VictorJuiz/thesis huggingface dataset:
Unravelling the structural, metamorphic and strain history of the "Aegean Orogeny", Southern Greece with a combined structural, petrographic and geochronological approach

The Cycladic Islands in the Aegean region, southern Greece, has been indisputably under lithospheric extension throughout the last 10 Myrs but there remains a limited understanding of the regional tectono-metamorphic evolution prior to extension. In this thesis, new structural mapping, petrography, thermobarometry, phase equilibria modelling, U–Th–Pb and Lu–Hf garnet geochronology is presented from the islands of Tinos, Naxos and Delos and reveal the Cyclades have experienced a complete cycle of mountain building. The Tsiknias Ophiolite on Tinos formed at 161.9 ± 1.3 Ma and is underlaid by a metamorphic sole which displays a highly condensed and inverted temperature gradient, with partial melting directly below the ophiolite contact at P–T conditions of 8.5 kbar, 850°C. The timing of metamorphism is constrained as 74.0 ± 3.3 Ma from leucosomes and 66.6 ± 2.0 Ma from garnets in the underlying meta-sediments, and is interpreted to represent the initiation of a NE-dipping subduction zone that remained active for ~ 20 Myrs associated with the closure of the Vardar Ocean to the NE. The arrival of the leading edge of the Cycladic continental margin caused high-pressure metamorphism (22–26 kbar, 500–570°C at 46.4 ± 3.4 Ma on Tinos and 14.5 kbar, 470°C at 49–46 Ma on Naxos. Crustal thickening resulted in regional metamorphism and climaxed with kyanite-grade conditions (10 kbar, 670–730°C) at 18.5–16 Ma followed by sillmanite-grade anatexis (5–6 kbar, 690–730°C) at 15.5–14 Ma on Naxos. The transition from overall crustal shortening/thickening to extension is constrained to 15 Ma in the Naxos migmatite dome. I and S–type granites intruded contemporaneously between 14.6–12.2 Ma, suggesting a regional-scale partial melting event affected the deepest levels of the Cyclades, possibly associated with the onset of extension and exhumation.

Keywords: Metamorphic Core Complex
Tsiknias Ophiolite
Cyclades
Kyanite and Sillimanite Migmatites
Cycladic Blueschists
Tinos
Naxos
Aegean Orogeny
Advisor: Searle, M
Waters, D
Roberts, N
Politics and space in the Cairo peri-urban fringe

The subject of this study is local politics in Cairo’s peri-urban fringe in the Mubarak era (1981-2011). It aims to propose a new theoretical model for understanding the social dynamics at a local level that have led to a specific form of socio-political mobilization, in which social space has been central. Each chapter in this study is based on the premise that Cairo’s peri-urban fringe during the Mubarak era witnessed the rise of a dominant cognitive structure that has been responsible for shaping most of the collective political practices of local social agents. This cognitive structure has placed the representation of social space at the foreground of political representation. I call this cognitive structure ‘neighbourhoodism’. Through neighbourhoodism, social agents have been able to translate their social, cultural and symbolic capitals into political capital, thereby qualifying themselves to be locally recognized as political representatives.
As this study will show, nearly all social agents in Cairo’s peri-urban fringe who sought to play a role in local politics were involved in politicizing their social spaces, at least at one stage in their political life. Those agents were from different ideological and cultural backgrounds. They encompassed actors from the local NDP, Islamists and other local figures. However, the constructing of neighbourhoodism did not happen overnight. It was an outcome of sustained social practices, individual and collective, formal and informal, which eventually resulted in an intense competition over the representation of social spaces. Although neighbourhoodism first emerged in the late 1970s, it came to dominate the political field from the late 1980s. Local communities in Cairo’s peri-urban fringe experienced an intense struggle between social agencies, who tried to protect their positions and acquire recognition by developing strategies that involved symbolic violence.
Neighbourhoodism has pervaded most social groups and has led to differing cultural and ideological outcomes. Firstly, it has provided the autocratic regime with new means of control, enabling it to make clientelism more efficient and rational. Secondly, it has created a basis for the rise of new movements, most importantly the Islamic movement, by allowing it to cultivate allies from different sectors of society. Furthermore, it has motivated local groups to produce new strategies, such as clannism, in order to consolidate their position in the battle for recognition. Moreover, it gave local groups sufficient grounds to confront the state in times of conflict.
The contribution of this work is to intellectually capture a social medium where the interaction between the macro and the micro can be examined to show how the local and the national/ global interact to produce localized politics, or how the local is localizing the national and vice versa.

