VictorJuiz/thesis huggingface dataset:
Vertex model approaches to epithelial tissues in developmental systems

The purpose of this thesis is to develop a vertex model framework that can be used to perform computational experiments related to the dynamics of epithelial tissues in developmental systems. We focus on three example systems: the Drosophila wing imaginal disc, the Drosophila epidermis and the visceral endoderm of the mouse embryo. Within these systems, key questions pertaining to size-control mechanisms and coordination of cell migration remain unanswered and are amenable to computational testing.
The vertex model presented here builds upon existing frameworks in three key ways. Firstly, we include novel force terms, representing, for example, the reaction of a cell to being compressed and its shape becoming distorted during a highly dynamic process such as cell migration. Secondly, we incorporate a model of diffusing morphogenetic growth factors within the vertex framework, using an arbitrary Lagrangian-Eulerian formulation of the diffusion equation and solving with the finite-element method (FEM). Finally, we implement the vertex model on the surface of an ellipsoid, in order to simulate cell migration in the mouse embryo.
Throughout this thesis, we validate our model by running simple simulations. We demonstrate convergence properties of the FEM scheme and discuss how the time taken to solve the system scales with tissue size. The model is applied to biological systems and its utility demonstrated in several contexts. We show that when growth is dependent on morphogen concentration in the Drosophila wing disc, proliferation occurs preferentially in regions of high concentration. In the Drosophila epidermis, we show that a recently proposed mechanism of compartment size-control, in which a growth-factor is released in limited amounts, is viable. Finally, we examine the phenomenon of rosettes in the mouse embryo, which occur when five or more cells meet at a common vertex. We show, by running simulations both with and without rosettes, that they are crucial facilitators of ordered migration, and are thus critical in the patterning of the early embryo.

Keywords: Drosophila imaginal wing disc
partial differential equations
cell migration
vertex models
tissue size regulation
Advisor: Maini, P
Baker, R
Kay, D
Reformed sacramental piety in England 1590-1630

England in the late-Elizabethan and early-Stuart period saw a surge of pastoral writings intended to provide lay-readers with information and advice about sacraments. Using sixty-four such texts from the period 1590-1630, this thesis analyses the conceptions of sacraments offered by cleric-authors to their audience. As a group these works had two structural features in common. First they were concerned to outline the ‘qualities’ of a ‘worthy’ receiver of the Lord’s Supper, foremost amongst which were knowledge, faith, newness of life and repentance. Second they tended to divide the concept of worthiness into three temporal chunks comprising the times before, during, and after the Supper.
Using these rubrics as guidelines the thesis compares and contrasts the content of the corpus. In opposition to stereotypes of puritans neglecting sacraments, it is found that sacraments were presented by Reformed English clerics as highly efficacious entities, which truly communicated something to the believer. The importance of faith to the Reformed conception of sacraments is affirmed, with the caveat that the dominance of this concept did not prohibit clerics from extolling the sensuous or ceremonial aspects of sacraments. It is further contended that sacraments continued to be seen as spurs to moral amelioration, occasions for charity, and a demonstration of community – and that receiving sacraments did not become a wholly individualised enterprise.
Building on this analysis the thesis offers three broader conclusions. Firstly it is shown that sacraments played a key part in the quest to gain assurance of salvation. Secondly it can be seen that in England there was a way of extolling sacraments and their use which is not usually thought about – a species of ‘sacramental piety’ which used mainstream Reformed ideas about sacrament to urge believers to comfort and increased Godliness. Thirdly it is contended that key Reformed theological distinctions were often submerged by the contingencies of pastoral writing.

Keywords: sacraments
Advisor: Heal, F
Accuracy estimation for sensor networks

With sensor technology gaining maturity and becoming ubiquitous, we are experiencing an unprecedented wealth of sensor data. In most sensing scenarios, the measurements generated by sensor networks are noisy and usually annotated with some measure of uncertainty. The problem we address in this thesis is how to estimate the accuracy of the sensor systems based on the probabilistic measurements they provide. This problem is increasingly common in many settings, such as multiple sensing services are competing for the same group of users, detecting faults in large scale networks, or establishing trustworthiness of different individuals in social sensing. It is also challenging in many ways, for instance, the ground truth of the monitored states is absent, the users often lack a clear view of the implementation details of the sensor systems, and the reported accuracy can be misleading.
To address theses challenges, in this thesis we formulate the problem of estimating the accuracy of sensor systems in a general manner that applies to a broad spectrum of sensing scenarios. We then propose an accuracy estimation framework that breaks the problem into layers, which can be implemented in different ways. We present a novel inference-based accuracy estimation approach, which assesses the accuracy of sensor systems by comparing the reported measurements with the states inferred with the probabilistic measurements from all systems and available prior knowledge. We also propose a new learning-based approach for accuracy estimation, which employs novel parameter learning techniques. The learned parameters are either used to improve estimating the accuracy of sensor measurements, or to derive the accuracy of sensor systems directly in certain cases. We perform a systematic experimental evaluation on two datasets collected from real-world sensor deployments, where an array of different approaches are juxtaposed and compared extensively. We discuss how they trade accuracy for computation cost, and how this trade-off largely depends on the knowledge of the sensing scenarios. We also show that the proposed approaches outperform the competing ones in estimating accuracy and ranking the sensor systems.

