VictorJuiz/thesis huggingface dataset:
Sedimentology and sedimentary geochemistry of the Eagle Ford Group, Texas

The Eagle Ford Group is an organic-rich succession of rhythmically interbedded packstones and wackestones, deposited in the southern Western Interior Seaway during the Cenomanian-Turonian of the Upper Cretaceous. Recent investigations have suggested that either eustatic sea level change, astronomical forcings, change in primary productivity and dilution, or changes in local and global benthic oxygenation may be responsible for the Eagle Ford Groups lithological and geochemical variations. However, no consensus has yet been reached. Chapter 3 examines cm-scale geochemical, mineralogical and sedimentological changes to investigate the temporal and spatial variabilities of the Eagle Ford Group. This study suggests the stratigraphical cyclicity of the Eagle Ford Group is a function of alternating periods of high and low primary productivity and accumulation rates possibly modulated by the fertilizing effect of ash falls. Lateral variabilities are determined by the reworking of pelagic sediment by bottom currents, below storm wave base. Chapter 5 investigates changes in water-mass exchange, climate, water-column anoxia and hydrodynamics during the deposition of the Eagle Ford Group. The results of this study show four distinct stages in the deposition. The lowermost stratigraphic third of the Lower Eagle Ford was deposited under a humid climate with high continental runoff, anoxic/euxinic benthic conditions and exchange with a nutrient-rich water mass. The upper stratigraphic two thirds of the Lower Eagle Ford was deposited during a more arid climate, with lower continental runoff, a highly restricted anoxic benthic zone with some periods of euxinia, and little siliciclastic input. The lowermost stratigraphic half of the Upper Eagle Ford was deposited during a mostly humid climate with high continental runoff and the presence of a suboxic benthic zone that experienced multiple periods of oxygenation related to a more open water mass exchange. The upper stratigraphic half of the Upper Eagle Ford exhibits deposition under a more arid climate with lower continental runoff and reduced benthic oxygen content. Global controls, such as perturbations of the global carbon cycle, exert a fundamental role in the large-scale deposition of organic carbon. As such it is important to understand the effect and causes of global events when studying sedimentary systems. The Eagle Ford Group contains one such event Oceanic Anoxic Event 2 (OAE 2). However, the fundamental cause of OAE 2 is still poorly constrained. As such in Chapter 4 mercury concentrations are examined in sedimentary successions spanning the Mid-Cenomanian to Early Turonian interval. The data presented here are consistent with an initial magmatic pulse at the time of the MCE, with a second and greater, pulse at the onset of OAE 2, possibly related to the emplacement of LIPs in the Pacific Ocean and/or the High Arctic.

Advisor: Cartwright, J
Ruhl, M
Hesselbo, S
Skill and scepticism: an enquiry concerning the nature and epistemic value of intuitive judgement

This thesis concerns two main questions: What is intuition? And can it be a source of knowledge or justification? In addressing these questions, it advances several ongoing philosophical debates, and does so in two main ways: firstly, by formulating a general account of the nature of intuitive judgement that establishes common ground amongst the often disparate views of scholars working on intuition (or intuitions) in psychology, linguistics, philosophy and various other disciplines; and, secondly, by developing a new epistemological position that combines scepticism about the evidential value of intuition with a new account of philosophical skill.
The general account of the nature of intuitive judgement mainly consists in drawing a distinction between intuitive judgement and intuitive appearance which is analogous to a distinction that can be drawn between perceptual judgement and perceptual appearance. It is argued that a common type of paradox entails the distinction for the non-perceptual case; it is then demonstrated how various related notions, such as intuitive belief, intuitive thinking and intuition as a cognitive faculty, can be derived from the notion of intuitive judgement.
The epistemological account receives additional support from a new theory regarding the objects of intuition, according to which the analogy between intuition and perception holds specifically for what is sometimes called 'aspect perception': it is argued that some intuitive appearances are partially constituted by an appearance of meaning and that, consequently, the analysis of intuitive judgement must distinguish between two types of object, an intentional object (typically, a thought) and a causal one (typically, an expression of thought). It is further argued that the focus on evidential value that has been prevalent in the philosophical literature is too restrictive. By contrast with the prevalent view, it is demonstrated that intuition plays a significant role in human thinking, including in philosophical and scientific enquiry, independently of whether intuition is of great or only of minimal evidential value.

