VictorJuiz/thesis huggingface dataset:
Detection of cerebral small vessel disease signs on brain MR images

Introduction: Accurate and automated detection of brain disease signs could aid in studying their clinical associations in large populations. This research aims to detect on magnetic resonance images two signs of cerebral small vessel disease- white matter hyperintensities (WMHs) and cerebral microbleeds (CMBs)- and to analyse their spatial distribution and characteristics.
Methods: We modelled the distribution of WMHs at the population-level with respect to various parametric factors (e.g. age) using Bayesian inference. For improving the performance of FSL's WMH segmentation tool, BIANCA, we used the above population-level WMH distribution probabilities as an additional feature, tested different classiers and proposed a locally adaptive thresholding method (LOCATE). Furthermore, we developed a triplanar U-Net ensemble model (TrUE-Net), based on deep learning (DL), spatially-weighted cross-entropy and Dice loss functions to improve WMH segmentation, and explored various domain adaptation techniques. For CMBs, we developed an end-to-end analysis: CMB candidate subject preselection pipeline using machine learning, CMB detection using DL and atlas-based automated CMB rating.
Results and conclusions: Our distribution modelling provided comparable error values, with lower computational load, with respect to existing methods on simulated data. On real data, periventricular WMH probabilities showed signicant increases with age, while the probabilities for deep WMHs were higher in hypertensive subjects, in line with literature. Among the proposed improvements for BIANCA, LOCATE gave the highest performance increase on 7 datasets with dierent lesion characteristics. TrUE-Net performed better than BIANCA on 5 dierent datasets, especially on low lesion load subjects. The CMB preselection pipeline provided robust performance despite dierent training modalities. The CMB detection method provided performance comparable with existing methods and higher precision than the state-of-the-art method. Future directions for this work could include improving the DL-based CMB/WMH detection methods and studying the clinical impact of CMBs at the population-level.

Keywords: image analysis
deep learning
small vessel disease
machine learning
white matter hyperintensities
segmentation
structural MRI
cerebral microbleeds
Advisor: Jenkinson, M
Griffanti, L
Zamboni, G
A shift in time: music and temporality in 1913 Paris

Temporality is an integral—and often overlooked—aspect of music. This thesis seeks to understand the relationship between music and time. Rapid social, cultural and technological change affected the perception and experience of temporality in fin de siècle Paris. The year 1913 offers a fascinating case study for understanding the plethora of cultural and musical reactions to these changes. To that end, this thesis draws on a range of primary and secondary sources such as journalistic texts, letters, notes, philosophical texts, visual arts, cinematic and musical sources, and makes use of interdisciplinary methodology, drawing upon historical musicology, socio-cultural history and philosophies of time.
This thesis presents a kaleidoscopic portrait of musical life in 1913 Paris. Chapters 1 and 2 examine time and space respectively—the former details definitions of time, while the latter explores Paris as a city of temporal change, looking at changes in transport and architecture and its impact on musical culture. Chapter 3 examines landscape and Satie’s relationship with time; Chapter 4 considers the connections between Bergson, Proust and Ravel; and Chapter 5 looks closely at parallels between early cinema and Debussy’s Jeux. Finally, Chapter 6 brings together these cultural and musical moments. It is in 1913 that we can see the consequences of this rapid period of change in musical terms as a palpable trend for the first time, rather than as individual moments. By using the example of 1913 Paris, this thesis proposes that there are useful parallels to be drawn between experiences of time and the cultural and musical manifestations of temporality.

