VictorJuiz/thesis huggingface dataset:
Adaptive immune evasion in clinically latent HIV infection
Keywords: Immune evasion
HIV
AIDS
Evolution

HIV is a master of immune evasion, utilising a range of different techniques to not only survive the human immune system, but also mediate its eventual catastrophic decline. Understanding how HIV evades the adaptive immune response is paramount to developing effective treatments and vaccines. This thesis aimed to investigate three key ways in which HIV-1 and HIV-2 mediate immune evasion in the context of clinically latent infection. Chapter three summarises a study into selection pressure and mutation in the gp120 envelope gene in a narrow-source HIV-1 cohort of former plasma donors (FPDs) from China. This study further characterised the cohort, and identified specific mutations in the gene consistent with antibody and CTL-driven selection pressure. Chapter four describes an investigation into the downregulation of HLA-I mediated by primary isolates of HIV-1 and HIV-2 Nef. Nef-mediated HLA-I downregulation contributes to the evasion of CTL responses. In stark contrast to previous reports, no evidence for differential downregulation of HLA-A and HLA-B was detected, but primary isolates invariably showed reduced activity relative to laboratory-adapted and consensus variants. In performing this study, a number of limitations came to light regarding how bifurcate analyses are used to interpret flow cytometric data collected in studies of receptor modulation. A novel technique - SWARM - was therefore developed to address these limitations, and is described in chapter five. Chapter six aimed to address why CTL responses against HIV-2 Nef are rare, despite HIV-1 Nef being highly immunogenic. A series of in vitro (immuno)proteasomal processing assays revealed HIV-2 Nef is more extensively digested than HIV-1 Nef, but further experimentation is required to explain the difference in response. Finally, chapter seven briefly summarises a successful collaborative attempt to resolve the first ever crystal structure of HIV-2 Nef.
Towards a structural model of adherent knobs on the surface of Plasmodium falciparum infected erythrocytes
Keywords: pfemp1
Malaria
structural biology

The Plasmodium falciparum proteome is enriched in intrinsically disordered proteins, three of which are directly linked to malaria severity; P. falciparum Erythrocyte Membrane Protein 1 (Pf EMP1), Knob-associated Histidine-rich Protein (KAHRP) and Plasmodium He- lical Interdispersed Sub-telomeric family member (PHIST) PFE1605w. Pf EMP1, KAHRP and PFE1605w all localised to protrusions (knobs) on the P. falciparum-infected erythrocyte surface, which enable pathogenic cytoadherence of infected erythrocytes to uninfected erythrocytes and endothelial cells. In this thesis, I have employed a combination of biophysical and computational methods to characterize the interactions of Pf EMP1 and KAHRP with host erythrocyte spectrin, and of Pf EMP1 with two PHIST family proteins, PFI1780w and PFE1605w. These interactions are likely to assist knob formation and, thus, promote cytoadherence. I derived atomistic structural models of complexes formed between the PHIST domain of PFI1780w and the disordered C-terminal region of the cytosolic domain of Pf EMP1, of the folded core of the Pf EMP1 cytosolic domain and domain 17 of the host erythrocyte α spectrin, and between the KAHRP 5' sequence repeat and domains 10-14 of β spectrin. Combining these structural models with previous electron microscopy information allows us to propose a detailed model as to how knobs form and how Pf EMP1, KAHRP, PFE1605w, and other possible factors could locate therein.
The volatile history of past volcanic eruptions
Keywords: Petrology
Mineralogy
Geochemistry
Volcanology

Volatile elements play an important role in almost every aspect of sub-volcanic systems, from the generation and storage of magma, to the timing and style of volcanic activity. Currently, the most common method for assessing pre-eruptive magmatic volatile contents is through analysis of trapped melt inclusions. However, the reliability of this record is uncertain, necessitating development of new, independent petrologic methods for determining the pre-eruptive volatile contents of past eruptions. This thesis combines physical and chemical models with empirical analyses to develop the use of apatite as a magmatic volatile 'probe'.
The first research chapter investigates well-documented difficulties in electron microprobe analysis of apatite volatile concentrations. These are found to be caused by electron-beam induced heating and electric field generation. In determining these effects, it is possible to identify optimal operating procedures for apatite analysis. The next chapter explores the theoretical evolution of apatite volatile compositions as a function of magmatic evolution, building on previous work to develop thermodynamic models that relate crystal compositions to fluid systematics during fractional crystallisation. These provide a qualitative framework for interpreting apatite compositions in natural volcanic systems.
The remainder of the thesis is dedicated to identifying new insights that can be gained from the use of apatite as a magmatic volatile 'probe'; this method is applied to constrain pre-eruptive processes at Campi Flegrei, Italy. Texturally-constrained apatite analyses are used to create a time-series of magmatic volatile evolution in the build-up to eruption. This reveals that volatile saturation occurred late in magmatic evolution, and represents a potential eruption trigger. Apatites from different eruptions show a long-term temporal variability in the H2O contents of primitive melts feeding Campi Flegrei, which correlates with different epochs of activity. Melt inclusions from all eruptions have reequilibrated post-entrapment. This study demonstrates the potential utility of apatite for investigating pre-eruptive volatile behaviour in apatite-saturated magmas.
Using student views to develop a formative assessment policy in a sixth-form History department
Keywords: MLT
MLT2016
History
Formative Assessment

