VictorJuiz/thesis huggingface dataset:
The geopolitics of climate change in Greenland: superpowers and small states

This dissertation asks why and how Greenland became a focal point of U.S.–China competition between 2009 and 2021. The answer is climate geopolitics: the anticipated impact of long-term climate change on geography and its implications for national power, interest, and strategy. I posit that the anticipation of future climate change can have significant geopolitical consequences before the salient geophysical impacts actually arrive. Under certain conditions, this can give small polities substantial leverage to bargain for better outcomes. Taking Greenland as a case study, I show how the China and the United States conceptualize Greenland’s geographic significance in a future Arctic transformed by climate change. I then show how Greenland has exploited these perceptions to bargain for profit and autonomy. I discuss how this geopolitical dynamic shaped negotiations over three Chinese-proposed mega-deals with Greenland: to acquire land, build critical infrastructure, and operate a mine. Finally, I show that China is now extrapolating the logic of climate geopolitics to acquire access and influence in other climate-exposed island states: the Faroe Islands, Iceland, Maldives, and Kiribati. Analytic methods are discourse analysis and process-tracing. Sources include 36 elite interviews and government reports, company documents, academic papers, and newspaper articles in English, Chinese, and Danish.

Keywords: climate geopolitics
Maldives
geopolitics
China
Faroe Islands
Iceland
climate change
Greenland
Kiribati
Arctic
Advisor: Crookes, P
Mitter, R
Ancient scholarship on papyrus: new light from Oxyrhynchus

This thesis presents editions of twenty-one previously unpublished papyri from the Oxyrhynchus Papyri collection in the Sackler Library, Oxford. Every papyrus is edited with introduction, commentary, and translation, according to the conventions of The Oxyrhynchus Papyri (London, 1898–). All the papyri deal in some way with ancient scholarship. There are new commentaries on Homer, Apollonius Rhodius, and Herodotus; new grammatical treatises dealing with the letters of the alphabet, with nouns/adjectives, with doxography, and with various other matters; new scholia minora on the Iliad and the Odyssey; new texts displaying ancient marginal annotations; and a few miscellaneous pieces dealing with mythography， biography, and other varied subjects. These papyri bring to light interesting evidence. There are new testimonia for ancient scholars, including Philitas of Cos, Zenodotus of Ephesus, Apollodorus of Athens, Istrus of Paphos, and Aristonicus of Alexandria. There are also new citations of classical literature, including a superior text of Alcman, PMG fr. 80, and references to lost works of drama, Euripides’ Tennes and Sophocles’ Tereus. The main significance of these papyri lies however in the extent to which they enlarge the current state of knowledge about scholarship in the Roman period. Some pieces, such as the commentary on Herodotus, provide rare and substantial new evidence for ancient scholarship on a particular author, while others, such as the scholia minora, contribute usefully to the stock of evidence for types of ancient scholarship that are already well known.

Keywords: textual criticism and editorial technique
ancient scholarship and ancient education
Roman Egypt
Graeco-Roman society
ancient manuscripts
Advisor: Benaissa, A
Molecular mechanisms underlying the pathogenesis of dengue fever: dengue virus co-opts innate type 2 pathways to escape early control of viral replication


Dengue is a mosquito borne tropical infection caused by the dengue virus with a dramatic global spread over the last few decades. Dengue infection can present as dengue fever (DF) or the severe forms such as dengue haemorrhagic fever (DHF) and dengue shock syndrome (DSS). There is a recognised clinical link between asthma and other allergies associating with severe dengue. Furthermore, mast cells are known to be activated in dengue infection and high levels of type 2 cytokines are known to be associated with DHF. Group 2 Innate Lymphoid Cells (ILC2) are type 2 cytokine secreting cells that respond to different stimuli including lipid mediators such as prostaglandin D2 (PGD2) and leukotrienes. Here, the hypothesis was tested that ILC2 contribute to dengue pathogenesis. First, increased peripheral blood ILC2 frequency was observed in dengue-infected individuals compared to healthy controls (HC). From ex vivo RNA sequencing data of ILC2 sorted from peripheral blood mononuclear cells (PBMC) of patients with DF and DHF, it was found that ILC2 were activated and infected, supporting viral dissemination. In vitro, ILC2 were permissive to infection particularly when activated and led to productive viral replication. From ex vivo RNA sequencing data it was evident that in DF the type I interferon related genes were highly expressed by ILC2 and in DHF this response was impaired.
Blockade of CRTH2, a PGD2 receptor, reduced dengue viral infection in ILC2 by inhibiting action of both exogenous and endogenously produced PGD2; and PGD2 reduced the ability of ILC2 to respond to type I IFN. Moreover, LTE4, another lipid mediator in the group of leukotrienes produced by mast cells increased infectivity of ILC2, and this could be inhibited by leukotriene receptor blockade. It was found that activated ILC2 supernatants promoted differentiation of monocytes to monocyte-derived dendritic cells (MoDCs) and could upregulate expression of DC-SIGN and MMR, which are key receptors facilitating attachment of dengue virus. Additionally, activated ILC2 supernatants increased dengue virus infection in differentiating monocytes in a GM-CSF dependent mechanism. Lastly, urinary PGD2 metabolites were elevated in severe dengue when reaching the ‘critical phase’ of the disease.
In summary, ILC2 are highly activated during acute dengue infection and can be infected by dengue virus ex vivo and in vitro. Dengue virus co-opts the innate type 2 pathways to escape protective type I interferon responses. We propose CRTH2 inhibition could be a novel mechanism to reduce viral replication in dengue infection.

