VictorJuiz/thesis huggingface dataset:
The mathematical structure of non-locality and contextuality
Keywords: cohomology
sheaf theory
contextuality
Bell theorem
non-locality
Hardy's paradox
quantum theory

Non-locality and contextuality are key features of quantum mechanics that distinguish it from classical physics. We aim to develop a deeper, more structural understanding of these phenomena, underpinned by robust and elegant mathematical theory with a view to providing clarity and new perspectives on conceptual and foundational issues. A general framework for logical non-locality is introduced and used to prove that 'Hardy's paradox' is complete for logical non-locality in all (2,2,l) and (2,k,2) Bell scenarios, a consequence of which is that Bell states are the only entangled two-qubit states that are not logically non-local, and that Hardy non-locality can be witnessed with certainty in a tripartite quantum system. A number of developments of the unified sheaf-theoretic approach to non-locality and contextuality are considered, including the first application of cohomology as a tool for studying the phenomena: we find cohomological witnesses corresponding to many of the classic no-go results, and completely characterise contextuality for large families of Kochen-Specker-like models. A connection with the problem of the existence of perfect matchings in k-uniform hypergraphs is explored, leading to new results on the complexity of deciding contextuality. A refinement of the sheaf-theoretic approach is found that captures partial approximations to locality/non-contextuality and can allow Bell models to be constructed from models of more general kinds which are equivalent in terms of non-locality/contextuality. Progress is made on bringing recent results on the nature of the wavefunction within the scope of the logical and sheaf-theoretic methods. Computational tools are developed for quantifying contextuality and finding generalised Bell inequalities for any measurement scenario which complement the research programme. This also leads to a proof that local ontological models with `negative probabilities' generate the no-signalling polytopes for all Bell scenarios.
Development of enzymatic H2 production and CO2 reduction systems
Keywords: carbon monoxide dehydrogenase
solar fuel
hydrogenase

One of today’s most pressing scientific challenges is the conception, development and deployment of renewable energy technologies that will meet the demands of a rapidly increasing population. The motivation is not only dwindling fossil fuel reserves, but also the necessary curtailment of emissions of the greenhouse gas carbon dioxide (a product of burning fossil fuels). The sun provides a vast amount of energy (120,000 TW globally), and one major challenge is the conversion of a fraction of this energy into chemical energy, thereby allowing it to be stored. Dihydrogen (H₂) that is produced from water is an attractive candidate to store solar energy (a ‘solar fuel’), as are high energy carbon-containing molecules (such as CO) that are formed directly from carbon dioxide.
One key aspect is the development of catalysts that are able to offer high rates and efficiencies. In biology, some microbes acquire energy from the metabolism of H₂ and CO. The biological catalysts - enzymes - that are responsible are hydrogenases (for the oxidation of H₂ to protons); and carbon monoxide dehydrogenases (CODHs, for the oxidation of CO to CO₂). These redox enzymes, containing nickel and iron as the only metals, are extraordinary in terms of their catalytic characteristics: many are fully reversible catalysts and offer very high turnover frequencies (thousands per second are common), with only tiny energy input requirements.
This Thesis uses a hydrogenase from the bacterium Escherichia coli, and two CODHs from the bacterium Carboxydothermus hydrogenoformans, as the catalysts in H2 production and CO₂ reduction systems. Chapter 3 describes the concept and development not of a solar fuel system, but of a device that catalyses the water-gas shift reaction (the reaction between CO and water to form H₂ and CO₂) - a process of major industrial importance for the production of high purity H₂. Chapters 4, 5 and 6 detail photochemical CO₂ reduction systems that are driven by visible light. These systems, operating under mild, aqueous conditions, involve CODHs attached either to TiO₂ nanoparticles that are sensitised to visible light by the co-attachment of a ruthenium-based dye complex, or to cadmium sulfide nanomaterials that, having a narrow band gap, are inherently photoexcitable by visible light.
The motivation here is not the construction of technological devices; indeed, the enzymes that are used are fragile, highly sensitive to oxygen, and impossible to scale to industrial levels. Rather, the drivers are those of scientific curiosity (can the incorporation of these remarkable biological catalysts enable the creation of outstanding solar fuel devices?), and of producing systems that serve as benchmarks and inspiration for the development of fully synthetic systems that are robust and scalable.
Investigating a role of HER3 in anti-HER2 target therapy in breast cancer
Keywords: trastuzumab
HER3
MET
HER2
nuclear localisation

