VictorJuiz/thesis huggingface dataset:
Structural and functional studies on a prokaryotic homologue of the mammalian SLC7 cationic amino acid transporters

The Amino acid/Polyamine/Cationic transporter superfamily is among the largest of the sec-ondary active transporters. APC family members use either a proton or sodium gradient to drive substrate translocation across the membrane. Members of the APC superfamily are responsible for the uptake of amino acids and are found in all kingdoms of life. Amino acids, and their derivatives, are crucial for both prokaryotic and eukaryotic cell biology, being the building blocks of a variety of macromolecules and play important roles in metabolism and cell signalling. Therefore, the systems responsible for their transport are important targets of further study, in particular to gain greater insight into how these proteins recognise and discriminate between different types of amino acids. The transport mechanism of several APC members has been elucidated using a variety of structural, biophysical and functional approaches. However, these studies have focussed on sodium coupled transporters due to their function as neurotransmitter transporters. Here, the crystal structure of the first pro-ton-coupled amino acid transporter of the APC superfamily, from Geobacillus kaustophilus, GkApcT, is presented. GkApcT closely related to the mammalian cationic amino acid trans-porters (CATs) of the SLC7 family, responsible for the transport arginine and lysine into the cell. The mechanism of transport was further investigated using liposome-based functional assays to characterise the substrate specificity and kinetics. The crystal structure was used to guide a detailed site-directed mutagenesis study, which identified several conserved res-idues involved in substrate binding and proton-coupling. The current structure serves as a template to further understand proton coupled amino acid transport in bacteria and to un-derstand mammalian amino acid transport via the SLC7 and SLC36 families.

Advisor: Garman, E
Newstead, S
The health impact of health and nutrition claims in the UK, Germany, the Netherlands, Spain and Slovenia

Background: Health-related claims (HRCs) are statements to be found on food packets that convey the nutritional quality of a food and/or its impact on a health outcome. It is unknown whether HRCs improve, hinder, or have negligible effects, on diet and/or health.
Aims: To estimate the impact of HRCs on dietary choices; measure the prevalence of HRCs in five European countries, and the nutritional composition of foods carrying HRCs; compare nutrient profile models aimed at regulating HRCs; and model the impact of HRCs on non-communicable disease (NCD) mortality.
Methods: This thesis reports on a systematic review of the impact of HRCs on dietary choices; a survey of HRCs on pre-packaged foods available to purchase in the UK, Germany, the Netherlands, Spain, and Slovenia; analyses of the nutritional quality of foods that carry HRCs and foods that do not; and the development of a model to predict the current impact of HRCs on NCD mortality in the UK, and the impact of using a nutrient profile model to regulate the use of HRCs.
Results: Foods carrying a HRC are 75% (OR 1.75, 95% Confidence Intervals [95% CI] 1.60, 1.91) more likely to be chosen than identical foods without a HRC. In the five countries surveyed, 26% (95% CI 24%, 28%) of foods carry a HRC and these foods, on average, have a more favourable nutritional composition than foods without a HRC. Modelling suggests that removing HRCs from food labels would result in an additional 2808 deaths per year (95% Uncertainty Intervals -2993, 7392), and that regulating the use of HRCs with a nutrient profile model (such that only foods that pass the model can carry a HRC) would also be detrimental to health. However, the uncertainty intervals associated with these results are large and cross zero. The largest contributor to this uncertainty is the insufficient statistical power of the food composition data.
Discussion: Regulation of HRCs in the EU is the focus of much debate. Current EU law requires the development of a nutrient profile model for their regulation. In order to make an evidence-based health impact assessment of such regulation it would be necessary to collect data on a much larger dataset of foods than that used for this thesis.

