VictorJuiz/thesis huggingface dataset:
Navigation in Procellariiform seabirds

Much of what is known about avian navigation results from half a century of displacement experiments with the homing pigeon, the main model in avian navigation. Whether the same processes underpinning navigation in the homing pigeon are also integral to navigation in other species remains an open question. In particular, how Procellariiform seabirds, which routinely travel huge distances over open ocean, might navigate is of interest because of the contrast in sensory environment compared to terrestrial species. In this thesis, I have three aims. First, to investigate whether the mechanisms involved in homing pigeon navigation might also guide Procellariiform seabirds over the ocean. Second, to establish whether GPS-tracked, free-ranging Procellariiform seabirds might be able to offer insights into avian navigational mechanisms. Third, to investigate some of the ecological drivers of long-distance movement facilitated by these navigational mechanisms in Procellariiform seabirds. By combining novel experimental and analytical approaches, I attempt to answer some of these questions. I find that many of the mechanisms though to guide homing pigeons also appear to underpin Procellariiform navigation. In particular, the involvement of information from the time-compensated sun-compass, central to structuring spatial representation in terrestrial species, seems to be very similar to that observed in pigeons. Furthermore, like pigeons, olfaction seems to play a specific role in Procellariiform seabirds’ map sense. However, there are differences too. I make the tentative discovery that, perhaps unlike pigeons, shearwaters might be able to derive information exocentrically about their location at sea in the form of a vector of direction and distance from the home colony, implying a geometric cognitive representation of large-scale environmental gradients. Finally, in terms of ecological drivers of long-distance movement, I find that Manx shearwaters’ migratory phenology is probably constrained by their environment and not by their condition, in-keeping with the idea that long-distance movement comes at a low cost for Procellariiform seabirds.

Keywords: Scopoli's shearwater
Sun compass
Cognitive Map
Navigation
Olfactory navigation
Procellariiform seabirds
Manx shearwater
Advisor: Guilford, T
Drawing: the point of contact

This thesis is a study of the point of contact between pencil and paper during certain acts of drawing. It comprises three elements. Firstly, five ‘drawings’ which together raise the central question of the thesis: what arrests me, in the manner of a Barthesian punctum, about the point of contact between pencil and paper (and their proxies) in these particular drawings? These drawings are in evidence through written accounts introducing each chapter, and they are: (1) a practice of ‘half-blind’ life drawing; (2) a line drawn around the internal perimeter of a house; (3) several voice recordings made while walking in the dark; (4) a biro line drawn across a bed sheet; (5) a row of ink blots at the foot of a page. Secondly, the present document, which shows the endeavour of answering this question. Thirdly, a display of artefacts left over from the five drawings and the writing, which pose a question at the close of the thesis: when the writing is completed, what is left of the drawings that set it going?
The present document is undertaken ‘drawingly’: employing a methodology and form learned from the point of contact at its centre and developed as a mode of enquiry adequate to this punctum’s apparent resistance to being named or wholly analysed. Building upon Jean-Luc Nancy’s characterization of a working drawing as a search for form, Derrida’s description of the ‘aperspective’ of the drawing stylus, and Laura U. Marks’ analysis of haptic visuality, this methodology lies at the intersection between the blindness associated with drawing, the association of vision with knowledge, and the association of creative work with not knowing. It is characterized by moving forward with acute attentiveness and close proximity to the object under scrutiny; paying myopically close attention to associations when and where they arise; accepting and thematizing the fact—and the risk—that such a perspective restricts the view of an end-point, of the wider imaginative and critical landscape around, and indeed of a blind spot at the centre of the object; and heeding the prospect—and, again, the risk—of ‘surfacing’ from myopia into circumspect analysis. Like Nancy’s working drawings, the completed thesis is proposed as a working document that bears the marks of the search for form it constitutes.
In these terms, the present document arrives at a description of the point of contact as a figure for the ultimately frustrated attempt to consummate or cancel out some experience that is felt to be excessive. Finally, the document itself is proposed as such a figure, a proposal that in turn revises the original assumption that the punctum is the point of contact in drawing, instead revealing this point of contact as a highly wrought description of some further object that remains unidentified and unconsummated, but somewhat changed by being described.

Keywords: drawing
haptic visuality
blindness
practice-based research
phenomenology
Advisor: Taylor, B
Martin, D
Invariants of D-modules

Let K be a complete, algebraically closed, non-trivially valued and non-Archimedean field of mixed characteristic (0, p). We investigate D-module theory on rigid spaces over K in the sense of Ardakov–Wadsley [5], with particular attention to module invariants, and focusing on the 1-dimensional disc X = SpK〈 x〉 as a base space. Highlights of these investigations are to provide tools for calculating lengths of 1-related modules, and to introduce a type of characteristic variety for coadmissible D(X)-modules. Proposals for applications and directions of future study are important features of the discussion.

