VictorJuiz/thesis huggingface dataset:
Up-down ordered Chinese Restaurant Processes: representations and asymptotics
Keywords: scaling limit
branching diagram
Ray-Knight theorem
Chinese Restaurant Process
stable process
composition
mixing time
Kingman lattice
squared Bessel process

We study composition-valued Markov chains that appear naturally in the frame-work of up-down Chinese Restaurant Processes (CRPs), introducing first discrete time models as in a similar way to those introduced by Petrov (2009), and also in continuous time via a Poissonisation technique similar to that used in Pal (2011).
As time evolves in the continuous time model, new customers arrive (up-step) and existing customers leave (down-step) at suitable rates derived from the ordered CRP of Pitman and Winkel (2009). We relate such up-down CRPs to the splitting trees of Lambert (2010) inducing spectrally positive Lévy processes. Conversely, we develop a theorem of Ray–Knight type to recover more general up-down CRPs from the heights of Lévy processes with jumps marked by integer-valued paths. We further establish limit theorems for the Lévy process and the integer-valued paths that connects to work by Forman et al. (2018+) on interval partition diffusions.
Fulman 2009 shows that the framework of commutation relations can be used to study the behaviour of discrete time down-up Markov chains, and he applies this to the unordered up-down (α,θ)-CRP from Pitman 2006. We demonstrate that these techniques still yield valid results when applied to the ordered down-up (α,θ)-CRP of Pitman and Winkel 2009, and generalise a theorem of Fulman 2009 on the explicitform and asymptotics of the maximal separation distance from the case θ= 1 to general the case θ > 0.
Seeing the utan from the orang:  A decolonial Indigenous approach to orang utan conservation in Sarawak. 
Keywords: Sarawak
indigenous
Borneo
decolonial
orangutan
conservation

This thesis takes an Indigenous decolonial turn for a rich, empirical analysis of the seemingly paradoxes of human-environment or human-animal relationships within the multi-scalar forces of conservation. Indigenous relations is more-than-human relations and further, necessitates fresh inquiry into specific politics and strategies of concealment that rural Indigenous communities may employ in response to conservation actions. This thesis seeks to understand the multiple Indigenous strategies to maintain relations with lands and orang utans through an interdisciplinary approach of decolonial and political ecology frameworks, including decolonizing ethnographic methods. In considering human-orang utan relations in ecological time and subtle Indigenous responses to conservation forces and action in Sarawak, Malaysian Borneo, I build on lndigenous decolonial and political ecology frameworks, including Vizenor’s (2008, 1999) Indigenous survivance and Simpson’s (2007, 2014) politics of refusal. I demonstrate the multiple ways human-orang utan relations are realized within the power relations of conservation work. These findings provide a theoretical and decolonial grounding of understanding the different ways of Indigenous Iban presencing, and provide a way forward in developing a decolonial political ecology of orang utan conservation.
Learning models in quantum computation and quantum control
Keywords: Quantum machine learning
Quantum mechanics
Quantum computation

We investigate learning models for implementing arbitrary unitary operations and perform quantum machine learning tasks. First, we discuss efficient constructions for building unitary transformations in U(d), thus providing upper bounds on the minimum time required to implement them. Second, we study the hardness of learning unitary operations in U(d) via gradient descent on the time parameters of an alternating operator sequence, and numerically find that, despite the nonconvexity of the loss landscape, gradient descent always converges to the target unitary when the sequence contains d2 or more parameters. Third, we introduce the first quantum boosting algorithm for converting a weak quantum learner into a strong accurate quantum learner for a Boolean concept class C; thereby achieving a quadratic quantum improvement over classical AdaBoost in terms of VC(C).
A Franc appraisal: the political economy of macroeconomic policy in the CFA zones
Keywords: Francophone Africa
Macroeconomics
CFA franc
Post-colonial
Africa
Monetary unions
Macroeconomic policy
Currency unions

