VictorJuiz/thesis huggingface dataset:
Language teacher motivation in Slovakia: a case study of Slovak teachers of English

This research study investigated the changing language teacher motivation of nine Slovak English as a foreign language (EFL) teachers at a private, bilingual university preparation school in Bratislava, Slovakia. The aim of the research was to better understand why these teachers chose to teach and what factors in their work motivated or demotivated them over the course of the 2021-2022 school year.
For this research, a qualitative, longitudinal design was used to examine the nine participants in a multiple case study. The participants were asked to fill in journal entries regarding their motivation at the beginning of each month from October 2021 to June 2022. Semi-structured interviews were conducted with them in October, March, and June of that school year to add more details to the data from the journals. Thematic analysis and magnitude coding were then used to examine their changes in motivation, what factors affected their motivation, why they chose to become teachers, and why they are still in the profession.
The findings of this research are that all nine teacher participants experienced varying levels of motivation throughout the year, though there was a noticeable difference between their levels at the beginning of the school year compared to the end. The principal factors affecting their motivation included their age and teaching experience, student interest in the classes, and interaction with students. The effect of vision (Dörnyei & Kubanyiova, 2014) on these teachers' motivation is assessed in this work, in particular in two of the highlighted case studies.

Keywords: semi-structured interviews
language teacher motivation
multiple case studies
journals
Advisor: McKinley, J
Thomas, N
Visitation returns and nineteenth-century Anglicanism in Oxford and its surrounding parishes

This thesis examines 528 nineteenth-century visitation returns from Oxford and its surrounding parishes. In chapter one it is established that Oxfordshire’s unusually high survival rate of these documents makes it possible, with the development of a relational database, to examine data longitudinally over an entire century. A core aim of the thesis is to establish if doing so yields significant insight. Chapter two considers the visitation itself, and how it was reformed over the century to ensure its usefulness. Chapter three is a prosopographical study of the 467 clergy listed in the returns, and identifies the mid-century as an important pivot point in discussing parochial Anglican activity. A reinvigoration — perhaps a revival of sorts — is identified over the second half of the century and University reform is found to be a crucial factor. Chapter four examines two key issues raised in the returns: inadequate room for church services and meetings, and competition from protestant nonconformity and Roman Catholicism. Despite being a significant drain on time and resources much church building took place over the century. A key reason that justified this was the building’s potential to convey a religious message of spiritual authority and value, but the ministers also made great use of lower-status structures for mission rooms and halls. At Oxford dissent and Roman Catholicism struggled during this time. Chapter five measures seating capacity, communicants, and service attendees. The figures that are calculated corroborate chapters three and four by identifying significant increases, with communion participation and church attendance rising faster as a percentage than population growth. The overall conclusion is that by the end of the nineteenth century the Church remained a substantial influence on life in the parishes of this review, more so than in the first half of the century.

Keywords: Oxford movement
Nineteenth-century church communion
Nineteenth-century church attendance
Nineteenth-century Anglicanism
Visitation returns
Nineteenth-century history of  the city of Oxford and the University of Oxford
Nineteenth-century church / religious architecture
Parochial system
English local history
Advisor: Smith, M
The ECJ’s precedents as means of EU integration: National courts’ treatment of European case-law under scrutiny

This thesis investigates how national judges treat the case-law of the European Court of Justice in their run-of-the-mill adjudication outside preliminary reference mechanism. It shows that the ECJ formally instructs all national judges to follow its previous rulings and as a result, the Luxembourg’s jurisprudence theoretically enjoys precedential force in the wider sense. Nevertheless, it is argued that in reality, there is a great variety of patterns in how national judges apply and engage with the Court’s previous case-law. In order to examine those patterns, the study surpasses traditional indicators of compliance and instead embraces a broader concept of judicial treatment of previous case-law. Consequently, a three-level methodological framework for empirical analysis of the domestic referring practices consisting of a mix of quantitative and qualitative approaches is introduced. It is argued that combining automated text analysis with more traditional legal research methods offers a rather holistic approach which could contribute to the reconstruction of a more realistic and systematic picture of EU judicial choice-making. That framework is then applied to the pilot study of the Czech Supreme Administrative Court.

