VictorJuiz/thesis huggingface dataset:
The iridium-catalysed alkylation of aromatic ketones via hydrogen borrowing
Keywords: Hydrogen Borrowing
Organic Synthesis
Catalysis

This dissertation explores how the scope of hydrogen borrowing reactions can be further expanded to use both primary and secondary alcohols to form α-, β- and α,β-branched aryl ketones. ortho Substituents were critical in enabling the hydrogen borrowing alkylation by inducing a non-coplanar geometry of the aryl–ketone motif, which provides various beneficial effects that contribute to the success of the reaction.
The versatility of the hydrogen borrowing reaction was further improved by introducing a vinylcyclopropane rearrangement into the reaction manifold prior to enone reduction. Control studies and modified substrate provide insight into the mechanism of the reaction.
The synthetic utility of pentamethylphenyl (Ph*) ketones was enhanced through electrophilic cleavage to form various carboxylic acid derivatives. Phenol derivatives of Ph* ketones were also found to undergo a related oxidative cleavage of the derivatised Ph* group to form esters and carboxylic acids.
Phenol and aniline derivatives of Ph* ketones formed tetrasubstituted α-keto centres in the hydrogen borrowing reaction, a remarkable result that could not have been possible using conventional aldol chemistry. Attempts were made to explore the formation of tetrasubstituted α-keto centres in the hydrogen borrowing reaction with other aryl ketone derivatives.
Structural changes were observed by X-ray crystallography that were consistent with the alleviation of steric interactions between the aryl group and ketone substituent, providing evidence that ortho-substitution provides multiple benefits that drive the hydrogen borrowing reaction. Substituents at the meta and para positions of the aryl ring result in structural distortions that are directly responsible for the "buttressing" effect. IR, 13C and 15N NMR spectroscopy were also employed to study the effects of non-coplanar geometries of the amino, nitro and carbonyl groups.
Non-contact monitoring of respiration in the neonatal intensive care unit
Keywords: neonatal
breathing rate
camera
physiological signs
respiratory rate
apnoea
non-contact monitoring
respiration
vital signs

Camera-based monitoring is an emerging sensing modality which has attracted widespread interest due to its potential to offer comfortable and concurrent measurements of the cardiorespiratory vital signs: the cardiac pulse rate, respiratory rate and peripheral capillary oxygen saturation.
In recent years, several methods have been proposed for the processing of visible and infrared video data and subsequent extraction of the respiratory rhythm. However, due to the low signal-to-noise ratio (SNR) of these signals, their application has so far been limited to adult subjects and controlled research environments. In this thesis, we aim to improve the signal processing aspects of non-contact respiratory measurements by developing a novel technique for extracting this signal in a clinical setting. The main contribution of this work is a multi-channel source separation method which combines information from multiple image domains and uses a priori information about the distinctive temporal structure of the signal of interest to improve the quality of the respiratory signal extracted.
Considering the neonatal breathing component as an extreme case of poor SNR in video signals, we present a case study of the extraction of respiratory signals from video signals recorded from a CCD camera placed above an incubator inside which critically-ill infants are nursed. Evaluation results were obtained from recordings on 30 neonatal patients nursed in the Neonatal Intensive Care Unit at the John Radcliffe Hospital, Oxford, UK. The respiratory signals extracted using the methodology described compare favourably against those derived from direct and indirect sources during periods of manual breath counts. In addition, we show that a classification algorithm which uses features of these signals to identify periods of cessation of breathing can successfully distinguish between true and artefactual decreases in respiratory rate in a range of critically low values of this vital sign.
Oil and state capture: the subnational links between oil revenues and armed conflict in Colombia
Keywords: Royalties
Subnational governments
Resource curse
Colombia
Armed clientelism
Armed conflict
Oil

While there is strong evidence of the association between oil wealth and internal armed conflicts, the literature is less conclusive about the processes linking the two. Despite myriad mechanisms hypothesised by the literature, much uncertainty still exists about the causal pathways between oil and armed conflicts. How does oil revenues affect the occurrence and course of internal armed conflicts in contexts of political decentralisation? The main argument of the thesis is that the control of abundant oil revenues by subnational governments contributes to shape the strategies undertaken by armed groups at the local level. Subnational governments become a prize for armed groups, which pursue oil revenues through the political capture of local democracy. The armed groups interfere with democracy through a mix of violent and non-violent strategies. The thesis identifies political connections between oil revenues and armed conflicts and traces mechanism which I term the subnational-government-as-target. The pathway contributes to explain how oil revenues can undermine the workings of the subnational government through the dynamics of the armed conflict.
A comparative case study approach was implemented to examine how oil revenues affected conflict and public management at the subnational level in Colombia. Drawing on data collected over five months of fieldwork in oil-royalty-abundant municipalities, the thesis also constitutes one of the first studies to examine the effects of oil revenues accrued by non-oil-producing municipalities in Colombia. The qualitative and quantitative data was triangulated to carry out a process-tracing analysis covering the period from the early 1960s to 2017.
Bridging the gap between JavaScript analysis and web analysis
Keywords: Web page analysis
Web forms
Symbolic execution
JavaScript
Program analysis
Web information extraction
Concolic testing
Software testing

