VictorJuiz/thesis huggingface dataset:
Functional analysis of Xist-mediated silencing

The lncRNA Xist is the master regulator of X chromosome inactivation in female mammals. Its mono-allelic expression triggers a cascade of well characterised events leading to the stable silencing of the X chromosome. However, how Xist coordinates these events is still unclear. We developed a system to dissect Xist function by making a library of deletions of Xist cDNA. The cDNAs were then stably transfected into a male ES cell line under an inducible promoter. The parent cell line was derived from an interspecific cross between different mouse strains, allowing subsequent allele-specific analysis based on a previously described set of strain-specific SNPs. This approach allowed full and partial loss of silencing activity to be discriminated by isolating nascent transcripts upon prolonged Xist expression, and using them to make libraries for high-throughput sequencing. It was therefore possible to map regions of Xist required for specific functions, notably gene silencing and recruitment of Polycomb repressor proteins. Using this approach, the B-repeats were identified as the segment of the RNA crucial for de novo recruitment of both PRC1 and PRC2 Polycomb complexes, whereas the A-repeats were confirmed to be essential for Xist-mediated early silencing of genes. To complement these analyses, an in vitro assembly system was set-up to study the direct interaction between key regions of Xist RNA and defined nuclear proteins at the biochemical/proteomic level, obtaining a comprehensive list of functional candidates. Interestingly, the nuclear matrix protein hnRNP-K was found among the factors significantly enriched over the segment of Xist previously identified as essential for Polycomb recruitment. We thus investigated the functional role of hnRNP-K in mediating the interaction between Xist and Polycomb with a number of in vivo and in vitro assays, and found that hnRNP-K is required to mediate contact between PRC1 and Xist through its KI domain.

Advisor: Brockdorff, N
Lower Cretaceous climate records and the correlation between marine and lacustrine settings (Europe and South America)

Major changes in watermass chemistry during the opening of the central segment of the South Atlantic, and oceanic anoxic events (OAEs 1a to 1d), represent dramatic events that affected the ocean–atmosphere system during the Early Cretaceous. This thesis addresses the chemostratigraphic correlation of Tethyan and South Atlantic sections based on carbon-, sulphur- and strontium-isotopes (δ13C, δ34S and 87Sr/86Sr) integrated with other methods to explore the causal links between these phenomena. Firstly, the sedimentation of massive evaporite deposits is discussed and its relationship with the Early Aptian OAE 1a explored. The proposed coincidence in timing between massive evaporite deposition and OAE 1a enhances the understanding of carbon and sulphur cycles in the Early Cretaceous. Secondly, the top of sub-evaporite carbonates in the southern Brazilian basins is identified as having been deposited in a continental environment, and further evidence for its deposition during part of the OAE 1a interval is presented. Thirdly, it is suggested that the formation of the Ontong Java Plateau, already linked to the genesis of OAE 1a, promoted a eustatic sealevel rise responsible for rapid seawater entrance into the southern Brazilian basins during the Early Aptian. Fourthly, the first record of OAE 1a from northeastern Brazil (Sergipe- Alagoas Basin) has been recognized, allowing stratigraphic correlation with southern Brazilian basins. Stratigraphic correlation between the southern Brazilian basins is extended to the Falkland Plateau, where the decrease in the content of organic matter upwards in the stratigraphy of DSDP Site 511 through the Barremian–OAE 1b interval can be related to the evolution of South Atlantic basinal geometry. Finally, in the context of a Tethyan reference section, the record of the Barremian-Aptian boundary and the OAE 1a interval has been characterized in the Tethyan Poggio le Guaine scientific core from Marche–Umbria, Italy.

