VictorJuiz/thesis huggingface dataset:
Functional analysis of POLE exonuclease domain mutations in cancer

POLE encodes the polymerase and exonuclease domains of the leading strand replicase, DNA polymerase ε. Somatic and germline POLE exonuclease domain mutations (EDMs) occur in colorectal and endometrial cancer and are associated with tumour ultramutation, a distinct mutation signature and an excellent prognosis. However, the mechanism by which POLE EDMs cause mutagenesis and the molecular consequences of this are unclear.
Previous functional studies in several POLE EDM knock-in cell and mouse models have been performed, however they all have limitations regarding their clinical relevance. In addition, the timing of POLE EDMs in tumour development is based purely on genomic data from advanced POLE EDM tumours with no direct evidence of their occurrence in pre-cancers. The aim of this thesis was to study the function of POLE EDMs in clinically relevant human cell-line and mouse models and determine their timing in cancer development.
Corrected somatic POLEP286R EDM isogenic colorectal cancer cell lines were generated using CRISPR-Cas9. Correction of the POLE mutation resulted in a striking reduction in the HPRT1 mutation rate (11-75-fold), consistent with a causal role in tumour ultramutation. Furthermore, the POLE EDM cell line somatic mutation spectra exhibited a significant bias towards POLE signature mutations: TCT>TAT, TCG>TTG and TTT>TGT (P<0.0001).
Analysis of uterine and intestinal-specific tissue and constitutive germline PoleL424V EDM knock-in mice revealed no gross morphological or histopathological phenotype, however constitutive models demonstrated elevated Cleaved-Caspase-3 expression in the small intestine (P<0.05). Germline PoleL424V expression increased the colonic polyp burden in ApcMin mice (P<0.05), although there was no significant difference in the small intestinal polyp burden.
Finally, a somatic POLEV411L EDM was identified in a colorectal pre-cancer with an elevated T-cell infiltrate, increased somatic mutation burden and a bias of POLE EDM-associated amino acid substitutions.
Overall, this work provides strong evidence that POLE exonuclease domain mutations cause tumour ultramutation, a distinct mutation signature and are an early event in cancer. POLE EDM mice only developed a gross morphological phenotype when crossed with ApcMin mice, raising interesting questions regarding the mechanism of tumour initiation in cancers with POLE exonuclease domain mutations.

Advisor: Church, D
Tomlinson, I
Kearsey, S
Designing and evaluating repointing lime mortar for the conservation of historic buildings in highly exposed environments

Many historic buildings are under threat due to their severe exposure to wind, rain and high humidity. One of the main conservation challenges for historic and traditional buildings is to ensure water ingress is mitigated and moisture that has entered a wall evaporates, contributing to drier and less damp conditions. These are some of the main roles of mortar joints in a masonry: absorbing moisture from the surrounding stones and contributing to its evaporation. When mortar deteriorates or when inappropriate mortar, that traps moisture inside the wall and encourages evaporation through the porous stone, has been used, it has to be replaced by a new mortar called repointing mortar. This thesis focuses on repointing in a common UK situation of high exposure to wind and rain and masonry with low permeability, as found in the south-west of England. It aims to investigate the role of repointing mortars in the conservation of historic buildings in exposed environments: What would be the most effective mortar to repoint dense stone masonry in exposed locations? How do the environmental conditions found on-site affect these mortars? Can these repointing mortars mitigate driving-rain ingress? This thesis addresses these research questions with a multi-method and multi-scale methodological approach, from laboratory samples to test walls, to optimise, evaluate and validate twenty-three compositions of lime mortars. This work is therefore relevant to other high humidity environments and to a multitude of structures. Key scientific findings are made on the effect of specific materials in lime mortars, such as the use of wood ash, porous aggregates and quicklime, qualifying them as suitable materials to optimise repointing mortar. Wood ash contributes to increase the capillary absorption capacity of mortar while giving a potential pozzolanic activity, a positive outcome when applied under humid conditions. The thesis brings further understanding of the impact of humid environmental conditions on the properties of lime mortars, and showed that laboratory evaluation should be made on samples cured under realistic conditions if information on the early to medium-term (up to 90 days) characteristics of NHL mortar is required. Findings from experiments on test walls demonstrate that repointing mortar, by being more compacted, helps mitigate rain ingress after a short intense rainfall event. The novel pilot scoring system developed could have considerable implications for more effective and durable repointing interventions. Together, these findings have significant implications for decision-making on repair interventions for the conservation of historic buildings, especially in building resilience in a context of climate change.

