VictorJuiz/thesis huggingface dataset:
The intellectual context for the development of Quakerism, 1647-1700

This thesis considers the development of Quakerism from 1647 to 1700. Changes affecting the movement in this period are often explained as the result of the Quakers' desire for socio-political respectability – that is, their desire to reduce persecution and social exclusion. This thesis does not deny the importance of socio-political factors. However, it argues that they have been exaggerated as a historical force, and that theological factors driving change have been comparatively neglected. The thesis therefore explores the Quakers' desire for 'theological respectability', by examining the scope and impact of their constructive engagement with outsiders. The project begins with an investigation into the Quakers' understanding of their personal experience, noting both continuities and underlying theological changes which cannot be explained in socio-political terms – namely, a changed view of divine immanence, a strengthened group identity, and the loss of a sense of prophetic vocation. The rest of the thesis explains these developments in their theological context. The Quakers' engagement in Christological debate forms the central case-study. Individual chapters examine the Quakers’ earliest Christology, first responses to criticism, the early career of William Penn, the intellectual development of Robert Barclay's Vehiculum Dei, the Quakers' place in the early Enlightenment, and the Keithian controversy. In particular, the need to articulate a positive theology of the Incarnation led the Quakers into conversation with many influential figures outside the movement, which in turn encouraged an increasingly derivative understanding of the Light within and more optimistic view of physical matter. These shifts relate directly to the religious changes explored in the first part of the thesis. This study illustrates the necessity of theological analysis as part of historical investigation and provides a sustained intellectual history of seventeenth-century Quakerism, demonstrating its important contribution to the intellectual landscape of the early Enlightenment.

Keywords: Keithian controversy
Quakerism
Christology
Religious experience
Robert Barclay
Enlightenment theology
Light within
Advisor: Southcombe, G
Apetrei, S
R21, a novel particle based vaccine for a multi-component approach to malaria vaccination

Malaria is a major cause of mortality and morbidity and an effective vaccine is an urgent global health priority. This thesis evaluates the liver stage viral vector regimen ChAd63 – MVA ME.TRAP in humans and demonstrates the induction of partial protective efficacy (21%) against sporozoite challenge, mediated by high levels of antigen-specific T cells. Although this efficacy is suboptimal, the only subunit vaccine regimen found to elicit greater efficacy has been the particle vaccine, RTS,S/AS01B. This vaccine has been evaluated in large phase 3 trials in Africa and elicits between 30-50% efficacy, mediated predominantly by antibodies that target the circumsporozoite (CS) protein at the sporozoite stage of infection. The aim of this thesis is to enhance pre-erythrocytic stage subunit vaccine efficacy using two approaches. Firstly, by increasing the immunogenicity of a CS-based particle vaccine and secondly, by combining the particle vaccine with ChAd63 – MVA ME.TRAP. To enhance the immunogenicity of the CS-based particle an improved RTS,S like vaccine called R21 was developed. The major improvement is that the R21 particle is formed from a single CS-HBsAg fusion protein and contains a much higher percentage of CS antigen than RTS,S, which may lead to enhanced immunogenicity and efficacy. R21 was found to be immunogenic at a very low dose, used alone or in a range of adjuvants and elicited sterile efficacy when administered with ISCOM adjuvants. Concurrent induction of both cellular and humoral immunity was achieved by combining R21 with ChAd63 – MVA ME.TRAP and no immunological interference was seen. Furthermore, sterile efficacy against sporozoite challenge was significantly enhanced when R21 was administered with TRAP based viral vectors. These pre-clinical studies have provided important information for the selection of a suitable adjuvant and proof of concept that these vaccines can be combined. R21 is now being taken forward for evaluation in Phase 1/2a clinical trials with the future aim of combining it with the ChAd63 - MVA ME.TRAP regimen in humans.