Keywords: empirical research
mixed methods
CJEU
ECJ
national courts
automated text analysis
EU integration
Court of Justice of the European Union
EU judicial system
precedents
national judges
systematic content analysis
Advisor: Bogojević, S
Improving our mechanistic understanding of cell cycle dynamics

The mammalian cell cycle is regulated by a well-studied but complex biochemical reaction system. Computational models provide a particularly systematic and systemic description of the mechanisms governing mammalian cell cycle control. They facilitate a detailed understanding of cell cycle control mechanisms and are in part also able to aggregate this knowledge into full cell cycle models that explain periodic cell cycle oscillations. This dissertation aims at improving on these models along four dimensions: model structure, validation data, validation methodology and model reusability.
Presented is a core model structure of the full cell cycle that qualitatively explains the behaviour of unperturbed and perturbed cells. Using rule-based model descriptions, the core model was conveniently extended by a DNA damage checkpoint and a separation in a nuclear and cytoplasmic compartment. The dissertation conceptualises a methodology for generating highly informative validation data, including cell cycle perturbation with CRISPR interference. More specifically, time courses of 292 features as measured by indirect immunofluorescence imaging experiments are reconstructed from single cell snapshot data using the reCAT algorithm. This data and the cell cycle model are then cast into the PEtab format for specifying parameter estimation problems in biochemical reaction networks. By combining a powerful hybrid global-local optimiser with hierarchical optimisation of parameters, a cell cycle model that explains the validation data is presented. The PEtab specification allows any modeler to reuse the model, the data and/or the optimisation results.
Further experimental conditions, for instance in form of CRISPR interference, are expected to significantly improve parameter identifiability and provide a way for testing the predictive power of the model. Given the central role of the cell cycle in health and disease, such a predictive model may aid in the discovery of new therapeutic targets.

Keywords: cell cycle
BioNetGen
immunofluorescence
differential equations
inverse problem
scatter search
systems biology
PEtab
Advisor: Novak, B
Retrospection and re-orientation in Dante's Ante-Purgatory

This thesis investigates Dante’s use of retrospection in Ante-Purgatory or, more specifically, of intratextual eches of Inferno in Purgatorio I-IX. Building upon earlier work on intratextuality in the poem, the thesis highlights and discusses vertical echoes between cantos of the same number, diegetic, and episode-related parallels, as well as other forms of repetition, including recalls of specific lexical fields, syntagms, and rhyme patterns. In so doing, the thesis aims, firsltly, to demonstrate that Ante-Purgatory constitutes a privileged space for retrospective reading, and secondly, to broaden the manner in which we conceive of intratextuality within the Commedia. This is achieved through considering the ways in which Dante develops a programme of recalls across the Ante-Purgatory cantos to the beginning of Inferno, to Limbo, and to the encounter with Ulysses, and by considering several less-established modes of retrospection, including thematic parallels, similarities in the presentation of certain figures, and landscape echoes. In Chapter 1, I consider how retrospection in Purgatorio I and II contributes to the re-orientation of the reader at the beginning of the new cantica. In Chapter 2, I explore the thorny and problematic issue of Virgil’s damnation which, I argue, is developed especially in cantos III-VI through recalls to Inferno IV. In Chapter 3, I explore the value of landscape reading and how the poet makes important recalls to infernal landscapes and modes of travel through Hell. Overall, we see that in the liminal and transitional zone that is Ante-Purgatory, the preoccupation with retrospection interrogates and problematizes the division between the damned and the saved in the passage from Hell to Purgatory. Though retrospective elements are of course present throughout the Commedia, I argue that Ante-Purgatory is a particularly privileged space for retrospection precisely because of its liminal textual and geographic position.

Keywords: Ante-Purgatory
intratextuality
formula
Dante
liminality
liminal
repetition
Advisor: Gilson, S
Southerden, F
Development of novel nuclease inhibitors as potential anticancer agents

SNM1A and SNM1B are 5' to 3' exonucleases that are involved in the repair of DNA interstrand crosslinks (ICLs); the endonuclease SNM1C is involved in the repair of DNA double strand breaks via non-homologous end-joining. Cells depleted in SNM1A and SNM1B show increased sensitivity toward clinically used ICL inducing drugs, such as cisplatin or mitomycin C and those cells depleted in SNM1C display increased sensitivity towards ionising radiation. Inhibitors of SNM1A, SNM1B, and SNM1C could potentiate the effects of these commonly used cancer drugs or prevent the development of resistance to them.
A high-throughput screen was carried out to identify SNM1 hits for use as a foundation for the development of new inhibitors. Building on these hits, sets of structural analogues were synthesised to investigate structure-activity relationships (SAR). The developed compounds were initially tested using a fluorescence-based assay, with activity for apparent inhibitors being validated by radioactive gel-based assays.
The hydroxamic acid group was identified as a pharmacophore targeting the active site of SNM1 nucleases. Initial sets of hydroxamate-based compounds inhibited all three SNM1 nucleases, demonstrating no selectivity. By application of iterative rounds of SAR analysis informed by crystallographic data, improved hydroxamate-based inhibitors were developed. The work culminated in a series of compounds that selectively inhibits SNM1B with IC50s in the low nanomolar range. Although potent inhibition was observed against purified, recombinant SNM1B, achieving a similar result in human cell lines was more challenging despite the use of a prodrug strategy.
Overall, the work reveals that potent and selective inhibition of human SNM1 nuclease isoforms is viable. Future work can focus on optimising the cellular potency of SNM1 inhibitors.

