VictorJuiz/thesis huggingface dataset:
EEG complexity as an ASD biomarker: a data-driven study for the identification of electrophysiological correlates of ASD

Autism Spectrum Disorders (ASD) are a group of lifelong neurodevelopmental disorders, described by three core deficits which are thought to be consequences of atypical cortical activity. Abnormal neural connectivity underlying ASD could be inferred from dynamical system characteristics of the brain measured from electroencephalography (EEG) time series. Simple EEG measurement have the potential to provide important clinical biomarkers for early identification, risk assessment and monitoring the progression of ASD, while spanning the spectrum’s heterogeneity of severity. The explicit goal of this project was to use Multiscale Entropy (sample entropy) measures and Recurrence Quantitative Analysis (RQA) on EEG to identify quantifiable neural correlates of behaviours associated with an ASD diagnosis. The hypotheses were tested on two cohorts: the Kenyan cohort with data collected in Kilifi, Kenya from both neurotypical children as well as children diagnosed with ASD and the NDAR cohort from the National Database for Autism Research (NDAR), also containing data from both groups. The results showed that complexity measured using sample entropy is useful in distinguishing the two groups, both at a whole brain level in the alpha, beta and gamma bands, and at a single electrode level, mainly in the theta band in the frontal, occipital and parietal electrodes and in the high gamma band in the frontal and prefrontal areas. RQA variables analysis showed that determinism can delineate ASD in the theta, gamma and high gamma bands in all electrode locations, in the delta band in the left frontal and temporal areas and in the alpha band in the left hemisphere in the occipital, parietal, temporal and central electrodes; laminarity is useful in delineating ASD in the frontal, temporal and parietal regions in the theta band and the occipital, parietal and temporal regions in the delta band; l_entropy played a role in ASD delineation in the central, temporal and occipital areas in the theta frequency; lastly, l_max accurately distinguished the two groups, mainly in the frontal and central areas in the theta band and in the parietal region in the alpha frequency. These findings represent pilot evidence of potential high utility of this method, which can have great impact on clinical practice, in the early screening and diagnosis stages of ASD.

Keywords: Autism
Entropy
Electroencephalography
EEG
Advisor: Newton, C
Accelerating computational diffusion MRI using Graphics Processing Units

Diffusion magnetic resonance imaging (dMRI) allows uniquely the study of the human brain non-invasively and in vivo. Advances in dMRI offer new insight into tissue microstructure and connectivity, and the possibility of investigating the mechanisms and pathology of neurological diseases. The great potential of the technique relies on indirect inference, as modelling frameworks are necessary to map dMRI measurements to neuroanatomical features. However, this mapping can be computationally expensive, particularly given the trend of increasing dataset sizes and/or the increased complexity in biophysical modelling. Limitations on computing can restrict data exploration and even methodology development. A step forward is to take advantage of the power offered by recent parallel computing architectures, especially Graphics Processing Units (GPUs). GPUs are massive parallel processors that offer trillions of floating point operations per second, and have made possible the solution of computationally intensive scientific problems that were intractable before. However, they are not inherently suited for all types of problems, and bespoke computational frameworks need to be developed in many cases to take advantage of their full potential.
In this thesis, we propose parallel computational frameworks for the analysis of dMRI using GPUs within different contexts. We show that GPU-based designs can offer accelerations of more than two orders of magnitude for a number of scientific computing tasks with different parallelisability requirements, ranging from biophysical modelling for tissue microstructure estimation to white matter tractography for connectome generation. We develop novel and efficient GPUaccelerated solutions, including a framework that automatically generates GPU parallel code from a user-specified biophysical model. We also present a parallel GPU framework for performing probabilistic tractography and generating whole-brain connectomes. Throughout the thesis, we discuss several strategies for parallelising scientific applications, and we show the great potential of the accelerations obtained, which change the perspective of what is computationally feasible.