Advisor: Rayner, M
Scarborough, P
Philosophical readings in Virgil's Aeneid

This study examines how and why Virgil makes reference to philosophy and engages with contemporary philosophical debate in the Aeneid. Each of the six chapters has a different philosophical focus, and offers literary analyses of the poem that are supported and enriched by situating it within its philosophical context. Cicero and Lucretius are our principal sources for Roman philosophy during the 1st c. BC, and Stoics, Epicureans and Academics were the most influential philosophical schools. The topics I explore include: the relationship between words, especially names, and their referents; the characterization of fate in the Aeneid as Stoic, and the meaning of F/fortuna; Virgil's engagement with Lucretius' explanation of visual perception, which I argue embodies a refutation of the materialism integral to Epicurean philosophy; and, given that Cicero and Lucretius provide the first extant references to 'free will' (libera...voluntas Lucr. 2.256-7; voluntate libera Cic. Fat. 20) in Western literature, the articulation of this concept in the Aeneid. I conclude that Virgil's use of philosophy is both politically and poetically motivated: he shows that poetry and literature are valuable philosophical and political tools by demonstrating that our experience of reality is fundamentally mediated through language and texts.

Keywords: Virgil
Philosophy
Aeneid
Advisor: Trimble, G
Nielsen, K
'Pour une poésie mineure': linguistic experimentation in the work of Dominique Fourcade, Olivier Cadiot and Christophe Tarkos

In a passage in Mille plateaux, Gilles Deleuze and Félix Guattari refer to the 'expressions singulières' of the American poet E. E. Cummings ('he danced his did ou they went their came'), arguing that Cummings offers an example of how, in literature, the atypical stylistic and syntactic variations of an author push language towards its limit, extending it 'vers un en-deçà ou un au-delà de la langue' (125-6). This comment forms part of an analysis, introduced in Kafka: pour une littérature mineure (1975), developed in Dialogues (1977), Mille plateaux (1980), Critique et clinique (1993) and elsewhere, which elaborates the notion of 'littérature mineure'. Deleuze and Guattari's analysis situates literature within the language system more broadly; this system, which they conceptualise as a socio-political phenomenon, structured around relations of power, sees two opposing forces at work. On the one hand, there is a 'major' or 'territorialising' impulse, which seeks to suppress the intrinsic variation of language, and to assert, in its place, a homogenous system, characterised by norms and constants. On the other hand, there is a 'minor' or 'deterritorialising' impulse, which serves to resist this former impulse, and to highlight instead the heterogeneous reality of the continuous variation of language. The stylistic variation of certain types of literature present prime examples of the deterritorialisation of a major mode: they disorder language, rendering it strange, agrammatical and foreign. Thus, in Cummings's example, his subversive use of syntax highlights the homogenising tendency of prescriptive grammar, pointing toward novel possibilities in language, new 'outsides' to the parameters established by a dominant discourse. Deleuze and Guattari call this type of literature ‘mineure’, and argue that it is intrinsically political in so far as it destabilises a major linguistic mode, which is itself a discourse of power.

Advisor: Maclachlan, I
Developing the theoretical foundation for faith-based reentry programming  in the United States

Against a backdrop of high incarceration and staggering recidivism rates, faith-based reentry programming has emerged as a solution to assist the successful reintegration of former prisoners in the United States. Despite increasingly popular partnerships between the government and faith-based organizations in the reentry context, the theoretical and evidentiary basis for this type of programming remains weak. Moreover, almost no evidence exists on the application of faith-based reentry programming to cultural and faith minorities, specifically American Muslims, who make up a significant segment of the incarcerated population. In accordance with evidence-based practice, this dissertation develops a theoretical foundation for understanding, developing, and evaluating faith-based reentry programming. The literature review component examines existing theories in criminology, sociology, and evidence-based practice regarding the process of desistance, the relationship between religion and crime, and the process by which faith-based programming affects re-offending. The qualitative research component interviews 37 "experts" on faith-based reentry programming for a niche population—namely, formerly incarcerated African-American converts to Islam. These experts include formerly incarcerated individuals in three cities, administrators of two existing faith-based programs, researchers, and policymakers. Findings from the literature review and qualitative research are synthesized to produce a theoretical framework for understanding and evaluating faith-based reentry programming generally, and this framework is used to design a sample program for the population interviewed. The research reveals that voluntary faith-based programming may be an effective way of promoting long-term desistance among the reentering African-American Muslim population given their unique challenges and needs, but several practical challenges remain. Finally, the dissertation recommends ways in which faith-based programs may partner with government while remaining effective, abiding by the law, and addressing infrastructural and capacity-related needs.

