VictorJuiz/thesis huggingface dataset:
The Polish-Russian mixed code in the Polish community in Lithuania

The aim of this thesis is to investigate the patterns of language alternation in the Polish community in Lithuania, which can be described as an indigenous ethnic group that has been living on the territory of modern-day Lithuania since the fourteenth century (Potašenko 2007). Following two language ideologies, Russification during Soviet times and Lithuanisation post-independence, the Lithuanian Poles developed complex linguistic repertoires, consisting of the regional and standard variety of Polish, Russian and Lithuanian. One of the most significant consequences of the prolonged language contact has been the emergence of frequent and regular language alternation between the regional variety of Polish and Russian, which constitutes the focal point of the present study.
As the existing research suggests, the linguistic phenomena arising as a result of language contact can be situated along a continuum, which starts with code-switching, then gradually moves towards code-mixing and finally evolves into a conventionalised fused lect (Auer 1999). 'Classic' code-switching is characterised by the locally meaningful juxtaposition of the two languages, code-mixing can be described as a type of interaction where the switched mode of speaking becomes the norm while a fused lect is an even further development of bilingual speech, which presupposes loss of variation and an increase of linguistic structure.
The data for the present study come from a corpus of spontaneous conversations involving members of the Polish community. The recordings were collected in the city of Vilnius and feature 25 respondents in their twenties. The data analysis reveals that all three types of language alternation feature in the present corpus; however, code-mixing is clearly the preferred type. It immediately manifests itself in the frequent insertion of Russian single switches and larger constituents into the Polish base. As a result of its wide spread and frequency, language alternation has lost its immediate local meaning and the pattern of frequent Polish-Russian mixing has become the accepted mode of speaking within the Polish speech community.

Advisor: Fellerer, J
Patient and public involvement: ethical justifications, expert knowledge, and deliberative democracy

Across many countries worldwide, support for patient and public involvement (PPI) in health care has grown significantly over the last two decades. Calls to democratize the health care system have resulted in a system where patients are increasingly involved in the design of medical research and members of the public have been called upon to help make decisions concerning various elements of national, regional, and local health care policy. In some countries, like the UK, laws on the books now mandate that health care institutions meet certain benchmarks in PPI in order to be eligible for national funding. Though many scholars have sought to understand how society can make PPI efforts more "effective," they have largely neglected to provide an overarching justification for involvement in the first place. This thesis seeks to understand whether such a justification exists.
I examine two sets of arguments in support of PPI: one that maintains PPI simply improves the quality, relevance, or effectiveness of medical research and health care provision (the outcomes-based argument) and one that appeals to notions of democratic legitimacy and representation. I argue that the outcome-centered argument wrongly presupposes an agreement on which outcomes should be prioritized while the democratic legitimacy argument fails to adequately identify the relationship between PPI and greater transparency, accountability, or reasonability. Since supporters of PPI often use the framework of deliberative democracy as support for the democratic legitimacy argument, I use it as well as a starting point for analysis. In short, though PPI may appeal to certain democratic intuitions, there is little reason to think that in practice it has strengthened bonds of democratic legitimacy.
I conclude by suggesting ways in which those core democratic virtues might be strengthened outside the realm of PPI. Despite increased patient involvement, the processes of resource allocation (rationing) in health care remain opaque in many countries. In addition, there exist few mechanisms for individual appeal of an unjust decision, a feature that most deliberative democrats consider essential to a just system of resource allocation. Ultimately, I contend that a greater focus on the processes that facilitate transparency and accountability will better serve citizens and their health care systems.