This thesis analyses how economic policies and outcomes in 14 countries in Western and Central Africa are shaped by the CFA franc monetary arrangement with France. This is a complex institution that reflects tensions between macroeconomic policy considerations, ambitions on regional integration and the reality of post-colonial international relations. In light of increasing scrutiny, and reforms announced in 2019, the three main chapters examine leading contemporary issues and contribute to the current debate concerning the future of this Franco-African arrangement.
The first chapter analyses how a fixed exchange rate may restrict the ability of low-income, resource-rich economies to reap long-term benefits from natural resource endowments. Through the lens of the so-called resource curse, CFA members are shown to have a less favourable experience than neighbouring non-CFA countries.
The second chapter considers how the CFA arrangement may influence fiscal policy decisions in unintended and undesirable ways. The empirical findings show fiscal policy to be on an unsustainable path in the zones. They also show that countries’ fiscal stances are affected by the policies of fellow member countries, and that this effect is much stronger than in non-CFA Sub-Saharan African countries. Lastly, it argues that conventional fiscal frameworks are inadequate to address such an unconventional arrangement.
Chapter Three argues that a number of the economic and political factors that have supported the continuation of the CFA arrangement have receded markedly over the six decades since its members gained independence. In addition, policy restrictions imposed by the arrangement remain as relevant as ever, as the prior two chapters highlight.
Brought together, these chapters paint the CFA arrangement as increasingly difficult to justify in its current form from an economic and political perspective. However, the thesis conclusion describes why a growing case against the CFA franc may not be enough to precipitate sweeping changes.
The HMGB1-CXCL12 heterocomplex and its interaction with CXCR4 as a target for tissue repair
Keywords: CXCL12
HMGB1
CXCR4
DAMPs

Reduced High Mobility Group Box 1 (HMGB1) protein binds to CXC Ligand 12 (CXCL12), signals through CXC Receptor 4 (CXCR4) to promote tissue regeneration and accelerates repair by transitioning stem and progenitor cells to GAlert. Therefore, administration of fully reduced HMGB1 (FR-HMGB1) could prove beneficial in clinical practice. However, local conversion of FR-HMGB1 to the disulfide form (DS-HMGB1) may result in deleterious inflammation through signalling via Toll-Like Receptors 2 and 4, and the Receptor for Advanced Glycation End Products (RAGE).
Engineering HMGB1 to eliminate these potentially deleterious properties requires knowledge on the mechanism of its interaction with CXCL12, for which there is sparse literature. I identified the residues involved in formation of the heterocomplex using a combination of peptide arrays, biolayer interferometry and nuclear magnetic resonance. With these, and the published literature on the interaction of HMGB1 with its proinflammatory receptors, I designed a panel of HMGB1 derivatives aimed at removing the deleterious activities. I identified a construct comprising two HMG B Boxes in tandem (DbB-HMGB1) which is unable to signal through either TLR-2 or TLR- 4 and has greatly decreased RAGE binding but retains regenerative activity equivalent to FR-HMGB1 in vivo and in vitro.
A CRISPR-Cas9 screen for hepatocyte receptors for malaria parasite invasion
Keywords: CRISPR
sporozoite
liver stage
CRISPR-Cas9
malaria

More than 2 billion people are at risk of contracting malaria, and around half a million die every year. Malaria is transmitted by sporozoites from Anopheles female mosquitoes to human host during a blood meal. From the host dermal layer, sporozoites travel to the liver, traverse through multiple hepatocytes until stopping in one last cell. They then establish a productive cell invasion, followed by a parasitophorous vacuole formation. Inside this vacuole, sporozoites develop into thousands of merozoites which are later released by hepatocyte rupture. Then, merozoites travel to the blood vessel to invade erythrocytes where malarial clinical symptoms appear– as such, preventing the liver stage infection can protect infectees from clinical onset. However, the liver stage remains a poorly understood malaria stage today owing to its complex molecular cell invasion mechanism. Therefore, in order to understand how sporozoites establish a hepatocyte invasion and which host cell surface receptor-sporozoite surface ligand interaction is involved in this event, CRISPR-Cas9 screen technology was applied in this study. 480 genes were knocked out, and their impact on the sporozoite invasion was assessed. Initially, results showed ITGAV, RPN1, ATP2B1, TMEM30A, FCGR2B, ITGB5, SLC35A2, MGAT1, EMC1 and APOH genes as hits. Amongst these, ITGAV and ITGB5 (αVβ5 integrin) were investigated as αV-integrin is a known binding partner of TRAP. However, further experiments revealed that ITGAV and ITGB5 hits were false positives induced by a lack of cell adhesion due to integrin disruptions rather than a direct binding activity with the sporozoites. Nevertheless, the CRISPR-Cas9 screen method used for this study remains a useful tool in studying hepatocyte-sporozoite protein interactions due to its success in identifying hepatocyte surface proteins, SR-B1 and ApoH, which are known to be important for the malaria liver stage. Therefore, this study presents an effective method to study parasite-host protein relationships by incorporating a sporozoite invasion assay with a CRISPR-Cas9 screen.
Effects of altering CpG dinucleotide composition in small DNA viruses
Keywords: CpG dinucleotide
TpA dinucleotide
zinc antiviral protein
codon optimisation
minute virus of mice
parvovirus

