VictorJuiz/thesis huggingface dataset:
Online higher education experiences for First-Generation and/or Low-Income students during the Covid-19 pandemic: an explorative study through the lens of Self-formation
Keywords: first-generation student
elite higher education institution
self-formation
online education
inequality
low-income-student
Covid-19
capital

The experiences of First-generation and/or Low-income (FGLI) students in elite higher education institutions (EHEI) are important to analyze as often they are further disadvantaged due to the large discrepancies between them and peers who are not FGLI. Through the lens of the COVID pandemic this research seeks to understand what experiences FGLI students had and how it led to their outcomes. This case study focuses on Columbia University due to its location, reputation, and proximity to Covid. In thinking about their institutional experience students discussed disparities/stressors, their livelihood, and prestige. Through the impact of Covid, issues of housing, mental health, and loss were expressed. With the transition to online learning students examined academic policies, digital inequality, and the importance of interior spaces. Through these difficulties’ students brought forth concepts of Simon Marginson’s (2022) higher education as self-formation. Through independent conscious action, growth/moral responsibility, motivation/drive, and transformational change. These FGLI students had a mutually beneficial relationship with their higher education institution in which they helped create programs for students as well as improve their personal outcomes. Many participants were able to overcome these obstacles, and many spoke about coming out better in the end through self-formation. In looking at higher education as self-formation we can see how these high achieving individuals consider higher education as a means to better their lives and advance their livelihood. By examining this population, we can further understand the needs of this marginalized community, and in learning some of the difficulties these students face, institutions can be better prepared to assist current and future students.
Structure and uncertainty in deep learning
Keywords: Bayesian machine learning
deep learning
machine learning
uncertainty
machine vision

Designing uncertainty-aware deep learning models which are able to provide reasonable uncertainties along with their predictions has long been a goal for parts of the machine learning community. Such models are also frequently desired by practitioners. The most widespread and obvious method to provide this to this is to take existing deep architectures and attempt to apply existing Bayesian techniques to them, for instance, by treating the weights of the neural network as random variables in a Bayesian framework. This thesis attempts to answer the question: are existing neural network architectures the best way to get reasonable uncertainty? In the first part of this thesis, we present research on the uncertainty behaviour of Bayesian neural networks in an adversarial setting, which demonstrates that, while a Bayesian approach improves significantly on deterministic networks near the data distribution, the extrapolation behaviour is undesirable, as standard neural network architectures have a structural bias toward confident extrapolation. Motivated by this, we then explore two alternatives to standard deep learning architectures which attempt to address this issue. First, we describe a novel generative formulation of capsule networks, which attempt to impose structure on a learning task by making strong assumptions about the structure of scenes. We then use this generative model to examine whether these underlying assumptions are useful, arguing that they in fact have significant flaws. Second, we explore bilipschitz models, a family of architectures which address the more limited goal of ensuring prior reversion in deep neural networks. These are based on deep kernel learning, attempting to control the behaviour of neural networks out of distribution by using final classification layers which revert to a prior as the distance to a set of support vectors increases. To maintain this property while using a neural feature extractor, we describe a novel 'bilipschitz' regularisation scheme for these models, based on preventing feature collapse by imposing a constraint motivated by work on invertible networks. We describe various useful applications of these models, and analyse why this regularisation scheme still appears to be effective even when the original motivation behind it no longer holds, in particular, where the feature dimensionality is lower than the input.
Quantitative analysis of the mode and tempo of virus molecular evolution
Keywords: virus evolution
pathogen dynamics
excess mortality
population genetics
molecular epidemiology
molecular evolution

Estimating the rate of nucleotide and amino acid substitutions is fundamental to our understanding of how fast species evolve. It also enables us to reconstruct their natural history. The development of sophisticated statistical methods and software in molecular sequencing analysis has made it easier for biologists to test and compare various evolutionary hypotheses and infer evolutionary parameters. However, the use of these software packages as a ‘blackbox’ without paying close attention to the underlying assumptions can lead to spurious rate estimations across different timescales which often result in erroneous inferences of virus evolutionary histories. In this thesis, I develop quantitative methods to understand biological mechanisms that can alter the molecular evolutionary rate of viruses over time and investigate the implications of having a time-dependent rate of evolution for reconstructing the phylogenetic history of viruses. I also explore alternative methods to estimating the time of origin and reconstructing the evolutionary trajectory of viruses using mobility data, national vital statistics, and serology surveys. I show how three evolutionary processes of rapid within-host evolution during chronic infections, purifying selection, and site saturation can determine the changes in evolutionary rate of viruses over different timescales, from a few weeks to millions of years. I also leverage excess mortality and seroprevalence data to correct for under-reporting of COVID-19-related deaths, reconstruct early transmission dynamics of SARS-CoV-2, and estimate the start of the Iranian epidemic as well its growth rate in the absence of high-quality genome sequence and province-level epidemiological data. This work will build towards the goal of making more accurate estimations of the timescale of phylogenetic histories and the rate at which species evolve. It also further strengthens the conceptual link between phylogenetics, population genetics, and molecular evolution.
J.M. Coetzee's Hispanic worlds
Keywords: Argentine literature
English literature
Miguel de Cervantes
Jesus novels
Australian literature
South
Pablo Neruda
Chilean literature
Don Quixote
Hispanic
world literature
South African literature
world-making
J.M. Coetzee
J.L. Borges

