VictorJuiz/thesis huggingface dataset:
Algorithms for trigonometric polynomial and rational approximation

This thesis presents new numerical algorithms for approximating functions by trigonometric polynomials and trigonometric rational functions. We begin by reviewing trigonometric polynomial interpolation and the barycentric formula for trigonometric polynomial interpolation in Chapter 1. Another feature of this chapter is the use of the complex plane, contour integrals and phase portraits for visualising various properties and relationships between periodic functions and their Laurent and trigonometric series. We also derive a periodic analogue of the Hermite integral formula which enables us to analyze interpolation error using contour integrals. We have not been able to find such a formula in the literature.
Chapter 2 discusses trigonometric rational interpolation and trigonometric linearized rational least-squares approximations. To our knowledge, this is the first attempt to numerically solve these problems. The contribution of this chapter is presented in the form of a robust algorithm for computing trigonometric rational interpolants of prescribed numerator and denominator degrees at an arbitrary grid of interpolation points. The algorithm can also be used to compute trigonometric linearized rational least-squares and trigonometric polynomial least-squares approximations.
Chapter 3 deals with the problem of trigonometric minimax approximation of functions, first in a space of trigonometric polynomials and then in a set of trigonometric rational functions. The contribution of this chapter is presented in the form of an algorithm, which to our knowledge, is the first description of a Remez-like algorithm to numerically compute trigonometric minimax polynomial and rational approximations. Our algorithm also uses trigonometric barycentric interpolation and Chebyshev-eigenvalue based root finding.
Chapter 4 discusses the Fourier-Padé (called trigonometric Padé) approximation of a function. We review two existing approaches to the problem, both of which are based on rational approximations of a Laurent series. We present a numerical algorithm with examples and compute various type (m, n) trigonometric Padé approximants.

Keywords: rational approximations
algorithms
periodic functions
Hermite integral formula
numerical algorithms
Advisor: Trefethen, N
The mammalian EMC in membrane protein biogenesis

The mammalian Endoplasmic Reticulum Membrane protein Complex (mEMC) has previously been implicated in a range of cellular activities, including the biogenesis of oligomeric plasma membrane receptors, endoplasmic reticulum (ER)-mitochondrial phospholipid transfer, and as a host factor modulating viral pathogenicity. Despite its evolutionary conservation in all eukaryotes, the biological functions and molecular mechanism of the EMC remain poorly understood. Here, the requirement of the mEMC for integral membrane protein biogenesis is investigated. It is reported that the mEMC is involved in the biogenesis of squalene synthase (SQS), an integral ER-resident cholesterogenic enzyme with tail-anchor protein topology. The mEMC is assembled from 10 subunits (EMC1 - 10). Quantitative proteomics on mEMC-deficient ΔEMC5 and ΔEMC6 U2OS Flp-In cells revealed reduced steady-state levels of select cell surface and intracellular proteins. In particular, both EMC5 and EMC6 knockout cells exhibited substantial co-depletion of SQS. The enzyme was significantly destabilized and rapidly degraded by the ubiquitin/proteasome system (UPS) in ΔEMC6 cells. Cells lacking the mEMC were viable under replete media conditions, but were prone to enhanced cell death upon acute cholesterol depletion. Sensitivity to cholesterol loss in EMC6 knockout cells was reproduced by direct deletion or pharmacological inhibition of SQS. mEMC depletion also caused imbalances in the mevalonate pathway, likely leading to increased shunting of the farnesyl pyrophosphate precursor into the isoprenoid pathway, increasing the detection of prenylated proteins. It is proposed that the mEMC is a maturation factor for SQS, and potentially other transmembrane proteins sharing critical molecular features with the biogenesis of this enzyme.

Advisor: Christianson, J
Food environments in Islamabad, Pakistan

This dissertation examines how concerns about food system transformations affect how middle class consumers in Islamabad, Pakistan, perceive and approach food consumption in their everyday lives. The dissertation is situated in the context of risky food environments and food fears resulting from intensified, industrialised, and increasingly lengthened global food systems. Working within food geography and food environments paradigms, this dissertation explores how the transformation of food systems is associated with increasing anxiety about food security and safety for middle class urban consumers in Islamabad. Qualitative data gathered from semi-structured interviews and participant observation is used to illustrate the effects external influences, such as energy scarcity and violent events, have on everyday food environments. The dissertation examines the ways in which conceptualisations of 'good food', and trust relationships are negotiated in these dynamic food environments. The intensely geographical nature of these food environments and food systems, and the role of place-specific contexts on perceptions and adaptations related to food anxieties are emphasised. Situated in literatures on food anxiety and food consumption emerging from geography, food studies, and anthropology, this dissertation challenges dominant discourses on alternative and ethical consumption in a globalising food system. The results of this research not only contribute to literature on South Asia, but also contribute to consumption practices of a burgeoning middle class in developing countries.