Advisor: Viles, H
Epigenetic modification of the frataxin gene for the treatment of Friedreich’s ataxia

Friedreich's Ataxia (FRDA) is a recessive neurodegenerative disease caused by the partial silencing of the frataxin gene (FXN). Long GAA triplet repeat expansions in the first intron of FXN are responsible for the reduced levels of frataxin, an essential mitochondrial protein involved in iron-sulphur cluster biosynthesis. The precise mechanisms of FXN silencing remain unclear, but in the last few years, epigenetic silencing of FXN was reported to have a major role in the development of FRDA. The presence of expanded GAA repeats has been shown to induce a repressive heterochromatin environment at the FXN locus, with increased levels of methylated histones H3K9me2/3, H3K27me3 and H4K20me3, as well as reduced acetylation of histones H3 and H4, demonstrating epigenetic repression of FXN.
In this thesis, first HDAC3 and G9a were targeted by siRNA-mediated knockdown to increase overall acetylation and reduce methylation and promote transcription of FXN. Using a human FXN-GAA-Luciferase (FXN-GAA-Luc) repeat expansion reporter model of FRDA, HDAC3 knock-down was shown to increase FXN mRNA levels with no effect on protein, while G9a knock-down did not show an effect on either FXN mRNA or protein levels.
Next, the Structural Genomics Consortium epigenetic compound library set was screened in the FXN-GAA-Luc reporter model of FRDA to identify compounds that can restore FXN expression. Amongst the hits was a group of compounds targeting methyltransferases which increased frataxin protein expression, assessed by the FXN-GAA-Luciferase assay. Concentration-response curves and direct siRNA-mediated knock-down of the targets showed that the methyltransferases SUV4-20 play an important role in the silencing of FXN. The specific inhibitor of SUV4-20, the probe A-196, was then tested in FRDA patient-derived fibroblasts and was able to increase the expression of mature FXN protein by 1.5-fold in the FRDA line GM04078. When A-196 was tested for its ability to modify a wide range of cellular phenotypes in FRDA patient cells, such as altered mitochondrial membrane potential and mitochondrial ROS generation, it showed only modest effects that did not reach statistical significance. Therefore, in collaboration with Oxford SGC, more stable and potent A-196 analogues were synthesized and tested in the FXN-GAA-Luciferase reporter cell line, and two new variants were found to increase FXN protein expression.
In summary, the work has defined SUV4-20 as a novel therapeutic target for FRDA and identified compound A-196 as a potential small molecule candidate for hit-to-lead development as a new drug for this fatal disease.

Keywords: SUV4-20
H4K20
Histone methylation
Advisor: Wade-Martins, R
Moral manoeuvres: cybersecurity in Egypt and the Gulf states

Cybersecurity is a complex and contested issue in international politics. The existence of radically different conceptions of cybersecurity is recognised by many scholars in International Relations (IR), but rarely explored outside the cyber ‘great powers’: the US, the EU, Russia and China. This thesis investigates cybersecurity in Egypt and the states of the Gulf Cooperation Council (GCC), a region between two poles of internet governance that has close military and security ties to the US and Europe and authoritarian features more reminiscent of Russia or China. Given this hybrid position, the research question of this thesis is: how can we explain the nature of cybersecurity in Egypt and the Gulf states? This question is not merely academic, as it directly affects the creation of international agreements, laws and institutions, as well as corporate and state surveillance practices.
The thesis argues that cybersecurity is primarily an expert discourse incorporating both technical and value claims. The content of this discourse – who cybersecurity protects from what – is ambiguous due to both professional incentives and technological characteristics. Relevant actors use this ambiguity to perform what I call ‘moral manoeuvres’: altering values and technical concepts within this professional discourse for their own ends. I identify four separate moral manoeuvres, which I call alignment, appropriation, manipulation and elision. These manoeuvres are performed by human rights NGOs, government organisations, international surveillance suppliers, and the wider cybersecurity industry respectively. The overall result of these moral manoeuvres is the preservation and even amplification of contradictions and ambiguities present in expert cybersecurity discourses. This thesis makes three original contributions to IR: first, it provides a more nuanced account of the construction of security domains than critical theories of securitisation; second, it explains struggles over values in cybersecurity better than alternative accounts of ‘cyber norms’; and third, it presents detailed empirical data on an important region and issue area with few existing treatments.

