VictorJuiz/thesis huggingface dataset:
Generating evidence to improve childhood cancer health outcomes and resource use in Egypt
Keywords: resource use
global health
childhood cancer
health outcomes
evidence synthesis

The aim of this thesis was to generate evidence to improve childhood cancer health outcomes and resource use in Egypt. Childhood cancer is an urgent priority in Egypt, owing to the large numbers of children with cancer, limited resources, and inferior survival. Therefore, there is a need to improve childhood cancer health outcomes (survival) with optimal resource use. The thesis generates three types of evidence using hybrid research methods: (1) Real-world evidence through conducting observational cohort studies in a local setting in Egypt (Chapters 3–5); (2) systematic evidence from the literature through conducting a systematic review study (Chapter 6); and (3) qualitative evidence from experts’ opinions in the local context through conducting a qualitative interview study (Chapter 7). In Chapter 3, I determined the survival rates and temporal trends in survival for 14,808 children with cancer treated at Children’s Cancer Hospital Egypt (CCHE) between 2007 and 2017, and identified cancers with inferior survival compared to international benchmarks. In Chapter 4, I determined childhood cancer hospital resource use and associated costs for 8,886 children with cancer treated between 2013 and 2017, and identified cancers with the highest resource use/costs. In Chapter 5, I estimated treatment cost-effectiveness at CCHE and found that it was not cost-effective for children with relapsed/refractory acute leukaemia. Accordingly, In Chapter 6, I conducted a systematic review on costs/cost-effectiveness of treatment for relapsed/refractory paediatric acute leukaemia. In Chapter 7, I conducted interviews to determine the clinicians’ perceptions of barriers and facilitators to implementing cost-effective evidence-based treatment at CCHE. Overall, I have reported that the 5-year overall survival rate for children with cancer at CCHE was 72.1%, where 12 (out of 18) cancer types had inferior survival compared to international benchmarks, and that children with acute myeloid leukaemia had the highest costs/resource use. Also, I found that treatment of relapsed/refractory acute leukemia was not cost-effective at CCHE, and the systematic review findings have shown that CAR–T cell therapy was a cost-effective treatment option, besides other novel therapies. I have identified four themes of barriers and facilitators to implementing cost-effective evidence-based treatment at CCHE. In conclusion, the thesis provides evidence-based recommendations for improving childhood cancer survival, resource use/costs, and treatment cost-effectiveness, addressing the implementation gaps at CCHE/Egypt. In Chapter 8, I discuss the implications of my thesis, and I propose a context-specific conceptual framework of evidence synthesis to improve childhood cancer health outcomes and resource use in Egypt.
English literature in Latin translation, 1580-1750
Keywords: Chaucer
Pope
translation
Dryden
Milton
Early modern
Latin
English literature
eighteenth century
seventeenth century
Spenser
Latinization

In early modernity, as classical literature was rapidly translated and absorbed into English, the opposite phenomenon also took place: English literary texts were translated into Latin. This thesis is the first study of the ‘Latinization’ of English literature during a crucial period of development for the English language and literary tradition. It discusses Latin translations of Chaucer, Spenser, May, Marvell, Fletcher, Milton, Dryden, and Pope, by translators including Richard Fanshawe, Christopher Smart and Samuel Johnson.
In this period, Latin was not only a language of the past composed of fragments of ancient texts and history; it was also a living lingua franca, imagined by these translators to be the language of futurity. English poetry was Latinized for both posterity and international readers. Latin acted as the medium for English literary texts to move from Portugal to Poland and across the Atlantic. This literary history of ‘Latinization’ reveals the real and imagined place of English poetry in the world and the relationship between two competing literary languages as the vernacular rose, showing how contingent that ‘rise’ appeared to be as it happened. The translations also disrupt existing models of translation, Latinity, bilingualism, allusion, and reception.
Latin translation goes through three broad phases in this period. In the first phase, c.1580-1635, it is primarily a response to changes in the English language that may soon render Chaucerian and Spenserian language unintelligible; it is also a European, ‘transmarine’ project to put English literature and politics on the map. The second phase, c.1635-1681, sees English texts Latinized, often self-translated, to explore political and diplomatic identities during the Civil Wars and Restoration. In the third phase, c.1681-1750, Latinization adapts Milton (alongside Dryden and Pope) to new Augustan contexts, and fraudulency and failure become increasingly characteristic of Latin translation in this changed literary environment.
Structural techniques in descriptive complexity
Keywords: finite Model theory
Courcelle's Theorem
Ehrenfeucht Fraisse games
bounded tree-depth
finite quantifier rank
bounded tree-width
categorical semantics
descriptive complexity
locality
homomorphism preservation Theorems
finite variable logic