CpG dinucleotides are underrepresented in mammalian genomes and in many viruses infecting them. Previous studies have shown that increasing CpG frequencies in various RNA viruses and retroviruses reduces replicative fitness but the effects of this compositional modification are unknown in DNA viruses. To investigate this, the effects of increasing CpG frequencies were determined in the parvovirus minute virus of mice (MVM) at various stages of the viral life cycle and a system was set up for the murine polyoma virus (MPyV).
Part of the VP gene (24.4 % of the viral genome) of MVM was replaced by synonymously coded inserts with a CpG-high sequence and several other compositional mutations. Infection time courses and TCID50s were performed to test replicative fitness. Genome copy numbers and viral RNA levels were measured via RT-qPCR. Immunofluorescence, western blots and in vitro translation were used to visualise and measure protein production and distribution. Knockout cell lines were used to find antiviral mechanisms involved.
Compared to the wild type and scrambled virus, CpG-high viruses showed impaired growth curves in vitro. Immunofluorescence assays showed that the CpG-high viruses could establish infection and protein production in fewer cells. RT-qPCR revealed that viral mRNA levels were reduced in the CpG-high mutant, a phenotype that partially reverted in ZC3HAV1 (ZAP) knockout cells.
Increasing CpGs in MVM led to reduced mRNA levels, which impacted all aspects of the viral life cycle, leading to fewer productively infected cells and reduced viral progeny numbers though there might be further restriction later in the replication cycle. This is thought to be due at least in part to selective recognition of CpGs in RNA by ZAP.
Mechanics and control of perching flight
Keywords: flight
motion capture
eagle
landing flight
flight control
bird flight
flight kinematics
Harris hawk
wing motion
flight mechanics
morphing wings
perching

Perching is an example of high risk, high reward behaviour executed within tight physical constraints. Despite the high risks posed by collision and stall, perching is performed routinely by most birds. However, surprisingly little is understood about the energetics and control of aerodynamic braking, nor the detail of wing and tail kinematics during perching.
In this thesis, detailed wing and tail kinematics were quantified for over 1000 indoor perching flights by Harris hawks using high-speed motion capture. Similar measurements were also taken from 15 outdoor flights by a Steppe eagle, and trajectories were tracked from wild passerines landing on a fixed or oscillating feeder. Aerodynamic braking is typically achieved in raptors through a rapid pitch-up manoeuvre executed at the end of a gliding approach. This manoeuvre produces high drag as predicted by published unsteady aerodynamic models, but unexpectedly the data shows no accompanying peak in lift. The complexity of wing-tail morphing and rotation during the rapid pitch-up manoeuvre points to the careful control of aerodynamic forces during unsteady deep stall.
A high degree of variation in the perching manoeuvre was evident in the Steppe eagle flights, likely in response to local air conditions. However the hawk flights were exceedingly consistent under the controlled experimental conditions. Different perch distances were used to induce variation in the hawks’ braking strategy. Braking was achieved in a flapping rather than gliding approach in the shortest flights, although the observed pattern of body pitch-up was consistent across flight distances. Systematic inter-individual variation was recorded in both wing motion and trajectory shape.
As a visually-guided flight behaviour, braking is controlled precisely with respect to the target such that the bird may land with low impact force and avoid injuries. Flights from the eagle and hawks show evidence for control of braking in line with the predictions of tau theory: during approach to the perch, both the rate of change in the optic flow variable tau and the rate of deceleration were constant. This was not the case for wild passerines using intermittent flight, although they might still use optic flow in feedback control.
Towards healthier diets and more sustainable food systems: Developing and evaluating behavioural interventions to reduce meat consumption
Keywords: sustainable food systems
healthy diets
systematic review
meat consumption,
randomised controlled trial
behavioural science

