VictorJuiz/thesis huggingface dataset:
Self-supervised video understanding

The advent of deep learning has brought about great progress on many funda- mental computer vision tasks such as classification, detection, and segmentation, which describe the categories and locations of objects in images and video. There has also been much work done on supervised learning—teaching machines to solve these tasks using human-annotated labels. However, it is insufficient for machines to know only the names and locations of certain objects; many tasks require a deeper understanding of the complex physical world—how objects interact with their surroundings, for example (often by creating shadows, reflections, surface deformations, and other visual effects). Furthermore, training models to solve these tasks while relying heavily on human supervision is costly and impractical to scale. Thus, this thesis explores two directions: first, we aim to go beyond segmentation and address a wholly new task: grouping objects with their correlated visual effects (e.g. shadows, reflections, or attached objects); second, we address the fundamental task of video object segmentation in a self-supervised manner, without relying on any human annotation.
To automatically group objects with their correlated visual effects, we adopt a layered approach: we aim to decompose a video into object-specific layers which contain all elements moving with the object. One application of these layers is that they can be recombined in new ways to produce a highly realistic, altered version of the original video (e.g. removing or duplicating objects, or changing the timing of their motions). Here the key is to leverage natural properties of convolutional neural networks to obtain a layered decomposition of the input video. We design a neural network that outputs layers for a video by overfitting to the video. We first introduce a human-specific method, then show how it can be adapted to arbitrary object classes, such as animals or cars.
Our second task is video object segmentation: producing pixel-wise labels (segments) for objects in videos. Whereas our previous work is optimized on a single video, here we take a data-driven approach and train on a large corpus of videos in a self-supervised manner. We consider two different task settings: (1) semi-supervised object segmentation, where an initial object mask is provided for a single frame and the method must propagate this mask to the remaining frames, and (2) moving object discovery, where no mask is given and the method must segment the salient moving object. We explore two different input streams: RGB and optical flow, and discuss their connection to the human visual system.

Keywords: deep learning
computer vision
Advisor: Zisserman, A
How is the bike made mobile? Learning from bicycle activism and mobilities in Latin America

Over the course of nearly thirty years, cycling activism has proliferated throughout Latin America and, from two independent initiatives in opposite ends of the continent, it has grown into a vibrant social movement with manifestations in almost every major city in the region. Still, there is a significant knowledge gap with regards to cycling activism in Latin America, both in the Spanish-language and anglophone literatures. Hence, this research is an exploratory enquiry into the geographies of cycling activism in this region, working through a multi-sited field comprised of Santiago de Chile, Mexico City, and the World Bike Forum in Lima and Quito, to interrogate how the bicycle is mobilised by activists in Latin America today. In asking “How is the bike made mobile?” this research seeks to understand the spatialities, knowledge-practices, and moments of tension and dissent that make up this social movement. To do so, it draws on a wide body of literature, encompassing vélomobilities, the geographies of social movements, and research into the production and circulation of knowledge. Working with a qualitative militant research approach, this thesis unpacks the politics of cycling activism in three moments: first, I conceptualise cycling activism in space as simultaneously territorial and networked, working through multiple scales, and assembling as a regional phenomenon. Situating cycling activism in space lays the groundwork for interrogating the strategies and techniques by means of which activists construct the bicycle as a particularly appropriate vehicle for the city, and how the knowledge they produce is made to circulate. Finally, I examine the challenges and possibilities that Latin American feminism presents to cycling activism, identifying mobility not just as a site where gender inequalities find expression, but also where patriarchal domination and machismo can be resisted. In presenting my arguments, I advocate for a more worldly research practice that meaningfully engages with the scholarship, knowledge, and ambitions of researchers and activists in Latin America.