Keywords: food consumption
Pakistan
organic food
sustainability
food environment
food systems
middle class
urban design
alternative food networks
rhythm
local food
commodity geography
fuel scarcity
Advisor: Lora-Wainwright, A
McConnell, F
A P450BM3 toolkit For C-H activation synthesis

Cytochrome P450s are a superfamily of haem-dependent enzymes that catalyse the oxidation of natural organic compounds, most commonly via insertion of an oxygen atom from atmospheric dioxygen into a carbon-hydrogen bond. Since there is widespread interest in the selective functionalisation of C–H bonds, P450s have been extensively studied and evolved, particularly P450BM3 from Bacillus megaterium, which is catalytically self-sufficient. In this thesis, a P450BM3 variant library has been developed based on four 'generic accelerators', which have showed enhanced activity towards a broad range of non-natural substrates such as polyaromatic hydrocarbons and terpenes. The library was refined to 48 variants based on the screening results in order to maintain diversity of substrate pocket topology for oxidising a broad coverage of organic molecules. Successful applications include drug metabolism, drug fragment diversification, synthesis of flavour and fragrance compounds, steroid oxidation, late-stage functionalisation in total synthesis, and C–H amination. Total conversion was observed in most cases with a sufficient turnover number that enabled all the products to be fully characterised by NMR and MS. Two novel P450 activities were discovered as oxidative decarboxylation of an α-hydroxy carboxylic acid and C–H amination. The substrate range and varied product profiles suggest that this enzyme library is a good basis for developing selective C–H activation catalysts while expanding the P450 catalytic repertoire to include reactions important in synthetic chemistry, potentially opening new opportunities for biocatalysis.

Advisor: Wong, L
The intimate and the impossible: analogy without similitude in Jean-Luc Marion

In this thesis I argue that the constructive philosophical project of Jean-Luc Marion offers a new way of thinking the analogical relation between God and the human person. I particularly examine his concept of the saturated phenomenon in order to show how we might construct the relation between incommensurable terms (God and the human being) without requiring a similitude to mediate the relation.
I argue that for Marion God's transcendence is understood as what he describes as "impossibility" and that his immanence is understood through Augustine's interior intimo meo, the God more intimate to me than I am too myself. I demonstrate that radical immanence is God's transcendence insofar as the event of the impossible precedes the being-possibility correlation of metaphysics. Thus I develop the relation of God and the human being as a coincidence of opposites more than an analogy: the infinite distance of radical alterity becomes a belonging together of the human being with God. As a consequence of this analysis, I develop a new concept of relation, which I call "hyperbolic relation." If similitude always threatens to abolish the alterity of the terms of the relation (as was Barth's objection to the analogia entis), in this case, alterity is maintained not by removing relation but by increasing it to the level of hyperbole. Like Marion’s God who is "without Being," this analogy is "without similitude" by means of excess. The concept of God that I develop (impossible as intimate and vice versa) will consequently lead to a deepening of the concept of the human person through the transfiguration that saturation precipitates within the concept of relation.

Advisor: Ward, G
Fictions of youth: childness in selected West African novels, 1991-2009

This thesis examines child figures in Anglophone West African novels by Ben Okri, Chris Abani, Uzodinma Iweala, Delia Jarrett-Macauley, Helen Oyeyemi, and Yaba Badoe. A "child" here is defined as a human person under age 18 and is referred to using the term childness, drawing from the work of children's literature scholar Peter Hollindale. The thesis begins by reviewing some of the ways literary scholars have discussed images of childness in West African novels to date, exploring common themes such as "Empire," "nationhood" and "identity." The next three chapters, then, seek to move beyond some of these established readings. Chapter 1 investigates Ben Okri's "Azaro" in The Famished Road (1991) as a means of exploring aspects of the artist's creative life. Okri’s child figure, I propose, shares much in common with the "artist" from his earlier fictions, Flowers and Shadows (1980) and The Landscapes Within (1981). Chapter 2, similarly, considers the way in which child figures have a versatile function in Chris Abani’s Song for Night (2007), Uzodinma Iweala's Beasts of No Nation (2005), and Delia Jarrett-Macauley's Moses, Citizen and Me (2005), propping up an implicit argument in favor of humanitarian intervention in civil war. Yet here the thesis also considers some of the downsides to children’s instrumentalization: Jarrett-Macauley and Iweala depersonalize the child figure in their fictions, I argue. The child is drained of a convincing sense of an individuality and agency of his or her own.
Chapter 3 continues to explore the figure of the child as a complex and multivalent symbol. However, it finds that Helen Oyeyemi's The Icarus Girl (2005) and Yaba Badoe's True Murder (2009) do not disavow children's personhood, as Iweala and Jarrett-Macauley appear to do. Rather, the "otherness" of children, which is explored in their novels alongside the alterity of black persons, cultural minorities, and women, helps to draw attention to the agency of children. That is to say, Oyeyemi and Badoe show us children as subversive, contributing their own social meanings to the category of "youth," even whilst they are passively constructed or "othered" by adults in the novels. As an additional concern, the thesis also examines how authors have recourse to western conceptions of childness, not only to the traditions of their native countries, as we might as expect. The goal throughout is to highlight the child as a multifunctional figure, while also bringing attention to several specific ways in which African child figures function, including as a means of exploring human creativity, of arguing implicitly for more humanitarian involvement in African civil wars, and of establishing the full extent of the migrant's "outsiderness" in the space(s) of diaspora.