Advisor: Hill, A
Gilbert, S
Colloidal particles for confocal microscopy and optical tweezing

A novel colloidal model system is developed for the purpose of achieving simultaneous three-dimensional (3D) confocal imaging and optical tweezing of impurity probe particles embedded in a dense material of colloidal host particles. First, the colloidal host particles are developed from 3-trimethoxysilyl-propylmethacrylate (TPM), and the solvent mixture is tuned to match the refractive index and the density of the particles. A sedimentation-diffusion equilibrium profile of the TPM particles was imaged in 3D to establish suitability of the system for 3D confocal laser scanning microscopy, and to study its phase behaviour and particle dynamics. Then, core-shell particles, which consist of a high refractive index core and a TPM shell, are synthesised to be used as the impurities. The versatility of the two-step coating procedure with TPM has been demonstrated on several core materials, and the optical properties of the core-shell particle are established using digital holographic microscopy and their optical trapping strengths. Together with the TPM host particles, the core-shell particles are shown to be suitable impurity probes in dense colloidal materials, as they can be manipulated using optical tweezers in all three-dimensions, whilst the structure and dynamics of the surrounding host particles can be imaged simultaneously using fast confocal laser scanning microscopy. Subsequently, to demonstrate the capability of the TPM-based colloidal model system, the depletion potential of a pair of core-shell probe particles embedded in a sea of TPM host particles has been measured using optical tweezing. This is derived from comparing the direct pair potential between the core-shell particles in a TPM refractive index matching solvent, and the potential of mean force for the core-shell particles embedded in a dense fluid region of the TPM host particles. Direct visualisation of the liquid structures of the TPM host particles in the binary system around the probe particles has been linked to the form of the depletion potential, and its oscillatory nature as a function of the particle separation. Lastly, the formation of colloidal dumbbell particles is discussed. The dumbbell formation has been rationalised in terms of the total surface energy of droplet formation on spherical surfaces and the calculations are compared with experimental results from coating various seed particles with TPM. Using optically anisotropic dumbbell particles and tuning the refractive index of the dispersion medium, a preliminary two-trap experiment has been conducted which shows unusual trapping behaviour when a time-delayed feedback trapping trajectory has been applied.

Keywords: Confocal Microscopy
Optical Tweezing
Colloids
Advisor: Dullens, R
Characterisation of lipid-protein interactions through computational modelling

Parallel advances in lipidomics and the structural biology of membrane proteins over the past decade have revealed the highly diverse and complex nature of cell membrane composition. These compositional complexities influence the behaviour of embedded proteins, and a number of biomedically important membrane proteins are now known to be modulated via interactions with their lipid environment. This project aims to apply an array of computational tools to probe and characterize the molecular level detail of these interactions, and obtain information to complement experimental studies. In particular the interactions of modulatory lipid species with the transmembrane domain of the epidermal growth factor (EGF) receptor were addressed using coarse-grained potential of mean force (PMF) calculations. The results suggest this approach, widely applied in other areas of computational biology, may be successfully adapted to probe the strength and selectivity of lipid-protein interactions, and the effects of protein mutation. Subsequently these calculations were applied in tandem with equilibrium simulations to explore cardiolipin interactions with a key mitochondrial transporter, the ADP/ATP Translocase. The data show the coarse-grained model employed is capable of accurately identifying three specific cardiolipin binding sites on the protein, in agreement with prior crystallographic and NMR data. These sites were shown to be specific to cardiolipin, rather than general phospholipid interaction sites. In the third project, prospective predictions were made as to the location of PIP2 lipid binding sites on the membrane-exposed surface of a class A GPCR, the Neurotensin Receptor 1 (NTS1). A protein known to specifically bind these lipids from native mass spectrometry (MS) measurements at hitherto unknown regions. The results suggest PIP2 binds to defined loop regions on the intracellular portion of the protein. Finally, atomistic simulations are applied to examine the effect of a crystallographically resolved cholesterol molecule on the dynamics of a class F GPCR, Smoothened. The data suggest a marked influence of bound cholesterol on intra-domain dynamics of the extracellular region of Smoothened.