Keywords: Epistemology
Intentionality
Metaphysics
Justification
Cognitive science
Psychology
Philosophy of mind
Intuition
Scepticism
Philosophy
Experimental philosophy
Advisor: Child, W
Williamson, T
Axonal mechanisms underlying presynaptic short-term plasticity of dopamine release in striatum

Dopamine (DA) signalling plays a central role in the functions of the basal ganglia, supporting behavioural processes such as action selection and reinforcement learning. Consequently, dysfunction of DA release is implicated in a wide range of neurological and psychiatric disorders, including Parkinson’s disease and addiction.
DA is released from an extensively-branched axonal arbor in the striatum, but it remains unclear how the characteristics of these complex axons influence the short-term plasticity of DA release. This thesis uses fast-scan cyclic voltammetry and patch-clamp electrophysiology in slices of mouse striatum to study the axonal factors that shape the conversion of firing activity in midbrain DA neurons to DA release in the striatum.
Firstly, short-term plasticity of DA release was shown to be governed by a region-specific hierarchy of mechanisms related to Ca2+ dynamics at DA release sites, and to excitability of DA axons in striatum, which was maintained by the dopamine transporter (DAT). Second, tonic background activity in DA neurons was shown to enhance the contrast of DA signals evoked by bursts, in a region-specific manner, and was also regulated by the DAT. Third, release of γ-amino butyric acid (GABA) from DA axons was shown to be insensitive to regulation by the DAT, in contrast to the release of DA.
These data suggest that the characteristics of DA axons, particularly expression of the DAT, can powerfully regulate short-term plasticity of DA release in a region-specific manner. These findings extend our understanding of the regulation of DA signalling and may have implications for the manner in which presynaptic activity in DA neurons is read out as DA release across striatal regions.

Advisor: Cragg, S
Changing the conversation: An exploration into the impact of structured feedback and consultation in the English classroom

Identity as a learner in the classroom is a field that needs negotiating. As a teacher one must remember that the learners of any given class bring with them their own identities, pedagogies and experiences of learning. Thus it is worthwhile, as a researcher, thinking about the dynamics of the classroom and the need for both learners and teachers to negotiate the environment and educational climate we foster as a school.
All learners and teachers must mediate identities in the classroom in order to be effective learners. These identities have been defined by curriculum demands, targets, schools and the continual cycle of testing, assessment and reporting that we place upon students to see if they are, according to external parameters, characterised as effective learners
The question is; how do learners negotiate these identities successfully and to what extent can they really feel they have some sense of control or say within the context of the classroom?
From my perspective, in order to solve such questions, one must strive to create a conducive learning environment and foster a love of learning, hence, it is of the utmost importance; to consider how we as teachers create an inclusive classroom which promotes self-efficacy and self-reflection. The paradigm? A classroom where one is not just concerned with the whole but the individual and the relationship between these two is the ideal; a classroom that develops learners to be self-regulating, empowered and in control of their learning.

Keywords: MLT
English classroom
MLT2015
What impact do pedagogies that encourage students to take ownership of their own learning have on self-esteem and attainment?

This research and development project expands on research conducted at a comprehensive school in South West London over the last two years. Its aim is to explore the link between self-esteem and attainment, particularly considering whether there is a link between pedagogies that offer students more control in the classroom and their levels of self-esteem and academic attainment. My previous research had highlighted the fact that students in lower sets felt that they were not a high priority for the school and as a result, they felt that their efforts and achievements did not matter as much as some of their peers. Participants were selected using Key Stage 4 prior achievement data and their responses to Rosenberg’s Self Esteem test (1965). Three students were selected to act as ‘teachers’ in a whole-class setting or as ‘experts’ in group work, taking responsibility for their learning and the instruction of others. In addition, the class was permitted to select their own groups for small-group tasks, allowing them to decide whether they worked with their friends or other classmates to complete specific tasks. Self-esteem tests were then re-administered at the end of the action research phase as well as an academic assessment to measure progress. The action research revealed that in general, the self-esteem scores of the ‘teachers’ did improve, and along with the levels of some of their classmates. Academic results also improved but with much greater success than self-esteem levels, as all students showed progress when re-assessed at the end of the test phase. Again, ‘teachers’ showed a similar rate of progress to their classmates which suggested that while they had been empowered to a greater degree by being placed in positions of authority, they had not been unduly advantaged by this process. Students preferred student-led lessons and expert sessions to self-selected groups which some felt offered them the chance to socialise rather than learn. However, data collected did suggest that these sessions were successful and created a collaborative learning environment that was not present before the action research had taken place.