Keywords: social movements
cycling
feminism
Latin America
spatiality
mobilities
Advisor: Schwanen, T
Scrub typhus in northern Thailand

Scrub typhus, a neglected infectious disease caused by obligate intracellular bacteria Orientia tsutsugamushi, is a major cause of acute non-malarial fever in the tropics. Difficulties surrounding diagnosis have hampered our understanding of disease burden, which in turn negatively impacts awareness. Using national surveillance data, I highlighted the high burden of scrub typhus in Thailand with a substantial rise in cases over time. Spatially, disease burden was greatest in the northern region and geographical and meteorological factors may contribute to disease prevalence. Scrub typhus contributes significantly to the febrile disease burden in Chiangrai, northern Thailand, with 22.5% of adults admitted to hospital with acute undifferentiated fever diagnosed with the disease. I described the disease in adults and found presence of eschar and elevated liver enzymes to be predictive of scrub typhus. Scrub typhus in children remains understudied and in this thesis, I characterised paediatric scrub typhus in Chiangrai, showing that the disease was frequently severe and potentially fatal with complication and treatment failure rates of 40% and 23%, respectively. Severe hepatitis was found to be predictive of treatment failure in this cohort.
In the 1990s, reports of putative drug resistant scrub typhus emerged from northern Thailand. This proved controversial at the time as doxycycline resistant Orientia tsutsugamushi had not been described. Studies on treatment outcome and its determinants were not pursued, leading to uncertainty regarding optimal scrub typhus treatment. I reviewed the evidence on drug resistant scrub typhus extensively and concluded that doxycycline resistance may have been misconceived. Finally, I described my ongoing role as principal investigator for the Scrub Typhus Antibiotic Resistance Trial, a randomised controlled trial comparing the efficacy of 7 days of doxycycline versus 3 days of doxycycline versus 3 days of azithromycin in northern Thailand. Detailed immunological, microbiological and pharmacological analyses are embedded, which should provide clarity on the determinants of treatment outcome and whether drug resistance is illusory.

Keywords: Scrub typhus
Orientia tsutsugamushi
Advisor: Day, N
Newton, P
Tarning, J
Mukaka, M
Salvaging democracy? The United States and Britain in British Guiana 1961-1964

This thesis, based upon recently released British and American government documents, considers Anglo-American intervention in British Guiana in the years 1961-1964, when the American and British governments successfully engineered the removal from office of the democratically elected government of self-confessed marxist and alleged international communist, Cheddi Jagan.
The thesis examines the sources of the Kennedy administration's hostility to the Jagan government, locating its concerns in the demands of American domestic politics and in the perceived need to preserve the international credibility of the United States in the bipolar zero-sum context of the Cold War.
The administration realised its objectives in British Guiana through a multitrack process of intervention in the political, economic and industrial life of the colony and through sustained diplomatic pressure on the British government. The thesis investigates the instruments of intervention employed in Jagan's removal, highlighting particularly the role of the American and international trade union movements as agents of American foreign policy, and the political ramifications of American economic aid or non-aid for developing countries. It also examines the symbiotic relationship between Washington and leaders of British Guiana's political opposition who encouraged and facilitated intervention in the colony.
The thesis is more than a self-contained case study in the means and motives of intervention. It uses intervention in British Guiana as a base from which to approach broader Cold War, alliance and hemispheric issues. Placing events in the colony in the multiple contexts of the Cuban revolution, the globalisation of the American doctrine of 'containment', and the colony's volatile internal political situation, the thesis examines how an ostensibly peripheral country of little demonstrable interest to the United States became drawn into the Cold War. Finally, the thesis analyzes the conflicts over often bureaucratically defined policy preferences both within and between the British and American governments. In particular it demonstrates the distortion of British policy-making which resulted from the priority given to the preservation of the 'Special Relationship' with the United States.