Advisor: Gardner, F
Diagnosis and prognosis of degradation in lithium-ion batteries

Lithium-ion (Li-ion) batteries are the most popular energy storage technology in consumer electronics and electric vehicles and are increasingly applied in stationary storage systems. Yet, concerns about safety and reliability remain major obstacles, which must be addressed in order to improve the acceptance of this technology. The gradual degradation of Li-ion cells over time lies at the heart of this problem. Time, usage and environmental conditions lead to performance deterioration and cell failures, which, in rare cases, can be catastrophic due to res or explosions. The physical and chemical mechanisms responsible for degradation are numerous, complex and interdependent. Our understanding of degradation and failure of Li-ion cells is still very limited and more limited yet are reliable and practical methods for the detection and prediction of these phenomena.
This thesis presents a comprehensive approach for the diagnosis and prognosis of degradation in Li-ion cells. The key to this approach is the extraction of information on electrode-speci c degradation through open circuit voltage (OCV) measurements. This is achieved in three stages. Firstly, a parametric OCV model is created, which computes the OCV of each electrode. Secondly, a diagnostic algorithm is devised, through which the OCV model is tted to OCV measurements recorded on Li-ion cells at various stages throughout their cycle life. The algorithm identi es the nature and quanti es the extent of degradation experienced by the cells. Lastly, the outputs of the algorithm are used to identify the likely failure modes of the cells and predict their end-of-life.
The presented methods improve safe operation and predictions of remaining useful cycle life for commercial Li-ion cells. Greater certainty about the reliability, safety, required maintenance and depreciation of Li-ion battery systems can signi cantly enhance the competitiveness of battery electric storage in both automotive and stationary applications. The ndings presented in this work are therefore not only of technological but also of commercial interest.

Keywords: Diagnostics
Open circuit voltage
Battery management
Degradation
Advisor: Howey, D
Essays on Unconventional Monetary Policy

Monetary policy since the global financial crisis of 2007/08 has contended with the 'unknown unknowns' associated with Knightian uncertainty rather than the 'known unknowns' associated with risk. We find that when a policymaker knows neither the parameters of his model nor the probability distribution from which those parameters are drawn, more fear of model misspecification calls for more aggressive use of both conventional and unconventional instruments. Moreover, the greater the policymaker's doubts about the effect of asset purchases relative to the effect of interest rate changes, the greater the relative zeal with which he should pursue the former. Critics of the U.S. Federal Reserve argue that "unwarranted pessimism" about the effectiveness of quantitative easing (QE) inhibited the postcrisis monetary policy response. We find that this relative passivism during QE2 may instead have been the optimal response to less fear of model misspecification following QE1. Rather than the FOMC's return to activism during QE3 implying that its passivism during QE2 was undue, it may be the latter that was warranted and the former that was undue.

