VictorJuiz/thesis huggingface dataset:
Anatomical and functional analysis of cardiac MRI scans using deep learning
Keywords: Cradiac MRI
Mouse heart
Deep learning
Left ventricle
Neural network
Segmentation
3D shape reconstruction

Cardiac magnetic resonance (CMR) is the current gold standard imaging technique to assess myocardium anatomy and regional and global function of the heart. The accuracy and robustness of CMR imaging has been validated using manual segmentation. However, the quality of manually traced contours is critical for the assessment. Manual segmentation is tedious and time consuming and suffers from inter- and intra-observer variability. Therefore, much research work has been focused on automating the segmentation of CMR images. The rapid developments and applications of deep learning algorithms have dramatically improved the accuracy of automated segmentation methods and open the possibilities for alternative approaches.
In this thesis, we first investigate and show the importance of the segmentation method for calculating cardiac anatomy and function parameters using deep neural networks. We then develop and validate our segmentation neural network using both human and mouse CMR images for both short-axis (SAX) slices and long-axis (LAX) slices in order to utilise all available information for more meaningful and accurate evaluation. We then develop our three-dimensional (3D) neural network for reconstructing ventricular surfaces using sparse contours extracted from both SAX and LAX two-dimensional (2D) slices, with or without spatial consistency between them. Finally, we integrate our segmentation and reconstruction networks into a fully automated pipeline for the assessment of mouse heart using CMR images and achieved promising results by validating against our database with both normal and infarct hearts coming from two imaging centres.
Affective vision: urban landscape photographs and their paratexts
Keywords: affect
counternarrative
urban landscape
photography
Mexico
Oxford
image/Text
practice-based Research
photobook
documentary photography

This practice-based research project focuses on how artists use paratexts to communicate extravisual phenomena such as affect and emotion in photographs of the urban landscape. I construe these environments as ‘repositories’ of personal experiences and sociopolitical histories that only become fully apparent to the viewer through texts such as titles, captions, and artist statements.
In the first three chapters, I discuss a range of photographic practitioners, describing some critical differences between photographs that share the built environment as their subject. Then, in more extended case studies, I examine the tensions that arise when artists use paratexts to elicit affective readings of their works since this external information links the images with their biography and intentions.
In the closing sections, I offer some observations on the two photobooks that constitute the practice component of my degree. The first, Border Documents, brings together short narratives of my father’s youth in Ciudad Juárez, with recent photographs of the places where those events unfolded, in an attempt to avoid the graphic violence shown in most depictions of the city. The second, A Certain Logic of Expectations, is a psychogeographical exploration of Oxford that seeks to capture the current cultural moment of Brexit. These works share a view of everyday life as a complex matrix of interconnected events that can reveal some of the social, historical, and political idiosyncrasies of the urban environment through the combination of images and texts. As such, they can be seen as counter-narratives to the cities they depict, contesting their hegemonic reputation and foregrounding what is at stake when images reinforce cultural cliches. The conclusion reached through the different strands of this research project is that the visual indeterminacy of photography can be preserved despite the involvement of language, as long as the works avoid semantic redundancy.
Photocatalytic reductive synthesis of α-functionalised amines and ethers
Keywords: umpolung
catalysis
photoredox

Chapter 1 introduces fundamental notions of photocatalysis as well as its evolution into mod- ern photoredox catalysis with seminal contributions of the past decade.
Chapter 2 describes the development of a photocatalytic three-component one-pot umpolung methodology for the diastereoselective synthesis of 1,3-diamines based on the in situ formation of nucleophilic α-amino radicals species. The method provides access to a broad range of 1,3- diamine products with a wide variety of functionalities and demonstrates its application as an entry point to bioactive molecules.
Chapter 3 details the design and application of a reductive synthetic methodolgy for the construction of challenging α-tertiary dialkyl ether compounds from readily accessible starting materials. The coupling approach pivots on a novel photocatalytic single-electron reduction of oxocarbenium ion intermediates.
Chapter 4 illustrates our efforts towards the development of a photocatalyst-free approach for the synthesis of biologically relevant α-trifluoromethyl-α-amino acid derivatives. Visible light-mediated homolytic cleavage of substituted radical precursors (RPs) is used to generate open-shell alkyl species which are believed to engage in radical addition reactions.
Halide segregation in mixed-halide perovskites
Keywords: semiconductor physics
solar cells
halide segregation
perovskite
spectroscopy