Advisor: Sheehan, M
Cardinal Bessarion and the transmission and interpretation of Plato in the fifteeenth century

Cardinal Bessarion came from his native Byzantium and settled in Rome in the mid fifteenth century. He was a Basilian monk and, at the time, a Greek Archbishop. His cultural background was in the rationalist tradition of Greek theology. As the Byzantine Empire succumbed to the invading Turks he made it his mission to preserve as much of Greek cultural heritage as possible. Part of this mission was to set out for the Italians (or Latins as he called them) the teachings of Plato of which they had only scanty knowledge. His work in Calumniatorem Platonis was intended as a defence of Plato's teachings against the criticisms of the militant Aristotelian George of Trebizond. This thesis examines Bessarion's exposition of Plato's teachings in that work on a range of philosophical questions that were litmus tests of theological orthodoxy at the time. It argues that Bessarion's exposition of Plato is heavily interpreted through a prism of later commentaries and thinkers particularly the Neo-Platonists. It shows how these interpretations and Bessarion's use of his sources is determined by his aim of showing that Plato’s philosophy was closer to Christian orthodoxy than Aristotle’s and, therefore, provided a firmer philosophical base than the prevailing Aristotelianism.

Keywords: Interpretation of Plato
Cardinal Bessarion
Advisor: Heyworth, S
Gertz, S
Wilson, N
Nourishing the nation: manifestations of Catalan national identity through food

In this thesis I ask whether food can be used to express Catalan national identity, and if so, in what ways this occurs. In doing so, I consider the lived realities of nationalist movements, rather than simply the ideas and political claims that inform such movements. The Catalan Autonomous Community in northeast Spain is an ideal place to research this issue, due to the strengthening of nationalist sentiments there in light of the rise in support for independence from Spain. I wished to see whether this had any effect on the connections between food and national identity (or gastronationalism).
National identity and food are connected in many diverse and varied ways. Food culture allows us to reflect on national identity as a whole. Themes which commonly appear in nationalist discourse, such as cultural specificity, historicism, or landscape (to name but a few), also inform discussions of national food identity. In the present case, while other markers of identity (e.g. language) are also important, ideals of Catalan nationalism may take the guise of Catalan gastronationalism as well. The current pro-independence movement has had the effect of making Catalans more aware of their cultural symbols, including cuisine, which is now one of many such symbols that can be mobilized for the expression of national identity.

Keywords: Culinary identity
Catalanism
Gastronationalism
Catalan cuisine
Anthropology of Food
Development of mycobacterial growth inhibition assays for the early evaluation and gating of novel TB vaccine candidates

Tuberculosis poses a serious global health threat, with an estimated 9 million new cases and 1.5 million deaths annually. The current vaccine, BCG, is inadequate but development of an effective alternative is severely hampered by the lack of an immune correlate of protection. Candidate vaccines are currently tested using preclinical animal models such as mice and non-human primates. Large numbers of animals are required and subjected to procedures classified as 'Moderate' in severity. Experiments are long and costly and it is unclear whether outcomes are predictive of efficacy or safety in humans. Work in this thesis describes the optimisation and evaluation of a functional in vitro Mycobacterial Growth Inhibition Assay, the MGIT, which takes into account a range of immune mechanisms and their interactions. Applying this assay, a BCG-induced reduction in mycobacterial growth was detected in humans, NHPs and mice. A correlation was observed between the in vitro MGIT response and in vivo protection from challenge in the mouse and NHP models. There was also concordance between the MGIT and epidemiological data or in vivo outcome in humans. Comparison of whole blood and PBMC compartments indicated that haemoglobin may act as a confounder and suggested a role for complement, but not antibodies, in determining mycobacterial growth. Classical monocytes and CD16- NK cells played a crucial role in PBMC MGIT. Cytokines correlating with mycobacterial growth represented a mixture of subsets, and the immunoregulatory cytokine IL-10 was highly influential. Genes correlating with mycobacterial growth were enriched for the immune response pathway, which included CD14 and HAMP, supporting the importance of monocytes and iron. Although further work is required, the MGIT assay represents a potential correlate of protection that may be applied in preclinical vaccine testing, reducing the number of animals used in challenge experiments and accelerating the development of an effective vaccine.