Keywords: Non-linear optimisation
GPGPU
Diffusion MRI
Tractography
Scientific computing
Connectome
Brain Modelling
Brain microstructure
Advisor: Reguly, I
Giles, M
Smith, S
Sotiropoulos, S
Targeting BRCA2 deficiency with GSK3 inhibitors

BRCA1 and BRCA2 tumour suppressors are essential for homologous recombination-mediated double-strand break repair and replication fork protection. Therefore, BRCA1 and BRCA2 are essential for cell viability. Deactivating mutations in one of these genes lead to genome instability and are associated with breast and ovarian cancer. We thus performed a chemical library screen and identified glycogen synthase kinase 3 (GSK3) inhibitors as a potent tool to kill BRCA2-deficient cells.
One of the best-characterised cellular functions of serine/threonine kinase GSK3 is its role in the WNT pathway. Here, it acts as a regulator of β-catenin, with the inactivation of GSK3 leading to the stabilisation of β-catenin.
In this study, we show that inhibition of GSK3 reduces the viability of human BRCA2-deficient cells. In addition, GSK3 inhibition leads to replication stress, DNA damage and genome instability in the context of BRCA2 deficiency. GSK3 inhibition sensitivity can be reversed by depleting β-catenin. Furthermore, GSK3 inhibition-induced replication stress and checkpoint activation is reduced when β-catenin is depleted.
BRCA1-deficient cells that have lost 53BP1 are able to overcome PARP inhibitor olaparib sensitivity by reactivating homologous recombination. Interestingly, we find that olaparib-resistant Brca1-/- , 53BP1-deficient cells are sensitive to GSK3 inhibition, whilst Brca1+/+ cells remain unaffected.
In summary, these results demonstrate that GSK3 inhibitors may be used to target HR deficiency, including cells that have acquired resistance against currently used therapies.

Advisor: Tarsounas, M
Ryan, A
Data challenges in pulsar searches

Technological advances coupled with a decline in digital storage costs have resulted in a profusion of data being created, collected and consumed. These data give rise to new challenges and opportunities in many disciplines ranging from science and engineering to biology and finance.
An example of a future project in radio astronomy that promises both Big Data and Big Discoveries is the Square Kilometre Array (SKA) radio telescope project. Astrophysicists are confident that the Big Data amassed by the SKA will not only answer fundamental questions regarding the Universe but also contain big discoveries not yet postulated. The transformational potential of the SKA and its ensuing data and algorithmic challenges, in particular for the discovery and study of pulsars, drive the research of this thesis.
Discovering all pulsars beaming towards Earth is one of the key science goals of the SKA. However, in addition to low signal strengths, searching for pulsars is extremely difficult due to the intrinsic weakness of their signals, propagation effects and the presence of anthropogenic interferences. Numerous techniques have been developed to overcome some of these difficulties and to assist in the quest to find more pulsars. However, despite the success of these techniques, the number of pulsars discovered in recent surveys (Swiggum et al. 2014, Lazarus et al. 2015) has fallen well short of the number predicted by pulsar population synthesis models (Lorimer 2011). This shortfall in pulsar detections can be attributed to radio frequency interference (RFI), red noise and scintillation (Lazarus et al. 2015).
For this thesis, and in order to investigate and quantify these claims, I first developed a new technique to simulate pulsar search data that contain different types of RFI and varying noise baselines (i.e. red noise). This surrogate modelling technique was then used in a framework that I developed to inexpensively explore the sensitivity of pulsar search pipelines for different noise and RFI settings. The results from this framework highlight the necessity to develop algorithms that are able to identify and remove non-stationary variations from the data before RFI excision and searching is performed in order to limit false positive detections.
To address the shortcomings identified with the framework which assessed the performance of existing pulsar search pipelines, I developed a new real-time algorithm for excising RFI while simultaneously normalising the variability in time and frequency inherent to pulsar observations. Processing synthetic data with the algorithm resulted in an expansion of the noise/pulsar spin period parameter space for which we are able to successfully detect pulsars. Furthermore, the algorithm is shown to reduce the number of false positive detections.
In conclusion, the insights gained from the work presented in this thesis and the improvements achieved will contribute to the development of a new realtime pulsar search pipeline adept at dealing with the challenges posed by the SKA.