In 2017, Abramsky, Dawar, and Wang published a paper which gave a comonadic characterisation of pebble games, tree-width, and k-variable logic, a key trio of related concepts in Finite Model Theory. In 2018, Abramsky and Shah expanded upon this to give an analogous comonadic characterisation of Ehrenfeucht Fraisse games, tree-depth, and bounded quantifier rank logic. A key feature of these papers is the connection between two previously distinct subfields of logic in computer science; Categorical Semantics, and Finite Model Theory. This thesis applies the ideas and techniques in these papers to give a categorical account of some cornerstone results of Finite Model Theory, including Rossman’s Equirank Homomorphism Preservation Theorem, Courcelle’s Theorem (on the model-checking properties of structures of bounded tree-width), and Gaifman’s Locality Theorem.
(Re-)claiming the social contract: state-society relations in three former socialist towns in the Baltics
Keywords: Lithuania
neoliberalism
Latvia
social contract
comparative ethnography
Estonia
state anthropology
(post-)socialism
citizenship

This thesis is an ethnographic study of the social contract between the state and society as imagined and lived by the predominantly Russian-speaking residents of three former socialist towns in the Baltics: Visaginas in Lithuania, Daugavpils in Latvia, and Sillamӓe in Estonia.
This thesis argues that the residents of Visaginas, Daugavpils, and Sillamӓe define “the state” and their relationship with it primarily as a social contract. For Russian-speaking residents of Visaginas, Daugavpils, and Sillamӓe, who are deprived of recognition to various degrees, the social contract offers an ideal of an equal, fair, reciprocal, and perceivably apolitical relationship with the state that they yearn for, yet feel the lack of. Thereby, the language of the social contract becomes a way for Russian speakers to try and claim membership in the national Lithuanian, Latvian, or Estonian collectives as good, deserving, and loyal state subjects. However, I show in this thesis that the social contract is also the only language available to the residents that allows them to challenge the dominant narrative in Lithuania, Latvia, and Estonia, which often depicts Russian speakers as alien and potentially threatening to the national state.
This thesis then raises the following questions: what is entering into the social contract with the state in Lithuania, Latvia, or Estonia contingent upon, and can the Russian-speaking (non-)citizens effectively challenge the exclusionary state narratives and practices by employing the language of the social contract. The thesis examines how the predominantly Russian-speaking residents of Visaginas, Daugavpils, and Sillamӓe attempt to redefine the very political community of which they strive to become a part, as well as the ways and forms of governance that the residents believe would allow them to achieve their ideal state-society relationship.
Understanding video through the lens of language
Keywords: multimodal
video understanding
vision &amp; language
deep learning

The increasing abundance of video data online necessitates the development of systems capable of understanding such content. However, building these systems poses significant challenges, including the absence of scalable and robust supervision signals, computational complexity, and multimodal modelling. To address these issues, this thesis explores the role of language as a complementary learning signal for video, drawing inspiration from the success of self-supervised Large Language Models (LLMs) and image-language models.

First, joint video-language representations are examined under the text-to-video retrieval task. This includes the study of pre-extracted multimodal features, the influence of contextual information, joint end-to-end learning of both image and video representations, and various frame aggregation methods for long-form videos. In doing so, state-of-the-art performance is achieved across a range of established video-text benchmarks.