Background
HER2-positive breast cancer is a poor prognostic subgroup, even if treated with anti-HER2 directed therapy. Trastuzumab is an important HER2-targeting antibody but only limited patients respond to this drug, and acquired resistance is a common problem. HER3 has been shown to be a key candidate in mediating resistance to trastuzumab and other ErbB inhibitors. The aims of the project are to investigate the resistance mechanisms and the relevant biomarkers in relation to trastuzumab treatment and resistance in HER2-positive breast cancer, in particular, HER3 subcellular localisation and HER3 phosphorylation.
Methods
Effects of trastuzumab on HER3 subcellular localisation and HER3 phosphorylation in relation to MET receptor were studied using western blots, nuclear fractionation, confocal microscopy, and immunoprecipitation in a panel of HER2-positive cell lines, including SKBr3 and BT474 breast cancer cells in which trastuzumab resistance was induced by long-term drug exposure. Effects of drug and knockdown experiments were tested by cell viability and proliferation assays. HER3 and MET expression was assessed by immunohistochemistry in xenograft tumours and human tissue samples, and clinical impact was assessed in different cohorts of HER2-positive breast cancer patients.
Results
Acquired trastuzumab resistant SKBr3 cells showed an increase of nuclear HER3100kD, which was derived from C-terminus of HER3. Nuclear HER3100kD could be due to the proteolytic cleavage of HER3 since it was reduced by ADAM17 or gamma-secretase inhibitor. In a panel of HER2-positive cell lines and xenograft samples, nuclear HER3 was observed only in the resistant cells. In addition, nuclear HER3 was associated with poor progression-free and overall survivals in HER2-positive breast cancer patients. It was also found that HER3 phosphorylation was maintained in acquired trastuzumab resistant cells, which was contributed by the ligand independent interaction of MET and HER3. Higher MET expression was associated with better overall survival in HER2-positive, breast cancer patients who were not treated with trastuzumab.
Conclusions
Nuclear HER3 was found in trastuzumab resistant cells and appeared to result from HER3 proteolytic cleavage mediated by ADAM17 and gamma-secretase. Further studies are required to investigate its mechanism and to identify the HER3 cleavage sites. MET was a key factor in maintaining HER3 phosphorylation during trastuzumab resistance. Lastly, nuclear HER3 and MET could be two potential biomarkers in HER2-positive breast cancer.
Stochastic partial differential equations applied to hydrocarbon reservoir modelling
Keywords: Stochastic biharmonic equation
Gaussian Random Fields
Stochastic Partial Differential Equations
Inverse Problems

This thesis describe the generation of random fields using elliptic stochastic partial differential equations driven by Gaussian white noise. The intended application is that of sampling from a prior probability density in the solution of an inverse problem.
In the first part of thesis, we will study two specific examples of isotropic models, namely the stochastic Helmholtz equation and stochastic biharmonic equation. We will address the analytical properties of a particular solution and the conditions required for the uniqueness of the Green’s function. A useful formula is also derived linking the computation of the covariance function of the solution to that of the Green’s function. Moreover, in each example the correlation function and approximate realizations are computed and simulated.
In the second part of the thesis, we will investigate the possibility of using vector fields to guide the random fields. The vector fields will be used to build tensor coefficients for an elliptic stochastic partial differential equation. The model considered is capable of producing non-stationary random fields on curved layers. Approximate realizations of this model will be drawn by using the finite element method, which is applied using the MATLAB PDE toolbox.
A Leader without Followers? European Union Relations with China and India on Climate Change, 1990-2009
Keywords: Climate Change
Energy
Environment
China
European Union
India

The EU has, for a long time, portrayed itself as an international leader on climate change. Previous studies have tended to focus on the characteristics of EU leadership, but have failed to examine the extent to which EU leadership generates “followership”. Going beyond these existing approaches, this dissertation analyzes not just EU attempts at leadership but also the response of two potential followers: China and India.
Based on extensive fieldwork, the dissertation explains the pattern of EU engagement and the response to engagement in each case, and makes three key arguments. First, EU engagement was driven by a desire to build the international role of the EU, but also from 2000 onwards in particular by growing normative concern and material interest within the EU regarding combating climate change. The development of engagement was also conditioned by the broader development of EU relations with China and India. Second, EU engagement took the form of institutionalized dialogue and capacity-building projects. These were generally more extensive in the EU-China case; the EU-India relationship was significantly more limited. Both cases were characterized by a lack of EU capacity—particularly the EU-India case and to some extent by inconsistency and incoherence. Third, the Chinese Government responded through limited normative emulation and limited but growing lesson-drawing through bilateral cooperation in specific sectors. While the Indian Government also responded through limited normative emulation, the principal Indian response was resistance. Moreover, both the Chinese and Indian Governments resisted the EU approach to the international climate change negotiations.
This pattern of engagement and significant resistance stemmed partly from the EU’s failure to develop sufficient capacity for effective engagement, but also partly due to significant differences in the way each side has framed the issue of climate change. Based on these findings, the dissertation concludes that while the EU was not entirely a leader without followers, it has acted as a highly restricted leader in its relations with China and India on climate change.
Priors for new view synthesis
Keywords: markov random field
prior model
new view synthesis
optimization