Metal halide perovskites have garnered a great deal of interest over the last few years due to their impressive – and rapidly increasing – performance as materials for solar cells. In particular, mixed-halide perovskites are essential for use in all-perovskite or perovskite-silicon tandem solar cells due to their tunable bandgap. However, one major obstacle to their use is the compositional instability some mixed-halide perovskites experience under illumination or charge-carrier injection, during which the perovskite material demixes into regions of differing halide content. Such segregation of halide ions adversely affects the electronic properties of the material and severely limits the prospects of mixed-halide perovskite technology. While, empirically, the crystallinity, stoichiometry, and optoelectronic properties of the perovskite – alongside other factors – are known to influence the halide segregation dynamics, the underlying mechanisms are still poorly understood. The work of this thesis elucidates many issues regarding the halide segregation phenomenon, and helps to explain the fundamental dynamics at the heart of this instability problem.
The dependence of the halide segregation mechanism on the atmospheric environment surrounding the perovskite is investigated, revealing that encapsulation of the films with a thick layer of poly(methyl methacrylate) allows the segregation dynamics to be fully reversible and repeatable. From measurements of photon efficacy on halide ion separation, electronic trap states are revealed to play a pivotal role in the segregation mechanism. A predictive, empirical model is created to quantify this relationship, and is shown to match results in the literature.
An investigation is conducted on full mixed-halide perovskite photovoltaic devices to study the impact of electric fields on both the dynamics of halide segregation and other mobile ionic behaviours. Three distinct defect species are identified in the perovskite, and their influence on the perovskite material is determined. Additionally, charge-carrier extraction from low-bandgap regions of perovskite suggests the existence of charge-carrier percolation pathways through grain boundaries.
Finally, simultaneous, in situ X-ray diffraction and photoluminescence measurements are made utilising a home-built setup, and are used to study the role of stoichiometry on halide segregation in two different perovskite compositions. Fast ionic pathways – proposed to exist at grain boundaries – are found to strongly impact the ionic movement associated with halide segregation, resulting in extremely different compositional evolutions in high- and low-stability materials.
Cardiovascular phenotype and response to exercise training in preterm-born adults
Keywords: hypertension
prematurity
trial of exercise
cardiac structure and function

Preterm birth affects more than 10% of live births worldwide and associates with significant increases in cardiovascular risk in later life. It occurs during a critical window for organogenesis, disrupting normal organ development, with an early, physiologically demanding transition to the extrauterine environment. This thesis aimed to further investigate the cardiac phenotype of adults born preterm and whether a prescribed aerobic exercise training intervention can beneficially modify prematurity-related cardiac changes. The first results chapter focused on normotensive adults born preterm and term (n=101) and used multimodality cardiac imaging (echocardiography and cardiac magnetic resonance, CMR) to determine whether previously observed changes in right ventricular (RV) function in preterm-born adults were out of proportion to changes seen in the pulmonary system. It was demonstrated that those born preterm had reductions in RV function, independent of any alterations to lung physiology, but that the RV remained hemodynamically coupled to the pulmonary circulation. In the second results chapter, adults born preterm and term (n=468) were studied to explore the relationship between systolic blood pressure elevation and cardiac remodelling. Using CMR, it was found that left ventricular (LV) mass index and LV mass to end-diastolic volume ratio increased more per 1mmHg rise in systolic blood pressure in preterm-born adults than in term-born adults, with the greatest change in those born very and extremely preterm. In the third results chapter, cardiac remodelling was explored by CMR following a 16-week prescribed aerobic exercise training intervention in adults born preterm and term (n=100) with elevated blood pressure. Preterm-born adults showed significant increases in systolic myocardial deformation parameters for both the RV and LV following the intervention. Overall, these findings have contributed to the growing body of research into the long term cardiovascular risk of being born preterm and the potential benefit of lifestyle interventions in this at-risk population.
The understanding and development of rhodium-catalysed asymmetric cross-coupling reactions
Keywords: reaction development
catalytic mechanism
asymmetric catalysis