Keywords: MLT
MLT2015
Life has value, but non-existence does not

Epicurus argued that death is not bad for the one who dies, because death is annihilation of the experiencing subject and we need a subject of badness for anything to be bad. Epicurus' argument is widely thought to lead to indifference about death, as well as indifference about creating new life, and thus is mostly rejected.
In his essay “Death and the Value of Life,” McMahan offered an alternative framing of the Epicurean position on death. He called this the “Epicurean Reconciliation Strategy” (ERS). The ERS entails that non-existence is not intrinsically good or bad, and non-existence is not comparatively better or worse than existence, but that existence can be non-comparatively bad or non-comparatively good. This non-comparative value provides axiological reasons to create and extend good lives, and to avoid creating and avoid extending bad lives.
In this thesis, I will defend the premises that underlie the ERS, before defending the ERS more directly. I will look at implications that the ERS has on the value of creating and ending lives, and defend it from objections.

Keywords: Population
Value
Ethics
Death
Advisor: McMahan, J
Improving simulation training in orthopaedics

The way surgical trainees acquire technical skills is changing in modern surgical training programmes: simulation is proposed as a key part of those changes. Arthroscopy is a surgical technique that is increasing in both incidence and technical complexity; where simulation is becoming common, but evidence is limited. Real-world performance improvements can be measured following simulation training in other fields, but equivalent measures of intra-operative performance are inadequate. Thus, although surgical simulation is popular and improves simulated performance, there is little objective evidence that it improves intra-operative performance.
The original contribution of this thesis is to objectively demonstrate the transfer of simulation training into improved intra-operative technical skills. To achieve this, a systematic literature review investigated the quantitative metrics currently used to measure arthroscopic performance, identifying wireless motion analysis as a potential method to assess performance intra-operatively. Motion analysis is a recognised objective method to measure surgical activity which correlates with surgical experience, so wireless motion analysis was validated against a wired motion analysis method commonly used in simulation but not feasible for intra-operative use. Wireless motion analysis metrics were further validated with a simulated arthroscopy list: this environment allowed deliberate practice of arthroscopic sub-skills with proximate feedback for independent practice.
This simulated arthroscopy list with wireless motion analysis was used in two randomised studies: the penultimate study of this thesis investigated the impact of simulated practice on the arthroscopic learning curve and showed that performance improved rapidly with independent practice but was not modified by feedback, while the final study investigated additional simulation practice during early surgical training, and objectively demonstrated that additional simulation training improved intra-operative performance compared to traditional training alone.
This thesis is the first to objectively show that simulation affects intra-operative behaviour. It sets the groundwork for further investigations into efficient, cost-effective simulation and the impact of simulation training on patient outcomes.

Keywords: Orthopaedics
Arthroscopy
Motion analysis
Simulation
Learning curve
Feedback
Advisor: Rees, J
Alvand, A
Global and local patterns of population structure and their role in the evolution and demography of Plasmodium falciparum

In this thesis, I study the role of genetic population structure in the evolution and demography of Plasmodium falciparum by focusing on the recent onset of artemisinin resistance in Southeast Asia, an alarming event for global public health. I describe the population structure of Plasmodium falciparum in the Thai-Cambodian border region, characterizing sympatric but differentiated subpopulations associated with artemisinin resistance. I show evidence that they are the product of recent founder events and seem the primary force spreading resistance. Next, I study a superset of the kelch13 mutations associated with artemisinin resistance, assessing their relationship with population structure and recent founder effects. Each resistant subpopulation possesses a distinct kelch13 allele that, in conjunction with a particular genetic background, seem to have driven recent founder effects. I examine the demography of these resistance alleles using patterns of haplotype sharing and show that the primary mode of spread consists of independent mutational events, with limited gene flow within countries in East Southeast Asia. Subsequently, I assess the origin of kelch13 mutations observed in African isolates, concluding that they are indigenous and have originated independently. These observations undermine localized resistance containment as a strategy for malaria control and suggest that population structure and founder effects may predate and facilitate the emergence of resistance. Therefore, monitoring these phenomena could warn about the development of resistance before phenotypic evidence materializes. Next, given the importance of demographic inference to inform malaria control programs and the advent of large genomic datasets, I develop a fast and scalable method to build the ancestral haplotype graph. I show that this data structure, composed of a collection of local haplotype trees, is informative about the recent genealogical history of the sequences and can be used to summarize and study shared haplotype patterns along the genome. I describe a set of algorithms with quasilinear time complexity as a first step in the development of scalable demographic inferential methods that can be applied to several thousands of sequences. I also evaluate how mixed infections affect the analysis of deep sequencing data and review the FWS statistic, a relative measure of inbreeding and complexity of infection. In doing so, I show that the original FWS estimator discards the diversity encoded by rare variants and provide an alternative estimator without such bias that is simpler, more intuitive and has a better resolution.