Advisor: Jenkyns, H
Robinson, S
Monetary mythology: the West German central bank and historical narratives, 1948-78

This thesis examines the emergence, and then development, of what I call 'monetary mythology', a historical narrative, or version of history, concerning the inter-war period of Germany. Following the Second World War, it was left to West German elites to establish a new federal central bank, the Deutsche Bundesbank. A three-way power struggle emerged between the existing West German central bank – the Bank deutscher Länder - the federal government and the various state governments, all vying to influence the institutions and structure of this new monetary authority. In justifying their arguments, West German elites used various lessons derived from the turbulent experiences of the inter-war era. Monetary mythology, for its part, emphasised the lessons of Germany's two inflations; and the Bank deutscher Länder, and its allies, explicitly tied these lessons to the need for an independent central bank. And though it was once challenged by other competing historical narratives in the period 1949-51, monetary mythology emerged by 1956 triumphant in the public sphere in terms of framing the parameters through which West Germans viewed their monetary history.
The doctoral project at hand approaches economic history from a cultural angle. In doing so, it offers an alternative history of the Bundesbank, as well as an alternative explanation for the cultural preoccupation surrounding inflation in West Germany. The thesis explains this cultural preoccupation in institutional terms. In providing for a central bank that was independent of political instruction, the Bundesbank Law of 1957 allowed for conflicts between the federal government and central bank to emerge. These conflicts often became 'dramatised' in the public sphere, creating controversies surrounding the Bundesbank's independence, and, in turn, giving rise to circumstances in which the lessons of the two inflations continued to remain relevant, geared in support of central bank independence.

Keywords: Bundesbank
West Germany
Inflation
Central Banking
Bank deutscher Länder
Reichsbank
Advisor: O'Rourke, K
Betts, P
The feasibility of ultrasound elastography in monitoring high-intensity focused ultrasound therapy

High-intensity focused ultrasound (HIFU) therapy is a non-invasive therapy method for the treatment of solid tumours. One of the main barriers to wider clinical adoption of HIFU is the lack of reliable and cost-efficient therapy monitoring. One promising technique is acoustic radiation force (ARF) ultrasound elastography, which relies on the temperature dependence of tissue properties to affect displacement amplitudes.
An extensive literature review of tissue acoustic, thermal and mechanical properties identified an absence of data on the temperature dependence of the viscoelastic properties. Experiments were carried out in ex vivo liver to determine these properties over the range of temperatures and frequencies relevant to ARF.
ARF induced displacements were quantified experimentally in a tissue-mimicking phantom. The comparison of sine and square modulated ARF excitation showed that square modulation results in higher peak amplitudes and smaller second harmonic components in the frequency domain. A simulation model was developed, which accurately reproduced the observed displacements with different modulation frequencies and power levels.
The effect of temperature on ARF displacements was measured experimentally during HIFU therapy in ex vivo liver. Simulations captured the same phenomena as observed in the experiments. ARF displacements during HIFU therapy were shown to initially depend on attenuation before ablation, but once the temperature exceeded the ablation threshold, viscoelastic properties dominated.
A second barrier for HIFU is the need to reliably deliver acoustic energy to the target. Nonlinear acoustic simulations were conducted using patient derived computed tomography (CT) data to evaluate the HIFU therapy in the kidney. The simulations revealed that attenuation and refraction contributed roughly equally to intensity loss. Focal splitting associated with refraction was found to be the main effect reducing the heating efficacy, and a method to employ phase correction at the source was proposed to mitigate the effect.

Advisor: Cleveland, R
Edwards, D
Methods for modelling human functional brain networks with MEG and fMRI