Advisor: Sansom, M
Dynamics and entanglement of exotic quantum liquids

This thesis focuses on the one-dimensional Hubbard model, considering both dynamical response functions and also particular entanglement measures of highly excited eigenstates.
In Chapter 2 we discuss how to describe the optical conductivity at finite energy scales. In order to calculate the dynamical response of this interacting system, it is necessary to go beyond the conventional Luttinger liquid picture. Using mobile impurity models and integrability we make quantitative predictions which can be compared with numerics.
In Chapter 3, we investigate the existence of the so-called "quantum disentangled liquid" (QDL) in the same system. The diagnostic for the QDL involves understanding the bipartite entanglement entropy of highly excited eigenstates. Here we use results from integrability and strong-coupling expansions to argue that such a state of matter is realised in the Hubbard chain in a specific sense.

Advisor: Essler, F
The role of the HSV-1 ICP22 protein in regulation of expression of host cell genes

The eukaryotic RNA Polymerase II (Pol II) is responsible for the synthesis of all mRNA and many small regulatory RNAs. The Herpes Simplex Virus 1 (HSV-1) relies exclusively on the host Pol II to synthesise viral RNA during productive infection. A repeating structure on the carboxy terminal domain (CTD) of the Pol II largest subunit consisting of consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7, has to be phosphorylated to drive Pol II-mediated transcription. The ICP22 protein of HSV-1 is capable of interacting with P-TEFb, a kinase phosphorylating the Ser2 position of the CTD. Ser2 CTD phosphorylation is a mark associated with Pol II productive elongation. ICP22 has been shown to cause loss of Ser2 CTD phosphorylation.
In the first part of this thesis, I show that transient expression of ICP22 affects the level of transcribing Pol II at the beginning and end of a model gene, which mirrors the effect caused by CDK9 inhibitors. This result suggests that ICP22 possibly inhibits Pol II elongation due to inhibition of the Ser2 CTD kinase, P-TEFb.
In the second part of the thesis, I describe the ICP22 interactome. I performed ICP22 pull-down assays with HeLa cell extract and the cellular protein complexes bound to ICP22 were analysed by mass spectrometry. This work confirmed the interaction between ICP22 and CDK9 and identifies novel proteins that interact, directly or indirectly, with ICP22.
In the last part of the thesis, the interaction of ICP22 and P-TEFb was further characterised. Using recombinant protein of subunits of P-TEFb; CDK9 and Cyclin T1, I demonstrated that ICP22 interacts with both subunits of P-TEFb. In addition, I validated the ICP22 proteomic hits using immunoblots. Here, I reveal that ICP22 possibly interacts with transcriptional kinases other than P-TEFb.
The in vitro experiments presented in this thesis involved transiently expressed ICP22 or recombinant proteins ICP22 and VP16 thus eliminating the effects of viral proteins other than ICP22 or VP16. Based on these findings, I have extended our understanding that ICP22 induces alteration of host cellular transcription by inhibiting P-TEFb and possibly other transcriptional kinases. These works serve as a platform for genome-wide analyses of the effect of ICP22 on host gene transcription and structural biology to characterise the interaction of ICP22 and P-TEFb.

Advisor: Murphy, S
Moving-mask volume growing: a novel volume segmentation algorithm for medical images

Various physiological modelling studies require isolating the anatomy of interest from medical imaging. There exist a variety of segmentation algorithms, each particularly tailored for a specific anatomical region, imaging modality or physiological modelling study. Simulations of blood flow in brain vasculature require that the arterial and venous vasculature be isolated from angiographic modalities such as rotational planar angiography, computer tomography angiography and magnetic resonance angiography studies. Due to the tortuousity and apposition of the cerebral vessels to the highly vascular meninges and cranium, segmentation of these vessels is generally difficult. This work focuses on a novel algorithm for anatomy segmentation for specific use in the isolation of a particular region of the cerebrovascular anatomy associated with vessel pathology such as aneurysms and arteriovenous malformations. The algorithm uses geometric volume growing by means of comparing the intensities of neighbouring voxels originating from a user-determined seed point rather than fully automated segmentation by means of statistical algorithms that erroneously assume a normal distribution of intensity values in the image data. The research carried out shows that this novel algorithm can easily be incorporated into a simple processing chain for transoperative use by clinicians as the total time from a DICOM stack being imported to a STL geometry being created was on average under 5 minutes. Measurements carried out by clinicians of the anatomy in imaging data strongly correlate with the same measurements on the segmented volumes indicating high accuracy and precision in segmentation. In conclusion, although this algorithm is not suitable for all anatomies, modalities or applications, it shows promise for cerebrovascular studies in particular those where computer fluid dynamics or finite element method simulations of treatment are carried out. Further work should focus on improvements and tailoring the algorithm for other specific data and applications.