Keywords: Jagan
Anglo-American special relationship
Cold War
PPP
British Guiana
US intervention in Latin America
US foreign policy 1961-1964
Anglo-American relations
British decolonisation
Advisor: Lewis Gaddis, J
Dallek, R
Affinity and activity profiling of agrochemical-metabolising enzymes

Agrochemical detoxification involves the consecutive action of several families of detoxifying enzymes. Cytochrome P450s (CYP450s) and Glutathione transferases (GSTs) are two large and diverse superfamilies of enzymes that play important roles in xenobiotic detoxification in many living organisms. Many efforts have been taken in order to identify the selectivity of these enzymes and understand their biological function. However, just a few specific CYP450s and GSTs have been identified as the actual cause of agrochemical modifications and little is known about the specific role and mechanisms by which these enzymes contribute to response to abiotic and biotic stress.
In this research we aim to establish and use activity-based protein profiling (ABPP) to monitor, identify and characterise the activity of CYP450 and GST enzymes in plants and fungi. To do so, we present a first chapter describing the relevance of agrochemical metabolising enzymes in agriculture and their importance for crop protection and food safety. Second, we studied the labelling of mouse and plant (Arabidopsis, maize and Nicotiana benthamiana) CYP450s by a set of CYP450 activity-based probes, identifying key aspects between mammal and plant CYP450 profiling. CYP450 probes label many CYP450s in mouse liver microsomes in a NADPH-dependent manner; however, the relatively low abundance and reactivity of CYP450s in plant tissues limit their activity-based profiling in plant extracts. Third, we identified the main targets of CYP450 activity-based probes in the fungal plant pathogen Zymoseptoria tritici and described the specific blockage of ZtCYP5080H1 labelling by the fungicide cyprodinil. Fourth, we validated the use of the glutathione-based photoaffinity probe, GST-G, to target GSTs in several plant species. We demonstrated the potential use of GST-G photoaffinity profiling to study the activation of GST upon safener application in wheat and identified the activation of several members of GSTU and GSTF classes upon the BION treatment of Arabidopsis plants. Overall, these innovative tools have great potential to support the development of more effective agrochemicals and identify new enzymes involved in the metabolism of pesticides.

Keywords: GSTs
CYP450s
Agrochemical detoxification
ABPP
Advisor: van der Hoorn, R
Opera after Stalin: Rodion Shchedrin and the search for the voice of a new era 

Until recently, Russian opera after Stalin has been an almost entirely neglected topic. In this thesis, I analyse the development of operatic style and culture in Russia between 1953- 2020 by examining four operas by the most prominent late Soviet and post-Soviet composer, Rodion Shchedrin, and by bringing these operas into conversation with those of his peers during each phase of his career. Mining previously untapped archival sources, I set opera in dialogue with aspects of Soviet cultural history, engaging with the central themes that have occupied scholars of the late Soviet and post-Soviet periods: Socialist Realism, modernism, consumer culture, relations with the West, political ideology, Soviet morality, religious revival, and negotiations with power and censorship. In Chapter 1, I address the re-formation of operatic standards during the Thaw, using the bizarre production history of Shchedrin’s first opera, Not Love Alone (1961) as a case study. Chapter 2 explores the operatic culture of the 1970s, identifying four major camps of composers: the ‘officials’, the ‘rebels’, the revival of 1920s modernism, and the fourth way – Shchedrin, and his opera Dead Souls (1976). Chapter 3 probes the fault lines of Perestroika exploiting the lens of Shchedrin’s third opera, Lolita (1989-1994), and examines the musical and professional fate of composers navigating this transition. In Chapter 4, I analyse Russian opera in the twenty-first century. First, I expose the contemporary culture of censorship that has developed in the past two decades, and its effect on opera; next, I chronicle the formation of a new style in Russian opera that is both national and divergent from trends in Western opera: ‘Russianist Realism’. I demonstrate how Shchedrin’s adaptability, which helped him thrive in the Soviet era, has enabled him to meet the demands of a new political moment, and rise to a position of prominence among living Russian composers. Ultimately, I hope this thesis will contribute to the growing literature addressing the need for closer scrutiny of Soviet life and culture after Stalin, and especially, that it will spark new interest in late Soviet and post-Soviet opera.