MEG and fMRI offer complementary insights into connected human brain function. Evidence from the use of both techniques in the study of networked activity indicates that functional connectivity reflects almost every measurable aspect of human reality, being indicative of ability and deteriorating with disease. Functional network analyses may offer improved prediction of dysfunction and characterisation of cognition.
Three factors holding back progress are the difficulty in synthesising information from multiple imaging modalities; a need for accurate modelling of connectivity in individual subjects, not just average effects; and a lack of scalable solutions to these problems that are applicable in a big-data setting. I propose two methodological advances that tackle these issues.
A confound to network analysis in MEG, the artificial correlations induced across the brain by the process of source reconstruction, prevents the transfer of connectivity models from fMRI to MEG. The first advance is a fast correction for this confound, allowing comparable analyses to be performed in both modalities. A comparative study demonstrates that this new approach for MEG shows better repeatability for connectivity estimation, both within and between subjects, than a wide range of alternative models in popular use. A case-study analysis uses both fMRI and MEG recordings from a large dataset to determine the genetic basis for functional connectivity in the human brain. Genes account for 20% - 65% of the variation in connectivity, and outweigh the influence of the developmental environment.
The second advance is a Bayesian hierarchical model for sparse functional networks that is applicable to both modalities. By sharing information over a group of subjects, more accurate estimates can be constructed for individuals' connectivity patterns. The approach scales to large datasets, outperforms state-of-the-art methods, and can provide a 50% noise reduction in MEG resting-state networks.

Keywords: MEG
Connectome
fMRI
Gaussian graphical model
Bayesian statistics
Functional connectivity
Volume conduction
Imaging genetics
GGM
Magnetic field spread
Advisor: Woolrich, M
Smith, S
The origins of the Reagan Doctrine Wars in Angola, Central America, and Afghanistan

This diplomatic and military history offers a new interpretation of the origins of the three fighting fronts during the final phase of the Cold War in Angola, Central America, and Afghanistan. Vaguely remembered today as proxy wars on the periphery, in fact, these were protracted revolutionary civil wars and regional contests for the balance of power in which millions died, while at the same time they were central to global superpower confrontation. Analysis focuses on the strategy and policy of the United States. The chronology from 1975 to 1982 covers the Ford administration's covert action intervention in the Angolan Civil War, which came to grief at the hands of Cuban troops; Jimmy Carter's effort to conduct foreign policy based on principles, which ran foul of power considerations in Angola, Nicaragua, El Salvador, and Afghanistan; and Ronald Reagan's embrace of these wars early in his first term as part of the revival of U.S. strength in its competition with the Soviet Union.
The principal argument is that, while generally undervalued as controversial small wars of dubious significance, these wars were in fact integral to U.S. experience of limited war during the Cold War following victory in World War II. In strategic terms, the main conclusion is that the U.S. restricted itself to conducting economy of force contingency operations in Angola, Central America, and Afghanistan as a result of its costly struggles in Korea and Vietnam. Despite declaring these peripheral wars to be central to the Cold War, avoiding the costs of involving U.S forces directly in Third World conflicts and minimizing the risks of escalation with the Soviet Union were overriding political and military imperatives.

Keywords: Revolution
Civil War
Cold War
Reagan Doctrine
Third World
Irregular Warfare
Strategy and Policy
Advisor: Strachan, H
Johnson, R
Statistical structure of plasma turbulence from BES measurements in MAST and the effect of flow shear

The suppression of turbulent transport is a key requirement for enabling nuclear fusion to become a viable energy source. One possible route to achieving this suppression is through toroidal flow shear. We investigate the effect that flow shear has on the structure of turbulence by analysing data from both measurements of the fluctuating intensity field using the Beam-Emission-Spectroscopy (BES) diagnostic on the spherical tokamak MAST, as well as from numerical simulations of the fluctuating density field in MAST. We develop a procedure to map from the correlation parameters of the intensity field to the correlation parameters of the density field. This procedure is illustrated using the MAST BES system and the validity of the underlying assumptions is tested on fluctuating density fields generated by direct numerical simulations using the gyrokinetic code GS2. By using this procedure, we demonstrate how, in experiment, the flow shear associated with the differential toroidal rotation of tokamak plasmas breaks an underlying symmetry of the turbulent fluctuations imposed by the up-down symmetry of the magnetic equilibrium. Indeed, in both experimental BES measurements and gyrokinetic simulations, this symmetry breaking in ion-scale turbulence in MAST is shown to manifest itself as a tilt of the spatial correlation function and a finite skew in the distribution of the fluctuating intensity (density) field. The tilt is a statistical expression of the "shearing" of the turbulent structures by the mean flow. The skewness of the distribution is related to the emergence of long-lived density structures in sheared, near-marginal plasma turbulence. The extent to which these effects are pronounced is argued (with the aid of the simulations) to depend on the distance from the non- linear stability threshold. Away from the threshold, the symmetry is effectively restored.