Keywords: Maurice Ravel
Erik Satie
technology
time
Claude Debussy
Advisor: Cross, J
Neutrino cosmology and large scale structure

The topic of this thesis is neutrino cosmology and large scale structure. First, we introduce the concepts needed for the presentation in the following chapters.
We describe the role that neutrinos play in particle physics and cosmology, and the current status of the field. We also explain the cosmological observations that are commonly used to measure properties of neutrino particles.
Next, we present studies of the model-dependence of cosmological neutrino mass constraints. In particular, we focus on two phenomenological parameterisations of time-varying dark energy (early dark energy and barotropic dark energy) that can exhibit degeneracies with the cosmic neutrino background over extended periods of cosmic time. We show how the combination of multiple probes across cosmic time can help to distinguish between the two components.
Moreover, we discuss how neutrino mass constraints can change when neutrino masses are generated late in the Universe, and how current tensions between low- and high-redshift cosmological data might be affected from this.
Then we discuss whether lensing magnification and other relativistic effects that affect the galaxy distribution contain additional information about dark energy and neutrino parameters, and how much parameter constraints can be biased when these effects are neglected.
We conclude by describing current fields of active research in cosmology, and how the work presented in this thesis contributes to them.

Keywords: relativistic effects
neutrino masses
dark energy
Neutrino physics
Advisor: Ferreira, P
Calabrese, E
Alonso, D
The crust and upper mantle structure of the UAE-Oman mountains: insights from new gravity and seismological data

The UAE-Oman mountains are a ~700 km long mountain belt located on the north-eastern margin of the Arabian plate, extending from the Musandam peninsula in the north, through the United Arab Emirates (UAE) and Oman to terminate at the eastern tip of Arabia. These mountains contain a series of stacked thrust sheets that incorporate a full “half ocean” sequence, including: deep ocean sediments and volcanoclastic exotics; shelf and slope sediments; and an obducted slab of oceanic crust and upper mantle known as the Semail ophiolite. The obduction of these thrust sheets emplaced a significant load on the Arabian margin, and the resulting flexure and subsidence led to the formation of a foreland basin inland from this load. Significant sedimentation has also occurred on the seaward side of the ophiolite since its obduction, with up to 10 km of deposition since the end of the Cretaceous, concealing the eastern termination of the ophiolite, and the present day transition from continental to oceanic crust.
This thesis utilises passive seismic and gravity data acquired across two east-west profiles. We aim to constrain the thickness and subsurface geometry of this ophiolite, investigate its offshore extent, constrain the crustal thickness of the underlying Arabian margin, and investigate the transition from continental to oceanic crust offshore in the Gulf of Oman.
Receiver functions and gravity modelling across these profiles revealed: a ~15 km sedimentary sequence and a ~36 km Moho in the foreland basin to the west, suggesting a stretching factor for the rifted Arabian margin of 1.49; a ~10 km flexural root beneath the UAE-Oman mountains, offset ~20 km landwards from the primary ophiolite load; that the Semail ophiolite dips eastwards at ~30◦, increasing from 5 − 10 km depth near Masafi to ~25 km depth near the Gulf of Oman coastline; that high ophiolite densities (~3120 kg m−3) are required to reproduce the ~160 mGal Bouguer anomalies observed across the ophiolite, implying minimal bulk serpentinisation (< 30%); that the ophiolite extends offshore below the hinterland sediments in the Gulf of Oman in a steep normal fault; and that the Moho thins rapidly east of Masafi to transition from thinned continental crust of the Arabian margin to in situ oceanic crust of the Gulf of Oman ~30 km offshore.