This project sought to explore the views of sixth-form history students concerning the efficacy of their department’s formative assessment policy, and builds on my part 2 research into student views of self and peer marking. The project first consisted of a literature review in order to provide the grounding needed to adapt the department’s current assessment policy. This policy was then implemented by all staff in the department at the start of the academic year. Questionnaires and group interviews were carried out to explore how the students responded to this policy, with the intention that their responses would then be mediated by staff to produce an adapted policy for the start of the next academic year.
One of the key findings of this project was that despite increased student confidence in self assessment, students still reported considerable reliance on the teacher. Among other conclusions drawn, it will ultimately be suggested that to further shift the balance of power in assessment away from the teacher, students need greater ownership not only over the assessment of their work, but also the assessment policy itself. Therefore, although the original aim of the project was for the staff to redraft the department’s assessment policy based on student views, instead the outcome developed into a decision to give students a role in regularly revising the policy, encouraging a more organic and embedded approach.
Although this approach to policy-making in general is far from novel, it is rarely applied specifically to formative assessment, where educationalists tend to empower students within the narrow boundaries of teacher-determined assessment activities. It is still often the teacher ultimately who ‘owns’ and ‘provides’ formative assessment activities, with students required only to play their ascribed role. Therefore, this approach contrasts considerably with some of the contemporary literature that sees formative assessment as a concern of teacher pedagogy rather than student ownership.
A bridge too far? Volunteering, voluntary associations, and social cohesion
Keywords: Civil society
Labour market
Segregation
Social capital
Integration
Volunteering

In this thesis, I seek to advance our knowledge about the factors that make people start and stop volunteer work, thus shedding light on the capacity of volunteering and voluntary associations to foster social cohesion. In particular, my goal is twofold: first, to reveal to what extent voluntary associations function as meeting places for people from different social backgrounds, and second, to assess the resilience of civic participation in the face of labor market experiences that might undermine such engagement.
I make three core contributions to the literature on voluntary association involvement. First, I pay special attention to the organizational contexts in which volunteers are embedded. Second, I adopt a dynamic approach, analyzing decisions to start and stop volunteering. Third, I attempt to disentangle alternative mechanisms that could drive the associations observed between volunteering and its potential determinants. Analyzing data from The Netherlands and the United States, my findings expose limits to the integrative capacity of voluntary association involvement.
As it turns out, the civic landscape is strongly segregated. People tend to sort into voluntary associations where they mostly meet people with similar characteristics as themselves. Such sorting occurs along multiple social dimensions, including educational attainment, religiosity, gender, and ethnicity. This constrains the opportunities for building relationships that cut across existing social boundaries. Indeed, these sorting processes can reproduce in the civic domain fault lines that dominate other spheres of life.
Furthermore, civic engagement and participation in the labor market are shown to be strongly intertwined, with the former breaking down when labor force exits occur. Voluntary association involvement is, therefore, of limited value for drawing labor force outsiders into public life. However, this chain of events does not necessarily unfold, as long as labor force outsiders retain aspirations to participate in social life.
Digital era local government in England
Keywords: Big data
Web crawling
Webometrics
Network analysis
Digital Era Governance
Local government
Methodology
Internet
e-government

Local governments have been developing online services, aiming to better serve the public and reduce administrative costs. However, the impact of this work, and the links between governments' online and offline activities, remain uncertain.
Using a new full-population dataset of the UK government web, this thesis directly analyses the structure and content of government online. It argues that recent digital-centric public administration theories, typified by the Digital Era Governance quasi-paradigm, are not empirically supported by the UK local government experience. Instead, it argues for a positive but critical attitude to the value of technology in public administration.
New methods are developed for full-text empirical analysis of government web crawl data and the use of machine learning approaches for adding attributes to full-population data. Webometric and content analyses of the .gov.uk web are conducted, together with a time-series panel regression of English local government cost, service quality, satisfaction, and an expert assessment of web provision.
English local government online is highly heterogeneous and there is remarkably little intrinsic structure to the .gov.uk web. Geography is weakly visible in online government structures, but there is little evidence that online structures closely reflect the offline activities of government.
Empirically, English local governments' web development levels are found not to be associated with improvement in the cost of, quality of, or satisfaction with council services, challenging the merit of online approaches to service improvement.
Overall, the importance of digital-centric approaches to local government service improvement is challenged. A more nuanced theoretical approach to online service delivery is advocated, which discards utopian enthusiasm and focuses on concrete service improvements.
It is recommended that full-population quantitative analyses be used more broadly in political science, with awareness of both the opportunities and the challenges associated with them.
Exploring the testing 'effect' to enable knowledge retention and deployment in the Key Stage 3 History classroom
Keywords: MLT
MLT2016
Key Stage 3
History