Keywords: music
soviet
opera
russia
Shchedrin
socialist realism
ballet
music and politics
Advisor: Cross, J
Bullock, P
Investigating new physics with high power lasers

This thesis presents theoretical studies of different aspects of axion physics. First, we review the origin of axions from the Peccei-Quinn (PQ) solution to the problem of charge-parity (CP) non-violation in the quantum chromodynamics (QCD) sector of the standard model (SM) of particle physics. An overview of the most common direct and indirect detection efforts is then presented before three distinct, new methods are presented and put in perspective.
Chapter 2 proposes a stimulated version of light shining through wall (LSW) type searches which utilises the large photon numbers in high power laser beams to achieve strong bounds around axion masses of ma ∼ 1 eV. The sensitivity is evaluated and special care is taken to consider stimulation effects stemming from the large number of photons present. In chapter 3 a new axion-photon parametric decay instability is found and analysed. The coupling of a strong pump and a weaker probe pulse is found to result in an exponentially growing axion mode. The prospect for direct detection experiments is discussed and put into perspective of ongoing searches. The axion's coupling to fermions is investigated in chapter 4 in which the decay of axions to electron-positron pairs in a strong background field is investigated. The chapter starts with a review of strong field quantum electrodynamics techniques and then proceeds by applying them to the axion coupling to identify different regimes based on the axion's mass and the background field strength.
The second part of the thesis investigates the cosmological implications of including axions into the SM. A review of the standard ΛCDM cosmology is followed by a discussion of the cosmological importance of the axion by an investigation of the energy density in a coherent axion field throughout the universe which could constitute the dark matter. An investigation of topological defects formed during the symmetry breaking stages of the axion then leads to the introduction of the domain wall problem. Chapter 6 is dedicated to the solution of the domain wall problem and finishes with a lookout onto avenues for future investigations and attempts at solutions.

Keywords: Axion Detection
Axion Cosmology
Axion Physics
Advisor: Gregori, G
Sarkar, S
Computational, psychological and neural mechanisms of prosocial motivation

Prosocial behaviours are essential for healthy social interactions, with established impacts on life satisfaction, mental and physical health, and economic success. Yet, how willing people are to act prosocially varies considerably between individuals and across contexts. When making decisions that can result in others’ pain, people can be highly prosocial, and will typically not profit from other’s harm. In contrast, people are much less motivated to exert effort to benefit others compared to themselves. However, the psychological and neural mechanisms of these behaviours remain largely unknown. In this thesis, I examine the affective, cognitive, and neural processes that underpin harm aversion and effortful prosocial behaviours and their variability between people. First, I propose a theoretical framework where individual differences in prosocial behaviour across domains are due to idiosyncratic sensitivities to personal costs and others’ benefits, giving a conceptual and methodological overview on what factors might be hypothesised to influence cost-benefit prosocial evaluations. Second, I show that harm aversion and prosocial effortful actions share variance despite their differences at group level, and are linked by responses in the anterior cingulate cortex (ACC) and the anterior insula (AI) to others’ benefits. Third, I identify an affective profile characterised by high empathy and low apathy as crucial for predicting prosociality. Fourth, I find that people who are highly hypocritical, i.e. fail to live up to their moral standards, are more sensitive to effort costs, suggesting motivational aspects in moral hypocrisy. Fifth, I disentangle the role of ACC and AI in others’ rewards representations, with the dorsal AI linked to interoceptive processes and the ACC linked to motivational aspects of others’ rewards. Finally, I propose a new experimental framework to investigate prosocial motivation, examining how the alternative opportunities in the environment shape prosociality. In sum, in this thesis I show that being motivated to benefit others depends on cost-benefit evaluations, which are modulated by affective traits and interoceptive sensibility, with crucial, but differential, roles of ACC and AI in prosocial behaviour.