Advisor: Roberts, S
Karastergiou, A
Unravelling the role of AKR1D1 in human hepatocytes

Non-alcoholic fatty liver disease (NAFLD) is the hepatic manifestation of the metabolic syndrome and is rapidly becoming one of the leading indications for liver transplantation worldwide. The cellular processes and molecular targets that govern disease development and progression remain to be fully defined and currently there are no licensed treatments. Steroid 5β-reductase (AKR1D1) is highly expressed in human liver where it inactivates steroid hormones and catalyses a fundamental step in bile acid synthesis. I have hypothesised that AKR1D1 plays a crucial regulatory role in hepatic metabolic homeostasis.
In human hepatoma cell lines, genetic manipulation of AKR1D1 altered primary bile acid biosynthesis and steroid hormone action. Furthermore, gene silencing of AKR1D1 increased hepatocyte triglyceride accumulation through increased de novo lipogenesis and decreased β- oxidation, fueling hepatocyte inflammation as well as increasing glycogen synthesis. I have shown that AKR1D1 has a potent ability to regulate the metabolic phenotype of human hepatocytes suggesting a crucial role in the pathophysiology of NAFLD.

Advisor: Hodson, L
Tomlinson, J
'Inte' at intersections: deaf and hard-of-hearing mainstreamed Japanese youth and the search for belonging

This dissertation explores the lived realities of young deaf and hard-of-hearing (DHH) Japanese who were educated in mainstream schools. Colloquially known as 'inte', a shortened form of the loanword 'integration', these youth are poised at intersections: between special education and academic integration, deaf and hearing, and signed and spoken languages. This study focuses on how participants negotiate this distinct positionality. Inte are 'the other' in the private sphere of the family and the public sphere of the school. I aim to illuminate how inte negotiate this in-between status as they search for belonging. The integration of DHH students is a relatively recent phenomenon. For nearly 100 years, deaf students were educated in separate educational institutions. Therefore, I begin by situating the inte's experiences in a historical and comparative context by exploring the shifts in educational trends for DHH students and the debates regarding the most appropriate communication modalities for their education. I argue that the first phase of integration does not occur within schools but within the home. Inteare typically born into families in which the taken-for-granted shared vertical (inherited) identity and language must be re-examined and re-configured. As a minority in mainstream schools, inte demonstrate agency by employing 'covering' strategies to mitigate difference and perform 'communication competence'. Upon encountering signing DHH peers, inte re-evaluate their positionality and sense of self. By utilizing a number of methodological approaches, including an approach developed for this research, 'peer interviews', this dissertation contributes to the understanding of anthropological concepts of belonging, personhood, intimacy, 'passing' and identity. Through an actor-centered approach that concentrates on the voices of 'youth', I explore how members of this marginalized group in society (re)negotiate their position in the mainstream.

Advisor: Goodman, R
Konishi, S
A re-assessment of text-image relationships in Christine de Pizan’s didactic works