Keywords: Sensor Network
Accuracy Estimation
Advisor: Trigoni, N
The end of the affair: Britain's turn to Europe as a problem in Anglo-Australian relations (1961-72)

This thesis is an historical account based on primary sources in Australia and Britain. It seeks to explain why Anglo-Australian relations underwent radical change during the 1960s and why the ties of empire which had once bound Australia and Britain, became, for all practical purposes, inconsequential by the early 1970s. It is the main contention of the thesis that this radical change can be broadly attributed to what has been described as Britain's turn to Europe. In the 1960s Britain's foreign, defence and trade policies underwent a profound revision as Britain endeavoured to redefine its emerging post-imperial role. British policy-makers gradually turned away from an imperial and global focus and their orientation became increasingly more European. This process of reorientation can be seen principally in the series of policies implemented by successive British governments during the 1960s and early 1970s: the three applications for EEC membership between 1961 and 1972 and the decision taken in 1967-68 to withdraw from east of Suez. Both the EEC applications and the withdrawal from east of Suez brought about an irreconcilable conflict of interest between the two countries. The relationship suffered under the strains imposed by Britain's reassessment of its imperial policy-making. This thesis explains how Australia perceived these challenges, the manner of its response to them and the policies successive Australian governments implemented to minimise their impact. The thesis argues that, anxious not to antagonise Britain for fear it would drift further away, Australian policy-makers avoided too confrontational a stance. They gradually accepted the developing new realities and sought to diversify their country's trading options away from its traditional markets in Britain towards the Asia-Pacific region, while also cautiously redefining its strategic priorities in Asia.

Keywords: EEC
Anglo-Australian relations
Britain
Australia
Advisor: Deighton, A
On securitisations of assets

In the first chapter we introduce securitisations and discuss the current state of structured finance in Europe; we also explore the main trends in securitisations and future prospects. Next, we provide a general introduction to the theoretical and empirical literature concerning securitisations and structured finance more generally: we discuss theoretical hypotheses concerning different rationales for structured credit and explore the empirical literature on the topic.
In the second chapter, we look at financial contracts determining implicit boundaries of a firm. In the spirit of the incomplete contract theory, we analyse optimal allocations of control in financial contracts involving limits on managerial discretion and legal separation of assets. Our model explores the interplay between different groups of creditors and managers in a symmetric information environment. The results display optimality conditions for different contracts from asset-backed securities through project finance to debt with covenants vis-a-vis a standard debt contract.
In the third chapter, we provide the first systematic testing of the theories of tranching. We find support for asymmetric information and market segmentation explanations for tranching and present evidence on how such different rationales influence the structuring process in practice. We also investigate the impact of tranching on the price of securities at the issue level.
In the fourth chapter, we investigate determinants of launch spreads in securitisation transactions. First, we develop a reduced-form pricing model of tranches across different transaction types and test it. We document the importance of credit ratings for prices of structured securities. Next, we test for the effect of tranching on pricing of individual securities. Finally, we develop a simultaneous equations supply and demand model with endogenous structuring to further investigate the effects of structuring on prices at launch.
In the fifth chapter, we investigate returns to equity around securitisation dates, and explore how different factors influence the size and the direction of the potential effects. We find significant, positive, and consistent abnormal returns to equity on the pricing date, over longer event windows, and over the period immediately prior to the issue date. We find support for the theory that equity holders in well-capitalised banks and firms with low gearing benefit from securitisations. Furthermore, we show that more developed securitisation markets, larger issuers, and banks in particular all benefit from securitisations.