Advisor: Kwiatkowski, D
McVean, G
Schizophrenic justice: exploring ‘justice for victims’ at the International Criminal Court (ICC)

This thesis examines how the promise and institutionalization of ‘justice for victims’ has shaped the ICC’s justice vision and identity. Drawing on interviews with 90 practitioners in The Hague, Kenya and Uganda, it undertakes a sociological and institutional analysis of how ‘justice for victims’ has evolved in the Court’s first two decades through the definitions and redefinitions, pushes and pulls, strategies and miscalculations of the Court’s diverse actors both in The Hague and in the field. It argues that the introduction of ‘justice for victims’ has led to a rift within the Court between those who embrace a narrow understanding of justice as ‘fair trials’ and those who see the ICC as an opening for broader justice processes.
These rifts and gaps are reinforced by the Court’s actors in the field such as victims’ lawyers and intermediaries who sometimes assume political advocacy roles beyond what the Court’s judges envisaged or follow their parochial interests on the ground. While the ICC’s judges have increasingly curtailed victim participation and reparation in the court room, the Court’s practices on the ground reflect an uneasy fusion of legal justice, development, local and national politics with a proliferation of new justice concepts including ‘transformative justice’ and ‘gender justice’. So far, these justice contestations have not chipped away, much less undermined, the Court’s legitimacy. Rather, the Court has thrived on its justice contradictions; its failure to commit to any particular justice vision while loosely relating to all possible visions, has made the Court impervious to critique. But the thesis will also show that ‘justice for victims’ at the ICC is schizophrenic: it is inherently unstable and its contradictory dynamics may at some point rip the concept apart - and with it the Court’s legitimacy.

Keywords: Transitional Justice
International Criminal Court
Kenya
Restorative Justice
Uganda
Victims
International Criminal Justice
Advisor: Hoyle, C
Against indexicality: photography as a formation of thought

Guided by the question of what does photography bring into being, ‘Against Indexicality’ is a proposition to rethink the foundation of the philosophy of photography – to rethink the supposed relation of truth between the photograph and the world. Taking Indexicality as a messy and convoluted conceptual field comprised of the notions of pointing, stillness, and fragmentation, this study works to untangle the three from each other, separately challenging each individual notion. In analysing each of the three through their conceptualisation by prominent thinkers, including Charles S. Peirce, Susan Sontag, Henri Bergson, Walter Benjamin, André Bazin, Rosalind Krauss, Jacques Derrida, and Roland Barthes, and examining them against and through examples of photographic images, this study points to the imprecisions, insufficiencies, and incompatibilities of Indexicality in relation to the photographic image and form. Undoing Indexicality as a field, this study resists Indexicality as a paradigm, proposing a new theoretical framework for photography: rather than looking at photographic images as truth bearers that can evidence the photographed, it proposes to look at photographic images as formations that form a thought out of the photographed. In that, this study works to remedy the Indexicality fever, or compulsion, which it identifies as the root cause of theoretical mess within the philosophy of photography. By evincing that Indexicality is a wrong, albeit necessary, solution to a problem that is to do with identifying the relation of the photograph to the world, it not only lifts photography out of a Procrustean bed in which it was never comfortable, but also allows for a new solution to develop. This solution is the theory of photo-poiesis: a move beyond the materiality and away from the referentiality of photography towards its being in the world and the thought that it forms and brings-forth – towards thinking.

Keywords: poiesis
indexicality
photography
phenomenology
Advisor: Grootenboer, H
Coombes, J
Computational approaches to vaccine development for multi-strain pathogens

This thesis presents a number of computational approaches that I have used for the study, design, and optimization of vaccination strategy. An effective vaccination regimen against an infectious disease will elicit immune responses that target carefully selected regions of the parasite, and will be implemented in such a way that maximum benefit can be had. Here, I present research into various steps of the vaccine development pipeline, from developing new methods by which targets can be selected, to the best way that a therapy can be implemented in the field. Existing understanding of the ways in which populations of pathogens are structured is used to develop methods for selecting novel vaccination targets, that is, regions of pathogens against which a vaccine might be highly effective. These approaches are combined with mathematical modelling of vaccination at both within-host and population levels to assist in the development and implementation of vaccines against pathogens of global health importance. My within-host model suggests that a highly efficacious sterilely protective malaria vaccine may be possible by combining existing therapies. An epidemiological approach provides evidence that mass vaccination with a malaria vaccine of moderate efficacy, in combination with other interventions, may drive eradication in many transmission contexts. Considered together, the works contained within this thesis explore the ways in which both existing and novel therapies may be combined to gain maximum benefit.

Advisor: Lourenco, J
Gupta, S