects directly or indirectly conserving carbohydrate and protecting the brain. This work is the first to show the metabolic effects of an exogenous (dietary) ketone ester in human, particularly on carbohydrate metabolism, and the effect of substrate availability on ketone oxidation.

Advisor: Clarke, K
Brain markers of cumulative stress response and allostatic load in the ageing Whitehall II cohort

The Whitehall II (Stress and Health) study is a prospective study based on originally 10,308 British civil servants. Since 1985, rich socio-demographic, health and life-style measures have been acquired every 2-5 years. Eight hundred participants were randomly selected from the remaining 6,308 participants of Phase 11 for magnetic resonance imaging (MRI) and further examination in Oxford (2012-14).
There is evidence of changes in brain anatomy and mental health following traumatic events, such as combat stress or sexual abuse, in patients with posttraumatic stress disorder, mood or personality disorders, but little is known about the association between everyday stress, brain structure and function, and mental health in the general population. The secondary stress markers, Allostatic Load (AL) index, Framingham Stroke Risk score (FSRS) and Metabolic Syndrome (MetS) were selected as potential predictors of brain changes at follow-up. This thesis focuses on measures of structural grey and white matter (GM, WM) integrity, collected with the Siemens 3T Verio scanner in the first 563 participants of the Oxford study.
As hypothesised, stress markers measured as early as 20 years prior to the scan, predicted lower GM and WM integrity in older age. Unique linear relationships remained even after controlling for socio-demographic confounders between each stress marker and GM density but not with measures of WM integrity. This suggests that some, if not most variance is shared between the stress markers and the usual correlates of general health, such as age and employment class.
The three markers did not have equal power to predict brain measures: AL added more unique predictive variance to GM density than MetS and FSRS. On the other hand, FSRS was the more powerful predictor of poor WM integrity compared with AL and MetS, and after removing confounding variable effects.
This thesis thus provides some empirical support for the concept of allostatic load, linking 'everyday' stress and features of the ageing human brain.

Keywords: stress
MRI
human brain ageing
Advisor: Ebmeier, K
Methodology development and synthesis of a biologically relevant natural product and targeted scaffold discovery for serine hydrolase inhibition

The phenomenal potential of synthetic chemistry to influence small molecule therapeutic development represents my overarching theme. The goal of designing or discovering a novel clinical candidate or biological target can be achieved through a variety of avenues available to synthetic organic chemists. The potential of natural product total synthesis and inhibitor development as impactful projects were pursued with the use and development of methodology.
The natural product streptonigrin, a potent antitumor antibiotic, showed promise in clinical trials ultimately terminated in the 1970s. The underexplored mechanism of action prompted a reexamination of this potential therapeutic. The Donohoe group successfully designed a modular total synthesis accessing streptonigrin in 11 steps and 14% yield. The introduction of an asymmetric Suzuki– Miyaura reaction yielded a key intermediate in 42% ee and 65% yield, which represents the first example of purely synthetic access to enantioenriched late-stage streptonigrin analogues.
The "hydrogen-borrowing" method allows the functionalization of ketones with methanol and transition metal catalysts, but examples lacked application to further α-functionalization. The successful development of a novel "interrupted- hydrogen-borrowing" method allowed the use of iridium and methanol to trap the reactive enone intermediates by preventing the subsequent "hydrogen returning". Thus, this enabled these reactive intermediates to be subjected to a 1,4-conjugate addition with a nucleophilic ketone enolate and subsequent cyclization and oxidation to form highly substituted pyridines from simple ketones.
The exploration of serine hydrolases, an important mammalian enzyme class with a large portion still uncharacterized, requires inhibitors with new chemotypes that can covalently and irreversibly bind. The small library of urea- and carbamate- containing scaffolds with varied aromatic backbone substitutions was subjected to activity-based protein profiling to allow expedient examination of the whole serine hydrolase family. The predicted strong electronic effect of the p-substituent was confirmed, modulating the reactivity of the electrophilic urea or carbamate moiety. MudPIT analysis of a subset supported the demonstrated reactivity profile and identified the uncharacterized serine hydrolase PNPLA4 as a selective target of one inhibitor. This potent and selective inhibition was verified by in vitro and in cell assays and validates this chemotype as a family of serine hydrolase inhibitors.

Advisor: Donohoe, T
Boger, D
Weighted discounting, time inconsistent stopping and their applications

This thesis studies groups whose members disagree about the method of discounting. In particular, we provide a comprehensive treatment of discount functions that are given by the weighted average of the group members’ discount functions. This class of "weighted discount functions" admits a natural notion of group diversity, which has consequences for behavior. We show that more diverse groups discount less heavily and make more patient decisions. Within a real options framework, for example, greater group diversity leads to delayed investment. Then, we show that well-known behavioral discount functions can be written as a weighted discount function. Therefore, all results in this thesis find a correspondence in a single agent setting with non-standard, behavioral time preferences. In particular, we provide an equilibrium stopping result for individuals who are aware of their time-inconsistency, but lack commitment. Finally, we propose an example which shows that the Bellman system for the equilibrium stopping problem may not admit any proper solution and illustrate that the non-existence is caused by group diversity or decreasing impatience.