Keywords: dengue fever
group 2 innate lymphoid cells
type 2 immunity
prostaglandin D2
Advisor: Ogg, G
Hardman, C
Puritan conformity, Church polity, and Anglican identity, 1628-88


There have been many attempts to define what Anglicanism is, through both “reformations” of the Church of England as well as rewritings of its history. Yet none have proposed a definition that can satisfy all. Instead of searching for one, static Anglican identity, this thesis follows recent scholarly endeavours to highlight the confessional diversity and conflicts that characterised the Protestant English Church, challenging traditional, and yet inaccurate dichotomies, such as puritan/conformist or puritan/episcopalian, to showcase how the very nature of the Church of England was one of struggle and fluidity rather than a definite triumph of specific strains of piety. To break through the puritan/conformist antithesis still prevalent in current scholarship, this thesis adopts a biographical approach to investigate a wide range of puritan contributions to the shaping of Anglican identity. The careers of the four protagonists in this study, William and Thomas Gouge, John Davenport, and Edward Reynolds, demonstrated that not only were the boundaries between conformity and dissent ever-changing, but both conformists and dissenters were active, self-conscious reformers of the Church of England.
While scholars in the past often narrate a story of dissent when they explore transatlantic congregationalism and presbyterianism, the four protagonists in this story show that they considered themselves active participants in, rather than opponents of, the national Church, and that even their dissenting activities, in both Old and New England, were tireless attempts to reshape the orthodoxy of the English Church. Pre-war and post-1662 puritan conformity feature prominently in this story as well, especially in William Gouge’s and Edward Reynolds’ lives. Both their conformity to the Laudian Church as well as Reynolds’ return to episcopacy as Bishop of Norwich in 1660 urge scholars today to rethink puritans’ view of episcopacy and better appreciate puritans’ legacy on the emerging Anglican identity.

Keywords: English presbyterianism
Reformed conformity
episcopacy
Edward Reynolds
ecclesiology
John Davenport
church government
Thomas Gouge
puritan conformity
early modern England
Anglicanism
seventeenth-century England
English Civil Wars
church polity
New England
post-reformation
puritan
William Gouge
Advisor: Maltby, J
MacCulloch, D
Generating textual captions for ultrasound visuals in an automated fashion

Generating captions for ultrasound images and videos is an area that is yet to be fully studied and explored. The aim of the work in this thesis is to learn joint image-text representations to describe ultrasound images with rich vocabulary consisting of nouns, verbs, and adjectives. Preparing medical image captioning benchmarks is challenging for two reasons: (a) describing medical images with specific terminology requires expert knowledge of medical professionals; and (b) the sensitive nature of medical images prevents wide-scale annotation, for instance, using crowd-sourcing services (e.g. Amazon Mechanical Turk) and similar methods. Therefore, automatic image captioning has not been widely studied on ultrasound images before, the challenge being enhanced by the lack of readily available large datasets of ultrasound images with captions.
First, the thesis explores different combinations of recurrent neural networks, concatenation techniques, word embedding vectors in different model architecture configurations. We identify in this process the configuration most suitable for the fetal ultrasound image captioning task and the dataset at hand. We show that a configuration incorporating an LSTM-RNN and word2vec embeddings and using a merge-by-concatenation operation performed best. The thesis then explores three solutions to the challenge of working with real world datasets. We introduce a curriculum learning based strategy that incorporates the complexities of the image and text information to prepare the data for training. We show that by training captioning models with the order of data samples determined by the curriculum, we can achieve higher scores on the evaluation metrics with the same amount of data. We also look into augmenting the data through the creation of pseudocaptions to pair up with caption-less images. Finally, we explore leveraging other available data from a different modality, specifically eye gaze points, to supplement available image-text data. We find that using eye gaze data can help in training models that score relatively higher on the evaluation metrics; however since the improvements are small and the pre-training steps involved are considerable, this leads us to the recommendation that improving base models should take precedence over relying on data from other modalities to improve the performance of captioning models.
To the best of our knowledge, the work in this thesis is the first attempt to perform automatic image captioning on fetal ultrasound images (video frames), using sonographer spoken words to describe their scanning experience. The thesis can help serve as a blue print for future endeavours in fetal ultrasound captioning by providing guidelines to follow and pitfalls to avoid and as an aid for those attempting medical image captioning, more generally.