Keywords: Mubarak
Egypt
Political Mobilisation
Sociology
Cairo
State and Society
Middle East
Advisor: Armbrust, W
Development of procedures for real-time hybrid simulation and testing of a buckling-restrained braced structure

In real-time hybrid simulation (RTHS), a simulated structure is split into two substructures: one being a physical specimen, and the other a numerical model of the rest of the structure. These are connected in a real-time feedback loop to simulate the dynamic response of the combined structure. An issue in RTHS is the delay in the response of the servo-hydraulic actuators applying the displacements which can destabilise the feedback loop. The delay can vary significantly during the simulation, predominantly due to nonlinearity of the tested specimen. This thesis presents work developing and testing RTHS procedures, which are used to simulate buildings fitted with buckling-restrained braces (BRBs) as the physical substructure. An improved version of the well-known Adaptive Time Series (ATS) delay compensator is presented, retaining the performance of the original but significantly improving its computational efficiency. An online stiffness simulator is then presented which ensures stable force feedback using a continually updated numerical model of the BRB response. Accuracy is further improved by correcting for rig flexure using feedback from encoders measuring the BRB extension. Finally, a numerical model of the BRB is created which is then used in a multi-degree-of-freedom model. The performance of the modified ATS compensator and rig flexure correction was demonstrated through predefined displacement tests, achieving excellent displacement accuracy. This was combined with a single-degree-of-freedom numerical substructure and the stiffness simulator to form a RTHS system showing excellent accuracy and stability up to high frequencies – the compensator adapting effectively to changes in delay caused by yielding. A multi-degree-of-freedom numerical substructure was then implemented to simulate the nonlinear response of realistic structures designed to Eurocode 8. Finally, the system was applied to RTHS with a viscoelastic damper, demonstrating the versatility of the adaptive system.

Keywords: Buckling Restrained Brace
Real-Time Hybrid Simulation
BRB
Seismic
Hybrid
Earthquake
Advisor: Blakeborough, A
Williams, M
Fibroblast Growth Factor 2 (FGF2) in cartilage injury and repair

Fibroblast Growth Factors (FGFs) are important pleiotropic growth factors with a proven role in joint development and postnatal homeostasis. Previously our group has shown that FGF2 is released upon cartilage injury and Fgf2 knockout (KO) mice develop accelerated osteoarthritis (OA), suggesting it is chondroprotective in vivo. Work from others has shown that the accelerated OA phenotype in the Fgf2 KOs is phenocopied by deletion of Fgfr3 but not Fgfr1, suggesting that the FGFR may determine FGF2’s action in the joint.
In the work presented here, I investigate the role of FGF2 in promoting enhanced cartilage regeneration. I first explore the control and function of different FGF receptors (FGFRs) and ligands; then perform an in vivo model of focal cartilage injury in the Fgf2 KO mouse.
FGFR3 mRNA expression levels were rapidly down-regulated by injury in an FGF2-dependent manner, but recovered after chondrocytes were isolated and cultured in vitro. I did not observe significant differences in intracellular signalling or expression of a panel of FGF-dependent genes using receptor selective mutant ligands. In vivo, Fgf2 KO mice failed to repair focal cartilage defects compared with wild-type (WT) controls. Mesenchymal stem cells (MSCs) were activated by FGF2; leading to enhanced scratch assay closure and keeping cells in a more motile state but not in promoting cell adhesion to damaged tissue. FGF2 suppressed chondrogenesis of MSCs in vitro. Taken together, I identified a primary role for FGF2 in promoting intrinsic cartilage repair, which may be due to local activation of MSCs. These results provide mechanistic insights into how cartilage repairs and may have important clinical implications.