New view synthesis (NVS) is the problem of generating a novel image of a scene, given a set of calibrated input images of the scene, i.e. their viewpoints, and also that of the output image, are known. The problem is generally ill-posed---a large number of scenes can generate a given set of images, therefore there may be many equally likely (given the input data) output views. Some of these views will look less natural to a human observer than others, so prior knowledge of natural scenes is required to ensure that the result is visually plausible. The aim of this thesis is to compare and improve upon the various Markov random field} and conditional random field prior models, and their associated maximum a posteriori optimization frameworks, that are currently the state of the art for NVS and stereo (itself a means to NVS). A hierarchical example-based image prior is introduced which, when combined with a multi-resolution framework, accelerates inference by an order of magnitude, whilst also improving the quality of rendering. A parametric image prior is tested using a number of novel discrete optimization algorithms. This general prior is found to be less well suited to the NVS problem than sequence-specific priors, generating two forms of undesirable artifact, which are discussed. A novel pairwise clique image prior is developed, allowing inference using powerful optimizers. The prior is shown to perform better than a range of other pairwise image priors, distinguishing as it does between natural and artificial texture discontinuities. A dense stereo algorithm with geometrical occlusion model is converted to the task of NVS. In doing so, a number of challenges are novelly addressed; in particular, the new pairwise image prior is employed to align depth discontinuities with genuine texture edges in the output image. The resulting joint prior over smoothness and texture is shown to produce cutting edge rendering performance. Finally, a powerful new inference framework for stereo that allows the tractable optimization of second order smoothness priors is introduced. The second order priors are shown to improve reconstruction over first order priors in a number of situations.
Sharing the moment's discourse: Virginia Woolf, D. H. Lawrence and Albert Einstein in the early twentieth century
Keywords: Modernism
Literature and science
Physics in literature
Albert Einstein
D. H. Lawrence
Virginia Woolf

Using Gillian Beer's suggestion that literature and science 'share the moment's discourse' (Open Fields, 1996), this thesis explores the ideas associated with Albert Einstein's three revolutionary 1905 papers, examining the ways in which similar concepts appeared across disciplines during the early part of the twentieth century, and focusing in particular on their manifestation within the literary works of Virginia Woolf and D. H. Lawrence. The study seeks to distinguish between instances of direct influence and a shared contemporary discourse, arguing that the analysis of both is essential to studies within the field of literature and science.
Part I focuses on concepts of duality and complementarity, considering Max Planck's introduction of the quantum, Einstein's development of light quanta, Louis de Broglie's wave-particle duality and Niels Bohr's principle of complementarity. It analyses other contemporary discussions of duality and complementarity, and explores Virginia Woolf's attempts to simultaneously express both sides of dualistic models, suggesting that Woolf is a complementary writer.
Part II focuses on Einstein's theories of relativity, exploring D. H. Lawrence's adoption thereof in Fantasia of the Unconscious (1922), in particular his claim that 'we are in sad need of a theory of human relativity'. It argues that this proposed theory is directly relevant to Lawrence's fictional works, both those that precede Fantasia and those that follow it. It also analyses the impact on Lawrence of contemporary ideas of relativism, especially those of William James as expressed in Pragmatism (1907).
Part III explores the ways in which both Woolf and Lawrence write about individuals within crowds. It considers the possible links between such scenes and Einstein's paper on Brownian motion as well as contemporary studies of crowd psychology. It suggests that individual characters within modernist works can be considered as similar to the individual particles suspended in a mass which exhibit Brownian motion.
Mechanisms of genome regulation in human islets and their role in the pathogenesis of type 2 diabetes
Keywords: genetics &amp; genomics
type 2 diabetes
islet of langerhans