Keywords: norms
cybersecurity
cyber security
Egypt
Arab Gulf states
Advisor: Hall, T
Kello, L
Deighton, A
Modulation of cancer cell invasion by extracellular vesicles

The cancer microenvironment is a receptacle of stimuli necessary to promote tumour growth. The role of extracellular vesicles (EVs) in orchestrating a crosstalk between cancer cells and other cell types in the surroundings is integral part of the tumour network. Extracellular vesicles are subcellular structures that emanate virtually from any cell type and carry information both within the primary tumour site and to distant sites. Here I show that two oncogenic stimuli control the release of EVs to render cancer and untransformed cells more aggressive. Firstly, I show that loss of the tumour suppressor RASSF1A in breast cancer cells allows the alternative transcript and oncogene RASSF1C to exploit its tumourigenic activity through enhanced secretion of EVs. I characterise RASSF1C EVs as able to drive migration and invasion in recipient breast cancer cells and I show that RASSF1C elicits exocytosis through activation of the small GTPase RhoA. Secondly, I explore the role of the TGF β cytokine in altering extracellular vesicle secretion. Here, I report the selective enrichment of the tetraspanin CD9 on TGF β driven EVs. I show that CD9 is a positive mediator of TGF β pathway and conclude that TGF β employs exocytosis as a route to secrete CD9 from pathway activated cells, as a negative feedback on the signalling cascade. Finally, I describe a novel role of CD9 positive EVs in propagating TGF-β signalling in recipient breast cancer cells and in mediating TGF-β driven invasion in untransformed breast epithelium. This work highlights the importance of tumourigenic stimuli, both intracellular (RASSF1C) and environmental (TGF-β), in fostering a pro invasive cancer environment and the pivotal role that extracellular vesicles play in mediating oncogenic signalling.

Advisor: O'Neill, E
Adaptive Bayesian optimization for dynamic problems

This thesis studies the problem of tracking the extremum of an objective function that is latent, noisy and expensive to evaluate. This problem is notable because many large-scale learning systems with complex models operating on non-stationary data have meta-problems whose solutions require the tracking of an evolving extremum.
We start by describing dynamic optimization problems and model them using spatiotemporal Gaussian process priors. We construct an intelligent search mechanism that uses the learnt insights to skillfully guide the search by dynamically modifying the feasible search region as a device to keep track of the evolution. We also show that this mechanism induces a natural approximation scheme for cases where the number of samples for the model becomes too expensive for inference. We test the resulting method on synthetic and real-world problems.
In the next part of the thesis, we demonstrate the utility of the method on pertinent real-world meta-problems occurring in essential and widely-used large-scale learning systems.
We start by proposing intelligent meta-heuristics, which are derived from our resulting method, for the learning rate adaptation meta-problem that is part of many large-scale learning systems trained by stochastic gradient descent. We incorporate hyper-gradients into the model for the meta-problem and use the additional insights to aid the intelligent meta-heuristic search. We test the resulting adaptation scheme on training various types of neural network models to demonstrate its utility through the significant performance improvements.
We also exploit the wealth of prior art to construct a configuration oracle that adapts various types of system parameters in online trading algorithms as they interact with noisy and nonstationary financial data. We test the oracle on multiple algorithms operating using widely-accepted trading principles and demonstrate notable performance gains.
The importance of this study is that it proposes a mechanism for intelli- gently exploiting vast amounts of prior knowledge that exists for these meta- problems. The intelligent use of this knowledge significantly improves the performance of the primary learning systems, which are vital for solving many practical problems, operating in dynamic environments.

Advisor: Roberts, S
Osborne, M
Late modernist travel literature, 1930-1949: home, nationalism, and war

In the decades immediately following the First World War, convulsions along geopolitical fault-lines exposed the inherent instability of home for many; the disintegration of empires led to redrawn borders and population resettlement, while militant nationalism, revanchist and irredentist ideologies triggered the further displacement or exile of millions, the elective emigration of the more fortunate, and the travel of the more fortunate still – including those who sought to bear witness to the catastrophe. In this period, broad questions about the definition of a conceptual home had striking correspondence with those around the status of material homes, and in both cases were catalysed by travel and war. How was literature involved in complicating and challenging the idea of home? How did it stage encounters between the rooted and the displaced?
This thesis argues that a particular body of travel writing, encompassing the factual travelogue and travel fiction, discrete from the contemporaneous popular form of travelogue, and often notably merging with war writing, emerged in the interwar period and 1940s. In this late modernist genre, texts are permeated by thought about the homes from which writers set off, and yet typically resist certainties about mapping the space of a metaphysical home and homeland, or to trusting in anything more than their provisional parameters.
The first chapter establishes this thesis’ broader methodology of reading travel literature across modes and genres, and investigates the chronic instability of the English home as represented in the work of Evelyn Waugh. Chapter Two traces W. H. Auden’s poetic representation of travelled topographies and of the metonymic, elusive ‘elsewhere’ that signals a failure to finally arrive at real locations. Chapter Three is concerned with nationalism and its place in shaping personal and collective conceptualisations of home, focusing on the work of Rebecca West. The final chapter looks at Cyril Connolly’s contribution to the production and reception of the travel genre, and in particular his review of the arts and literature, Horizon (1940-1949) as a forum that brought together those who travelled or dreamed of travel, and that served as an important catalyst for the hybridisation of travel and war writing in the 1940s.