This thesis examines the understanding and development of Rh(I)-catalysed cross-couplings with arylboronic acids. Our group has previously developed an asymmetric Rh-catalysed Suzuki-Miyaura cross-coupling of racemic allylic halides and boronic acids. Based on a combination of experimental and computational studies, a mechanism is proposed for this highly enantioselective transformation. The first step in the catalytic cycle is irreversible transmetalation. Oxidative addition can happen via syn- or anti-pathways and, in cases where a diastereomeric starting material is used, the diastereoselectivity is set in this irreversible step. The stereochemistry of the product is set by reductive elimination from a η3 Rh-complex formed from both allyl halide enantiomers. This study has led to a better understanding of our group’s method and we believe it will contribute towards the broader understanding of Rh-allyl chemistry and of asymmetric reactions with racemic substrates in general.
Attempts to significantly expand our group’s Rh-catalysed asymmetric Suzuki-Miyaura method, with a particular focus on forming quaternary stereocentres, are next presented. These involve the use of substrates with unsymmetric allyl units which introduces regioselectivity issues. Inspired by our mechanistic insights, these regioselectivity issues can be solved by employing enantioenriched substrates in a regiodivergent transformation.
In the final chapter, a regioselective Rh-catalysed hydroarylation of cyclobutenes is discussed. This carbometallation method can be used to synthesise biologically relevant cyclobutane products. Our group, and likely others, will continue to explore the potential and limitations of transition-metal catalysed cross-couplings with cyclobutenes.
Overall, this thesis examines the mechanism of Rh-catalysed asymmetric Suzuki-Miyaura transformations with racemic substrates and details the development of a Rh-catalysed regiodivergent Suzuki-Miyaura reaction along with a Rh-catalysed regioselective hydroarylation.
Poetic effects in prose: Virginia Woolf and Emilio Cecchi
Keywords: Virginia Woolf
epiphany
Emilio Cecchi
poetic effects
poetic style
poetry in prose
Woolf and poetic drama
lyricism
essay genre
literature and pure form

This thesis in comparative literature explores the meanings of poetry beyond verse and the ways they influenced the creation of poetic effects in the prose of two early twentieth-century writers: Virginia Woolf (1882-1941) and the Italian essayist Emilio Cecchi (1884-1966). Both authors believe that poetry, as a quality independent from verse, can be conveyed through prose, but they explicitly distance themselves from the kind of writing referred to as prose poetry or poetic prose. By addressing the question of poetry in prose from the perspectives of these two writers, who worked in different languages, genres and contexts, this study proposes a new method to approach the elusive category of poetic style, without reducing it to a set of techniques and devices borrowed from verse, or to a generic quest for beauty and emotional suggestiveness. I reconstruct Woolf’s and Cecchi’s notions of poetic quality as time-bound and culturally specific ideas, emerging at the crossing between intellectual influences, the reception of older literary traditions, and personal creative associations. By analysing the two authors’ prose through these lenses, I argue that for both of them engaging with poetry involves experimenting with multiple styles, where poetic and prosaic qualities are closely tied together and set in contrast in order to offer a double perspective on the topics treated or narrated. I identify different categories of poetic effects, classified according to their literary sources and/or their features: ‘Romantic-lyrical’ and ‘dramatic-choral’ in Woolf’s novels, ‘of contrast’ in Cecchi’s essays, and ‘of pure form’ in both authors. The thesis shows how Woolf’s and Cecchi’s ideas of poetry in prose strikingly overlap, particularly in associating poetry with an epiphanic feeling and an abstract design, but also stress different aspects of its broad spectrum, concluding that, to bring these specificities into focus, poetic effects in prose are best understood through cross-cultural enquiries.
Safe model based policy search
Keywords: Model based
Policy Search
Gaussian process
Reinforcement Learning
Safety

In this dissertation we focus on safe model based policy search, a subfield of reinforcement learning with two main objectives: data efficiency and safety. To achieve data efficient learning, we use Gaussian process regression to model the dynamics of unknown non-linear systems. The flexibility and probabilistic nature of GPs, along with their useful mathematical properties that often allow for closed form calculations, facilitate building accurate models efficiently, and using these models to optimise control policies for the underlying systems. Furthermore, our safety objective, also probabilistic in nature, is formalised as predefined state space constraints. The model's predictions are used to certify the safety of a candidate policy before deploying it on the system, and we thus manage to avoid constraint violations while training. We present an open source, openly available software tool implementing our proposed algorithm for safe and data efficient policy search. Furthermore, we propose a novel method for planning over multiple time steps with Gaussian processes, and provide formal guarantees bounding the predictive uncertainty. We consider safety and data efficiency critical challenges for the wider adoption of reinforcement learning algorithms, and we hope that our contributions will be useful in this effort.
Technocratic capacity and policy change: shaping the universalisation of healthcare in China
Keywords: Universal Health Coverage
China
Welfare reform
Healthcare system