Keywords: Vaccine
Tuberculosis
MGIA
Advisor: McShane, H
Fletcher, H
The impact of adjustment for covariates on meta-analysis of randomised intervention studies for binary outcome

Background
Covariate adjustment analysis is often used in epidemiological studies but is less common in randomised controlled trials (RCTs) and RCT meta-analyses. There is a lack of consensus on whether the analysis of RCT data should adjust for important baseline covariates. The estimated treatment effect of a binary covariate can differ when logistic regression is carried out, even when the covariate is balanced between treatment groups.
Objectives
The objectives of this study were to examine the factors that affect the impact of adjusted analysis in different RCT scenarios and to explore the impact of adjusted analysis in RCT meta-analysis.
Methods
Simulation and sampling studies were conducted to identify the factors that affect the impact of using an adjusted logistic regression model. Two covariates, one continuous and one binary, were considered simultaneously. The event rate, treatment effect, binary and continuous variable distributions, covariate prognostic strengths, and correlation between the covariates were varied during the simulations. The impact of adjustment on RCT meta-analysis was investigated using individual participant data obtained from the Perinatal Antiplatelet Review of International Studies. Different methods of performing unadjusted and adjusted meta-analysis were compared.
Results
The simulation results suggest that adjustment only has a notable effect in extreme scenarios, such as a very large treatment effect or highly prognostic covariates. The relative difference between the unadjusted and adjusted odds ratios was found to be larger than 50% under these extreme scenarios. Covariate adjustment is likely to have a small effect on meta-analyses with many studies.
Summary
Adjusted analysis should be carried out by design. Performing adjusted analysis in a meta-analysis can be challenging as sufficient information about the covariates is often not available.

Keywords: covariate adjustment
clinical trials
Adjusted analysis
meta-analysis
binary outcome
Advisor: Altman, D
An investigation into persistent transgene expression from plasmid vectors in the lung

Gene therapy for chronic lung diseases will require vectors capable of persistent transgene expression in the absence of inflammation but few promoters have been identified that can fulfil both of these requirements. The development of plasmids devoid of CG dinucleotides (CpGs) has resulted in markedly reduced levels of pro-inflammatory cytokines. Furthermore, a novel synthetic enhancer/promoter, termed hCEFI, has been shown to direct high levels of sustained transgene expression in the murine lung, following aerosol delivery of non-viral formulations. A CpG-free plasmid containing the hCEFI enhancer/promoter has been evaluated in clinical trials for cystic fibrosis lung gene therapy. The aim of this thesis was to investigate the reasons for successful persistent expression achieved with this plasmid. An understanding of these reasons is also useful for the development of new gene therapy treatments. Cell culture models did not recapitulate the transgene expression profiles obtained in vivo; therefore, a mouse aerosol model of lung gene transfer was utilised. New variants of the hC enhancer present in the hCEFI promoter were constructed and tested in vivo. Studies demonstrated that a minimal enhancer sequence, comprising the final 93 bp of the full-length 302 bp hC enhancer, was necessary and sufficient for mediating persistent and high levels of transgene activity in the mouse lung. Support for the inclusion of multiple copies of the minimal enhancer to increase transgene activity was also obtained. Observations in a mouse model for gene transfer to the liver showed that the minimal enhancer could not mediate transgene activity at the same level as the full-length hC enhancer, indicating that the minimal enhancer does not uniformly direct transgene activity but may be specific to the target organ. An analysis of predicted transcription factor binding sites was performed to support such tissue-specific differences. Overall, these studies demonstrate that only a very small portion of an enhancer is required to direct high-level activity in the lung. This has implications for the future design of both non-viral and viral vectors for use in gene therapy applications.