Keywords: Tokamak
Plasma Turbulence
Beam Emission Spectroscopy
Advisor: Schekochihin, A
Field, A
Commutative K-theory

The bar construction BG of a topological group G has a subcomplex BcomG ⊂ BG assembled from spaces of commuting elements in G. If G = U;O (the infinite unitary / orthogonal groups) then BcomU and BcomO are E∞-ring spaces. The corresponding cohomology theory is called commutative K-theory.
In this work we study properties of the spaces BcomG and of infinite loop spaces built from them, with an emphasis on the cases G = U,O. The content of this thesis is organised as follows:
In Chapter 1 we consider a family of self-maps of BcomG and apply these to study the question when the inclusion map BcomG ⊂ BG admits a section up to homotopy.
In Chapter 2 we show that BcomU is a model for the E∞-ring space underlying the ku-group ring of &Copf;P∞. Thus we provide a complete description of complex commutative K-theory. We also study the space BcomO. Our results include a computation of the torsionfree part of the homotopy groups of BcomO and a long exact sequence relating real commutative K-theory to singular mod-2 homology.
Chapter 3 is self-contained. We prove a result about the acyclicity of the "comparison map" M∞ → ΩBM in the group-completion theorem and apply this to compare the infinite loop space associated to a commutative &Iopf;-monoid with the Quillen plus-construction.
Chapter 4 is concerned with a previously known filtration of Ω0∞S∞ by certain infinite loop spaces {hocolim&Iopf;B(q, Σ_)}q≥2. For each term in this filtration we construct another filtration on the spectrum level, whose subquotients we describe. Our set-up is more general, but the space hocolim&Iopf;B(q, Σ_) will serve as our main example.
Appendix A is an excerpt from the author's Oxford transfer thesis. There we gave a construction of an infinite loop space associated to certain subspaces B(q, Γg,1) ⊂ BΓg;1, where Γg;1 is the mapping class group of a genus g surface with one boundary component.

Advisor: Tillmann, U
Risk factors for ovarian cancer by histological phenotype in the Million Women Study

There is growing evidence that the different histological types of ovarian cancer have diverse origins. Many high-grade serous tumours (the most common type) are hypothesised to arise from the fallopian tubes, while endometrioid and clear cell tumours are hypothesised to develop from endometriosis, and the origins of mucinous tumours are uncertain. If these hypotheses are true, then the population-level risk factors for the ovarian cancer histotypes should likewise vary – but few epidemiological studies have sufficient cases to explore this. This thesis investigates the association between ovarian cancer and various exposures (including tubal ligation and reproductive factors), in a cohort of 1.3 million women, with 8,000 incident ovarian cancers. Participants completed a questionnaire at recruitment, and were followed up for routinely collected information on cancers and deaths using national registries. Cox proportional hazards models were used to estimate adjusted relative risks of ovarian cancer in women by different exposures. Tubal ligation was associated with reduced risks of cancers of the ovary, and also of the peritoneum and fallopian tube; parity and breastfeeding were also associated with reduced risks of ovarian cancer. These associations with ovarian cancer were highly heterogeneous between the different histological tumour types, consistent with hypotheses of their distinct origins. In particular, risks of endometrioid and clear cell tumours were substantially reduced amongst women with tubal ligation, but substantially increased amongst nulliparous women. For high-grade serous carcinomas, there was a smaller but significant reduction in risk with tubal ligation, and no significant association with parity. I also describe some methodological studies I set up for future tissue-based work: developing techniques in image analysis, and a pilot study of obtaining linked pathology reports and tissue samples. The population-level associations demonstrated by histotype are largely consistent with the new hypotheses of the different origins of ovarian cancer histotypes.