Producing meat generally leads to greater greenhouse gas emissions, deforestation, water use and pollution, and biodiversity loss compared to producing plant-based foods. While there are many supply-side measures that can help to mitigate livestock’s environmental impact, substantively reducing meat consumption is required to ensure that food systems can sustainably feed the growing global population and would result in some benefits for human health too. Behavioural interventions to encourage changes in eating habits could help to reduce meat intake, but few such interventions have been implemented and rigorously tested. The aim of this thesis is to contribute towards addressing this evidence gap by generating empirical evidence on the effectiveness of behavioural interventions to reduce meat consumption through (i) systematically reviewing and synthesising the evidence on the effectiveness of interventions targeting conscious behavioural determinants or restructuring physical micro-environments; (ii) the development of a novel behavioural intervention (Replacing Meat with Alternative Plant-based Products, RE-MAP) to reduce meat consumption through the provision of meat substitutes, infographics, success stories, and recipes; (iii) a randomised trial evaluating the impact of RE-MAP on meat consumption, wider dietary changes, markers of health risk, markers of environmental degradation, and psychosocial factors related to meat and meat substitutes consumption; and (iv) qualitative interviews exploring the mechanisms through which the intervention might have delivered impact and recipients’ experiences of the intervention. The results of my DPhil suggest that some behavioural interventions targeting conscious determinants of human behaviour and restructuring physical micro-environments can help to reduce meat consumption. Providing meat substitutes for four consecutive weeks along with supporting informational material is an acceptable strategy to help people eat less meat and emerged as one of the most effective interventions to reduce meat consumption tested to date. Specifically, RE-MAP led to a 63 g/d reduction in meat consumption at the end of the intervention and a 39 g/d reduction four weeks after the intervention completion. Based on these findings, future research should investigate how to translate the active components of the RE-MAP intervention into a scalable policy option.
Sigma-hole non-covalent interactions in anion host-guest chemistry and the mechanical bond
Keywords: Halogen Bonding
Supramolecular Chemistry
Intermolecular Interactions
Macrocycles
Rotaxanes and Catenanes
Mechanically Interlocked Molecules
Chalcogen Bonding
Host-Guest Chemistry

This thesis describes the use of σ-hole interactions in acyclic, macrocyclic and mechanically interlocked receptors for anion recognition and sensing.
Chapter 1 provides an overview of the field of supramolecular host-guest chemistry with particular focus on host systems bearing σ-hole donor motifs for anion guest binding, followed by a discussion of mechanically interlocked host molecules for anion recognition and sensing.
Chapter 2 describes the synthesis of air and water stable acyclic tellurium and selenium-based chalcogen bonding receptors followed by an investigation of their thermodynamic anion binding properties in organic and mixed aqueous/organic solvent media. The integration of halogen bonding and chalcogen bonding motifs into mechanical interlocked molecular structural frameworks is also explored.
Chapter 3 details combining σ-hole donors and the BINOL motif to form chiral host receptors. The synthesis of a chiral halogen bonding [2]rotaxane structure is described as well as chiral acyclic and macrocyclic receptors possessing four integrated halogen bond-donors which are shown to be capable of binding chiral carboxylate anions. The enantioselective properties of these receptors were determined by monitoring the fluorescence changes of the respective receptor’s integrated BINOL or pyrene fluorophore upon chiral anion guest binding.
Chapter 4 introduces the use of halonium cation species in supramolecular chemistry. Primarily, this chapter investigates the stability of iodonium species in pyridyl-based pseudorotaxane assemblies and mechanically bonded [2]rotaxanes using NMR spectroscopy.
Chapter 5 summarises the conclusions of this thesis.
Chapter 6 describes the experimental procedures carried out in this work detailing characterisation of novel compounds presented in chapters 2-4. Additional information pertaining to crystallographic data and computational work are provided in the Appendices.
Paperscapes: navigating books in Early Modern England
Keywords: paper
navigation
emblem
early modern
john taylor
volvelle
londinopolis
book history
renaissance
imprint
library
material texts
bookshop
samuel pepys
history of reading
print