Advisor: Gill, D
Hyde, S
Submesoscale dynamics in the open ocean

The seasonal cycle of submesoscale flows in the upper ocean is investigated through a series of numerical simulations in an idealised model domain. Subme-soscale processes become stronger as the resolution is increased from 4 km to 0.5 km. There is a seasonal cycle in the magnitude of horizontal buoyancy gradients and horizontal wavenumber spectra consistent with stronger mixed layer insta-bilities developing as the mixed layer deepens and energising the submesoscale. Up to 30% of the mixed layer volume in winter has negative potential vorticity and this negative potential vorticity is found in both mesoscale vortices and filaments. Further investigation of the filaments that arise in anticyclonic eddies show that they are generated in regions of negative potential vorticity and lead to the upwelling of fluid from the thermocline. Symmetric instability is found to be the most likely mechanism. The role of flow curvature is considered and it is shown that the angular velocity of mesoscale eddies, as well as relative vorticity, contributes to their stability. A numerical tracer release experiment shows that the filament generation process leads to downwelling of surface layer flows and a simplified biogeochemical experiment shows that the instability gives rise to much higher primary productivity in mesoscale anticyclones. Observations of a mixed layer front observed in the North Atlantic are presented which has a more diffuse cross-front buoyancy gradient at the surface than lower in the mixed layer and a strong ageostrophic cross-front velocity. The observations are used to motivate two dimensional simulations of Rossby adjustment. These simulations show that as the frontal strength increases the Rossby adjustment phase accounts for an increasing proportion of the restratification. The simulations become much more turbulent over the parameter range for frontal strength. The vertical profile in the observations can be re-produced when the adjustment is simulated with a thermocline, though definitive conclusions are difficult to draw.

Keywords: Anticyclones
Submesoscale
Advisor: Marshall, D
Unleashing power: Pathways to inclusion and representation in U.S. AIDS activist organisations

The thesis proposes a theory for the development of substantive representation among social movement organisations (SMOs). Substantive representation (SR) is the extent to which political institutions advance the policy interests of their constituents, in particular the most disenfranchised. Despite their noble proclamations, institutions of representative democracy often fail to advance the interests of groups who have been ignored and absent at the proverbial table.
The thesis establishes a causal process to explain the divergence in SR outcomes among informal SMOs, or all-volunteer groups that disavow formal hierarchy in favour of egalitarian modes of decision-making. It utilises a case study of the AIDS Coalition to Unleash Power (ACT UP), an umbrella organisation dedicated to ending the HIV/AIDS crisis in the United States and worldwide. It explains an anomalous story of SR attainment through the ACT UP Philadelphia chapter, compared to sister groups in New York City and Boston. The analysis draws from 92 semi-structured interviews, 13 months of participant observation, periodical review, and archival databases.
ACT UP Philadelphia translated common SMO intentions of inclusivity into the uncommon rituals of practice. It forged a deliberate pipeline to invest not only in the presence but also the power of disenfranchised people with HIV, people too dark and poor to interest counterpart groups in other cities. Through an analytic retelling of ACT UP’s history, the thesis argues that the fulfilment of SR depends on the ability of SMOs to appeal to member self-interest. Critically, SMOs can offer material incentives and nurture feelings of debt and obligation: causal steps to recruitment and sustainability of a heterogeneous membership. In building a crucial if contentious core of dissimilar people and partnerships, SMOs can unleash an oft-unrealised power for collective action and SR, by and for disenfranchised peoples who had thought change to be impossible.

Keywords: Philadelphia
Direct democracy
Activism
The AIDS Coalition to Unleash Power
Advisor: King, D
Studies on the Bacterial Potassium efflux system Kef in Shewanella denitrificans SdKef

