VictorJuiz/thesis huggingface dataset:
Alexander re-mapped: geography and identity in the Alexander Romance in Armenia 

This thesis examines the reception of legendary traditions of Alexander III of Macedon in a region peripheral to his historical empire: Armenia. Its interest is in the relationship between the edges of the world in the Alexander Romance, and Alexander’s place and identity in Armenian literature. The central question is: to what extent did writers in the Armenian language adopt, alter or subvert the image of Alexander and the geographical ideas expressed in the Alexander Romance?
It finds that the complexity of the Armenian response to Alexander is located particularly in a literary tradition of the medieval period: the composition of kafas (short monorhymed poems) to accompany the Alexander Romance narrative, starting in the late 13th, early 14th century by Xač‘atur Keč‘aṙec‘i and continued in the 16th century primarily by Grigoris Ałt‘amarc‘i and his pupil Zak‘aria Gnunec‘i.
This thesis first seeks precursors to the kafas’ contents in three genres of Armenian text relevant to Alexander: geography, history and apocalypse. Particular attention is paid to the use of Alexander as marker of geographical extremity, pursuing the ways that these texts presaged the kafas – and highlighting how often they did not. The second and larger section of the thesis turns to the kafas about Alexander’s encounters with remote regions and foreign kings as multifarious Armenian responses to the Alexander Romance. It translates and analyses their contents, as well as drawing lateral lines across text networks in and beyond the Armenian language that situate the kafas in the full breadth of their contexts. This thesis answers its central question: through these poetic interventions, Armenian traditors re-mapped the world of the Alexander Romance to suit a medieval Christian Armenian cosmological understanding.

Keywords: armenian poetry
Grigoris Ałt‘amarc‘i
armenian literature
alexander romance
Xač‘atur Keč‘aṙec‘i
Zak‘aria Gnunec‘i
Advisor: van Lint, TM
Language teachers' professional learning: in search of impact

There is a growing evidence base suggesting that the effectiveness of individual teachers is one of the most significant factors in predicting valued pupil outcomes. This has led to much debate about how in-service teachers might continue to develop and improve their practice.
This study takes a single subject area (Modern Foreign Languages - MFL) as the context in which to explore teachers’ Professional Learning (PL) needs, experiences and motivations from July 2016 to July 2018. During Year 1, data tracking the PL priorities, experiences, well-being and self-efficacy of 57 MFL teachers clustered in 14 state school languages departments were collected via four iterations of an online questionnaire. Year 8 Students of French in 13 of the 14 schools (n=1370) completed a student perception questionnaire to gauge their classroom experiences. Questionnaire data were followed up with in-depth, semi-structured interviews with Heads of Department in six of the schools. Two languages departments were subsequently identified as productive contexts for teacher PL and in-depth case-studies of these departments were conducted in Year 2.
Languages teachers expressed strong interest in accessing PL and they particularly identified the need to develop their preparedness to teach towards new examinations at GCSE and A Level. They also highlighted a need to develop students’ speaking skills and motivation. Over the course of the study, analysis shows very low levels of engagement in PL that shares characteristics with the effective PL practices identified by Cordingley et al. (2015). Very few teachers reported extended engagement in PL activities over the course of multiple sessions. Teachers’ access to PL experiences was shaped by a sharp focus on instrumental organisational aims related to the introduction of new examination specifications and curricula. Although no significant associations were found between teachers’ engagement in PL and pupils’ outcomes at GCSE, a strong correlation was noted between the size of the language department and pupils' value-added outcomes in language GCSEs. The possible underlying reasons for this pattern are discussed.
Some Heads of Department perceived the changing curriculum as an opportunity for development and innovation, whereas others conceptualised the changes as a threat to established ways of working and to colleagues’ wellbeing. Working conditions and the nature of relationships between colleagues within institutions shaped the conditions for PL, with accompanying impacts on individual teachers’ sense of self-efficacy, engagement and intention to remain in the profession. The findings of this study have implications for policy makers, school leaders and Heads of Department wishing to build better conditions for teacher learning.