Advisor: Boehmer, E
The role of tumour necrosis factor alpha stimulated gene-6 on bone

Osteoporosis, a metabolic disorder of the skeletal system, currently affects 200 million people worldwide. Osteoporosis is caused by an imbalance in bone resorption and formation due to either molecular mutations, oestrogen reduction at menopause, oxida-tive stress, as well as life style, leading to a characteristic low bone density and/or thin-ning that predisposes patients to skeletal fracture and breakage upon minimal physical trauma. Depending on the severity of the disease, most patients are often treated with calcium/vitamin D and anti-resorptive drugs such as bisphosphonates or calcitonin. However, there are few options for bone formation using anabolic agents- such as Teriparatide (PTH1-34), which have limited success, creating an unmet need for novel anabolic interventions.
The rapidly-advancing field of osteoimmunology recognises the close and finely-tuned interaction between the immune system and musculoskeletal organisation. In an at-tempt to identify immune-derived cells and soluble factors that induce the differentiation of stem cells towards the osteoblast lineage, the interaction between monocytes and osteoblast precursors has proven a potentially promising approach.
One of the factors identified from this screening was TSG-6 – a secreted protein with immunomodulatory and chondroprotective properties.
This study aimed to generate adequate amounts of biologically active TSG-6 protein to test its role on bone formation in vivo during physiology and disease - using oestrogen-deficiency induced bone loss in mice as a model of osteoporosis. TSG-6 was not found to protect bone tissue against the effects of oestrogen-deficiency induced bone loss, as determined by global TSG-6 knockout and systemic exogenous administration studies. However, local delivery of full-length TSG-6 significantly enhanced mineral apposition rate in a dose-dependent manner, and in vitro studies found TSG-6 significantly enhanced alkaline phosphatase levels of primary bone marrow-derived human mesenchymal stem cells in vitro, in the presence of BMP-2.
Contrary to its previously reported inhibitory effects on osteoblastogenesis, this thesis shows, for the first time, that TSG-6 displays context-specific anabolic properties. This finding implies a therapeutic value for the protein, with possibilities of being used in conjunction with BMP-2 to treat local bone injuries such as fractures.

Advisor: Horwood, N
Sabokbar, A
Mahoney, D
Rhodium-catalysed carbon-carbon bond formation and carbon-sulfur bond functionalisation

This thesis documents the development of synthetic methodologies utilising rhodium catalysis for the formation of carbon-carbon bonds and the functionalisation of carbon-sulfur bonds.
Chapter 1 provides an overview of the two main areas of research discussed in this thesis that include the key developments in the field of intra- and intermolecular rhodium-catalysed hydroacylation, and the major advances in cross-coupling reactions via the catalytic cleavage of carbon-sulfur bonds.
Chapter 2 details the development of a tandem rhodium-catalysed hydroacylation, sulfide elimination and subsequent enantioselective 1,4-conjugate addition sequence allowing the preparation of stereodefined β-substituted ketones. This process enables the formation of two carbon-carbon bonds and offers a general method to access highly functionalised traceless hydroacylation products.
Chapter 3 describes the development of a rhodium-catalysed alkyne hydroacylation, thio-Michael addition sequence in a one-pot fashion. This methodology enables the synthesis of a variety of sulfur-containing heterocycles.
Chapter 4 documents the efforts towards the development of a rhodium-catalysed cross-coupling reaction with alkenyl sulfides and boronic acids via C-S bond activation. This study explores both a tether-free and a traceless tether approach.
Chapter 5 summarises the research and the potential future work.
Chapter 6 provides experimental details and data.