Keywords: data augmentation
gaze tracking
fetal ultrasound
image description
deep learning
video captioning
natural language processing
curriculum learning
audio-visual
multi-modal
image captioning
recurrent neural networks
Advisor: Noble, A
An integrated immune -omic approach to unravel the sepsis response

Sepsis is defined as life-threatening organ dysfunction due to a dysregulated host response to infection. There is major unmet clinical need given the burden of all cause sepsis accounting for 20% of global deaths, in addition to the COVID-19 pandemic where SARS-CoV-2 can lead to viral sepsis. Multiple dynamic host pathophysiological mechanisms exist but are aggregated under a single umbrella syndrome description, leading to substantial patient heterogeneity. This thesis examines the sepsis response through a lens of immune multi-omics, focusing on single-cell transcriptomics with additional proteomic profiling.
Data are presented for novel sepsis patient cohorts recruited under different clinical emphases, including patients with COVID-19 (n=78), influenza (n=12), and all-cause sepsis (n=63), and reanalysis of existing cohorts (n=667). The host response to severe infection is explored via bulk and single-cell transcriptomics (scRNA-seq), and proteomics either simultaneous to scRNA-seq i.e. single-cell multi-omics, or in isolation with CyTOF. Comparisons are made between severe infection/sepsis comparator groups, within groups across transcriptomic subphenotypes, and with healthy and post-cardiac surgery control patients.
The host transcriptomic response showed substantial commonality between COVID-19 viral sepsis and all-cause sepsis although immunoglobulin pathways and the interferon response were elevated in COVID-19. The sepsis response signature (SRS) transcriptomic subphenotyping proved consistent in both cohorts, suggesting its utility as a unifying framework to view the host respnose to severe infection. At single-cell resolution, transcriptomics and cell surface proteomics of peripheral blood mononuclear cells revealed common and distinct aspects of the response to severe infection across cell types such as classical monocytes and CD4+ T cells, with a specific COVID-19 signature uncovered in the form of AP-1 pathway elevation. The basis of SRS was then dissected, revealing that SRS derived mostly from neutrophils with a minor contribution from PBMCs. Sepsis neutrophils displayed immunosuppressive properties, in particular SRS1 neutrophils, suggesting a potential role in sepsis pathogenesis.
Collectively, the work presented in this thesis advances our understanding of the host response to severe infection in terms of the cellular and molecular bases of the sepsis response. This biological understanding highlights potential therapeutic opportunities as we move toward a personalized infectious disease medicine in sepsis and beyond.

Advisor: Knight, J
Todd, J
Whalley, J
Contributions to the model theory of henselian fields

The thesis addresses certain problems in the model theory of henselian fields, with a special focus on decidability. Some new methods are introduced along the way, which are of independent interest. The following results are obtained:
• A transfer theorem for perfectoid fields, saying that a perfectoid field K is decidable relative to its tilt Kb, modulo a subtle (albeit natural) condition on K. As an application, we prove that the fields Qp(p1/p∞) and Qp(ζp∞) admit decidable maximal immediate extensions, thereby obtaining some of the first few decidabilty results for tame fields of mixed characteristic.
• A model-theoretic proof of the Fontaine-Wintenberger theorem, which states that the absolute Galois groups of K and Kb are canonically isomorphic. (joint with F. Jahnke).
• A general existential Ax-Kochen/Ershov principle for tamely ramified fields in all characteristics, conditional to a certain form of resolution of singularities. This extends well-known existential Ax-Kochen/Ershov principles in residue characteristic 0 and also unramified mixed characteristic. It also encompasses the (conditional) existential decidability result of Denef-Schoutens for Fp((t)), which we also strengthen by replacing the assumption of (global) resolution with local uniformization.
• An undecidability result for the asymptotic theory of {K : [K : Qp] < ∞} in the language of valued fields with a cross-section. The proof goes via reduction to positive characteristic, à la Krasner-Kazhdan-Deligne, ultimately adapting Pheidas’ proof of the undecidability of Fp((t)) with a cross-section. This answers a variant of a question of Derakhshan-Macintyre.
• An undecidability result for power series fields k((t)), equipped with a total residue map res : k((t)) ! k, which picks out the constant term of the Laurent series. Becker-Denef-Lipschitz showed that res : k((t)) ! k is definable in the language of rings with a parameter for t, when the base field k is finite. We show that (k((t)),res) is undecidable, whenever k is infinite.