Advisor: Castrejón-Pita, A
Revealed preference and welfare analysis

This thesis uses nonparametric revealed preference methods to derive new tests for consistency with models of consumer behaviour, and discuss the implications for welfare analysis. Chapter 1 demonstrates how to conduct revealed preference analysis when prices, and hence budget constraints, are only partially observed. This chapter extends the revealed preference results of Crawford and Polisson (2015), derived for the static case, to dynamic settings, allowing for storability of goods. Necessary and sufficient conditions for consistency with intertemporal models are derived, which do not require the researcher to distinguish between corner solutions and unavailability of the good, or to impute prices. Chapter 2 discusses the validity of using reported happiness measures as proxies of utility or social welfare, by testing for consistency between revealed and reported preference orderings in Japanese household survey data. Although the expenditure behaviour of most households is consistent with standard models of utility maximisation, it is generally inconsistent with the preference ordering given by their reported happiness. This inconsistency is likely due to reporting error in the happiness measure, and suggests that happiness and utility are empirically distinct and noninterchangeable. Chapter 3 investigates the effect of price inattention on inflation misperceptions and cost-of-living indices, by developing a behavioural model in which consumers only notice price changes above a certain threshold. A data application, using supermarket scanner data, demonstrates that this model generates plausible results; in particular, consumers have more accurate perceptions of inflation during periods of high or volatile inflation, but may substantially misperceive inflation when it is low. These results have important implications for conducting welfare analysis when consumers are not fully attentive to price changes.

Keywords: Applied microeconomics
Inflation
Cost of living index
Happiness
Welfare analysis
Household expenditure
Revealed preference
Econometrics
Advisor: Crawford, I
The characterization and engineering of human antigen-specific cytotoxic T cells

This D.Phil. thesis focuses on human antigen-specific cytotoxic T lymphocytes (CTLs). In the first part of the thesis, the impact of antigen stimulation strength on CTL activation was investigated by evaluating the global transcriptomes of a wellcharacterized CTL clone and some of its surface protein expressions, with particular focus on immune checkpoint receptors. Based on the gene differentiations, an 'EGR2-CCL1-4-1BB' pathway, which is sensitive to very low-strength antigen stimulation, was identified. We proposed to block CCL1/CCR8 for future cancer therapeutic treatment as this could be a key mechanism for attracting immune-suppressive cells to local tumour-specific CTLs. Further, an ‘inverse correlation of inhibitory signal and expression level’ model was developed to explain the expression patterns of five inhibitory immune checkpoint receptors (CTLA-4, PD-1, LAG-3, TIM-3 and TIGIT). These findings throw lights on the understanding of CTL functions and the future design of T cell-based cancer immunotherapy. In the second half the thesis, the potential use of CRISPR/Cas9 technology was explored in manipulating antigen-specific CTLs and the antigen-specific CTL clone gene delivery method was optimised. Successful disruption of PD-1 gene by CRISPR/Cas9 via lentivirus has been achieved on several antigen-specific CTL lines and clones. After disrupting PD-1 gene, CTLs function better when the target cells express high level of PD-1 ligand. This part of work is the first study to knock out PD-1 gene on human antigenspecific primary CD8+ T cells and has the potential for clinical applications such as the treatment of infection, autoimmunity and cancer.