Keywords: FGF2
Cartilage
Advisor: Vincent, T
Symptomatic illness and treatment of Plasmodium falciparum malaria in African children

Plasmodium falciparum malaria is a major cause of morbidity and mortality globally, with a disproportionate fraction of cases and deaths in children under five years of age in sub-Saharan Africa. Estimating the proportion of infected individuals and symptomatic cases that receive effective antimalarial treatment is essential for assessing effectiveness of response efforts to reduce the malaria burden and for identifying coverage gaps for interventions. This thesis aims to provide new insights into the clinical malaria burden, and provides estimates of the proportion of malaria-infected children in sub-Saharan Africa that receive antimalarial treatment.
The first major theme of this thesis was to develop a framework for estimating the prevalence of paediatric fever in sub-Saharan Africa, distinguishing between malaria-attributable fevers (MAF), and non-malarial febrile illness (NMFI) with and without an asymptomatic P. falciparum infection. Using household survey data and Bayesian geostatistical methods, continental cartographic estimates of paediatric fever prevalence were produced, separated by underlying cause.
The second research focus was to develop an essential adjustment to household survey data to assess the duration a P. falciparum-infected individual remains positive via rapid diagnostic test after being treated with antimalarial medication. This adjustment was used in subsequent chapters, allowing for more accurate assessment of the likelihood of a febrile individual in the household survey datasets having experienced a MAF or NMFI in the two weeks preceding the survey.
Current malaria burden estimation approaches typically enumerate the total number of malaria- positive fevers expected at a national-level. This approach systematically overestimates the clinical burden of malaria, as many of these malaria-positive fevers are causally attributable to NMFI (and the malaria infection is asymptomatic). In the third research chapter, estimates were produced of the proportion of paediatric malaria-positive fevers that are causally attributable to either malaria or NMFI that present at public health facilities in sub-Saharan African countries. The results presented in this chapter provide estimates of the potential scale of overestimation of the P. falciparum malaria burden using conventional burden estimation approaches.
Finally, estimates of effective antimalarial coverage amongst children under 5 residing in 41 country-years with a household survey were presented, and individual-, community-, clinic-, and national-level coverage gaps for effective antimalarial coverage were identified. The results and conclusions from these studies are presented alongside recommendations and implications for both caregivers in malaria-endemic countries implementing paediatric fever management policy, and for epidemiologists studying the burden of malaria and non-malarial febrile illnesses.

Advisor: Gething, P
Cameron, E
Gupta, S
The evolution of doctrinal religions: Using semantic network analysis and computational models to examine the evolutionary dynamics of large religions

How do large scale religions achieve social cohesion among their members? The divergent modes of religiosity (DMR) theory suggests that imagistic religions rely on rare and emotionally intense rituals to foster fusion by means of reflection (e.g. tribal initiations in small tribal religions), while doctrinal religions achieve cohesion, in the form of social identification, through the performance of frequent low arousal rituals (e.g. daily or weekly rituals in Judeo-Christian religions). Even though the DMR theory proposes that in doctrinal religions, high-frequency emotionally intense rituals should die out or transform, such rituals have become increasingly common in Pentecostal and Charismatic Christian communities. In order to explain the rise and spread of emotionally intense but frequent rituals in doctrinal traditions, this thesis makes the case for an Information Identity System (IIS), through which emotionally intense experiences in doctrinal religions generate a socially regulated process of reflection, that in turn creates conceptual ties, which are links between central aspects of one’s personal identity and essential beliefs in their group’s social schema. The IIS proposes conceptual ties are the basis for extended fusion. This research uses surveys and semi-structured interviews to test 3 key hypotheses: H1) There is a positive relationship between frequency of in-group ritual attendance and social identification, when controlling for fusion; H2a-b) The relationship between the intensity of emotional arousal associated with an experience and fusion to both a group (H2a) and the concept God (H2b) are mediated positively by a) the perceived frequency of reflection on the experience and b) how central one views that experience to their sense of self; H3) The relationship between frequency of in-group ritual attendance and social consensus is mediated a) positively by social identification and b) negatively by fusion. The results suggest support for hypothesis H1 but also found an interaction between fusion and frequency of in-group ritual attendance and that fusion has a greater effect than expected. Results also found support for H2a and H2b. However, the sample size used to test hypothesis 3 resulted in an underpowered study. In addition, two alternative hypotheses from cultural epidemiology were tested but the study was also underpowered. The findings suggest that the IIS’ proposal of conceptual ties may be a plausible explanation for extended fusion. In future research, larger sample sizes should be used in future studies testing H3. Additionally. future research may wish to investigate how conceptual ties may underpin religious extremism and its relation to sacred values theory. The dissertation ends by discussing how the methods devised here can be used in future studies.