Advisor: Ardakov, K
Evaluation of the non-specific effects of Bacille Calmette-Guérin (BCG) vaccination in healthy UK adults

Tuberculosis is the leading single infectious disease killer in the world, and the global burden of LTBI and TB disease, with the addition of antimicrobial drug resistance means there is a desperate need for a safe and effective TB vaccine. BCG is the only licensed vaccine and extremely variable in efficacy. However, BCG potentially exerts a non-specific beneficial effect - protecting infants from other causes of death such as respiratory infections and fever. Data from randomised and observational studies in support have been variable in quality; however the WHO reviewed the data and concluded that the effect was likely real, but that more robust data was needed. The aim of this my study was to evaluate the potential non-specific effects of BCG using an in-vitro whole blood growth inhibition assay as a surrogate marker of an individual’s ability to control growth of bacteria before and after vaccination with BCG. Identification of improved control of bacterial net growth following vaccination with BCG would provide evidence to support large, costly, randomised control trials in TB high burden countries. The assay did not demonstrate improved control of growth of four pathogens in the whole blood GIA following BCG vaccination and was subject to bacterial inoculum batch effect and other variables such as haemoglobin. A PBMC GIA potentially detected a subtle improvement in control of bacteria in the same volunteer cohort, but requires further optimisation. Volunteers who received BCG vaccination had an expected clinical and immunological reaction to vaccination with BCG. Pilot data exploring innate immune ‘memory’ through secondary antigenic stimulation of PBMCs did not demonstrate a significant increase in cytokine production, but numbers were small and more work is necessary.

Keywords: Non-specific effects of BCG
Vaccine
Bacille Calmette-Guérin
Advisor: McShane, H
Wyllie, D
A theory of non-compensatory damages

This thesis is about non-compensatory damages (NCD) which include the awards of exemplary, nominal, contemptuous, vindicatory, and disgorgement damages. In contrast with existing scholarship, which tends to look at the various types of NCD individually, it analyses all NCD collectively. I conduct this analysis mainly from a philosophical point of view. I aim to show that the law of NCD is unclear and incoherent and that no one has yet offered a satisfactory definition of NCD. The problem that I seek to resolve is whether NCD are a mere collection of disparate types of award or whether there are any commonalities amongst them. It is argued that NCD can be analysed as a unitary category because they have common justificatory grounds. Such understanding casts new light both on the law of NCD and the law of damages generally.
There are three main original contributions in this thesis. First, NCD is not and cannot be currently conceptualised as a reductionist doctrinal concept. Instead, it can be scrutinised as a meaningful philosophical category. Second, NCD may be collectively justified by recourse to damage to societal rights (as opposed to the claimant’s rights). These justificatory underpinnings are best explained as non-correlative justifying reasons. NCD pursue non-correlative justifying goals of punishment, declaration, prevention, and restitution, which may be collectively explained as distributive justice goals. In support of these claims, the thesis offers an original conceptual and ethical analysis of NCD and provides an original analytical framework for justifying damages awards. Third, it is argued that NCD, to be clearly and systematically distinguished from compensatory awards, are best described as ‘distributive damages’ and a coherent theory of these awards is offered. The theory also shows how these awards may be justified and why they should be treated as exceptional types of remedies.