Keywords: Affective Traits
Cost-Benefit Decisions
Anterior Cingulate Cortex
Anterior Insula
Prosocial Behaviour
Advisor: Apps, M
Crockett, M
Bird , G
Towards post-democracy: shifting responsibilities and facilitating dispute resolution under the British neoliberal state 

This thesis investigates the State’s responsibility to facilitate dispute resolution and the extent to which this duty is upheld. This investigation is approached through Hobbesian social contract theory, which contends that the State must enable its citizens to resolve their conflicts through the public legal system. The primary function of the courts is to uphold the law, provide remedies for wrongs, and enforce rights. A central claim of this thesis is that citizens require lawyers to reach just outcomes. Most people, however, cannot afford lawyers. In the absence of affordable lawyers, this thesis asserts that the State must provide access to lawyers through legal aid to uphold its duty to facilitate dispute resolution. Providing legal aid, however, increases the State’s costs. Using political theory, this dissertation considers how rising costs conflict with the State’s neoliberal ideology. It argues that, to reduce costs, the British neoliberal State has diminished its role in facilitating dispute resolution by restricting the availability of legal aid and has sought to shift its responsibility onto charities, volunteers, and the private dispute resolution sector. Doing so reduces people’s ability to resolve their disputes within the public courts justly. This dissertation then explores the consequences that this has for democracy. By enabling people to hold the State accountable and using dispute resolution to lead to developments of the law, litigation provides a way for people to engage in self-government. This thesis contends that, in undermining people’s ability to resolve their disputes through the public courts, the State’s attempts to shift its responsibility of facilitating dispute resolution pushes society towards ‘post-democracy’. Post-democracy is a situation where society maintains the façade of democracy, but its democratic institutions are hollowed out of their substantive value.

Keywords: Post-Democracy
Democracy
Jurisprudence
Public Law
Civil Procedure
Legal Aid
Neoliberalism
Social Contract Theory
Advisor: Zuckerman, A
Molavi, M
Identification of mRNA features which facilitate their long-range transfer in an in vivo Drosophila model

Extracellular vesicles (EV) are membrane bound carriers released by cells to mediate important aspects of intercellular communication; however, the basic principles of EV-biogenesis, in particular the mechanisms regulating mRNA EV-loading, are poorly characterised. Furthermore, a limited repertoire of tools has thus far made these processes challenging to research.
To address these fundamental biological questions, an RNA-sequencing analysis of Drosophila EVs and the cells from which they derive was carried out. A bioinformatic pipeline was subsequently developed with the aim of identifying molecular features within the 3’UTR of mRNAs which may encourage their EV incorporation and long-range transfer. In addition, the role of these EV-enriched features was assessed in vivo, in complex Drosophila tissues, using an adapted version of the Cre-LoxP reporter to visualise long-range cell communication.
These analyses revealed a distinct mRNA profile for Drosophila cells versus EVs and identified unique EV-enriched 3’UTR motifs. Motifs were preferentially arranged in distinct combinations and tended to occur in specific RNA secondary structures. These features may modulate their interaction with trans-acting factors, such as RNA binding proteins, with sequence similarity observed between these novel motifs and well-established RNA binding-protein binding sites. Subsequent in vivo analyses highlighted the potential for mRNA 3’UTR modifications to successfully modulate long-range mRNA transfer in complex tissues. EV-enriched motifs within these 3’UTR modifications, however, may only play a contributing role. Future work is needed to assess the effect of specific 3’UTR modifications on mRNA stability, length and GC content, as these factors have the potential to influence long-range mRNA transfer.
These investigations provide novel insights into the biological properties facilitating mRNA transfer between Drosophila cells without physical contact. Importantly, these biological features may be evolutionarily conserved, given that similar mRNA properties have been described in mammalian cells. Therefore, these findings could establish the basis to efficiently modulate mRNA transfer and cell function at a distance.

Keywords: extracellular vesicles
molecular biology
exosomes
RNA
bioinformatics
Drosophila
Advisor: Baena Lopez, LA
Carter, D