Keywords: professional learning
Modern (foreign) languages
language teacher education
student perception survey
language teacher evaluation
second language acquisition
CPD
Advisor: Burn, K
Mutton, T
Investigating the function of a pentameric ligand-gated ion channel with molecular simulation

Pentameric ligand-gated ion channels (pLGICs) are key players in mediating fast neurotransmission. Upon neurotransmitter binding, they undergo conformational changes that lead to the opening of the channel pore, allowing ions to flow in or out of the cell. They are involved in a range of neurological diseases which makes them important drug targets. The glycine receptor (GlyR) is a chloride-selective member of this receptor family, which is an excellent model system, because structures in key functional states are available and it has been extensively characterized experimentally. This thesis therefore seeks to investigate the function of the GlyR as a representative of the pLGIC superfamily with molecular dynamics (MD) simulations with four focal points.
1. Recent work has questioned the physiological relevance of the open state structure of the GlyR, since it rapidly collapses in MD simulations. I show that the collapse can be avoided by a careful equilibration protocol that reconciles the more problematic regions of the original density map and gives a stable open state that shows frequent selective chloride permeation. The stability can be explained by the 90 leucine gate residues being locked into so far unreported hydrophobic pockets that are functionally conserved across pLGICs.
2. pLGICs are known to be sensitive to their lipid environment, yet it is still poorly understood how lipids modulate receptor function. By embedding this receptor in a realistic model of a neuronal membrane and performing coarse-grained molecular dynamics simulations, I find that the lipid environment as well as the lipid-protein interaction strength are dependent on the receptor state, suggesting that lipids play a crucial role in stabilizing either the active or inactive state. Cholesterol can bind to the binding site of the positive allosteric modulator ivermectin, indicating that intrinsic membrane lipids might have positive modulatory function.
3. A molecular level of understanding of partial agonism in pLGICs has remained elusive thus far. Using atomistic MD simulations, I characterize the binding modes and determine the binding free energies of the full agonist glycine and several partial agonists. All agonists stabilize loop C, which covers the binding site like a lid, in a closed conformation, but the interactions in the binding site are less optimal for partial agonists than for glycine.
4. The atomistic details of the gating mechanism of pLGICs are still not fully understood. Via a combination of targeted MD and Markov state modelling, I reconstruct the equilibrium distribution and underlying kinetics of the gating process. The analysis reveals that the closed-to-open transition involves an intermediate shut state.

Advisor: Biggin, P
In search of utopia in post-political Beirut: The pragmatic turn and the decline of radical imaginaries in activist Lebanon

Drawing on two years of ethnographic fieldwork in Beirut, Lebanon, this dissertation examines the turn towards a pragmatic and technocratic approach to politics in Lebanese civil society, in the aftermath of the ‘garbage protests’ that gripped the country in 2015. It situates this development within a global political conjuncture characterized by what other scholars have designated an anti-political, or post-political turn amongst activists in disparate contexts. Such activists are seen as focusing increasingly on uncontroversial questions of livability and wellbeing imagined to have the capacity to transcend binaries of Left and Right and, in so doing, instigate change.
This dissertation tells the story of a middle class urban social movement concentrated largely in Beirut, which drew on the technocratic expertise of its adherents to market an alternative vision for the city and wider country. The activists that made up this movement rejected the divisiveness of ‘ideology’ and the messiness of ‘politics’ proper in favor of what they put forward as a neutral discourse of the ‘right to the city’ – a non-contentious approach to socio- political agitation. In addition to making sense of the appeal of this approach to activism, I highlight its limitations.
My research unfolded in the aftermath of a political event that activists saw as charged with potential, yet quickly fizzled out, stranding them in a post-evental moment of ‘dead time’ heavy with the debilitating sense of having yet again failed to facilitate transformative change. I examined the ways in which activists in Lebanon attempted to work their way out of this impasse and towards new moments of rupture in an endeavor to create new processes of political subjectivation.
This dissertation charts ways in which activists in Lebanon attempted to challenge the hopelessness that was assumed to have enabled mass complicity with the status quo. It employs ethnographic methods to discern the ways in which activists in contemporary Lebanon made sense of and worked against what was designated as a prolonged period of ‘stuckedness’. It asks how the experience of routine failure within Lebanon’s post-civil war activist scene transformed contentious politics in the country, examining the decline of once popular radical political imaginaries, and the emergence, in their stead, of a pragmatic approach to politics. In exploring the limitations of this form of activism, I explore the effects that neoliberalism as a governing rationality has had on the political imagination, and on the ability of dissenters to think a more radical socio-political otherwise.