Advisor: Watts, T
Searle, M
The ends of collage

The Ends of Collage is an attempt to reflect on the physical place where collage fulfils its calling and distinguishes itself from other forms of artistic making. The ends, or edges of a collage mark the sites of interaction where one piece of paper – picture, surface or text – is juxtaposed with another. Yet the notion of ‘ends’ in this context also implies a historical paradigm, one that considers collage as part of a particular period in time which I argue to have emerged in the first decade of the twentieth century and came to a close in the late 1970s with the emergence of a new material, technological and ideological reality that constituted the dawn of the digital age as well as the Postmodern moment. These abovementioned formal and historical paradigms are joined in this thesis in order to serve as the principal prism through which I examine the work of four artists who adopted collage into their practice as a fundamental question to guide their artistic pursuits.
Following an introductory chapter itself titled ‘The Ends of Collage’, the first of five main chapters surveys the many definitions that have mapped the activity of collage so far. The second concerns a group of works from 1919-23 by the German artist Max Ernst known as ‘seamless collages’, so-called due to the absence of physical evidence that testifies to their making. Chapter three explores a group of works from 1927-30 by the Belgian artist René Magritte that transpose collage directly into the medium of painting, with paradoxical effect. Chapter four is concerned with the early work of the American artist Sherrie Levine from 1973-80, particularly her engagement with pre-modern practices associated primarily with women and still regarded as detached from art history per se. Chapter five addresses the work of the British artist John Stezaker from the years 1970-78, and his development of the term ‘photo-collage’ to distinguish his work from that of Dada and Surrealist predecessors.
Those chapters in their turn are bounded by two edited conversations, titled ‘Ends I’ and ‘Ends II’ respectively, between myself and artists Richard Prince, Linder Sterling, John Stezaker and theorist David Campany, conducted in the course of several curatorial projects undertaken in parallel with this research. Further Appendices are provided.

Keywords: Sherrie Levine
Rene Magritte
John Stezaker
collage
pictures generation
Max Ernst
Advisor: Taylor, B
Essays on financial frictions, collateral and default

The first model of my thesis introduces a monetary Real Business Cycle model with incomplete markets, a durable good, collateralized securities and endogenous default. We establish that equilibria are inefficient since agents underinvest due to the existence of endogenous default. Moreover, the Pareto optimal equilibrium allocation cannot be achieved through monetary policy. Our analysis suggests the need of an additional policy tool to generate optimal investment and improve equilibrium allocations. In the second model of my thesis, we propose an integrated tractable framework that incorporates endogenous default in a continuous-time setting. Productive experts that face leverage constraints and aggregate risk, borrow from households and choose to partially default subject to a penalty that decreases their objective function. Our results show that default increases borrowing costs, lowers expert’s capital holdings, suppresses investment and subsequently leading to a recession. We show that the path of inflation under quantitative easing policies that target interest rates, is determinate in the presence of default. We achieve this through different payoff profiles that a collateralised defaultable bond achieves in different states of nature with distinct default outcomes. In the model, heterogeneous households trade this bond and other shorter maturity risk-free bonds to maximise their intertemporal utility of consumption and labour. The differentiated payoffs of the collateralised bond, in an equilibrium with active default, span the full state space giving determinacy of prices and inflation as an outcome.

Advisor: Tsomocos, D
Noe, TH
Normative foundations of corporate insolvency law

This thesis develops a novel framework for normative reflection about corporate insolvency law in terms of distributive justice. It begins by demonstrating that the dominant theoretical approach in this area—known as proceduralism—is incomplete and, in some ways, incoherent, and seeks to build on these failures in arguing for a new approach. It is argued that corporate insolvency law must address at least two connected sets of questions. The first concerns distribution and the second concerns debtor fidelity. The former questions are questions of distributive justice. While no fully specified theory of distributive justice is defended or developed, it is argued that in a society in which distributive shares are mediated by legal rights, individuals must have the capacity to hold and deal with such legal rights on equal terms. Some dealings with such rights will engage the principle of personal responsibility, such that apparent disadvantages for which individuals are responsible need not be condemned by distributive justice. The statutory order of insolvency distribution, as well as its mandatory character, is considered in the light of these arguments. As individuals make use of the capacity to create or deal with legal rights and obligations, they are bound by ordinary moral principles in so doing. The discussion of debtor fidelity, then, considers a range of such principles and pursues their implications for a range of corporate insolvency law doctrines. Debtor fidelity does not, however, offer a justification for the centerpiece transaction avoidance rules prohibiting mere undervalue transactions and mere preferences. These rules, however, may be justified in terms of distributive justice. A normative critique of a range of fraudulent trading and transaction avoidance doctrines is advanced in terms of such principles.