Second, this work explores the automatic generation of audio description (AD) – narrations describing the visual happenings in a video, for the benefit of visually impaired audiences. An LLM, prompted with multimodal information, including past predictions, and pretrained with partial data sources, is employed for the task. In the process, substantial advancements are achieved in the following areas: efficient speech transcription, long-form visual storytelling, referencing character names, and AD time-point prediction. Finally, audiovisual behaviour recognition is applied to the field of wildlife conservation and ethology. The approach is used to analyse vast video archives of wild primates, revealing insights into individual and group behaviour variations, with the potential for monitoring the effects of human pressures on animal habitats.
Structural investigation of receptor engagement and monoclonal antibodies targeting Plasmodium vaccine antigens
Keywords: malaria
Plasmodium
vaccine
X-ray crystallography

Malaria remains a disease of great global healthcare burden, with over 600 thousand deaths annually. With an increase of multi-drug resistant malaria, achieving current mortality reduction targets hinges on the development of an efficacious malaria vaccine. Leading malaria vaccine RTS,S contains the major repeat epitope and C-terminal domain, but not the N-terminal domain of the Plasmodium falciparum circumsporozoite protein, which has been under investigated. Herein, the structural basis binding of six novel human and mouse antibodies with their N-terminal CSP peptide epitopes reveal the capacity for an antibody response towards multiple novel epitopes. The MAL071 RTS,S trial has provided renewed interest in antibodies targeting the C-terminal domain of CSP as correlates for protection. The structural basis for engagement of the C-terminal domain of CSP by ten monoclonal antibodies from the MAL071 trials demonstrates the broad antigenic landscape of this domain, including six new antibodies targeting the highly conserved β-epitope. The newfound immunological breadth of the β-epitope is then used to inform second-generation immunogen design combining key protective B-cell epitopes, successfully protecting mice from sporozoite challenge. Plasmodium vivax is responsible for most of the remaining malaria-associated mortality. Region II of the P. vivax Duffy-binding protein is a key antigen for a blood-stage vaccine. Here, the complete structural basis of PvDBP-RII engagement with the DARC ectodomain is revealed in complex with inhibitory human vaccination-induced monoclonal antibody DB1. This study significantly improves our understanding of receptor engagement by providing structural basis for previously described binding determinants and antibody-mediated inhibition of erythrocyte invasion by P. vivax merozoites.
Ecologies of desire: cinema, masochism, time
Keywords: Gilles Deleuze
nonhuman turn
environmental humanities
psychoanalysis
Maurice Merleau-Ponty
French cinema
Roland Barthes
Sigmund Freud
slow cinema

This dissertation examines a corpus of contemporary French and international filmmakers (Claire Denis, Mati Diop, Lucile Hadžihalilović and Apichatpong Weerasethakul) interested in ecology and dilated temporalities. I begin with the premise that slow films are not simply endurance tests: in their evocation of time-scales beyond human cognition, these films are undeniably pleasurable, full of sensorial richness and detail. In inviting us to enjoy the protracted rhythms of the natural world, I argue that they elaborate a psychoanalysis of nature, allowing us to abandon the opposition between the nonhuman turn and psychoanalysis that remains operative within the humanities.

In my first chapter on Denis, I amend some of the extreme directions taken by recent non- anthropocentric theory, in the form of the ecological anti-humanism of the recent ‘Dark Deleuze’ trend. Reading this thought alongside Beau Travail (1998) and High Life (2018), I show how Denis can recuperate Deleuze’s anti-humanist death drive into a renewed human sociality. My chapter on Hadžihalilović functions in a complementary manner, as I follow Maurice Merleau- Ponty in retrieving much of Freud’s thinking of nonhuman life that has been de-emphasized by the linguistic emphasis of Lacanian theory. Following the Merleau-Pontian Freud, my readings of Innocence (2004) and Evolution (2015) argue that ‘normal’ adult sexuality requires recuperating childhood and nonhuman perversity. In my third chapter, I show how this time- straddling perspective takes on geo-political contours in Apichatpong’s Uncle Boonmee Who Can Recall His Past Lives (2010) and Cemetary of Splendour (2015), as communal and intersubjective relations depend upon Freud’s “animist” thinking. Finally, Mati Diop’s Atlantique (2019) elaborates a similarly ambiguous and magical form of kinship that grants agency to objects. Across all of these films, I outline how the relationality prized by psychoanalysis necessitates nonhuman life as its ecstatic unmooring towards the Other and reality.
Phase transitions in the early universe
Keywords: extra dimensions
phase transitions
gravitational waves
cosmology
topological defects
particle physics
dark matter