This thesis presents my work towards web interface analysis and web data extraction by making connections between high-level user actions on web pages and the corresponding low-level implementation details.
I have developed a concolic testing platform for web-based JavaScript code, which can be used to analyse JavaScript running as part of live web pages without support from the developers. This platform is used as the basis for ArtForm, a tool which analyses web forms to infer their validation constraints. This involves simulating which actions and input values are available to a real user at the interface. ArtForm includes a suite of manual analysis tools which demonstrate the concolic testing platform and allow manual tracing of JavaScript execution for low-level debugging. The concolic platform has also been applied to the problem of event delegation, where it can be used to determine which elements on a page will respond to user actions, and should therefore be considered interactive. Finally, ArtForm can be connected to third-party analysis tools to provide advice on which values and actions are likely to lead to new code paths being explored, thus extending the client tool with low-level analysis results about the targeted site.
I also present work on optimising data extraction wrappers. By analysing the low-level HTTP calls corresponding to the user-level actions made by typical browser-based wrappers, it is possible to synthesise new, equivalent wrappers which can run without a browser. These optimised wrappers can provide a drop-in replacement for many data extraction tasks, with a huge performance benefit.
Community- and ecosystem-level effects of insect herbivory on oak (Quercus robur)
Keywords: Herbivory
Caterpillar
Winter moth
Oak
Photosynthesis
Wytham Woods
Polyphenol

The interactions between plants and their insect herbivores are among the most common ecological interactions. By feeding on plant tissue, insects can influence plant physiology and chemistry, with potential implications for other herbivores associated with the same host plant and for ecosystem-level processes mediated by the plant.
In this thesis, I studied the community and ecosystem-level effects of insect herbivores associated with the pedunculate oak (Quercus robur, L.) in temperate woodlands in Oxfordshire, UK. First, I studied how early-season moth caterpillars affect photosynthesis and selected physical and chemical leaf traits. I then examined how herbivore-induced changes in the host plant affect tree performance, the structure of the sessile herbivore community associated with the host tree, canopy-level carbon sequestration, and forest-level primary productivity.
My work shows that moth caterpillars can substantially reduce the photosynthetic rate of their host plant. These leaf-level changes can reduce canopy-level carbon sequestration, and therefore affect the primary productivity of the ecosystem. In this system, insect herbivory did not affect any of the studied leaf traits, tree performance, or the structure of the herbivore community. Leaf chemical composition varied substantially between individual trees, was affected by the growth location of the tree, and covaried significantly with the associated insect community.
My results suggest that insect herbivores can have important ecosystem-level effects by inducing small-scale changes in the primary metabolism of their host plant. My work also emphasises the importance of abiotic conditions in influencing plant chemistry, and plant chemical composition in shaping the plant-associated insect community. I stress the need to quantify the effects of insect herbivores on carbon cycling in other systems and to include these effects in models on ecosystem productivity and biosphere-atmosphere interactions.
Reason to hope: economic, social and ecological virtuous circles in Chiapas, Mexico
Keywords: coffee
Stephen Gudeman
indigenous
Chiapas
Mision de Bachajon
social and solidarity economy
food sovereignty
Jesuits
agroecology
Tseltal

Today’s dominant economic system does harm and has little future; agro-food systems are a privileged lens for understanding both what is happening and what is at stake. There is reason to hope; many actors are experimenting with alternative models for a life-giving economy that combine agroecology, food sovereignty, and social and solidarity economy. This thesis is an exploration of one such initiative, the Misión de Bachajón (MB) in Chiapas, Mexico. In Chapter 1, I build a theoretical framework based on the economic anthropology of Stephen Gudeman. All economies consist of a dialectic tension between the realm of the market and the realm of mutuality. To ensure sustainability, the latter realm must be protected from the former’s tendency to colonize it. Chapter 2 explains my ethnographic, collaborative research design. Chapter 3 is an account of the MB’s overall project, which entails a sophisticated "middle peasant" model. On the one hand, the things that are essential for the community’s reproduction are withdrawn from the market. At the same time, though, the MB’s group of cooperatives and social businesses, Yomol A’tel, creatively engages global value chains (coffee and honey) from a position of strength. Chapter 4 shows how the model goes beyond "fair trade" to achieve very significant economic upgrading, in a way that benefits people and ecosystems. I argue that the MB’s model generates economic, social, and ecological virtuous circles by refashioning "economy’s tension" into a creative tension. Chapter 5 considers how the MB has achieved all of this by mobilizing its relationships with other actors. Its strategy of networked territories is not only a form of resistance to neoliberal globalization, but also contributes to building the "pluriverse," a world in which many worlds fit. In the Conclusion, I consider the ways in which the MB gives us reason to hope.
Normothermic kidney preservation
Keywords: Perfusion
Kidney transplantation
Urine recirculation
Preservation
Transplantation