Advisor: Ellison, M
Calabi-Yau manifolds, discrete symmetries and string theory

In this thesis we explore various aspects of Calabi-Yau (CY) manifolds and com- pactifications of the heterotic string over them. At first we focus on classifying symmetries and computing Hodge numbers of smooth CY quotients. Being non- simply connected, these quotients are an integral part of CY compactifications of the heterotic string, aimed at producing realistic string vacua. Discrete symmetries of such spaces that are generically present in the moduli space, are phenomenologically important since they may appear as symmetries of the associated low energy theory. We classify such symmetries for the class of smooth Complete Intersection CY (CICY) quotients, resulting in a large number of regular and R-symmetry examples. Our results strongly suggest that generic, non-freely acting symmetries for CY quotients arise relatively frequently. A large number of string derived Standard Models (SM) were recently obtained over this class of CY manifolds indicating that our results could be phenomenologically important. We also specialise to certain loci in the moduli space of a quintic quotient to produce highly symmetric CY quotients. Our computations thus far are the first steps towards constructing a sizeable class of highly symmetric smooth CY quotients.
Knowledge of the topological properties of the internal space is vital in determining the suitability of the space for realistic string compactifications. Employing the tools of polynomial deformation and counting of invariant Kähler classes, we compute the Hodge numbers of a large number of smooth CICY quotients. These were later verified by independent cohomology computations. We go on to develop the machinery to understand the geometry of CY manifolds embedded as hypersurfaces in a product of del Pezzo surfaces. This led to an interesting account of the quotient space geometry, enabling the computation of Hodge numbers of such CY quotients.
Until recently only a handful of CY compactifications were known that yielded low energy theories with desirable MSSM features. The recent construction of rank 5 line bundle sums over smooth CY quotients has led to several SU(5) GUTs with the exact MSSM spectrum. We derive semi-analytic results on the finiteness of the number of such line bundle models, and study the relationship between the volume of the CY and the number of line bundle models over them. We also imply a possible correlation between the observed number of generations and the value of the gauge coupling constants of the corresponding GUTs. String compactifications with underlying SO(10) GUTs are theoretically attractive especially since the discovery that neutrinos have non-zero mass. With this in mind, we construct tens of thousands of rank 4 stable line bundle sums over smooth CY quotients leading to SO(10) GUTs.

Keywords: Calabi-Yau Manifolds
Heterotic String Compactification
Symmetries
Advisor: Lukas, A
Once more to the body: an ethnography of mindfulness practitioners in the United Kingdom

This thesis explores embodiment and self-shaping among practitioners of mindfulness-based interventions for health and wellbeing in the United Kingdom. It draws on the anthropology of embodied experience, the body, and ethics, to delve beneath an ethnographic problem: why does mindful self-cultivation entail so many notions of 'mindfulness', the 'practitioner', and the 'body'? Based on fieldwork at a leading mindfulness research, teaching, and teacher-training centre, and participant-experience in mindfulness praxis, the thesis explores the making of mindful subjectivities. Practitioners cultivate a trajectory through distinctive temporal and embodied experiences of self-shaping: where the practitioner begins with hope of rapid transformation, she must realise that she is already and perennially 'mindful'; where she begins as impatient and 'heady', she becomes curious and ‘embodied’. The thesis argues that although practitioners' claims and practices of turning to the 'present' and the 'body' appear dualistic, it is through the turning itself that dualisms are ultimately undone, and new forms of attention and intention with regard to oneself emerge.
Nonetheless, the thesis demonstrates that this trajectory towards 'embodiment' may not be fulfilled at all. Indeed, practitioners must perpetually adjust their direction of travel. The thesis explores anthropology’s own concepts of embodiment by arguing that the felt sense of being a self-shaping mindfulness practitioner entails progression, but also stuckness, hesitation, and doubt, in which commitments feel noncommittal and embodied capacities unstable. Analysing these experiences within frameworks from the anthropology of ethics, the thesis calls for the perspective not just of manoeuvrability as a virtue but also of the subject's embodied sense of their perpetual forward motion: the ways in which subjects encounter and create their futures, amidst the diversities and instabilities of themselves and their world.