Advisor: Dong, T
McMichael, A
Upgrading informal settlements in Karachi, Pakistan: a neopatrimonial approach to the study of policy implementation

In this thesis, I examine the implementation of the upgrading policy for informal settlements effective in Karachi from 1987. According to the policy there are two possible outcomes for the allocation of leases according to the status of the applicant: legal settlements and illegal settlements. However, these distinctions are not respected in practice. This gap has been frequently overlooked in current literature, which analyses policy formulation and outcomes while ignoring the implementation stage. I focus on a single site case study of the implementing agency's Karachi Field Office to examine in depth the processes that contributed to differential outcomes in upgrading in Karachi. I draw on the concept of neopatrimonialism to capture the contradictory conduct in the public agency of KFO that leads to inconsistent patterns in outcomes. Analysis of ethnographic and qualitative data, collected over six months of fieldwork, suggests that in the case of Karachi, the use of bureaucratic discretion by a senior level bureaucrat has explained periods of implementation where lease allocation has been close to the formulated intent of the upgrading policy. In times when such discretion has not been used, lease allocation has been selective and occurred at the behest of patrimonial imperatives exercised by provincial level politicians. The significance of bureaucratic discretion in implementation has implications for policy practice and the reform and improvement of public welfare programmes to ensure continuity between policy and outcome. On a larger scale my research contributes to the study of public agencies in Pakistan and, more broadly, to social policy literature, particularly as regards policy implementation in developing countries. Significantly the nuanced effect of neopatrimonialism on the work of public agencies shows that institutions continue to matter in the delivery of welfare programmes.

Advisor: Noble, M
Cheeseman, N
The design of gene regulatory networks with feedback and small non-coding RNA

The objective of the field of Synthetic Biology is to implement novel functionalities in a biological context or redesign existing biological systems. To achieve this, it employs tried and tested engineering principles, such as standardisation and the design-build-test cycle. A crucial part of this process is the convergence of modelling and experiment. The aim of this thesis is to improve the design principles employed by Synthetic Biology in the context of Gene Regulatory Networks (GRNs). Small Ribonucleic Acids (sRNAs), in particular, are focussed on as a mechanism for post-transcriptional expression regulation, as they present great potential as a tool to be harnessed in GRNs. Modelling sRNA regulation and its interaction with its associated chaperone Host-Factor of Bacteriophage Qβ (Hfq) is investigated. Inclusion of Hfq is found to be necessary in stochastic models, but not in deterministic models. Secondly, feedback is core to the thesis, as it presents a means to scale-up designed systems. A linear design framework for GRNs is then presented, focussing on Transcription Factor (TF) interactions. Such frameworks are powerful as they facilitate the design of feedback. The framework supplies a block diagram methodology for visualisation and analysis of the designed circuit. In this context, phase lead and lag controllers, well-known in the context of Control Engineering, are presented as genetic motifs. A design example, employing the genetic phase lag controller, is then presented, demonstrating how the developed framework can be used to design a genetic circuit. The framework is then extended to include sRNA regulation. Four GRNs, demonstrating the simplest forms of genetic feedback, are then modelled and implemented. The feedback occurs at three different levels: autoregulation, through an sRNA and through another TF. The models of these GRNs are inspired by the implemented biological topologies, focussing on steady state behaviour and various setups. Both deterministic and stochastic models are studied. Dynamic responses of the circuits are also briefly compared. Data is presented, showing good qualitative agreement between models and experiment. Both culture level data and cell population data is presented. The latter of these is particularly useful as the moments of the distributions can be calculated and compared to results from stochastic simulation. The fit of a deterministic model to data is attempted, which results in a suggested extension of the model. The conclusion summarises the thesis, stating that modelling and experiment are in good qualitative agreement. The required next step is to be able to predict behaviour quantitatively.

Keywords: Gene Circuits
Gene Regulatory Networks
Tetracycline Repressor
Rhamnose Activator
System Biology
Synthetic Biology
Feedback
Advisor: Papachristodoulou, A