Advisor: Zhou, X
A study on dense plasmas using molecular dynamics and X-ray scattering techniques

Matter exists in the cores of planets and the crusts of neutron stars, as well as the inside of inertial fusion experiments, in the warm dense matter (WDM) regime. This type of matter, defined by temperatures of several electronvolts and densities comparable to solids, is characterised by long-range Coulomb interactions between ions and non-negligible electron degeneracy, and is therefore inherently difficult to model theoretically.
In this work, time resolved X-ray diffraction is used to study the temporal evolution of a laser-heated gold sample, from solid state towards WDM. The electron-ion equilibration time is extracted through the use of molecular dynamics simulations employing the two-temperature model, with the results compared to other methods.
Laser-produced X-ray sources are focused to high intensities, through the use of a polycapillary lens. This setup is thoroughly characterised, with the results suggesting a vastly improved signal-to-noise ratio could be achieved in many pump-probe experiments by employing this schematic.
Numerical predictions for the dynamic ion-ion structure factor of warm dense aluminium are presented, with significant changes observed when dissipative processes are included by Langevin dynamics. The results are compared to recent experimental data, suggesting electron-ion dynamical effects could play a crucial role in the dynamic properties of matter in the WDM regime.

Advisor: Gregori, G
Magnetic field amplification in laser-produced plasmas

The universe abounds with shock waves, from those arising during structure formation, to those driving supernova explosions that create the elements of which life is made and can even trigger star formation. In the early universe, matter was nearly homogeneously distributed; today, as a result of gravitational instabilities, it forms a web-like structure of clusters, filaments, and voids. Radio-Synchrotron emission and Faraday Rotation measurements have revealed that clusters, filaments, and voids are all magnetised from a few nG to tens of μG. When integrated over the whole universe, this magnetic energy represents a sizeable component of the cosmic energy budget, making magnetic fields essential players in the dynamics of luminous matter in the universe.
At present, the origin and distribution of magnetic fields are far from understood. The standard model for the origin of galactic and intergalactic magnetic fields is through the generation of small seed fields by some mechanism (e.g. Biermann Battery) and the amplification of these seed fields via dynamo or turbulent processes to the level consistent with current observations. Due to the advent of high-powered lasers, scaled astrophysical phenomena can be created in the laboratory - a supernova several parsecs in diameter can be scaled down to the size of a baseball. These laboratory plasmas are similar to plasmas in the universe in terms of localisation, heat conduction, viscosity, and radiation.
Here we report on experimental measurements of magnetic field amplification by turbulent motions in both laser-produced shock waves scaled to supernova remnants and laser-produced jets analogous to cluster merger events. These measurements of turbulent magnetic field amplification in a laser-produced plasma are a precursor to turbulent dynamo [11] in which amplification is no longer limited by diffusion, and a necessary component in explaining the magnetisation of luminous matter in the universe.

Advisor: Gregori, G
Catalysis for CO2 activation reactions with light alkanes

CO2, without question, the most famous greenhouse gas, is known to have an increasing concentration in both the atmosphere and oceans. To slow down the pace not only of global warming but also the ocean acidification, several routes are proposed to effectively reduce the net emission of CO2. Compared to Carbon Capture and Sequestration/Storage (CCS), Carbon Capture and Utilisation (CCU) has much more potential because of the lower costs of scale up and higher profitability to potentially attract capital investment.
Different from the conventional CCU route which is to reduce CO2 to fuels with hydrogen generated via renewable-energy-driving electricity, two processes are investigated in this thesis; that of Dry Methane Reforming (DMR) and the DeHydrogenation of Propane by CO2 (DHP by CO2). The projects on these two processes not only develop catalysts which would be suitable for the reaction performance, but also the ultimate aim is to link the processes with a renewable energy source (in the thesis we chose Solar Thermal Heating).Thermodynamic calculations and process simulations were also evaluated.
The results of DMR unfortunately did not indicate a promising future to link with Solar Thermal Heating due to the very high temperature required during the process. However, the results of thermodynamic calculations and process simulations in DMR project illustrate a good opportunity to utilise flue gas in industry through the so-called Tri- Methane Reforming (TMR). In the DHP by CO2 process, the catalysts developed were less promising than the ones in DMR due to the severe side-reactions occurred which significantly decreased the selectivity for the desired product. However - and importantly - through our thermodynamic calculations and process simulations, the DHP by CO2 process has a bright future if the Solar Thermal Heating can be applied with the relative lower temperature requirement, making the CO2 utilisation process much easier to be fulfilled than DMR.

Keywords: CO2 Utilisation
Hydrocarbons
Catalysis
Advisor: Edwards, P