Although the works of Christine de Pizan have been of interest to scholars for some time, technological advances and initiatives to make digital copies of manuscripts available online have only recently enabled close comparisons between the visual programmes of her works to be made. This thesis demonstrates that detail usually considered secondary or 'paratextual' in Christine's manuscripts actually formed a carefully-constructed part of the work itself that Christine explicitly asks her audience to read. Through 'reading' the text and image simultaneously, the visual programme proves to comprise additional layers of meaning that were woven into her didactic works. These meanings can serve to supplement the educational and moral aims of the works, or, conversely, can be inconsistent with the message conveyed in the text, leading the reader-viewer to contemplate further on the matters presented and form their own opinions on them. Sometimes, meaning is created by intervisual connections with pre-existing iconography, such that viewers may be creating associations between the miniatures seen in Christine's manuscripts and other imagery, leading them to make certain associations - this is notably the case in author-portraits of Christine. As manuscripts prepared under the author's supervision came to be copied, changes were made to the iconographic programmes, testifying to and enabling different types of readings to take place. The findings of this thesis have implications for editorial practices of medieval works in general, as these tend to circulate in editions without the visual programme, providing modern readers with only a partial view of the complete work.

Keywords: Medieval France
Christine de Pizan
Medieval literature
Text-image relations
Paratext
Advisor: Swift, H
Everyday mapping: the design, construction and calibration of a portable surveying device

The contributions of this thesis can be categorised into two main areas. (1) The design, construction and testing of a portable mapping device, and (2) the automatic cross-calibration of cameras with laser scanners.
The mapping device, whose entire chassis is manufactured using a 3D printer, is designed to produce high quality 3D maps using a suite of cameras and laser scanners. A key feature of the unit is that it allows for multiple sensors configurations, thus enabling it as a versatile research tool. At the time of writing, the model produced for this thesis was in regular use by the Oxford Robotics Institute and a commercial company.
The second component of this thesis is partly an outgrowth of (1); replacing or repositioning sensors on the device requires recalibration of those sensors. We propose and provide analysis for two automatic methods of calibration which use observations of the robot's surroundings to register a camera and laser. The first method uses the information theoretic measure normalised information distance, which is found to perform well but only under certain scene conditions. This leads to our proposal of a scene selection policy which ensures only effective scenes are used for the registration. The second camera–laser calibration method relies on the automatic extraction and matching of image point features between modalities.
Lastly, we propose a unifying calibration framework that formulates multi- ple sensor registrations as a pose graph constrained by known inter-sensor measurements. Using an alternating optimisation we are able to treat each expensive registration (as part of a global optimisation) independently.
Calibration methods are tested in diverse environments of on-road driving, warehouse and urban pedestrian sidewalks. We demonstrate successful, accurate calibration in each case.

Advisor: Newman, P
The early struggle of black internationalism: intellectual interchanges among American and French black writers during the interwar period

The thesis focuses on the interchanges which took place during the interwar period between the American and the French black communities. It explores the role of national and transnational frames of reference in the definition of the New Negro movement during the 1920s as well as in its reception by French black intellectuals during the 1930s. Black internationalism during the interwar period can be seen as a circuit of interconnections which resulted in multifaceted and shifting identifications encompassing national and transnational affiliations as well as, sometimes, a cosmopolitan sense of belonging. My work explores the difficulties and successes that the writers under consideration encountered at the time in their attempts to communicate with fellow black people across socio-cultural boundaries.
Although, during the interwar period, the perspective shifted from a preeminence of local paradigms to an emphasis on diasporic views of the black race, the national and the transnational, understood as sites of social positioning, cultural self-definition, and political agency, remained inextricably intermingled. All the examples presented in the thesis show that literature, often understood as a national category, does not exist in a vacuum. It is constantly formed and informed through transnational exchanges. The American Harlem Renaissance depended on external sources of inspiration to come to existence. Not restricted to the United States, it then spread across territorialized borders and, in turn, affected the French black community, becoming a major influence in the emergence of Négritude. The thesis successively explores five defining instances of black internationalism: René Maran's Batouala (1921), Alain Locke's The New Negro (1925), black Parisian newspapers from the mid-1920s to the early 1930s, Claude McKay's Banjo (1928), and the early theorization of Négritude. Through the use of Glissant's notion of detour, theorized in Le Discours antillais (1981), this thesis frames 'black internationalism' as a shifting web of negotiations expanding between national and transnational spaces.