The thesis describes the development of a transportable normothermic kidney preservation device which is able to perfuse discarded human and porcine kidneys for up to 24 hours for the very first time. Recirculation of the urine to facilitate maintenance of perfusate volume and homeostasis is a novel approach. Utilisation of this perfusion device could enable viability assessment, decrease organ discard rate and improve transplantation logistics. Thirty-six clinically declined human kidneys were perfused, 19 from donors after brain stem death and 17 from donors after circulatory death: n=4 kidneys were perfused using Ringer’s lactate to replace excreted urine volume, and n=32 using urine recirculation. In all cases, normothermic perfusion either maintained or slightly improved the histopathologically assessed tubular condition, achieved physiological arterial flow levels and effective urine production. Biomarkers, neutrophil gelatinase-associated lipocalin (NGAL), kidney injury molecule-1 (KIM-1) and liver fatty acid-binding protein (L-FABP) were detected and quantified in the perfusates with and without urine recirculation. NGAL could be promising for clinical use, as it was inversely correlated with median arterial flow. Only kidneys with urine recirculation were readily perfused up to 24 hours and exhibited physiological perfusate sodium levels, whilst kidneys without urine recirculation achieved reduced normothermic perfusion time and significantly higher perfusate sodium. Metabolomics analyses of perfusate samples detected urea and two sugars as the main difference between kidneys with and without urine recirculation. Proteomics analyses not only revealed that human kidneys have become metabolically active during normothermic perfusion, but they also detected that damage-associated molecular patterns known to contribute to ischaemia-reperfusion-injury, were significantly downregulated in biopsies from kidneys with urine recirculation compared to kidneys without. As a final part, porcine perfusion studies were performed with the aim to revisit the findings obtained during the human experiments and to render a valid comparison between urine recirculation and urine replacement in undamaged kidneys.
Funding flows for freshwater: the role of philanthropy in market-based freshwater conservation
Keywords: philanthropy
philanthrocapitalism
market-based
freshwater conservation

As freshwater development progresses around the world, institutions must shift from the paradigm of exploiting water resources towards managing water scarcity in a way that maintains adequate environmental flows to support the river’s functioning, biodiversity, and many ecosystem services. Amidst the rise of market environmentalism, market-based solutions have gained popularity as a promising approach to reallocate water from existing uses to in-stream environmental purposes. Successful water transactions require a number of enabling conditions; this dissertation explores these conditions, the ways in which they are created, and the role of different actors in facilitating institutional change. The results indicate that philanthropic funders play a major role by enabling collective action, encouraging collaboration and efficiency in creating the necessary preconditions for successful transactions. This is connected to literature on philanthrocapitalism and the role that foundations play in shaping conservation discourse.
Incentives for international publications in the humanities and social sciences: an exploratory study of Chinese universities
Keywords: China
Humanities and social sciences
Research incentives
International publications
Higher education

This research aims to investigate how Chinese universities have attempted to incentivise academics in Humanities and Social Sciences (HSS) to publish in internationally-indexed journals, in response to increasing emphasis on internationalisation in national policies and political discourses. In addition, it explores how HSS academics’ research activities and careers have been influenced by those incentives. Institutional incentives used monetary and career- related benefits to prioritise international publications, especially publications in journals indexed by the Social Sciences Citation Index (SSCI) and the Arts and Humanities Citation Index (A&HCI;). This phenomenon has provoked heated debates in China, particularly seen as detrimental to domestic publications and to other academic activities. The thesis aims to address the lack of systematic research on the scale and structure of those incentives in Chinese universities, and the lack of research on the incentive schemes’ influences on HSS academics’ research and careers.
The study applied a multiple-case study design, including six research- intensive universities in China, indicative of ‘985’ and ‘211’ universities in Chinese policy terms. It drew on interview data with 65 HSS academics, six senior university administrators, and four HSS journal editors in China. The study also included a documentary analysis of 172 institutional incentive policy documents across 113 of the ‘985’ and ‘211’ universities.
This research revealed that 84 out of the 113 research universities have been employing monetary bonuses or career-related incentives to promote HSS international publications. Incentives varied in their aims, the level of benefits, specific requirements, and models of policy-making. The findings suggested that higher prestige was being attached to SSCI and A&HCI; publications, as demonstrated by the higher bonus value for them and higher status in academics’ career development. The study also found that academic interviewees’ responses to incentives clustered around four profiles: proactive, adaptive, resistant, and hesitant. Academics from different sub-groups and various backgrounds reported direct and indirect influences of incentive schemes on their research and careers.
The theoretical contributions of the study include a conceptualisation of academics’ responses to research incentives, and a proposed framework for understanding the relationship between incentives and international publications. It identified specific dynamics in Chinese HSS, which challenged the widely-used centre-periphery model for explaining the internationalisation of knowledge production. It also reflected on unintended influences of incentives for HSS international publications. Drawing on the discussion, the thesis proposes implications for institutional policymaking and directions for further studies.
Phenotypic modelling of the polyfunctional T cell response
Keywords: T lymphocytes
T cells
Cancer Immunotherapy
Cell Signalling
Adaptation
Immunology
Systems Biology