My dissertation seeks to bring into critical focus the connections between J.M. Coetzee’s work and Hispanophone literature and culture, 1970 to the present day, in order to demonstrate in broad terms how he has used his symbolic capital to open a Hispanic and southern perspective onto Anglophone world literature. In four chapters, I develop different but complementary readings relating to what I call four distinctive Hispanic worlds. Having first established the methodology and the scope of Coetzee’s Hispanic involvements in the Introduction, in Chapter 1 I examine the translation, publication and reception of Coetzee’s works in the Hispanosphere (1983-2022) with a view to showing the distinctiveness of the circulation of world literature in a non-Anglophone global context with significant southern elements. In Chapter 2, I analyse Coetzee’s praxis as a reviewer, critic and scholar of Hispanophone letters (1973-2017), and demonstrate that throughout this period he was influenced by Hispanic literature even as he promoted it in diverse contexts and through varied intellectual praxes. In Chapter 3, I delve into Coetzee’s engagement with Borges and discuss how he develops his personal idea of the south in dialogue with the Argentine author, and through his academic, publishing and outreach efforts in the Southern Cone more broadly (2015-19). In Chapter 4, I show how these different worlds come together in the narrative landscape of the Jesus novels and their crepuscular fictional reality (2013-19) which, I argue, establishes a southern literature of Cervantean origin and allows for a Hispanic reading of Coetzee.
Mathematical modelling of macrophage functioning in inflammatory bowel disease
Keywords: cytokine interaction network
network inference
macrophages
mathematical immunology

Macrophages play a central role in host defence and the orchestration of the immune response. Macrophage functioning defects contribute to the development of inflammatory bowel disease (IBD), in particular Crohn’s disease. Mechanistic understanding of IBD is needed to improve clinical care. We combined mathematical modelling with existing and novel experimental data to drive insight in the role of macrophages in IBD.
We developed a method to extract a minimal, weighted network from cytokine interaction data using ordinary differential equations and the Akaike information criterion. By applying our method to an existing PBMC flow cytometry dataset, we extracted a network of the regulation of IL-23, a key cytokine in IBD. Our findings suggest that IL-1 is an important regulator of cytokine responses and a promising therapeutic target for IBD patient subgroups.
Genetic studies in IBD suggest that that the hyper-inflammatory phenotype in subgroups of Crohn’s disease patients could be driven by a degree of immunodeficiency causing defective antibacterial activity and subsequent inflammation. We studied this immunodeficiency component using a combination of mathematical modelling and killing and cytokine concentration assays. Our framework, complemented with literature data, suggests that, in the presence of an impairment in cytokine production capability due to genetic defects in the NOD2 pathway, elevated cytokine levels could be solely driven by an increased bacterial load during infection.
We constructed a bacterial-load structured model to study what factors drive granuloma formation and verified our model against an existing agent-based model. We parametrised our model to represent an in vitro granuloma model and found that macrophage fusion, implemented as non-local source and sink terms in our model, does not play a large role in this context.
In summary, we combined mathematical modelling with experimental data to drive insight in macrophage functioning in IBD, while focussing on cytokine signalling, anti-microbial activity, and granuloma formation.
Language teacher motivation in Slovakia: a case study of Slovak teachers of English
Keywords: semi-structured interviews
language teacher motivation
multiple case studies
journals

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.
Visitation returns and nineteenth-century Anglicanism in Oxford and its surrounding parishes
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

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.
The ECJ’s precedents as means of EU integration: National courts’ treatment of European case-law under scrutiny
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

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.
Improving our mechanistic understanding of cell cycle dynamics
Keywords: cell cycle
BioNetGen
immunofluorescence
differential equations
inverse problem
scatter search
systems biology
PEtab

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.
Retrospection and re-orientation in Dante's Ante-Purgatory
Keywords: Ante-Purgatory
intratextuality
formula
Dante
liminality
liminal
repetition

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.
Development of novel nuclease inhibitors as potential anticancer agents
Keywords: DNA repair
nuclease

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.