Phase transitions are a generic prediction of models in particle physics. In the Standard Model, for example, there are two phase transitions: the QCD confinement transition and the electroweak phase transition, both occurring in the very early stages of the universe. Many extensions to the Standard Model predict new phase transitions, all occurring at very high temperatures. Depending on how these transitions proceed they may lead to signatures which can be detected today, offering a way to probe the early stages of the universe.
This thesis is on phase transitions and their impacts on early universe cosmology. Chapter 1 is an overview of the physics of phase transitions, both in the Standard Model and extensions of it. The different phases of gauge theories are described before discussing the phase transitions in the Standard Model and general features of phase transitions in theories beyond the Standard Model. The cosmological implications of these transitions is then summarised, with a focus on the production of topological defects, the gravitational wave signal and constraints from supercooling.
Chapter 2 focuses on the confining transition in Randall-Sundrum models. The transition places severe cosmological constraints on the model, meaning the model is only marginally under parametric control as an effective field theory. In this chapter a mechanism is presented which circumvents the problematic phase transition by making the confined phase metastable at high temperatures. The phenomenological features of the model, in particular dark matter production, are also presented in this chapter.
Everyday phase transitions are often catalysed by the presence of defects or impurities in the material, leading to an enhanced transition rate. In cosmology, however, phase transitions are typically considered to proceed from a homogeneous initial state. In chapter 3 the possibility that magnetic monopoles could act as catalysts for cosmological phase transitions is considered, and an algorithm developed to solve the field equations describing the transition. A similar idea is pursued in chapter 4 for the case of domain walls catalysing the electroweak phase transition.
Genetic and molecular characterization of the regulation of chloroplast protein import in Arabidopsis thaliana
Keywords: UBX
PUX10
chloroplast
chloroplast protein import
Cdc48
CHLORAD

Plastids are a unique group of interconvertible organelles which are descended from prokaryotic endosymbionts. The most prototypical member of the group is undoubtedly the chloroplast, which carries out photosynthesis and many other essential biosynthetic processes. Within the course of evolution, over 90% of the retained ancestral protein-coding genes have been transferred into the nuclear genome. The encoded chloroplast-destined proteins must therefore be imported as precursor proteins from the cytosol, through the import apparatus comprising the TOC/TIC complexes. Over the last few years, a proteolytic system called the Ubiquitin-Proteasome System (UPS) has been recognized to target TOC proteins for degradation. The dynamic regulation of the import pathway enables plastids to respond to environmental and developmental cues. A recent discovery demonstrated that the ubiquitinated membrane-embedded TOC proteins can be extracted through a pathway called chloroplast-associated protein degradation (CHLORAD) before degradation by the cytosolic 26S proteasome. In CHLORAD, SP1 acts as the E3 ligase, SP2 functions as an exit channel, and the ATPase Cdc48 provides the motor force for extraction.
Cdc48 functions in a variety of cellular processes and its activity depends on a wide range of cofactors. The ubiquitin regulatory X (UBX) domain-containing proteins constitute by far the largest family of Cdc48 cofactors. PUX10, a member of the plant UBX domain-containing protein (PUX) family, is an integral chloroplast outer membrane protein that contains a UBX domain and a ubiquitin-associated (UBA) domain that interact with Cdc48 and ubiquitin, respectively. Although pux10 mutant Arabidopsis thaliana seedlings in general appeared phenotypically normal, PUX10 expression levels influenced the rapid degradation of over-accumulated TOC proteins under certain circumstances, such as senescence or abiotic stress. Thus, I propose that PUX10 is involved in the CHLORAD pathway, mediating the recruitment of Cdc48 from the cytosol to the chloroplast surface, and promoting Cdc48 binding to polyubiquitinated TOC proteins for degradation.
In a parallel genetic strategy to understand chloroplast protein import regulation, I studied a new suppressor of the plastid protein import 1 (ppi1) mutation in Arabidopsis called suppressor of ppi1 locus 3 (sp3). Preliminary characterization suggested that the SP3 encodes the GIGANTEA protein which regulates photoperiodic flowering and negatively regulates chloroplast biogenesis. Further investigation of the functional interactions of SP3 with CHLORAD and TOC components will be required to fully understand the nature of these relationships.
Development and evaluation of clinical prediction models for risk-stratified early detection, prevention and management of breast cancer
Keywords: breast cancer
machine learning
risk prediction