This project aims to explore two interrelated issues. First, it seeks to probe recent interest in with research from experimental cognitive psychology regarding the use of low-stakes tests as a learning and memory tool rather than a summative assessment instrument. The idea that frequent testing of key dates, names and information as a way to improve student learning, produce superior performance in examinations and overcome social and economic deprivation has been seen as an exciting opportunity within the history and wider education community in England. By transplanting the basic methodology and placing it into the real world context of a school classroom rather than the tightly controlled laboratory space, it seeks to analyse the performance of students over a term in comparison with a class not subjected to frequent low-stakes testing. Qualitative data in the form of written work and semi-structured interviews are used to probe student conceptions of tests as learning tools.
The second related aspect the project aims to explore is the interest in the teaching of 'knowledge' and increasing the capacity of student memory which has fuelled the desire to explore cognitive psychology as a vehicle to liberate students from limited historical understanding and poor academic performance which leads to poor life chances.
Promoting collaboration to enhance learning in modern foreign languages
Keywords: MLT
MLT2016
Modern Foreign Languages

This paper details school-based research conducted to gather pupil views on group work and promote collaboration to enhance learning in French lessons at a British junior school. A dual-phase intervention centred on a sample of 74 pupils in Year 5 and saw the collaborative design, implementation and evaluation, by four teachers, of tasks drawing on the cooperative learning principles of positive interdependence, individual accountability, social skills, group processing and promotive interaction. Questionnaires were employed to gather views at different stages of the enquiry, allowing for quantitative analysis; data was also gathered via qualitative techniques such as lesson observations and semi-structured interviews. A majority of pupils claimed to enjoy working together, learning from others and helping one another, with many citing teamwork as a key facilitator to effective collaboration and warning of the negative implications of arguing, bossiness and disruption. The role of the teacher was considered key to the efficacy of group work, with proficient task design and efficient classroom management seen as especially important. Overall, cooperative learning strategies were deemed effective in enhancing the quality of group work in French lessons, this judgment being based primarily on the observations and experiences of the pupils and teachers involved. The key findings from this study have been collated to form a set of guidelines, intended as a point of reference in the future planning and execution of group work in this setting.
The purpose of perichōrēsis in the polemical works of John of Damascus
Keywords: Interdisciplinary
Damascus
Byzantine Theology
Christological Controversy
Jerusalem
Sectarian
Umayyad

John of Damascus was an early eighth century theologian in the Jerusalem Patriarchate. His family supplied financial administrators in Syro-Palestine for most of the seventh century, who were involved in surrendering Damascus to the Arabs if not also to the Persians. They thrived in the sectarian environment under the Umayyads. Numerous Greek Lives paint John in legendary terms; however, these are late and unreliable. I deconstruct the Lives decoupling his timeline from Byzantine Iconoclasm, arguing that there is no evidence and good reason to think that he did not leave the Arab administration because of vexed piety, persecution or administrative language change. Rather, focusing on the chronicler's treatment of John's family, I argue that John left office for his own reasons. I propose that John was instrumental in a quid pro quo: cathedral for patriarchate negotiation. Consequently, the Arabs built the Damascus Mosque on the site of the cathedral church of St John the Baptist, and the (dyothelite) Chalcedonian party moved to Jerusalem, where they reestablished the Jerusalem Patriarchate. Thus, I argue the context of John’s polemical works is Jerusalem and patriarchal policy. Further, I argue that John was commissioned to produce something like 'proto-school' texts in the context of debate in the Anastasis with internal Maronite and external West and East Syrian interlocutors. Then I look at one example of John’s theological creativity to show how this context impinged on his theological program. John appropriates Maximus the Confessor's term perichōrēsis and reduces its scope to the Incarnation while moving it into the doctrine of God for the first time. I show that he does this for polemical reasons in order to contravene each of his interlocutors with a simple biblical rhetorical model providing Chalcedonian monks in debate with a simple formula against better educated foes. This thesis demonstrates that reading John out of context fails to appreciate his creative response to these local exigencies.
Coordination in crisis: the practice of medical humanitarian emergency
Keywords: famine
Médecins Sans Frontières
humanitarianism
medical anthropology
nutrititional
emergency
epistemology of
South Sudan