Advisor: van Zwieten, K
Green, L
Pathwise and probabilistic analysis in the context of Schramm-Loewner Evolutions (SLE)

On the pathwise analysis side, this thesis contains results between Rough Path Theory and Schramm-Loewner Evolutions (SLE). In the study of Rough Differential Equations questions such as continuity of the solutions, methods of approximations of solutions and their uniqueness/non-uniqueness depending on the behavior of parameters of the equation, appear naturally. We adapt these type of questions to the study of the backward and forward Loewner differential equation in the upper half-plane, conformal welding homeomorphism and the SLE traces. On the probabilistic analysis side, we study a coordinate change of the Loewner equation in which we obtain via a random time change, a stochastic dynamics on a specific line in the upper half-plane, that is depending only on the argument of the points. In this setting, we analyze this dynamics and obtain results about related objects.

Advisor: Belyaev, D
Lyons, T
Essays on risk, nutrition and poverty dynamics

This collection of essays explores questions on risk, poverty dynamics and early child development. The first essay analyses issues of cognitive development in early childhood. An extensive literature documents linkages between nutrition and cognition, but few studies show correlations to be causal. Building on Glewwe et al (2001) and Alderman et al (2006), we re-examine this relationship and find a negative cognitive effect of early nutritional disinvestments among a sample of Peruvian pre-schooling siblings.
The second essay examines nutritional catch-up growth among poor Ethiopian children and the role household wealth in this process. We find that nutritional catch-up patterns vary across socioeconomic groups: average catch-up growth in height-for-age is near perfect among children in better-off households. However, for children above 5 years of age, household wealth no longer affects height velocity. Our findings suggest that nutritional remediation is effective early on in life, but that this window of opportunity might already be closed by the age of five.
The third essay contributes to the literature on poverty traps and thresholds. In spite of their popularity, little empirical evidence supports their existence. Studies testing poverty traps often are restrictive in their methodology (e.g. Lokshin and Ravallion, 2004) or fail to provide causal estimates (Lybbert et al, 2004). This essay tests and finds evidence of multiple equilibria in income dynamics in rural India using a 30-year long panel. Simulations suggest the presence of two equilibria: a stable high-income equilibrium and a low-level unstable saddle point. To the best of our knowledge, the paper provides first evidence of multiple equilibria in income dynamics.

Advisor: Dercon, S
Optimising T cell vaccination strategies for the prevention of HCV infection

There remains an unmet global need to develop a vaccine for the prevention of HCV infection. Adenoviral and MVA vectors have been established as promising tools in the development of a prophylactic HCV vaccine strategy. A Phase I trial in humans has demonstrated the induction of broad, robust and polyfunctional HCV specific T cells following prime-boost vaccination with heterologous AdCh3/MVA-NS encoding the HCV non-structural (NS) region. An important next step therefore is to optimise strategies in which viral vectored HCV vaccines are administered. Furthermore, with the emergence of highly efficacious yet prohibitively costly directly acting antiviral therapy to treat HCV infection, an imperative question is whether individuals cured of chronic HCV infection may be amenable to vaccination to prevent re-infection.
The first section of this thesis assesses re-boosting strategies of AdCh3/MVA-NS following initial prime-boost in healthy adult volunteers. The primary aim was to establish whether either the peak magnitude and/or the memory ‘set-point’ of the HCV specific T cell response could be improved. Re-vaccination with AdCh3/MVA-NS could be demonstrated to re-boost the antigen specific T cell response, however this was more effective following a longer interval between primary and secondary vaccination rounds.
Next, in a separate phase I study, I sought to establish whether the co-administration of distinct adenoviral vectors encoding both HIV-1 and HCV immunogens could be safely administered without compromising immunogenicity of either vector. Co-administration was shown to be safe and did not compromise the immunogenicity of either immunogen.
Thirdly, I addressed whether the reversal of T cell exhaustion is possible following DAA mediated HCV cure. A functional analysis of HCV specific T cells prior to commencing and following treatment was performed. Little recovery of proliferation or cytokine production was observed, furthermore T cell responses were significantly attenuated in comparison to spontaneous viral resolution and vaccine induced T cell responses.
Finally, I performed a detailed ex vivo phenotypic analysis of HCV specific CD4+ T cells induced by vaccination and compared them with spontaneous viral resolution. Phenotypic markers suggestive of highly functional effector and memory CD4+ T cells were observed.