Advisor: Beasley, R
What was criminology? From photography to painting in Cesare Lombroso's (1835-1909) criminal anthropology

Despite the emergence of a new criminological subfield called visual criminology in recent years and a long-standing criminological subfield called historical criminology, the visual history of criminology remains neglected. Nowhere is this neglect more obvious than when it comes to the scholarship of Cesare Lombroso (1835-1909). Given that Lombroso is considered to be the so-called founding figure of criminology it seems natural that a visual-historical study of our discipline should begin with him. A mere cursory glance through Lombroso’s L’uomo delinquente in rapporto all'antropologia, alla giurisprudenza e alle discipline carcerarie [Criminal Man in relation to anthropology, jurisprudence and prison disciplines] (1876), his most well-known work in criminology, and especially the fourth volume of its fifth and final edition (1896-1897d), reveals it to be rich in terms of the quantity and quality of images therein. Nicole Rafter (1939-2016) began paying attention to the visual in Lombroso’s scholarship and was a pioneer in this regard. However, her untimely death in 2016 meant that her efforts were frustrated in this regard. As yet, no in-depth study on the subject has been published. In this dissertation, I undertake a sustained book-length examination of the visual component of Lombroso’s criminal anthropology. I focus on photography and, additionally, a visual medium that even scholars in the arts and especially literary and art histories are yet to analyse, namely painting especially as it manifests itself as fine art. I argue that Lombroso’s criminal anthropology was not merely visual—that was something that Rafter (2014) observed before her death—but that it was, additionally, a creative and even artistic enterprise. In so doing I revise the orthodox history of criminology by troubling the relationship between science (Lombroso’s criminal anthropology) on the one hand and the arts on the other. What was criminology? Not what we knew it to be.

Advisor: Bosworth, M
Carrabine, E
Improving biologically inspired protein structure prediction using satisfied predicted contacts

The number of published protein structures is vastly outnumbered by protein sequences - this gap is only increasing as sequencing technologies continue to advance. Experimental methods of protein structure determination are costly and slow; computational protein structure prediction could be a solution.
A major problem with current methods of protein structure prediction is the large amount of computational time needed to generate an accurate structure for one protein. For some cases, notably smaller proteins, structures can now be reliably and accurately predicted. However, for a large number of proteins, especially longer proteins, the computational cost means that structure prediction remains infeasible using current methods.
SAINT2 is a sequential, fragment-based de novo structure prediction method that has been demonstrated to be faster and comparably successful at predicting correct structures than other methods. The aim of this study is to increase the number of protein families that SAINT2 can predict correct structures for by utilising predicted contacts in a unique way.
This thesis finds that in some cases, evaluating the long-range satisfied predicted contacts in a partial model can give an indication as to the final model quality. Discarding partial models predicted to lead to an incorrect final structure leads to overall enrichment of the decoy pool for these proteins. However, it is still unclear how to identify cases that our new version of SAINT2 would be better at predicting.
We also find that during extrusion, correct and incorrect models can satisfy and break predicted contacts differently. Correct models may be forming stable sub-structures early on in extrusion, whereas incorrect models appear to be breaking contacts throughout extrusion. It may be possible to identify incorrect predicted contacts based on their rank by satisfaction in models. This may lead to an increase in model quality if contacts predicted to be incorrect are down-weighted in further SAINT2 runs.

Keywords: Protein structure
Advisor: Deane, C
de Oliveira, S
Socioeconomic inequalities in health

The aim of this thesis is to advance the understanding of how the relationship between health and socioeconomic status changes over the life-course and over time. Three different studies which address several important aspects of the socioeconomic inequalities in health are presented. First, the existence of a socioeconomic gradient in functional health at the end of life in England is investigated. The objective is to contribute to the empirical evidence concerning the existence of a disappearing association between socioeconomic status and health in old age, by analysing whether socioeconomic status is associated with disability trajectories in the final years of life. The second study examines how the changing demographic composition of different educational groups over time can help to explain the widening educational gap in self-reported health in the United States, connecting family demography with health inequalities. The third study explores whether, and to what extent, education has a causal effect on cancer outcomes in England and Wales. This thesis contributes to the existing literature in at least three ways. First, it conceptualises the last years of life as a life stage where socioeconomic inequalities in health might emerge. Differences in the disability-related pathways preceding death were found only wealth. Second, it highlights the increasingly important role of demographic factors and marital status in particular, when studying health inequalities over time. Indeed, the findings suggested an increasingly relevant contribution of marital status over time for educational inequalities in health in the United States, despite marriage representing only a small part of the explanation. Furthermore, it investigated for the first time the causal effect of education on survival after cancer diagnosis, providing evidence for the absence of a causal impact of an additional year of compulsory schooling on cancer incidence and survival after two educational reforms.

Advisor: Monden, C