Keywords: Pentecostal Christianity
social identity
ritual
divergent modes of religiosity
Charismatic Christianity
fusion
network analysis
Singapore
Advisor: Whitehouse, H
Lipschitz functions on unparameterised rough paths and the Brownian motion associated to the bilaplacian

This thesis is a tale of two halves. The first introduces the space of unparameterised geometric rough paths and develops a notion of Lipschitz function on this space. The second associates an expected signature to the bilaplacian and culminates in an analogue of the Feynman-Kac formula for high-order parabolic partial differential equations.

Advisor: Lyons, T
The α-alkylation of ketones using hydrogen borrowing catalysis

Introduction – Hydrogen Borrowing Alkylation Reactions Using Alcohols
The introduction reviews the origins of hydrogen borrowing catalysis and how it has been applied to utilise alcohols as alkylating agents. The predominant focus is on highlighting the scope for the use of primary alcohols in the α-alkylation of ketones. Other nucleophiles are discussed with respect to the use of secondary alcohols as alkylating agents. Examples of related methodologies are also briefly discussed.
Results and Discussion – Formation of α-Branched Products Using Primary Alcohols
This chapter explores the alkylation of several ketone substrates and identifies cyclopropyl ketones as key structural motifs that facilitate the formation of α-branched products using primary alcohols. The development of an iridium–catalysed protocol for this reaction is described, including the optimisation of reaction conditions and investigation of the substrate scope with respect to the ketone and alcohol. The derivatisation of the resulting α-branched cyclopropyl ketones is also explored through utilisation of several ring-opening reactions.
Results and Discussion – Formation of β-Branched Products Using Secondary Alcohols
This chapter focuses on the development of an Ir-catalysed procedure for the alkylation of methyl ketones using secondary alcohols to form β-branched products. In developing this procedure, ortho-disubstituted aryl ketones were identified as key structural motifs that facilitated the reaction due to the unique properties they possessed. An overview of the optimisation of reaction conditions is provided, followed by exploration of the substrate scope with respect to the methyl ketone and the secondary alcohol. Derivatisation of the resulting β-branched products through bromine-initiated release of the aryl group, followed by trapping with several nucleophiles led to the formation of carboxylic acid derivatives. The final part of the chapter introduces preliminary studies towards the development of an asymmetric route to β-branched products.
Results and Discussion – Formation of Cyclic Products Using Diols
This chapter explores the development of an unprecedented Ir-catalysed procedure for alkylation of a methyl ketone using diols to form five-, six- and seven-membered carbocyclic rings. The optimisation of the reactions conditions is described followed by a systematic investigation into the diastereoselectivity observed in the formation of the carbocyclic rings. With the formation of cyclohexane rings identified as being most effective under the reaction conditions, these were then explored further in a more general substrate scope. The derivatisation of the cyclic products was also explored through a bromine-mediated release of the aryl group followed by trapping with a variety of nucleophiles.
Experimental Section
Experimental procedures are provided along with full spectroscopic characterisation of the compounds synthesised.