This thesis in anthropology investigates how emergency is socially constituted as a named and actionable entity. Specifically, it asks how human values and techno-scientific practices contribute to the constitution of emergency in the context of medical humanitarian intervention. The study considers emergency from an ethnographic perspective, as a group of international medical humanitarian practitioners from the aid group Médecins San Frontières (MSF) come to understand and respond to the 2013 outbreak of armed conflict in South Sudan and the potential for mass starvation among certain groups within that country. Through the method of participant observation, it examines how emergency is understood or constituted at three different conceptual levels: at the level of the individual clinical encounter, the level of population statistics, and the level of political representations of crisis. By extension, it inquires as to how professional formation and moral categories determine appropriate response. The study reveals how values, ethics and conceptions of "the good" are embodied in—yet imperfectly translated through—numerical measures and institutional structures. This reveals a key paradox of medical humanitarianism: that rational, technocratic institutions simultaneously enable and debilitate the goals and means of humanitarian action. This study is based on 11 months of fieldwork (Oct 2013-Sept 2014) with the Amsterdam operational section of MSF. The fieldwork was multi-sited; it included participant observation of MSF activities in Amsterdam (The Netherlands), Juba, Leer and Bentiu (South Sudan).
Comparative study of archaeological contexts of silver hoards c. 800-1050 in Northern and Central Europe
Keywords: trade
silver
Pomerania
Baltic Zone
archaeology
Gotland
emporia
hoards
hoarding
Svealand
Viking Age
dirhams

The dissertation deals with the archaeological context of Baltic-zone silver hoards deposited in the Viking Age. Its main objective is to investigate the hoards and the context of their deposition to determine how hundreds of thousands of silver artefacts, mainly Oriental dirhams, arrived in Northern Europe, why they were put in the ground and never retrieved.
The review of the published sources on hoards was undertaken in three case studies: Gotland, Pomerania and Svealand. The data on hoards, archaeological sites, geology and topography was collected in geodatabases, and analysed in detail by applying descriptive and advanced statistical methods: regression modelling and GIS-based spatial analysis. The results were presented in the historical context depicted in contemporary literary sources.
Hoard deposition was most pronounced near sites which afforded conditions suitable for mercantile exchange and facilitated the flow of silver: the network of emporia, regional trade hubs, local power centres, and harbours, generally situated near major communication routes and within populated areas. However, exchange networks needn’t have been strictly hierarchical, and emporium-scale sites were not indispensable for a fair share of silver influx, and trade, to occur. Chronological changes in hoard distributions, their composition and fragmentation of objects indicate how these networks operated and meshed with economic and political conditions in c. 900 and c. 980.
A method, which uses the information about the presence/absence of a container, crossreferenced with the weight of silver, was devised to provide an indication as to whether particular hoards were deposited with the aim of retrieval – as savings accessed periodically, or for protection in the face of danger – or whether they were meant to be permanent ritual or symbolic offerings. Ritual behaviour took a variety of forms, but the most widespread were the depositions in recently occupied land in marginal soils, where they were aimed at forging a personal bond between the land and the owner.
French imports: English translations of Molière, 1663-1732
Keywords: Molière
Translation

This thesis explores the first English translations of Molière's works published between 1663 and 1732 by writers that include John Dryden, Edward Ravenscroft, Aphra Behn, and Henry Fielding. It challenges the idea that the translators straightforwardly plagiarized the French plays and instead argues that their work demonstrates engagement with the dramatic impact and satirical drive of the source texts. It asks how far the process of anglicization required careful examination of the plays' initial French national context.

The first part of the thesis presents three fundamental angles of interrogation addressing how the translators dealt with the form of the dramatic works according to theoretical and practical principles. It considers translators' responses to conventions of plot formation, translation methods, and prosody. The chapters are underpinned by comparative assessments of contextual theoretical writings in French and English in order to examine the plays in the light of the evolving theatrical tastes and literary practices occasioned by cross-Channel communication.

The second part takes an alternative approach to assessing the earliest translations of Molière. Its four chapters are based on close analysis of culturally significant lexical terms which evoke comically contentious social themes. This enquiry charts the changes in translation-choices over the decades covered by the thesis corpus. The themes addressed, however, were relevant throughout the period in both France and England: marital discord caused by anxieties surrounding cuckoldry and gallantry, the problems of zealous religious ostentation, the dubious professional standing of medical practitioners, and bourgeois social pretension. This part assesses how the key terms in translation were chosen to resonate within the new semantic fields in English, a target language which was coming into close contact with new French terms.