Advisor: Willis, M
The interaction of positive and negative intergroup contact

In the sixty years following Allport's (1954) formulation of the contact hypothesis, very little research has tested the effect of negative intergroup contact. In recent years, several authors (e.g., Barlow et al., 2012; Pettigrew, 2008; Pettigrew & Tropp, 2013) have expressed concern over this positivity bias within the contact literature. In particular, Barlow et al. (2012) presented evidence that negative contact may have a larger effect on prejudice than positive contact. Barlow et al. argue that this contact valence asymmetry could mean that in socially diverse environments (which provide opportunities for both positive and negative contact), negative contact could counteract (or even reverse) the beneficial effects of positive contact. However, a number of studies have shown that rather than combining additively, positive and negative contact may in fact interact (i.e., the effects of negative contact may change depending upon the level of positive contact, and vice versa, e.g., Birtel & Crisp, 2012; Christ, Ullrich, & Wagner, 2008; Paolini et al., 2014). Unfortunately, the extent of evidence for these valenced contact interactions (and indeed for valenced contact effects in general) is severely limited, making it difficult to build any degree of theoretical (or methodological) consensus. The aims of this thesis are therefore twofold: first, to expand the body of evidence for the effects of negative intergroup contact; and second, to test the possible interaction between positive and negative contact as predictors of outgroup attitudes. With these aims in mind, this thesis presents four survey studies and three experiments testing the main effects and interactions of positive and negative contact across six different contact settings. In so doing, it reports strong evidence for the existence of valenced contact interactions. Based on the profiles of these interaction effects, the thesis ends by discussing possible causal explanations, and their implications for the field of valenced contact research.

Keywords: Intergroup Relations
Valenced Contact
Social Psychology
Psychology
Intergroup Contact
Negative Contact
Advisor: Hewstone, M
The architecture of rights

This thesis concerns the various concepts of rights and philosophical accounts of them. Chapter 1 addresses some methodological issues affecting analytic legal philosophy and the philosophy of rights. Chapter 2 distinguishes between two kinds of philosophical accounts of rights: models and theories. Models outline the 'conceptually basic' types of rights, their differences, and their relationships with other kinds of 'normative positions' (e.g., duties, liabilities, etc.). Theories of rights serve two roles: first, to posit a supposed ultimate purpose for all rights; second, to provide criteria for determining what counts as 'a right' in the first place. The chapter also criticises both monistic models (ones positing only a single basic kind) for being under-inclusive and a subset of pluralistic ones (those positing several basic kinds) as over-inclusive.
Chapter 3 clarifies the concepts of rights exercise, enforcement, remedying, and vindication. Chapter 4 explains the Interest-Will Theories of rights debate, while Chapter 5 argues that its constituents are irredeemably flawed, unnecessary, and under-inclusive. Chapter 6 further analyses the concept of rights enforceability, showing why legal rights are not invariably enforceable by legal powers. It then explains why wholly unenforceable legal rights nonetheless constitute 'imperfect' or defective cases. Chapter 7 argues there are more ways to enforce legal rights than just via powers, elucidating two such modes: legal rights can generally be claimed or invoked using legal liberties in private and social circumstances. While Chapter 8 shows why it might not always be possible to make liberty-based claims or invocations of right, it also provides reasons for thinking that legal rights that cannot be enforced in these ways are also imperfect.

Keywords: Philosophy of Law
Philosophy of Rights
Hohfeld
Legal Philosophy
Rights
Jurisprudence
Advisor: Eleftheriadis, P
Exciton dynamics in disordered conjugated polymers

Conjugated polymers have been the subject of many experimental and theoretical studies in recent years, with the interesting behaviour of their low-energy excited states depending on both electron-electron and electron-nuclear interactions, as well as the disorder which is almost universally present in these materials. Their potential use in optoelectronic devices, such as LEDs and photovoltaic cells, adds to this interest, with the behaviour of the low energy excited states being primarily dictated by the π-conjugation.
In this thesis we model the transport of energy in phenylene-based conjugated polymers, where the primary low energy excited states are Frenkel excitons that can be described by the disordered Frenkel-Holstein Hamiltonian. Initially, the eigenstates of this Hamiltonian are investigated using the density matrix renormalization group method. The results of this investigation show that the vibrational phonons of the polymer cause only a small change in the exciton wavefunction, while the relevant torsional normal modes are low enough in frequency that they can be treated classically. This allows the exciton states in the dynamics simulations to be calculated using the more numerically tractable Frenkel Hamiltonian with the coupling of the exciton to the vibrational modes being treated by the inclusion of appropriate polaron binding energies in the energy of the state and of Franck-Condon factors in the transition rates.
The first dynamics simulations are an investigation into the intramolecular motion of excitons on polymer chains in solution, where it is the torsional motion of the polymer chain, modelled by a Langevin dynamics algorithm, that is the main driving force behind the exciton transport. The exciton motion in the solid state, where the exciton motion results mainly from intermolecular Förster resonant exciton transfer, is then investigated, with a Monte Carlo algorithm being employed to determine the exciton diffusion length for various polymer morphologies.

Advisor: Barford, W