Advisor: Barnes, E
Klenerman, P
Dynamics of resident memory B cell responses in the lung

Immunological memory is the central mechanism supporting the protective effects of vaccination. This phenomenon is mediated primarily by antigen-specific memory B and T lymphocytes, which enforce accelerated clearance of infectious agents and rapid return to health. Memory B cells can be found in the circulation, where they are thought to migrate between secondary lymphoid organs surveying the body for secondary infection. Following pulmonary viral infections, such as influenza, memory B cells can also be found in the lung. Recent findings have shown that these resident cells can persist for prolonged periods of time and may confer enhanced protection from secondary infection. However, the microanatomical site of retention of this population, their dynamic responses to infection and the cues guiding their positioning and responses are poorly understood.
Here, two-photon and confocal microscopy coupled with flow cytometry and RNA sequencing is used to study the positioning, migration patterns and expression profiles of memory B lymphocytes before and after rechallenge with influenza infection. Following primary infection with influenza, resident memory B cells are found distributed across the lung where they appear to continuously scan alveoli. Shortly after rechallenge, Bmem cells increase their migration speeds in response to innate stimuli and, guided by an as-yet unknown G-protein-coupled receptor, move towards sites of infection where they undergo local proliferation. Reinfection also leads to the later appearance of plasma cells within these infected sites, in a manner independent of recirculating Bmem. Plasma cell distribution into infected alveoli was also dependent on innate stimulation by viral RNA in an antigen-independent manner, and may permit local antibody secretion at the site of pathogen exposure. The finding of plasma cell establishment within sites of infection after virus rechallenge may indicate an early protective role of local humoral immune mechanisms.

Advisor: Arnon, T
Role of CD1a-restricted T cells in the immune responses to Staphylococcus aureus

CD1a has been demonstrated to contribute to anti-bacterial immune responses by presenting lipid antigens to T cells. Skin Staphylococcus aureus (S. aureus) colonization has been documented to be strongly associated with the severity of skin inflammatory diseases including atopic dermatitis (AD). However, there have been limited studies of how the bacterial colonization contributes to pathology and exacerbation of disease.
Here, we investigate the involvement of a S. aureus exotoxin, sphingomyelinase (SMase), in regulating T cell immune responses via CD1a. We show that SMase enzymatic activity plays an essential role in CD1a-reactive T cell activation in both peripheral blood and skin, leading to production of inflammatory cytokines, including IFNγ, IL-17A, and IL-22. These findings support the possibility that the ceramide product of SMase may serve as a permissive lipid neoantigen and that SMase may reduce the non-permissive effects of sphingomyelin. Patients with atopic dermatitis had reduced CD1a-dependent IFNγ responses to SMase compared to healthy controls.
The generation of CD1a-reactive SMase-specific T cell lines and clones facilitated the further study of mechanisms underlying CD1a antigen presentation, including the novel identification of a Vγ9/Vδ2 CD1a-autoreactive T cell clone which expanded our understanding of CD1a-reactive T cell repertoire and potential pathways of gamma-delta T cell activation. The work also identified that CD1a may be a marker of activation of peripheral T cells.
In conclusion, we have discovered a previously unrecognized pathway of inflammation where SMase derived from S. aureus can modulate CD1a ligands which are presented to lipid-specific T cells.

Keywords: Sphingomyelinase
Staphylococcus aureus
CD1a
Advisor: Ogg, G
Jackson, D