Accurately estimating individual-level risks of breast cancer incidence and mortality could inform stratified approaches to screening, prevention, and management that help reduce deaths from breast cancer and are more cost-effective. Increasing interest in ‘machine learning’ techniques and the integration of phenotypic and genetic data present uncertainty around the best approaches to prognostication in these settings.
In a scoping review, evidence deficiencies were highlighted regarding risk-based breast screening, and parallels explored between this and risk-based breast cancer prevention and management. Using the QResearch primary care database and its linked datasets, clinical prediction models were developed using regression and machine learning methods to estimate individual women’s 10-year risks of incident breast cancer, 10-year risks of developing and then dying from breast cancer, and 10-year risks of breast cancer mortality after diagnosis. These were comparatively evaluated in an internal-external cross-validation framework to assess performance and transportability. Second, the incremental effects of integrating genome-wide polygenic risk scores to models for the first two outcomes were assessed using the UK Biobank.
This thesis sought to develop and evaluate models in accordance with modern practice, with an emphasis on robust, fair comparisons between different approaches. A key output was the first work to develop models that estimate the risk of breast cancer mortality in women without breast cancer at baseline, which could be important in the context of screening-associated overdiagnosis. Second, models were produced that may provide reliable risk stratification for any woman with breast cancer. Third, integrating genome- wide polygenic risk to ‘phenotypic’ information may increase the performance of breast cancer incidence and mortality models in women currently eligible for screening. The clinical impact and cost-effectiveness of strategies structured around these models needs further assessment.
Calibrated geometry in manifolds of exceptional holonomy
Keywords: Spin(7) geometry
manifolds of exceptional holonomy
G2 geometry
calibrated geometry

In this thesis, we discuss some aspects of calibrated geometry in manifolds of exceptional holonomy. Manifolds of exceptional holonomy are Riemannian manifolds that are endowed with one of the following additional structures: a torsion-free G2-structure or a torsion-free Spin(7)-structure. G2 manifolds admit two special families of calibrated, hence volume minimizing, submanifolds: associative 3-folds and coassociative 4-folds. Spin(7) manifolds admit only one family of calibrated submanifolds: Cayley 4-folds. Understanding the geometry of such calibrated submanifolds is one of the key challenges in the study ofmanifolds with exceptional holonomy.
After recalling some basic notion on calibrated geometry and manifolds of exceptional holonomy, we deﬁne calibrated ﬁbrations, and we prove a rigidity result for these objects under some linear condition.
Then, we describe the construction of two Cayley ﬁbrations in the Bryant–Salamon Spin(7) manifold using a cohomogeneity one method. These are the ﬁrst explicit examples of Cayley ﬁbrations in a non-ﬂat Spin(7) manifold and the ﬁbres provide new examples of Cayley submanifolds.
Finally, we study the geometry of calibrated submanifolds in G2 manifolds that admit T2 × SU(2)-symmetry. We apply our results to C3 × S1 , to the Bryant–Salamon manifolds and to the manifolds recently constructed by Foscolo–Haskins–Nordström, where our analysis gives new large families of T2-invariant associatives. This is based on joint work with B. Aslan.