This thesis attends to the place of paper in early modern literature, both in actuality and in imaginary form. While a conventional set of (often gendered) tropes holds paper to be passive, blank, and static, these four chapters attend to texts and sites which resist those tropes, and which foreground paper’s role as an intellectual-material site that is both agentic and mobile. Paperscapes: Navigating Books in Early Modern England fuses literary scholarship, bibliography, and book history to engage with the affordances of paper as textual substrate and material form.
The structure of this thesis foregrounds paper on the move. The chapters focus on the paper volvelles that direct readers around George Wither’s Collection of Emblemes (1635), whose verse enables spiritual as well as bibliographic modes of navigation; on the stories that imprints tell about paper’s journeys through the city, which collide with the textual routes of James Howell’s Londinopolis (1657); on the moving sheets and books which trouble the rhetoric of Samuel Pepys’ aspirationally static library; and on the global narratives of circulation in which John Taylor’s The Praise of Hempseed (1620) implicates paper. Paperscapes takes its structure from actual sites through which paper moves – the book, the city, the library, and the globe – while simultaneously asserting that paper as substrate makes room for the texts in which imaginary journeys of readers and books play out. Reading early modern printed texts was and is to encounter paper in a contingent place and form. Noting both that paper moves around, and that place matters for how we read, this thesis argues that the mobility of paper has literary implications in unsettling the meaning of text. Paperscapes reverses the suggestion that ‘text is more legible than its substrate’, and provides a paper counterpoint to the codex which is grounded both in material readings and in the early modern imagination.
Affect and materiality in therapeutic spaces. A contemporary archaeology of hospices.
Keywords: Affect
Hospices
Material engagement theory
Homecoming
Wellbeing
Atmosphere
Architecture
Heidegger

Through a series of case studies I explore the affective impact of the therapeutic spaces of hospices on the communities they serve, their staff, volunteers and users. Hospices provide services for those with life-limiting conditions. Cure is not possible, the subjective wellbeing of patients and their loved ones is thus paramount. Hospices deliver a range of palliative care interventions but what distinguishes hospices is their buildings which have the potential to contribute to the enhancement of wellbeing. Drawing on Material Engagement Theory (MET), enactivist perspectives on affect, Heideggerian conceptions of dwelling, the philosophy of atmosphere, the theory of wellbeing and other resources I explore the therapeutic mechanism of hospice spaces. I argue that atmospheres are the affordances of Ingold’s “weather world” and are at least as important as the affordances of the object world. Therapeutic spaces exercise their agency through permutations of affordance and atmosphere which facilitate or constrain forms of affect/movement of the material and felt bodies of those who use the buildings.
I argue that through mechanisms of “enactive signification” hospice buildings mobilise the support of the communities they serve and concretise their identity. I suggest that changing regimes of clinical care are in unrecognised conflict with some aspects of the original philosophy of hospice care, which was closely aligned with Heidegger’s concept of “dwelling”, and that this conflict threatens the identity and sustainability of the hospice movement. I provide a number of illustrations of the ways in which aspects of design contribute to the experience of both hospice users and community and I make a number of suggestions as to how hospices could navigate the implications of changing regimes of care and how the differing functions of the hospice may be combined and facilitated by their design. This analysis of the relationship between mind and architecture opens an underexplored domain of research into MET, phenomenology, the extended mind and material agency with profound implications for the commissioners, designers and users of therapeutic spaces.