T cells are important mediators of adaptive immunity and promising agents in immunotherapies. When T cell receptors (TCRs) on the surface of CD8+ T cells detect pathogenic peptides presented by major histocompatibility complexes class I (pMHC) on antigen-presenting cells (APCs), a complicated intracellular signalling process is initiated that results, among other functional responses, in the secretion of cytokines to fight the pathogenic threat. An overwhelming number of molecular components that are involved in the translation of the pMHC stimulus into an appropriate cytokine response have been identified, but a mechanistic understanding of how the quality of the pMHC stimulus, i.e. pMHC dose and affinity, determines the response phenotype is lacking. Here, reductionist T cell stimulation experiments were combined with a coarse-grained phenotypic modelling approach to identify prevailing modules that shape the phenotype of cytokine secretion in response to stimulation with pMHC. CD8+ primary human T cells transiently produced the four cytokines TNFα, MIP-1β, IFNγ and IL-2 and adaptation was paralleled by rapid and sustained TCR downregulation. Direct fitting of a phenotypic model constructed from known features of T cell signalling to the experimental data showed that TCR downregulation was sufficient to explain adaptation as well as other striking features of the cytokine response, including high-dose suppression (bell-shaped dose-response curve). Interestingly, secretion of TNFα, MIP-1β, IFNγ and IL-2 ceased at similar time scales and appeared equally sensitive to pMHC dose and affinity, contrary to previous reports. These findings thus suggest that T cells possess an intrinsic adaptation mechanism and reveal a surprisingly uniform early activation phenotype for multiple cytokines.
Apathy and effort-based decision making: a cognitive mechanism underlying amotivated behaviour
Keywords: Foraging
Motivation
Apathy
Dopamine
Decision making
CADASIL
Parkinson's Disease
Reward

Apathy is a common, debilitating but poorly understood disorder of motivation that manifests in reduced goal directed behaviours. The integration of cost and reward information about potential actions is central to normal motivated behaviour. This thesis will argue that disruption of this normal process – often termed effort-based decision making – underlies the clinical syndrome of apathy.
Two broad sets of questions are investigated to address this hypothesis, in clinically apathetic patients with either Parkinson’s disease (PD) or a genetic form of cerebral small vessel disease (SVD). Firstly, are apathetic patients hypersensitive to effort costs, or insensitive to rewards when making decisions about potential actions? Do these changes associated with apathy map onto physiological alterations in reward processing and disruption of anatomical regions that underlie normal effort-based decision making? And do these behavioural changes occur along the same axis as those induced by dopamine depletion? Secondly, using an ecological framework of decision making in which participants must compare current (foreground) reward information to the background reward context to guide adaptive behaviour, this research explores whether apathy is associated with aberrant use of background reward information, and how this interacts with the dopaminergic system.
The studies demonstrate effort-based decision making is disrupted in patients with apathy, driven by reduced incentivisation by the rewarding outcomes of actions rather than hypersensitivity to effort costs themselves. Reward insensitivity manifests in both behavioural choices and physiological responses to incentives, is associated with reduced white matter integrity in tracts connecting regions crucial for effort-based decision making, but occurs along a separate mechanistic axis to changes induced by dopamine depletion. Furthermore, whilst healthy human decision makers are remarkably sensitive to changes in background reward environment, apathy changed the influence of this information – dependent on dopaminergic tone. Together, the work in this thesis presents evidence that disruption of a specific cognitive process underlies the apathetic syndrome. This advances understanding of normal motivated behaviour and identifies potential therapeutic avenues to treat this important clinical syndrome.