Keywords: Epidemiology
Ovarian cancer
Pathology
Advisor: Beral, V
Ahmed, AA
The figure of Hades/Plouton in Greek beliefs of the archaic and classical periods

The main aim of this work is the presentation, characterisation and review of the image of the Greek underworld deity, Hades/Plouton in Greek beliefs of the Archaic and Classical periods, on the basis of comparison of the preserved literary and epigraphic testimonies with the remains of material culture, and the reconstruction of the most coherent possible image of the god, claimed by scholars to be of little importance to Greek beliefs and to have no cult. The present dissertation liberates the god from long-standing scholarly misconceptions and returns him to his proper place within the Greek pantheon. Its main scholarly contribution and originality can be summarised as follows: (i) Hades is mainly an agricultural deity with a clear cult environment and has more in common with the world of the living than that of the dead; (ii) Hades influenced the representation of other male deities connected with earth: his main attribute, paradoxically the cornucopia or 'horn of plenty', appears for the first time in Greek art in the 6th century BC as exclusively his, and is later ascribed to other deities; (iii) Hades and Plouton were the same deity (Plouton – an Attic instantiation – spread throughout Greece with Attic literature and the Eleusinian cult of Demeter and Kore), sharing the same myths, and both, through the properties inscribed in their names (invisibility in Hades' and corn in Plouton's), referring to the earth; both names are products of the conceptualisation of the world of the dead; (iv) contrary to the prevailing scholarly view, the multiplicity of Hades' names is not exclusively the result of euphemism (which I propose to see rather as a by- product): the nomenclature is more complex and depends principally on cultic or mythological contexts and local tradition. My work not only reconstructs the repertoire of Greek ideas and opinions on Hades and the character of his cult, but also advocates a new understanding of the notion of Greek deity, as metonymy: Hades is representative of a wider class of deities who are concrete and abstract at the same time (like Gaia [the Earth], Uranos [the Sky], Okeanos [the Sea]): they denote a place, a god, a property of something, a form of matter.

Keywords: Greek gods
Underworld god
Greek religion
Hades
Advisor: Parker, R
Healing nature: green living and the politics of hope in Hong Kong

In Hong Kong, 'green living' (luksik saangwut 綠色生活) is promoted as a way of living that is kind to the Earth and good to the people. It is a grassroots movement that encourages people to take personal responsibility for the environment and the society at large. While most studies of Asia's environmental movements focus on green groups' lobbying tactics and mobilisation strategies, this thesis pays serious attention to individuals' experience of living a green life. Although Hong Kong’s green culture is highly influenced by the global appeal to sustainability and environmental protection, its specificities are shaped by the city's social and political climate in a unique historical conjuncture. By focusing on individual experience and their practices of green living in the everyday, I argue that green living in Hong Kong is best understood as 'technologies of the self' wherein new environmental, social, and political subjectivities are formed among the ordinary people. The perceived reciprocity between the act of healing nature and the healing power of nature is an essential element in the formation of green subjectivity in Hong Kong. Not only does green living help people heal and transform themselves, it has also given rise to an embodied politics (santai likhang 身體力行) that enables people to reimagine a social and political 'otherwise'. Such embodied politics has come to represent a politics of hope that empowers people to confront with the politics of fear that has been looming over Hong Kong since the former British colony was returned to China in 1997. In light of this background, I argue that what the Hong Kong people want to sustain is not just the natural environment, but also the social norms and the ways of living that are thought to distinguish themselves from their counterparts in mainland China.

Keywords: China
East Asian Studies
Sustainability
Hong Kong
Environmentalism
Subjectivity
Anthropology
Social Movements
Advisor: Lora-Wainwright, A
Xiang, B