Keywords: DNA repair
nuclease
Advisor: Schofield, C
Temporal prediction and the mammalian auditory system

Neurons in the sensory systems are tuned to diverse but specific features of the sensory environment. Various hypotheses have been proposed to explain how this particular tuning may be the result of optimisation to statistical regularities of natural sensory stimuli under a given principle, such as efficient coding, sparse coding, and slowness. In this thesis, we investigate whether the auditory system is governed by temporal prediction. This principle states that the sensory features represented by neurons are optimised to predict immediate future input from recent past input. Experimental evidence indicates that neurons in the retina extract the most predictive information at a near-optimal efficiency level. Recent theoretical work has also demonstrated that temporal prediction can explain tuning across different sensory modalities. An artificial neural network optimised for temporal prediction of natural moving images can explain many of the receptive field features exhibited by neurons at different stages along the visual pathway. An auditory counterpart applied to spectrogram-like representations of natural sounds similarly produces receptive fields resembling those in the primary auditory cortex. In this thesis, we present work that further explores this explanatory principle for the auditory system. First, we show that an artificial neural network optimised for temporal prediction of raw waveforms of natural sounds produces tuning properties that are both qualitatively and quantitatively similar to those observed in the cochlea. Second, we show that a decision model based on auditory temporal prediction can predict the behaviour of mice in multiple auditory discrimination tasks. Finally, we present work that investigates whether a recurrent temporal prediction model can explain functional connectivity and neural responses to natural sounds in primary auditory cortex. Together, these findings provide further support for the role of temporal prediction in accounting for diverse characteristics of the auditory system.

Keywords: generalization
normative model
behavior
prediction
auditory
discrimination
Advisor: Harper, N
Willmore, B
King, A
Pathways to inclusion and exclusion: An analysis of Medellín’s participatory budgeting process (2004-2017)

Political exclusion from public decision-making processes is one of the main causes of conflicts worldwide. The scholarship on the political inclusion of marginalised populations in a broad range of contexts and fields is growing rapidly. A specific subject that is receiving increased attention is participatory budgeting, a process that allows citizens to decide how to spend part of the local government budget. Still, the studies that examine the influence of offline and online participatory budgeting on political inclusion in peacebuilding contexts remain scarce. This thesis aims at contributing to the literature by analysing the influence of participatory budgeting on political inclusion in Medellín, Colombia’s second-biggest city.
A case study approach was used to explore the participatory budgeting process in Medellín, from its launch as a city-wide policy in 2004 until its last regulatory change in 2017. Instead of testing pre-specified hypotheses, the thesis uses grounded theory to identify the factors and pathways that contribute to explain the influence of Medellín’s offline and online participatory budgeting on political inclusion in the view of its participants. The qualitative data collected and analysed suggests that participatory budgeting could boost political inclusion, while sometimes, even simultaneously, also reducing it. Using a grounded theory approach, this thesis develops a framework that explains how power dynamics and the deployment of the public budget through the participatory budget might foster or hinder political inclusion, depending on the design and implementation of the participatory budgeting process. The thesis also advances the literature by providing a thick description of political inclusion in Medellín’s participatory budgeting process, that characterises who are the actors that participate in the process and the distinctive dynamics of their interactions, along with how this participation may influence political inclusion.