Advisor: Mayer, C
Policing integration: the inter- and intra-organizational coordination of police work

The thesis examines the coordination of public police organizations in an intra-national setting through interviews and observations with police officers and managers in multiple organizations in the Lower Mainland, BC, Canada, alongside documentary analysis of local, national and provincial law, policy and protocols relating to coordination. It produces a qualitative and inductive analysis of how police coordinate both within and between agencies, examining ‘interstices’ between police units and using recent ‘integration’ initiatives between public police organizations in the Lower Mainland as a focal point. It develops a recent local history of police activity and organizational change in the region; a novel typology of police organizational boundaries grounded in open-systems organizational theory; and an account of the dynamics of inter-unit coordination based on empirical findings. The thesis then sets out a governance problem for police coordination, developing the argument that coordination work is unique work and needs to be treated as such for purposes of accountability, transparency and equity of police practice in a democratic society. This governance problem is applied to broader developments in police work in Anglo-American societies, and an intellectual framework for assessing police governance under coordination is advanced.

Keywords: governance
police
ethnography
criminology
organizational sociology
Advisor: Loader, I
Multi-scale parameterisation of static and dynamic continuum porous perfusion models using discrete anatomical data

The aim of this thesis is to replace the intractable problem of using discrete flow models within large vascular networks with a suitably parameterised and tractable continuum perfusion model. Through this work, we directly address the hypothesis that discrete vascular data can be incorporated within continuum perfusion models via spatially-averaged parameterisation techniques.
Chapter 1 reviews biological perfusion from both clinical and computational modelling perspectives, with a particular focus on myocardial perfusion.
In Chapter 2, a synthetic 3D vascular network was constructed, which was controllable in terms of its size and properties. A multi-compartment static Darcy perfusion model of this discrete system was parameterised via a number of techniques. Permeabilities were derived using: (i) porosity-scaled isotropic (ϕI); (ii) Huyghe and Van Campen (HvC); and (iii) projected-PCA parameterisation methods. It was found that HvC permeabilities and pressure-coupling fields derived from the discrete data produced the best comparison to the spatially-averaged Poiseuille pressure.
In Chapter 3, the construction and analysis of high-resolution anatomical arterial vascular models was undertaken.
In Chapter 4, various anatomically-derived vascular networks were used to parameterise our perfusion model, including a microCT-derived rat capillary network, a single arterial subtree, and canine and porcine whole-organ arterial models. Allowing for general-connectivity (as opposed to strictly-hierarchical connectivity) yielded a significant improvement on the continuum model pressure. For the whole-organ model however, it was found that the best results were obtained by using porosity-scaled isotropic permeabilities and anatomically-derived pressure-coupling fields. It was also discovered that naturally occurring small length but relatively large radius vessels were not suitable for the HvC method.
In Chapter 5, the suitability of derived parameters for use within a dynamic perfusion model was examined. It was found that the parameters derived from the original static network were adequate for application throughout the cardiac cycle.
Chapter 6 presents a concluding discussion, highlighting limitations and future directions to be investigated.

Keywords: parameterisation
cardiac perfusion
Darcy flow
Advisor: Smith, N
Chapman, J
The development of electroanalytical techniques

This thesis describes the development of an electroanalytical technique for the estimation of compounds of biochemical interest. The technique involves titration with hypobromite using double electrode systems - the rotating ring disc electrode (RRDE) and the flow-through tubular double electrode (TDE). Hypobromite is continuously electregenerated at the upstream disc (generator) electrode and is transported by convection and diffusion to the downstream ring (detector) electrode where it is detected amperometrically. The presence of a reactive substrate in solution decreases the amount of titrant which reaches the ring, and from measurements of the generating and detecting currents the bulk concentration of substrate may be estimated.
At pH 9.2 the amine group of amino acids reacts with two hypobromite molecules and some side chains (e.g. cystinyl, tyrosinyl, tryptophanyl) will also react. The reactivity of these side chains permits the titration of proteins. The titration response may be described theoretically which enables the calculation of the number of hypobromite molecules which react with one protein molecule ( ~500 for haemoglobin). With this chemical amplification the detection limit of the technique is ~10-8 g ml-1 for proteins and ~10-8 M for amino acids.
An electronic circuit has been developed which enables the detector electrode to control the rate at which titrant is generated. This autotitrator produces a generator current which is proportional to substrate concentration, and with the TDE should enable the continuous estimation of proteins as they are eluted from a chromatographic column.
Proteins have been titrated at pH 9.2 and pH 5; the ratio of a protein's titration responses reflects its amino acid composition and, when combined with the extinction coefficient, enables the identification of proteins. Patent applications for this method of identification and for the autotitration technique have been submitted.