Keywords: Activism
Utopia
Protest
Lebanon
Technocracy
Political imagination
Pragmatism
Resistance
Social Movements
Anthropology
Neoliberalism
Advisor: Armbrust, W
Lexical opposition: an investigation into canonical and peripheral phenomena of antonymy

This thesis presents a multi-method approach to the investigation of lexical opposition, taking into account central as well as peripheral opposites. One of the distinguishing factors of the present research is the investigation of a wide variety of opposite pairs (e.g. converses) alongside the canonical gradable adjectival antonym pairs which have thus far been the focus of most of the research on lexical opposition. Three main questions concerning lexical opposition are addressed from a data-driven perspective. Firstly, the question of which factors determine the antonymic strength of a pair of opposites. Secondly, whether there is a clear distinction between good and bad opposites or whether the internal structure of the category of antonymy can be described in term of prototype theory. Lastly, whether antonymy is a relation between cognitive concepts (Murphy & Andrew 1993) or between the words which encode these concepts (Gross et al. 1989).
This study employs a wide range of methodologies: corpus analysis, judgement tasks, attribute listing and behavioural lexical decision tasks in English and German. This allows for the detection of discrepancies between the results of the separate investigations which provide the starting points for the analyses. The data shows that the existing criteria for ‘good’ opposites influence a pair’s antonymic strength to different degrees. All factors which have previously been put forward with the addition of those which are proposed in this thesis are integrated into a holistic approach based on the theory of cognitive concepts and cognitive models (Lakoff 1987).
The evidence shows strong support for antonymy as a prototype category with antonym pairs distributed along a continuum of antonym canonicity on which each pair’s place is determined by both its antonymic strength (which is influenced by a certain distribution of factors) and its associative strength. The contrastive data provides the strongest evidence for antonymy as a conceptual relation since opposite pairs in both languages exhibit very similar behaviour.

Keywords: Antonymy
English
(Cognitive) Semantics
Psycholinguistics
German
Advisor: Cram, D
Lahiri, A
Ideas about Social Rights: Changing Social Assistance in Britain and Ireland, 1985-2015

This thesis examines the significance of ideas of social rights in shaping social assistance policies for the unemployed and lone parents in Britain and Ireland over the period 1985-2015. Adopting a qualitative, comparative case study approach and based on a combination of elite interviews and primary and secondary data analysis, the study finds that different ideas about social rights account for substantive and otherwise unexplained social assistance policy variation across Britain and Ireland. A blended human rights-positive rights idea was consistently relevant to Irish social policy-making while varying ideas of positive rights and social citizenship rights were associated respectively with periods of Conservative and Labour Party governance in Britain. The thesis shows that cultural legacies and political ideologies were significant in determining the ideas of rights that became salient in each country context, suggesting important three-way interactions between ideas, interests and institutions and lending support to theoretical arguments about the ‘mutual constitution’ both of ideas and interests, and of interests and institutions.

Keywords: ideas and public policy
Britain
social rights
social assistance
Ireland
Advisor: Seeleib-Kaiser, M
White, S
Ebbinghaus, B
Pathogen evolution and spread in the face of host genetic diversity

Despite the strong forces of genetic drift and directional selection, virtually all natural populations are genetically diverse. Declining within-host population diversity is nevertheless a growing problem, with homogenous populations (known as ‘monocultures’) predicted to suffer the most from pathogen (and/or parasite, herein used interchangeably where the same principles apply to both) infection given the increasing likelihood of uniform susceptibility. The literature has shown conclusively that genetically diverse populations stand a better chance of limiting infection by natural pathogens (otherwise known as the monoculture effect) or pathogens for which genetic variation for resistance exists in the host population. However, the impacts of within- and between-host population genetic relatedness in the face of novel pathogens has not been tested. In this thesis, I combined meta-analytic and experimental evolution approaches to explore the impacts of host population genetic diversity on pathogen spread and evolution. Firstly, I gathered data from a wide range of host-pathogen interactions to test the effects of two levels of host within-population diversity (low and high) on parasite success in a formal meta-analysis. Among other findings, this study revealed broad-spectrum support for the observation that low diversity increases the chance of parasite success across systems. Secondly, I used experimental evolution and follow-on genomics analysis to track the evolutionary dynamics of Staphylococcus aureus as a novel infection in an array of natural, susceptible Caenorhabditis elegans isolates. I found that the pathogen evolved similar virulence in closely-related hosts, with infection load evolving along an independent trajectory. I also found that S. aureus performs better (i.e., more virulent and higher infection loads) in a diverse population of distantly-related hosts compared to a population of closely-related hosts. Thirdly, I investigated whether S. aureus maintained its generalist infection ability throughout evolution in the novel C. elegans populations. I discovered that despite evolving in monocultures of particular host isolates, evolved S. aureus was able to infect sympatric and novel hosts equally. Moreover, pathogen performance between these host types was not negatively related to the genetic distance between them. As a whole, this body of work confirms that the host genetic diversity shapes the ecology and evolution of natural and novel pathogens across the tree of life. It additionally extends on knowledge of the monoculture effect to the wider concern of novel infections, and thereby improves our understanding of how host population genetic composition might be used to control the spread and evolution of new emerging infectious diseases.