Advisor: Goudkamp, J
Arginine metabolism in cancer and immunity

Amino acid catabolism causing nutritional stress has emerged as a key immune escape mechanism in cancer to suppress tumour-specific lymphocytes. Here, we show that Arginase-2, the enzyme that breaks down arginine, is released in the blood of acute myeloid leukaemia (AML) patients and mouse models to deplete systemic arginine and inhibit T-cell proliferation and effector function, effects that are abrogated by use of Arginase inhibitors. Importantly, we reveal that the genetic reprogramming in response to arginine starvation differs between cancer cells and activated T-cells in a way that only cancer cells continue to proliferate in the absence of arginine by taking up and converting citrulline to arginine. This dichotomy is accounted for by the cancer-specific ability to upregulate ASS1, the enzyme controlling conversion of citrulline to arginine. ASS1 knockdown in cancer cells completely abrogates proliferation in arginine-free conditions. Furthermore, we show that ASS1 upregulation is regulated by the transcription factor ATF4, which binds an internal enhancer in the ASS1 locus, along with its partner CEBPß. ATF4/CEBPß binding at this enhancer is high in cancer cells and augmented further upon amino acid depletion, whereas it is absent in T-cells. This discrepancy is explained by the presence of DNA methylation, H3K27me3 and H3K9me2/3, epigenetic modifications that create repressive chromatin at the ASS1 enhancer in T-cells but not cancer cells. ATF4 knockdown or deletion of the ATF4-binding site in the ASS1 enhancer abolishes the proliferative advantage displayed by cancer cells in arginine-free conditions. Finally, we reveal the citrulline transporters used by cancer cells and confirm that our findings are clinically relevant since, compared to healthy controls, AML patients have higher serum citrulline levels and possess leukaemic blasts with greater ASS1 and ATF4 expression. In conclusion, we identify arginine metabolism as a cancer immune evasion strategy and elucidate the adaptive mechanisms by which cancer cells, but not T-cells, resist arginine depletion in the tumour microenvironment. Our findings identify the epigenetic basis of a clinically relevant phenotype and reveal potential targets for cancer immunotherapy.

Advisor: Cerundolo, E
Vyas, P
What is called schooling?

Much has been said about the accountable school, the performative school, the school wholly given over to a corporate cult of assessment and accountability; the monarchy of criteria; and the sovereignty of the exam. Lamentations resound as the trend deepens and the cult starts to bites. But let us look another way. Based on a two year ethnographic study of an inner city comprehensive school in North London, this thesis tries to illuminate all of those mechanisms, technologies, processes, and structures, through which an attempt is made to bind us to an order of truth, fix us to a regime of conduct, and render us subject to definite arrangements of knowledge and power. Regimes of truth, orders of conduct, and modes and mechanisms of attachment. Positing as problematic those studies which take as their object a part or aspect of a system or structure that exceeds them, this thesis tries to grasp something of the whole, standing beside the student and following the thing as they make their way through the school’s gauntlet, attempting to detail all of those moments in which they are analysed, classified, sorted, distributed, trained, punished, and corrected.

Keywords: Punishment
Ethnnography
Discipline
School
Managerialism
Accountability
Advisor: Loader, I
Mills, D
Electronic structure of topological quantum materials probed by angle-resolved photoelectron spectroscopy

This thesis investigates the electronic structure of four separate topological quantum material systems by angle-resolved photoelectron spectroscopy (ARPES):
1. LaBi is a semimetal with an extremely large magnetoresistance (XMR) that remains unsaturated even at large magnetic fields. Our ARPES measurements of LaBi indicate the existence of a strong topological phase that may be unique within the family of lanthanum monopnictides. Additionally, our characterization of its bulk electronic structure finds a large imbalance between the electron and hole carrier densities, which challenges the previously assumed scenario of perfect carrier compensation as the origin of the XMR.
2. Three dimensional topological insulators (TIs) can be divided into two classes: strong TIs that host TSSs on all surfaces, and weak TIs, which host TSSs only on some surfaces, which are expected to harbour novel physical phenomena. Yet, despite multiple theoretical proposals and experimental reports, "smoking-gun" evidence for the existence of a weak topological phase is still elusive. Here, by performing ARPES measurements for the surface states of two distinct crystal surfaces, we can conclusively confirm the existence of a weak topological phase in the semimetal TaSb2, which may be related to its negative longitudinal magnetoresistance. Additionally, we present evidence that TaAs2 and NbAs2 are also topologically nontrivial.
3. Graphene is predicted to be a quantum spin Hall insulator, but due to the weak spin-orbit coupling (SOC) of carbon, the predicted bulk energy gap at its Dirac point remains unresolved. Here, we grow ultrathin layers of germanium on Au(1 1 1) in the attempt to realize germanene, a buckled honeycomb structure of germanium atoms, which is predicted to host a similar band structure as graphene with a much larger energy gap. Our ARPES studies of those films reveal the existence of multiple Dirac-like bands that can be tuned by changing the film thickness.
4. The family of A3BO antiperovskites (A=Ca, Sr; B=Sn, Pb) is predicted to form topological crystalline insulators (TCIs). Our ARPES studies of intrinsically hole doped Sr3SnO, Ca3PbO, and Sr3PbO find good agreement with bulk band structure calculations, but cannot probe the predicted bulk and surface Dirac cones in the unoccupied states. For the superconducting hole doped Sr3SnO, which may realize unconventional odd-parity Cooper pairing, we can resolve a controversial question about its Fermi surface morphology that may be relevant for its pairing mechanism.