Advisor: Albery, W
Pattern Recognition in Astrophysics  and the Anthropic Principle 

The role of the Anthropic Principle in astrophysics and cosmology is examined in two principal parts. The first (minor) part takes a chiefly philosophical perspective and examines the manner in which human cognition features into discussions on cosmic origins. It is shown that the philosophical questions raised by the Anthropic Principle and ‘fine-tuning of life’ bear resemblances to problems within the philosophy of mind and we seek a common origin for this surprising parallel. A form of ‘epistemic structural realism’ is defended and used to critique the physicalist identity thesis. It is argued that equating ‘reality’ with mathematical structures, which is the basis of the identity thesis, leads to incoherent conclusions.
Similar reasoning is used to critique infinite Multiverse theories. In the second (major) part, we gradually transition into mainstream astrophysics, first presenting a new line of research to explore counterfactual universes using semi-analytic models (SAMs) and offering a preliminary study wherein the cosmological constant is varied and the effects on ‘advanced civilisations’ are examined. The importance of galaxy mergers is highlighted and leads to their study. We first try solving the pattern-recognition problem of locating mergers using the Galaxy Zoo database and produce the largest homogenous merger catalogue to date. We examine their properties and compare them with the SAMs of the Millennium Simulation finding good general agreement. We develop the Galaxy Zoo approach with a new visual-interface design and double the size of the merger catalogue of SDSS mergers in the local Universe.

Keywords: Counterfactual Universes
Galaxy Evolution
Pattern Recognition
Galaxy Mergers
Anthropic Principle
Advisor: Silk, J
Transnational trauma: trauma and psychiatry in the world and Taiwan, 1945-1995

This study considers the history of trauma, both as a psychiatric concept and as a diagnosis, and its social and cultural representation from a transnational perspective after WWII. The intellectual evolution of trauma was determined by various medical, social and cultural variables, institutions, and people who wielded influence in the postwar world order as well as diverse local contexts. This thesis focuses on the globalisation and localisation of such concept and diagnosis shaped by international and local mental health experts at the World Health Organization and the National Taiwan University Hospital. Through the efforts of these experts, trauma not only became one of the most globally diffused psychiatric diagnoses, but also a hyperbole appropriated by Taiwanese psychiatrists to account for extreme forms of social suffering.
Studies have criticised the universality and the Anglo-American-centred approach to the history of traumatic psychiatry. Scholars have also begun to explore transnational histories of psychiatry by systematically comparing or tracing the diffusion routes of psychiatric topics. Their methods of enquiry and problems solved, however, differ. My research analyses a disparate collection of evidence at the level of international organisations and from local aspects, allowing not only a critical reconsideration of trauma in the trend of global medicine, but also its reception, contestation and appropriation in the non-Western contexts. Guided by the works of medical historians, literary critics and cultural anthropologists, this project combines archival research with oral history interviews to challenge the existing historical accounts of trauma, and provide evidence of the limited capacity of globalised psychiatric norms and their reception and appropriation beyond the imagination of world citizenship. It argues that such scientific artefacts were not only produced through mutual reference between Eastern and Western experiences, but also measures of instrumental rationality employed by postwar internationalists to engineer their modernity in the Global South.

Keywords: history of psychiatry
global health
trauma
mental health
Advisor: Mahone, S
Gerth, K
The identification &amp; optimisation of endogenous signalling pathway modulators

Chapter 1 Provides an overview of drug discovery with particular emphasis on library selection and hit identification methods using virtual based approaches.
Chapter 2 Gives an outline of the bone morphogenetic protein (BMP) signalling pathway and literature BMP pathway modulators. The association between the regulation of BMP pathway and cardiomyogenesis is also described.
Chapter 3 Describes the use of ligand based virtual screening to discover small molecule activators of the BMP signalling pathway. A robust cell based BMP responsive gene activity reporter assay was developed to test the libraries of small molecules selected. Hit molecules from the screen were synthesised to validate activity. It was found that a group of known histone deacetylase (HDAC) inhibitors displayed most promising activity. These were evaluated in a secondary assay measuring the expression of two BMP pathway regulated genes, hepcidin and Id1, using reverse transcription polymerase chain reaction (RT-PCR). 188 was discovered to increase expression of both BMP-responsive genes.
Chapter 4 Provides an overview of existing cannabinoid receptor (CBR) modulating molecules and their connection to progression of atherosclerosis.
Chapter 5 Outlines the identification and optimisation of selective small molecule agonists acting at the cannabinoid 2 receptor (CB2R). Ligand based virtual screen was undertaken and promising hits were synthesised to allow structure activity relationship (SAR) to be developed around the hit molecule providing further information of the functional groups tolerated at the active site. Subsequent studies led to the investigation and optimisation of physicochemical properties around 236 leading to the development of a suitable compound for in vivo testing. Finally, a CB2R selective compound with favourable physicochemical properties was evaluated in vivo in a murine inflammation model and displayed reduced recruitment of monocytes to the site of inflammation.

Keywords: structure activity relationship
drug discovery
cannabinoid receptor
computer aided drug discovery
medicinal chemistry
bone morphogenic protein
Advisor: Russell, A