Keywords: perfectoid fields
Fontaine-Wintenberger
henselian fields
resolution of singularities
model theory
valued fields
Advisor: Hrushovski, E
Koenigsmann, J
Reinforcement learning for rule selection in end to end differentiable proving

Neural Theorem Provers (NTPs) are neuro-symbolic models that combine deep learning with a system of logic. They can learn representations for data, induce rules, are naturally interpretable, come with built-in explanations for conclusions, and demonstrate the capacity for systematic generalization. However, since they consider all possible rules for proving a goal, they suffer from high computational complexity, and are thus unsuitable for use on large or complex datasets. Conditional Theorem Provers (CTPs) are proposed as an extension to address this issue. Nonetheless, CTPs suffer from similar computational constraints, as they still consider multiple proof paths while reasoning. We propose RL-CTPs, where CTPs are augmented with reinforcement learning to select the proof paths most likely to succeed. This allows the model designer to specify the number of proof paths to consider, to conform to the computational constraints of their use case, while retaining all of the benefits of CTPs. Using the CLUTRR dataset to perform evaluations, we provide evidence for the computational issues in existing CTP models, show that RL-CTPs alleviate these issues, and demonstrate that, in certain scenarios, the accuracy achieved by RL-CTPs is higher than CTPs with equivalent computational complexity.

Keywords: reasoning
neuro-symbolic
reinforcement learning
machine learning
Advisor: Blunsom, P
Teachers’ perception of their job-satisfaction in private schools in São Paulo municipality

This research focuses on teachers and teaching in schools, specifically investigates teachers’ perceptions of job satisfaction and the interplay between their satisfaction and work conditions in a set of private schools in Brazil. Based on qualitative research, semi-structured interviews were conducted, and the study collected insights from an intentional sample group of 10 teachers who work in different school environments that offer different working conditions for teachers in São Paulo. The results showed that teachers in the study experienced satisfaction by working with and for students, which is the most important element of their perception of satisfaction. In that regard, teachers differentiated the satisfaction in their careers and job. Also, echoing previous studies, the teachers evoked four recurring aspects of the working conditions related to satisfaction; organized through the thematic analysis, they are (i) autonomy, (ii) space for authorship as intrinsic factors, (iii) collective work, as a school-based factor, and (iv) work management, with concerns to extrinsic factors such as overload and remuneration. Findings also suggested that intrinsic factors contributed to their satisfaction, while extrinsic factors, mainly work overload, were seen as problems in their current schools.

Keywords: Teachers’ work conditions
Teachers’ job satisfaction
São Paulo
Private Schools
The adjustment journey: writing challenges and self-efficacy of students in transition from high school to an English medium instruction (EMI) university programme in Japan


Research into language-related challenges confronting EMI students is accumulating but gaps in understanding remain. One skill – academic writing – has not received the close-grained attention it merits given the centrality of the essay as a means of assessing EMI students. There is also a dire need for longitudinal insights into the EMI transition and a richer exploration of its lived reality. Such research may also provide valuable pointers to improving this crucial adjustment period.
The current charts the writing challenges and task-based confidence (i.e., self-efficacy) of 40 freshman EMI social science students during their initial 14-week academic writing preparatory course at a university in Japan. It clarifies 1) what writing challenges are faced and how they evolve; 2) students’ self-efficacy beliefs about academic writing and how they develop; 3) the influence of language proficiency and self-efficacy on perceived writing challenges. A mixed-methods approach was chosen in pursuit of these goals. Quantitative data was gathered over four timepoints through an EMI Writing Challenges Scale and an EMI Writing Self-efficacy Scale. Qualitative data was collected via nine student journal entries written through the semester by all 40 participants and three semi-structured interviews conducted with nine students.
Findings reveal that writing challenges lessened somewhat over the semester, yet the trend was not linear nor uniform. Self-efficacy remained largely stable as the semester progressed, but key differences existed between the nature and robustness of students’ beliefs. Overall, the initial adjustment journey to full EMI study remained a challenging one for participants. Implications for EMI policy and pedagogy are discussed.

Keywords: academic writing
EMI
self-efficacy