The glutathione-gated potassium efflux system (Kef) is a K+/H+ antiporter found in the majority of Gram negative pathogens, which shows potential as a novel antibiotic target. Kef plays a vital role in the protection of bacteria against toxic electrophiles through the regulation of cytoplasmic pH. Kef is inhibited by glutathione (GSH), ɣ L-glu-L-cys-gly, and activated by glutathione S-conjugates (GSX). Healy et al. have quantified the affinities of GSH and a range of GSX for Shewanella denitrificans Kef (SdKef). GSH was found to have a weak affinity of 900 μM, whereas the strongest GSX, t
BuSG, was 400 nM.
This dissertation looks to understand the potency shown by t
BuSG for SdKef by exploring the binding contributions from each group of the tripeptide. Truncated analogues of tBuSG were synthesised and evaluated using a competition fluorescence assay and 1H CPMG NMR. In summary, removal of the glycine unit caused a complete loss in affinity for SdKef, whereas removing the glutamate unit resulted in a negligible loss. Interactions made by the Glu-Cys amide carbonyl oxygen, the Cys-Gly amide NH and a directional interaction of the conjugated thiol were also found to be important contributors to affinity.
The information obtained during this work allowed the development of a membrane permeant, truncated analogue of t
BuSG, which lacks the majority of the glutamate, for use in in vivo studies. The truncated analogue is able to activate SdKef to elicit K+ efflux, demonstrating that the majority of the glutamate is not essential for activity. Furthermore, application of this truncated analogue to Escherichia coli cells expressing the sdkef gene in a Kirby Bauer disc diffusion assay has demonstrated for the first time that small molecules activating SdKef can elicit inhibition of growth / cell death. Kef thus shows promise as a target for the development of novel antibacterial agents.

Keywords: chemical probes
novel mechanism
ion channel
bacteria
glutathione
antibiotic
antiporter
glutathione S-conjugate
efflux
Kef
potassium
Advisor: Conway, S
Morris, G
Suffering and Christianity: conversion and ethical change among the Newars of Bhaktapur

This thesis argues that conversion to Christianity in the Nepali city of Bhaktapur is closely connected with ethical attitudes towards suffering in Bhaktapurian churches. This argument is situated within broader debates in the anthropology of Christianity. Anthropologists have debated the extent to which Christianity is a force for cultural discontinuity, and have often connected it with modernity and individualism. I contribute to these discussions by showing how distinctively Christian conceptions of suffering may promote cultural change by stimulating new understandings of selfhood and ethics. The first three chapters explore the social life of Bhaktapur’s Hindu majority. I describe how the last fifty years have seen a process of cultural unsettlement in Bhaktapur; one aspect of this unsettlement has been a disruption of traditional norms of care and deference. It is in this context that the distinctive ethics of Christianity have proved attractive to some. Those who convert have typically experienced a significant episode of suffering, and have felt themselves to be failed by those around them. They find in churches a framework that emphasises the moral significance of inner experience (I call this ‘inwardness’) and addresses affliction more in terms of ethics than ritual. I describe these ethics in terms of ‘care’: they stress presence with the afflicted person, engagement with their experience, and appeal to God in prayer. After two chapters describing Christianity in Nepal and Bhaktapur in general terms, I devote four chapters to examining different categories of Bhaktapurian Christians: those who have experienced healing, women, leaders, and youth. I focus on four conversion narratives, and relate these narratives both to other ethnographic materials and to broader trends in Bhaktapurian and global Christianity. I highlight the significance of the values of inwardness and care, and of narrative itself, in the life-worlds of Bhaktapurian Christians.

Keywords: ethics
Christianity
Multisite phosphorylation in T cell receptor proximal signalling

T cell receptor proximal signalling represents a specific instance of a multisite phosphorylation system. Receptor phosphorylation is regulated by the opposing actions of the kinase LCK, and phosphatases such as CD45 and CD148. Particular phosphoforms recruit the kinase ZAP-70, which once bound, propagates downstream signalling. In this thesis we investigate the functional consequences of multiple phosphorylation sites on the dose-response profiles of receptor phosphorylation. We combine mathematical modelling with cellular reconstitution to assess the effect of multiple modification sites on the potency and sensitivity of receptor phosphorylation. We find that multiple sites enhance the potency of receptor phosphorylation, but do not alter the sensitivity of dose-response profiles. This correlation between the number of sites and response potency is consistent with a mechanism whereby phosphorylation mediates an enhancement in the enzymatic efficiencies of modification.

Advisor: Dushek, O
van der Merwe, A
Maini, P