Keywords: iridium
catalysis
hydrogen autotransfer
hydrogen borrowing
green chemistry
Advisor: Donohoe, T
Freedom and persuasion in the attention economy

In order to do anything that matters, we must first be able to give attention to what matters. However, as Herbert Simon predicted in the 1970s, the unprecedented abundance of information produced by digital technologies has resulted in a similarly unprecedented scarcity of attention. As the newly scarce resource, our attention is today the primary object of competition among our digital technologies. In the so-called ‘attention economy’ that has emerged, design wins when it captures as much of our attention as possible—and in order to win, it must increasingly exploit our non-rational psychological biases. This attentional capture is carried out with a view to directing our thoughts and behaviors toward predefined goals—goals that may or may not align with our own. Persuasion, then, is the dominant business model of the digital attention economy, and this persuasion is increasingly powerful, prevalent, and centralized. Major moral and political questions therefore lurk here: questions of attention management that to date have been largely passed over in favor of questions about information management, such as privacy or surveillance. As a result, a full ethical grappling with the digital attention economy is long overdue. But how should we begin to think about, let alone protect, human freedom in such an environment of industrialized persuasion? In this thesis I approach this topic via four main questions. First, what counts as a ‘persuasive’ technology? Second, what risks to freedom do persuasive technologies pose? Third, how does advertising ethics need to change in order to be useful in the digital attention economy? And finally, how does specifically digital advertising differ in its nature and ethics from advertising as historically understood? I broadly conclude that the digital attention economy has produced several direct as well as systemic effects that pose serious challenges for user self-determination. These challenges have received little serious ethical attention to date and therefore warrant a sustained project of critical analysis and intervention. I then close with a brief, high-level discussion of possible paths for reforming the digital attention economy moving forward.

Advisor: Floridi, L
Nash, V
Discovering genetic variation in populations using next generation sequencing and de novo assembly

The de Bruijn Graph is a simple and efficient data structure that is used in many areas of sequence analysis including genome assembly, sequencing error correction, sequencing read compression and variant discovery. The data structure has a single parameter k, is straightforward to implement and is tractable for large genomes with high sequencing depth. It also enables representation of multiple samples simultaneously to facilitate comparison. However, unlike the string graph, a de Bruijn Graph does not retain long range information that is inherent in the read data. For this reason, applications that rely on de Bruijn Graphs can produce sub-optimal results given their input.
We present a novel assembly graph data structure: the Linked de Bruijn Graph. Constructed by adding annotations on top of a de Bruijn Graph, it stores long range connectivity information through the graph. We show that with error-free data it is possible to losslessly store and recover sequence from a Linked de Bruijn Graph. Through simulation we show that links improve performance and reduce the sensitivity to the parameter k. Many algorithms can be built on top of Linked de Bruijn Graphs, which we illustrate by implementing read error correction, variant calling, genotyping and assembly algorithms in a software package called ‘McCortex’.
With assembly simulations we demonstrate that the Linked de Bruijn Graph data structure outperforms both the de Bruijn Graph and the String Graph Assembler (SGA). Using human whole genome sequence, we show that Linked de Bruijn Graphs scale up to mammalian genomes. Finally we apply McCortex to Klebsiella pneumoniae short read data to call SNPs, indels and large events, which we validate using PacBio sequencing data. Although kmer-based methods have reduced sensitivity for calling SNPs, McCortex finds 3x more polymorphic bases due to small events in K. pneumoniae versus mapping-based approaches and 48% more than existing de Bruijn Graph de novo assembly methods. We also find multiple 10kbp events that cannot be resolved with a plain de Bruijn Graph.
In conclusion the Linked de Bruijn Graph is a versatile data structure with utility in multi-sample variant calling of indels and large events, in both de novo and reference-aware scenarios.

Keywords: de Bruijn graph
genetics
algorithms
Advisor: McVean, G