Keywords: René Maran
Advisor: Mendelssohn, M
Pratt, L
Corporate governance and political economy in South Korea: family ownership, control of business groups, and state-led capitalism

The evolving nature of the Korean chaebol – both a business group and the founding family who control the corporation – continues to intrigue scholars of corporate governance (Khanna and Yafeh, JEL 2007). In my thesis, I investigate these multi-generational controlling families to explain the chaebol's significance in the historical evolution of South Korea’s political economy during the 20th century.

My research first describes the origins of chaebol entrepreneurs and details their role in the growth of light industry before the the rise of state-led industrialisation during the social revolution of the 1960s in South Korea. I then consider the specific institutional features which appear to work against family control, even though they would ultimately support its proliferation: 1) progressive politics; 2) inheritance tax; and 3) ownership dispersion. Notably, my analysis of these distinctive institutions provides a clearer understanding of the contemporary behavior of the chaebols and their ability to maintain family control over many decades of growth.

In order to better understand the role of controlling families, during the state-led industrialisation period (1961-1988), I analyse their corporate networks and their ability to wield political power. To do so, I employ an unconventional source of evidence: a database of marriages among chaebol families. This research is theoretically grounded in the contact capabilities hypothesis advanced by Amsden (1989) and Guillén (2001a, 2001b with Kock). My scholarly approach complements parallel research on human networks within the state. My findings have implications for: 1) the epochal nature of chaebol-political networks; and 2) the market reaction to such network events, thus demonstrating the economic significance of these informal networks.

In my last chapter on the post-1998 era of financial liberalisation, I explore the evolution of the ownership structure within the business group as it relates to policy history. I do this through an analysis of The Holding Company Act of 1999, and show how the controlling families in South Korea found novel ways to use the Act to support their family ownership and corporate control in spite of the original intentions of the regulators. As I show, share buyback programmes, first popularized in Anglo-American financial markets, were crucial to the maintenance of chaebol. As it turns out, liberal policies, imported from the West, proved no more able to limit family capitalism in South Korea than domestic policy had been during the preceding state-led industrialisation era. Nonetheless, activist investor has a special role to play.

Keywords: Holding Company Act
Family Capitalism
Contact Capabilities Hypothesis
Event Study Analysis
Activist Investor
Abnormal Equity Returns
Family Business Groups
Shareholder Activism
State-led Industrialisation
Advisor: Esteves, R
McKenna, C
Evolutionary models of antibody lineages

Antibodies are proteins released into the blood and mucosa to identify and neutralize invading pathogens by binding to structures on their surface (antigens). Before being exported as antibodies, these vital components of the adaptive immune system are expressed, and refined, as membrane-bound B cell receptors (BCRs). BCRs are initially formed through somatic recombination of germline DNA, creating a large repertoire of unique sequences. After encountering antigen for the first time, BCRs undergo an evolutionary process of somatic mutation and clonal selection leading to improved antigen binding. Recently, next-generation sequencing has provided an unprecedented ability to characterize the genetic diversity of BCRs within individuals. Chapter 1 of this thesis overviews the work done elsewhere in the field until now. Chapter 2 uses summary statistics applied to high-throughput sequence data from a clinical trial to explore the genetic changes that occur in the repertoire during HIV infection. The results of these analyses motivated a more rigorous, model-based approach to understanding BCR diversity. Chapter 3 introduces a new phylogenetic substitution model that relaxes common model assumptions that are violated by somatic hypermutation. Chapter 4 expands this model to incorporate previously defined empirical models of somatic hypermutation, providing a more complete model of B cell maturation. Chapter 5 uses the models developed in Chapters 4 and 5 to explore dynamics of clonal selection during the maturation of three HIV broadly neutralizing antibody lineages. Finally, Chapter 6 shows how this framework may be scaled up to characterize data from entire BCR repertoires from a phylogenetic perspective.

Advisor: Lunter, G
Pybus, O