Genome-wide association studies (GWAS) have made substantial progress in implicating genomic regions in type 2 diabetes (T2D) susceptibility. Whilst attributing causal mechanisms to loci has proved non trivial, these studies have provided insights into the genetic architecture underlying the disease. GWAS findings indicate a causal role for gene regulatory processes, and suggest that pancreatic beta-cells play a pivotal role in mediating common T2D association. Work presented in this thesis therefore sought to generate novel regulatory annotations from human islets, and to assess whether T2D-associated loci can be accurately fine-mapped using statistical approaches, with the aim of improving understanding of causal mechanisms underlying these associations through integration of the two approaches.
Using small RNA sequencing in human islets and enriched beta-cell populations (both n=3) and mRNA sequencing in a large number of human islets (n=130), I increased the number of available human islet annotations. These studies identified high or islet-specific expression in many micro RNAs (miRNAs) without previously known roles in human islets. It also provided the largest study of quantitative trait loci (eQTLs) and allele-specific expression (ASE) in human islets to date, identifying significant eQTLs for 1,636 genes and significant ASE at 8,754 genes. There was enrichment of active islet chromatin, compared to other tissues, at the best eQTL variant for each gene, but also substantial sharing of significant eQTLs between islets and other tissues.
Simulations were used to assess the utility of fine-mapping approaches for refining common disease-associated loci to smaller intervals or sets of variants likely to include the causal variant. The results demonstrated that fine-mapping can indeed refine these loci to sets or intervals of a size more amenable to functional follow-up or focussed intersection with high quality annotations. Furthermore, using an approximated Bayesian approach, I was able to refine twenty-one of the known common T2D-associated loci.
Finally, using the newly generated annotations, I demonstrated enrichment of T2D association signal for regulatory RNA annotations (islet lncRNAs and miRNA target gene sets). I also identified examples in which these types of annotation overlap common and rare variation suggestive of a role in T2D pathogenesis. Using further islet annotations, I also uncovered potential causal mechanisms at four of the twentyone fine-mapped common T2D loci.
These data therefore provide many novel islet regulatory annotations that can be intersected with T2D genetics, and provide a first example of how such an approach can lead to novel potential causal mechanisms underlying association loci.
Confronting crisis 
Keywords: argumentation
foreign policy
International Normative Theory
international relations
humanitarian intervention
International Relations Theory

The purpose of this thesis is theory development. It begins by evaluating existing explanations of why states undertake humanitarian intervention. Realists argue that states only intervene when their national interests are at stake. Normative scholars argue that states are at times motivated to save foreign citizens. Neither approach adequately accounts for the pattern of post-Cold War state practice. Building from this conclusion, the thesis conducts research based on two propositions derived from an analysis of existing debates: that examining state motive holds promise for elucidating the weaknesses in current approaches and that studying state argumentation can provide insight into state motives. To better investigate state motives, a theoretical framework is developed to explain how motives translate into state decision-making and manifest themselves in state argumentation.
By employing process tracing, argumentation analysis, and elite interviews, this framework is applied to three cases: Northern Iraq in 1991, Rwanda in 1994, and East Timor in 1999. Each case study constructs a theoretically informed narrative, assesses debates between states at the United Nations Security Council, and evaluates the consistency between state discourse and state practice. The cases are then used heuristically to identify opportunities for improving existing theory and developing new theory. This yields several conclusions. First, not only do states often possess mixed motives, but the humanitarian impulse also appears in some cases to have been a necessary condition for humanitarian intervention. Second, the norm of humanitarian intervention does not function as a general rule. Rather, it is a cluster of principles derived from just war theory and international law, but also connected to related norms about sovereignty, human rights, and self-determination. Third, state decision-making is a collective process structured by the prevailing post-Cold War institutional and normative context. The thesis concludes by outlining promising avenues of research for better understanding why states respond to some occurrences of mass atrocities and not others.
The edifying and the polemical in Kierkegaard's religious writings
Keywords: self and society
Kierkegaard
social theology

This thesis provides a theoretical framework that brings the unity of Kierkegaard’s ‘middle period’ into relief. I will analyse Kierkegaard’s writings between 1846 and 1852 when, I argue, the socially constructive dimension of his thought comes to prominence, involving two dialectical aspects of religiousness identified by Kierkegaard: the edifying and the polemical. How these two aspects come together and get worked out in the lives of individuals form the basis of what can be called a Kierkegaardian ‘social praxis’. I conclude that the tension between the edifying and the polemical can be coherently maintained in a communicative life that is also characteristic of a militant faith. This militant faith and life is presented as a critical guard against absolutisms, fundamentalisms, and intellectual aloofness; but the ‘militant’ individual is also utterly dependent, in need of edification and critique, and therefore chooses the risk of encountering others, seeking relationships out of a commitment to the development of persons and communities in co-operation. Therefore, not only does this dialectic provide readers with an important theoretical framework for understanding Kierkegaard’s ‘middle period’, but it is also a valuable resource for a constructive analysis of active social living suitable for theology in the twenty-first century.