Keywords: Host diversity
Novel infection
Pathogen evolution
Monoculture effect
Meta-analysis
Advisor: King, K
Confidence in protein interaction networks

Protein interaction networks are a commonly used tool in bioinformatics, e.g. for the purposes of gene function prediction or drug target identification. They are built from often heterogeneous and error-prone protein-protein interaction data. In this thesis we study the effects of data uncertainty on the structure of protein interaction networks and on downstream network analysis.
Some databases provide confidence scores for protein-protein interactions, and networks are built from the data after a minimum score cut-off, or threshold, is applied. We study the effects of threshold choice on network structure. We argue that robust, biologically-relevant network analysis results should be replicated across networks obtained at different thresholds, and develop a methodology for quantifying this robustness in the context of node metrics. Our results indicate that the same node metrics are robust across a range of protein interaction networks, but are not necessarily robust in synthetic networks.
We further investigate uncertain networks as a possible approach to incorporating confidence scores explicitly into network analysis. Uncertain networks are a way of conceptualising the difference between the "true" network of biologically-relevant protein-protein interactions and the observed scored data. We show that any inference on the structure of the "true" network is strongly influenced by assumptions made about the dependence - or lack thereof - between edges in the scored network.
Finally, we focus on networks constructed from gene co-expression data. Gene co-expression can be measured in a number of different ways. Moreover, when networks are constructed, different thresholds can be applied to the co-expression values. It is not always clear which network construction method should be preferred. We develop a software package, COGENT, designed to aid network construction choice without the need for external validation data.

Keywords: protein interaction networks
protein interactions
network analysis
Advisor: Deane, C
Reinert, G
Identification and analysis of novel regulators of cell radiosensitivity

Radiotherapy plays an important role in the curative management of cancer. Despite technical developments in treatment delivery, it is still associated with potentially severe side effects due to damage caused to normal tissues surrounding the tumour. Targeting tumour specific determinants of radiosensitivity has the potential to improve the therapeutic index. The identification of novel determinants of tumour intrinsic radiosensitivity is therefore a key-step to develop innovative therapies.
In this study, two high-throughput radiosensitivity screens using different functional genomics approaches are presented. The first one, an arrayed RNAi-based radiosensitivity screen, was used to investigate a subset of about 10,000 ‘druggable’ genes in order to identify novel potential clinical targets. The second one, a pooled loss-of-function CRISPR radiosensitivity screen, made use of a genome-scale approach and therefore interrogated over 20,000 genes in the context of radiation response.
Interestingly, TRIM37 was identified from both screens as a novel gene whose depletion causes radiation sensitivity. TRIM37 (tripartite motif containing 37) is an E3 ubiquitin ligase belonging to the TRIM family proteins. TRIM37 germline mutations are associated with a rare autosomal recessive disorder known as MULIBREY nanism. Some of the clinical features are growth failure, infertility and higher incidence of cancer. TRIM37 has a known oncogenic function in somatic cells and it is overexpressed in a subset of tumours, where high expression of TRIM37 is correlated with lower survival rates. The depletion of TRIM37 as a modulator of radiosensitivity was validated in a wide panel of cancer cell lines. Also, the mechanism underlying TRIM37’s role in the response to ionising radiation was investigated. As for the pleiotropic nature of E3 ubiquitin ligases, it was found that TRIM37 depletion impacts on different aspects of ionising radiation response, but mainly, on cell cycle regulation. The exact mechanism by which TRIM37 depletion modifies cellular response to radiation is yet to be identified. However, this study shows that cells lacking TRIM37 expression have increased genomic instability independently from radiation treatment, providing evidences in agreement with MULIBREY disease phenotype. Evidences of genomic instability were amplified in presence of IR-induced DNA damage.
Taken together with the observed overexpression of TRIM37 in cancer cells, our findings suggest that TRIM37 is a potential target to modulate tumour radiosensitivity.

Advisor: Higgins, G
McKenna, G
Rodriguez Berriguete, G