Keywords: ARPES
Advisor: Chen, Y
The impact of genetic variation on IFITM3 related influenza virus restriction

The IFITM3 protein is a prominent restriction factor of influenza virus that has been shown to antagonise the cellular entry of influenza virus. In 2012, the minor allele of a synonymous SNP in IFITM3, known as rs12252 (major T, minor C), was shown to be associated with severe influenza virus infection. Numerous studies have corroborated this association, showing clear links between the C allele and increased risk of severe influenza virus infection in East Asian and European populations. It was hypothesised that the observed effects of rs12252-C were related to aberrant splicing of IFITM3, causing an isoform coding for an N-terminally truncated variant of the protein. More recently, additional IFITM3-associated genetic risk factors for severe influenza virus infection have also been uncovered.
In this thesis, we investigated the molecular mechanisms of rs12252. In chapter 3, we show that the IFITM3 splicing profile is consistently dominated by the canonical isoform, and that truncated isoforms are produced at extremely low levels regardless of rs12252 genotype. In chapter 4, we investigated associations between rs12252 and expression of IFITM3 at mRNA and protein level, using in vitro systems and healthy donors. We show that rs12252 is an expression Quantitative Trait Locus (eQTL) for IFITM3, and its activity is potentially tissue dependent. We also uncovered potential effects of this SNP on blood transcriptional signature. Next, in chapter 5, we identified two novel eQTLs for IFITM3, which may be risk variants for severe influenza virus infection. Finally, in chapter 6, we analysed the association between rs12252 and severe influenza infection using several model systems. These findings uncovered potential associations between rs12252 and differential interferon signalling, although further experimentation is required to confirm this.

Keywords: SNP
Infection
Influenza
rs12252
IFITM3
Genetic
Advisor: Dong, T
Rehwinkel, J
Warlordism, insurgency and public opinion: explaining civil war in Afghanistan

Current explanations for civil war are divided between grievance and opportunity-based paradigms. This thesis bridges these two theoretical schools by emphasizing elite fragmentation as an understudied variable in the onset and spread of insurgent violence. The three articles of this thesis examine these dynamics through the case study of the post-2001 civil war in Afghanistan. First, I compare variations in political violence within two neighboring provinces of northern Afghanistan, demonstrating how fragmentation between armed groups produces heightened grievances amongst civilians, incentivising them to defect to insurgent groups. Second, I show additional evidence challenging the legitimacy of armed commanders through a conjoint experiment demonstrating that Afghan citizens have strong preferences for leaders who are young and highly educated over older leaders with military experience. Third, I examine why attempts to redress public grievances with large injections of foreign aid have largely failed to win over the population in insecure areas with a case study of the National Solidarity Program in Wardak province. Together, the chapters of this thesis contribute to current literature on civil war while suggesting important policy implications for how the international community should engage in civil wars in Afghanistan and elsewhere.

Keywords: Civil War
Afghanistan
Insurgency
Advisor: Kalyvas, S
Bermeo, N
Travel in the late antique Levant: a study of networks of communication and travel infrastructure in the 4th-7th centuries

The purpose of this thesis is to study the travel infrastructure that existed in the Late Antique Levant (defined as extending from southern Asia Minor to the Sinai Peninsula), and how it enabled people to travel around the region for a variety of official, professional or personal reasons.
What were the motivations, and what mechanisms facilitated or constrained travel for different groups of people? Road conditions and road maintenance are discussed, as is the availability of amenities, and the means of transport (wheeled vehicles, animals) and the various hazards that travellers might have faced.
Chapter 3 addresses the conception of space and distance. This includes not only how geographical space was described, but also how distance was measured and broken up into manageable increments for travel. This chapter details how the incremental landscape was applied, e.g., through the staging posts of the cursus publicus and set itineraries for pilgrimage.
Chapter 4 focuses on travel by water, examining the different factors, such as ship construction, seasonal weather patterns, navigation and hazards, to determine whether the risks and benefits were in balance. An examination of the Tigris, Euphrates, and Orontes and their role in transportation relies on a combination of texts and archaeology from Late Antiquity itself, and ethnographic comparanda from both earlier and later periods.
Chapter 5 is devoted to specific evidence for networks in the Late Antique Levant. The four case studies look at the connections between the Levant and the imperial capital, military routes to the Mesopotamian frontier, caravan routes through Syria, and pilgrim roads leading to Jerusalem. These strands are brought together in Chapter 6, a regional study of southern Palestine and Transjordan. Changes in routes over time reflect military and commercial concerns, as well as the interest of pilgrims in the holy sites of the area.

Advisor: Mango, M