Advisor: Hsu, E
Potter, C
Subcritical turbulence in the Mega Ampere Spherical Tokamak

The transport of heat out of tokamak plasmas by turbulence is the dominant mechanism limiting the performance of fusion reactors. Turbulence can be driven by the ion temperature gradient (ITG) and suppressed by toroidal equilibrium scale sheared flows. Numerical simulations attempting to understand, and ultimately reduce, turbulence are crucial for guiding the design and optimisation of future reactors.
In this thesis, we investigate ion-scale turbulence by means of local gyrokinetic simulations in the outer core of the Mega Ampere Spherical Tokamak (MAST).We perform a parameter scan in the values of the ITG and the flow shear. We show that nonlinear simulations reproduce the experimental ion heat flux and that the experimentally measured values of the ITG and the flow shear lie close to the turbulence threshold. We demonstrate that the system is subcritical in the presence of flow shear, i.e., the system is formally stable to small perturbations, but transitions to a turbulent state given a large enough initial perturbation. We propose a scenario for the transition to subcritical turbulence previously unreported in tokamak plasmas: close to the threshold, the plasma is dominated by a low number of coherent long-lived structures; as the system is taken away from the threshold into the more unstable regime, the number of these structures increases until they fill the domain and a more conventional turbulence emerges.
We make quantitative comparisons of correlation properties between our simulations and experimental measurements of ion-scale density fluctuations from the MAST BES diagnostic. We apply a synthetic diagnostic to our simulation data and find reasonable agreement of the correlation properties of the simulated and experimental turbulence, most notably of the correlation time, for which significant discrepancies were found in previous numerical studies of MAST turbulence. We show that the properties of turbulence are essentially functions of the distance to threshold, as quantified by the ion heat flux. We find that turbulence close to the threshold is strongly affected by flow shear, whereas far from threshold, the turbulence resembles a conventional ITG-driven, zonal-flow damped regime.

Keywords: fusion
ion temperature gradient
turbulence
flow shear
subcritical
plasma
Advisor: Schekochihin, A
Highcock, E
Roach, C
Sleep physiology, circadian rhythms, and the risk for developing psychosis

Sleep and circadian rhythm disruption (SCRD) is frequently found to co-occur in psychotic disorders. This can include a range of phenotypes such as insomnia, circadian delays, deficits in sleep spindles, and sleep-dependent cognitive impairments. However, increasing evidence suggests that psychosis occurs across a continuum of severity within the general population, yet few studies have investigated sleep and circadian rhythms prior to clinical diagnosis. Furthermore, SCRD and psychosis are posited to share underlying neuropathologies and although increasing evidence implicates shared genetic influence, little is known of the shared environmental risk. This thesis investigates sleep and circadian rhythms at multiple levels, from their occurrence in the general population, their disruption in high risk individuals, and a focus on sleep spindle oscillations in the brain. Firstly, the relationship between subjective measures of sleep and circadian rhythms, risk factors for psychosis, and psychotic-like experiences (PLEs) were studied in a large population sample. All three were highly related, with a subset of risk factors showing a strong association to both PLEs and SCRD. Secondly, sleep and circadian rhythms were assessed in individuals at high risk for developing psychosis based upon having a high load of risk factors and sub-clinical psychotic symptoms. High risk individuals showed subjective SCRD but this was not reflected in objective measures assessed by actigraphy and polysomnography. A subset of high risk individuals further showed substantially later melatonin rhythms compared to a low risk group. Thirdly, high and low risk individuals were assessed for measures of declarative and procedural sleep dependent memory consolidation. High risk individuals showed no evidence for sleep dependent cognitive impairment but did show a potential sensitivity in performance to the amount of sleep, not seen in low risk individuals. Finally, recordings in the somatosensory cortex (SCx) of mice were used as a model to explore the spatio-temporal dynamics and functional significance of sleep spindles. Distinct highly localised spindle events were discovered in the anterior SCx, with their complete absence just a fraction of a millimetre away, and their occurrence of which coincided with unique responses to global vigilance states. Together, this work pioneers research into sleep and circadian phenotypes associated with both sub-clinical psychotic symptoms and risk factors for disease and furthers our knowledge of particular sleep processes which could collectively help us to understand why SCRD and psychosis develop.

Keywords: Sleep
Advisor: Wulff, K
Porcheret, K
Vyazovskiy, V