Keywords: Peacebuilding
Participatory budgeting
Political inclusion
Transitional justice
ICTs
Advisor: Lange, B
Mapping the proteomes of endoplasmic reticulum domains by proximity biotinylation

The endoplasmic reticulum (ER) is the largest organelle in the cell and is involved in a wide range of functions such as biogenesis of membrane and secretory proteins, calcium homeostasis and lipid synthesis. To be able to carry out these functions, the ER depends on an elaborate architecture consisting of a network of flat cisternae-like sheets and narrow tubules. The ER also assembles the nuclear envelope (NE) which is formed by two membranes, the inner and outer nuclear membrane (INM and ONM), that separate the cytoplasm from the nucleoplasm. Despite continuous with each other, these ER domains serve different functions. Consistent with their diverse roles, ER domains also appear to harbour distinct proteins. However, the complete proteomes of the various ER domains have not been systematically analysed and annotated. The primary objective of this project was to map the protein compositions of the distinct ER domains. To this aim, an APEX2-based proximity biotinylation assay coupled to subcellular fractionation was established and a data analysis pipeline developed. The assay was capable to identify many of the well-characterised INM, ER tubule and ER sheet proteins in their anticipated domain. Additionally, a range of bona fide proteins, that have not previously been shown to enrich at any of these domains, were identified. Therefore, these data provide a valuable resource to enhance our understanding of ER organisation. Additionally, the developed assay and data analysis pipeline can serve as a discovery platform to probe how the protein compositions of the ER domains change in response to disease-associated mutations or upon external perturbances. As an example, the effect of LMNA knockout on the protein composition of the inner nuclear membrane was investigated, whereby a small number of proteins were identified to be affected by depletion of A-type lamins.

Keywords: proteome
endoplasmic reticulum
nuclear envelope
Advisor: Carvalho, P
Engineering small molecule-mediated communication between light-activatable synthetic cells and bacterial cells

Gene-expressing compartments are a minimal representation of living cells. By using DNA blueprints to inform an assembly line of biological machinery how to manufacture the proteins required for a particular function, these cell-like compartments, often referred to as synthetic cells, have been engineered to exhibit life-like behaviours, such as division and communication. Although, despite these advances, little emphasis has been placed on how their activities are regulated. For synthetic cells to become a mature and valuable technology, it is essential that we precisely control where and when their functions are executed. Should this be achieved, synthetic cells could be used for the controlled production of drugs or signalling molecules, and be interfaced with living cells/tissues to modulate their behaviours. This thesis delineates progress towards creating gene-expressing synthetic cells that are activated only in the presence of UV light and describes how light-activated synthetic cells could be interfaced with living cells.
Synthetic cells were constructed by functionalising giant unilamellar vesicles with a cell-free protein synthesis system and DNA template. The DNA template dictated which proteins were synthesised inside the vesicle and, therefore, the overall function of the compartment. Photo-sensitive blocking groups were subsequently installed into the promoter regions of the DNA templates to regulate in situ gene expression; transcription, and in turn, translation, was prevented until the promoter was uncaged with UV light. This method of regulation enabled the resulting light-activated synthetic cells to be controlled remotely and in a spatiotemporally-controlled manner. To demonstrate the versatility of this platform, light-activated synthetic cells that participated in one-way communication with living cells were constructed. These compartments expressed an N-acyl homoserine lactone synthase in response to UV light, which synthesised an N-acyl homoserine lactone that was released and detected by engineered E. coli cells.

Keywords: Synthetic biology
Advisor: Booth, M
Bayley, H
Shepherds of men: a reassessment of the Athenian 
strategoi in the classical period


This thesis analyses the Athenian strategoi in the fifth and fourth centuries BC. The work critically engages with existing literature on the matter and proposes a different reconstruction of the strategoi. Instead of being weak officers with limited powers, this work argues that the strategoi had substantial independence and authority within the limits of their mandate, which was often quite loose. The office accountability limited erratic behaviour and open insubordination, but did not totally hinder every commander's independence; some commanders acted more boldly than others, probably trusting that by achieving a positive outcome in battle they would avoid harsh repercussions for any misbehaviour.
The strategoi’s authority is also discussed in extra-legal terms. The personal authority of the strategoi is discussed, on the one hand, engaging with existing scholarship on non-institutional ways to exercise power. On the other hand, the phenomenon is studied in terms of charismatic authority. The formulation of ‘synergic charisma’ is here adopted to explain the most extreme cases of extra-legal authority and offers a sociologically sound explanation for its numerous examples.
The second part of the thesis focuses on the more practical aspects of the strategia. It is proposed that the strategoi had some control over their men, even amateur citizen-soldiers, which allowed them to execute basic tactics already in the fifth century. The trend of the professionalisation of the strategoi is here questioned in favour of a mellower development. The major changes are due to fourth century Athens' socio-economic conditions more than this alleged professionalisation, of which the evidence is limited.
Lastly, the strategoi's role in the campaign's morale management and organisation is discussed to demonstrate their considerable set of responsibilities, which suggests a considerable degree of independence.

Keywords: Athens
military history
Greek history
leadership
Ancient history
Athenian institutions
Advisor: Thomas, R
Sidebottom, H