In the first decade of the twenty-first century, the expansion of Social Healthcare Insurance coverage and public health service provision in China were compromised by regional policy fragmentation and correlated discrimination against the domestic migrant population, who moved across geographic areas. Nevertheless, how has the Chinese healthcare reform developed a new trend over the last decade, which has emphasised expanding effective Social Health Insurance coverage and equalised basic public health services to migrants, thus taking a crucial step towards Universal Healthcare Coverage? This trend is buttressed by a more unified and coordinated system that is amiable to benefit portability and wider healthcare access. Nevertheless, the received wisdom does not provide an effective explanation for such a trend. The literature shows that due to the hefty amount of autonomy enjoyed by local leaders who seek revenue-based or promotional opportunities through intense competitions with counterparts in other regions, localism is likely to persist. These local leaders have gained power from national leaders through top-down political delegation. While such a “principal-agent” framework facilitates the understanding of the complex policymaking and implementational processes within China’s multi-level governance structure, it does not show how the country overcomes some substantial institutional barriers and makes progress towards Universal Healthcare Coverage, albeit having not achieved full universalism. This thesis offers an explanation by bringing technocrats back in. I developed a nuanced “principal-agent” model, which considers the autonomy and policy impact of the technocratic community. This thesis argues that technocratic interests and actions generate an important counterbalancing impact on the policymaking tendency to fragmentation and localism, which is inherent in the incentive mechanism concerning leaders. Ministerial technocrats utilise the “promotion tournament 2.0” mechanism as an institutional guarantee to rein in local officials, while also mobilising subordinates on the basis of esprit de corps. With a collection of empirical papers, this thesis takes a mixed-methods approach to address academic debates situated at the intersection of Chinese politics, public administration and social policy disciplines.
Photochemical functionalisation of arenes and hetereoarenes
Keywords: Organic Chemistry
Photochemistry
Photocatalyst
DDQ
SNAr

This thesis describes work focused on the application of potently oxidising organophotocatalysts to synthetic methodologies. The main motivation for this work is to enable chemical transformation of otherwise unreactive species. There are many organophotocatalysts described in the literature, and they often exhibit from high reduction potentials. However, most of the work herein is centered around the common reagent 2,3-dichloro-5,6-dicyano- 1,4-benzoquinone (DDQ), 1.
An overview of the relative benefits of organophotochemistry and a discussion of DDQ photochemistry is given in Chapter 1. Also included in this chapter is an analysis of the chemistry of aryl radical cations – a key intermediate in the work that follows. Chapter 2 covers our investigations into net oxidative organophotochemistry. Chapter 3 covers the work undertaken on net redox neutral transformations. This later class was more productive on the whole, and led to a new defluorinative organophotochemical SNAr process. The conclusions of this thesis, and an outline for future work, is then provided in Chapter 4. Finally, all pertinent experimental details are provided from Chapter 5 onward.
Exploring the links between dengue epidemiology, population immune response, and vaccination
Keywords: Vietnam
vaccination
mathematical modelling
epidemiology
dengue
maternal immunity

Dengue is the most rapidly spreading mosquito-borne viral disease in humans, causing around 58.4 million symptomatic cases and leading to 10,000–20,000 deaths annually. The only licensed dengue vaccine to date—Dengvaxia®—has been found to increase the chance of severe illness among naive recipients, and thus is recommended to be used only in seropositive individuals. Therefore, assessment of the long-term risk and benefit of future routine vaccination (with a Dengvaxia®-like vaccine) is a complex task that requires an understanding of multiple aspects of dengue transmission and vaccination, such as: [1] the link between the dynamics of dengue and the immune response of the population, [2] how this link may affect the performance of a selected pre-vaccination sero-screening method (employed toidentify seropositive individuals), and [3] how vaccination may alter transmission and population immunity. This thesis consists of 3 major analyses that were designed to tackle the research questions above. The first analysis provides a statistical method to quantify the transmission intensity of dengue and to estimate the distribution of immunoglobulin G (IgG) antibody levels, using serological samples from 3 populations across Vietnam. The results of this work suggest the potential of using a quantitative approach to IgG levels to identify individuals with only 1 past infection (the primary targets of dengue vaccination). The second analysis develops a mathematical model to reconstruct the transmission dynamics of dengue in Hồ Chí Minh City (the most populous city in Vietnam) from case-record data of 2 major paediatric hospitals. Via this inference, the effect of maternal immunity on infants’ risk of hospitalisation was also estimated. The final analysis combines the findings of the 2 prior investigations in a simulation study to examine how routine vaccination may affect the number of dengue hospitalisations in Hồ Chí Minh City. Collectively, the methodology developed throughout this thesis provides a modelling framework for evaluating the future epidemiological impacts of dengue vaccination on a vaccine-free population, if a Dengvaxia®-like vaccine is to be used.