VictorJuiz/thesis huggingface dataset:
Learning structure-function interactions of the heart using generative deep learning methods

Cardiovascular diseases account for the highest number of annual deaths worldwide, a burden exacerbated by current limitations in disease understanding. Accurate clinical outcome prediction is key for reducing these fatalities. However, high phenotype heterogeneity of diseases like hypertrophic cardiomyopathy and myocardial infarction (MI) complicates this task. Current clinical methods used for assessing outcome risk, such as ejection fraction, are often seen as too coarse and non-specific, failing to take complex variations of myocardial shape and function into account. Thus there is a growing need for more holistic approaches. The rise of deep learning has revolutionised medical image analysis and boosted interest in generative methods for cardiac modelling, due to the networks’ inherent aptitude for capturing complex data distributions. The aim of this thesis was therefore to investigate their use in learning structure-function interactions in the heart to facilitate cardiac function modelling and aid with disease understanding and clinical outcome prediction.
This thesis shows that Generative Adversarial Networks (GANs) and Variational Autoencoders (VAEs) can be used for synthetic 2D Cardiac Magnetic Resonance (CMR) data generation, reaching high levels of image realness that can convince trained observers. It further explores modes of variation within CMR data sets and uses latent space manipulation to guide the image generation process towards creating sub-population specific cardiac data. Conditional GANs (cGANs) are then used for 2D and 3D cardiac function modelling whereby high levels of predictive accuracy are achieved. Aided by the inclusion of patient metadata, subpopulation specific cardiac contraction patterns are extracted for both healthy and diseased patient groups from which understanding of (patho)physiological differences between groups is derived. This thesis presents a state-of-the-art segmentation network for 2D long-axis UK Biobank CMR data using cGANs to achieve an epicardial Dice score of 0.971, thereby aiding in the development of 3D CMR reconstruction pipelines based on 2D slice segmentations. Additionally, a new state-of-the-art classification network for assessing the risk of developing Major Adverse Cardiac Events (MACE) in MI survivors is presented which achieves an accuracy of 74.8%. By using class activation maps, it thus enables the derivation of MACE-related pathophysiology understanding.
Overall the results presented in this thesis demonstrate the power of generative methods to capture structure-function interactions from CMR data and provide initial validation of their applicability in clinical problems.

Keywords: Variational Autoencoders
Generative Adversarial Networks
Heart
Cardiac
Deep Learning
Advisor: Grau Colomer, V
Senescence across multicellular organisms, with a focus on social species

Senescence, the increasing risk of mortality and/or decreasing rate of reproductive success, is, at first glance, detrimental to individual fitness. Developments in evolutionary theory for senescence across the 20th century, however, suggested that despite its detrimental effects, senescence is an inevitable outcome of evolution. The variable patterns of age-specific mortality and reproduction observed in nature suggest otherwise. In this thesis, I explore the variation in senescence across multicelluar organisms, with a particular focus on social species. Specifically, I: (i) review the current state of theoretical and empirical senescence research, suggesting evolutionary explanations for the variation in age-specific mortality and reproduction observed across species; (ii) quantify levels of covariation between metrics of actuarial (mortality) and reproductive ageing; (iii) model how social interactions between individuals might modulate ageing and senescence; (iv) comparatively test predictions of the model in social species; and (v) test for senescence in a wild population of a cooperative breeder. Overall, I suggest that the force of selection is still integral to understanding the evolution of senescence. The force of selection, introduced by Hamilton (1966), allows for the quantification of how strongly a detrimental allele will be selected against as a function of the age at which the allele invades. Hamilton’s results suggested that the force of selection is always a monotonically declining function with increasing organism age. By breaking assumptions from Hamilton’s model, however, we can observe forces of selection that need not always decline with age, and thus better predict the diversity of ageing patterns observed in nature.

Keywords: aging
evolutionary ecology
senescence
ageing
evolutionary theory
evolutionary biology
Advisor: Green, J
Bonsall, M
Salguero-Gomez, R
Transactions of minors in English and German law

This thesis is a comparative analysis of the ability of minors in English and German law to enter into and perform transactions, as well as of the protection that each jurisdiction provides them with. The core insight that this thesis offers is a better understanding of what the ‘protection of minors’ from improvident transactions means in each of the two jurisdictions by determining the underlying policies. English law allows minors to enter into and perform transactions and thereby dispose of their property. Minority bars only the enforcement of minors’ promises, whether directly or indirectly in tort or unjust enrichment, and subject to certain exceptions. By contrast, German law limits minors’ ability to participate in transactions autonomously nearly completely and confers all control over minors’ transactions on their parents. The latter can even act on behalf of their child as agents by statute and make their child party to transactions without the latter knowing. This thesis analyses the impact that ‘minority’ has in the areas of contract, (personal) property, and restitution of unjust(ified) enrichment in light of these policies. Following the far-reaching powers of parents over their children, a further important point of consideration in this thesis is the role which parents and the state play in protecting minors from improvident bargains. It can be shown that parents are generally in a fiduciary position in relation to their children and their property and are personally liable for breaches of duty in this regard. A proposal for English and German law to improve the protection of minors from misappropriations of their property by their parents is discussed in this context. In addition, the thesis assesses further particularities of English and German law concerning ‘minority’, such as the abstract design of German law versus the flexible and individualised approach taken in England.

Keywords: English law
Comparative private law
Property law
Underage persons
Unjust enrichment
Contract law
Minority
Comparative law
Restitution of unjust enrichment
German law
Unjustified enrichment
Contractual capacity
Advisor: Haecker, B
The impact of ageing on the human haematopoietic stem cell and memory T cell compartments through the lens of single cell transcriptome analysis

Human biological ageing comprises the molecular and physiological changes that negatively affect homeostasis with age and are strongly associated with susceptibility to disease and ultimately death.
This thesis utilises single cell transcriptomics to study the haematopoietic stem and memory T cell compartments in humans and how ageing impacts on their potential functionality in the context of health and disease.
Firstly, we have studied the human haematopoietic stem cell (HSC) compartment utilising single cell transcriptomic datasets from young and old males to address the existence in humans HSCs expressing a gene signature indicative of an output biased towards platelet generation and the inflation of this population with age. Secondly, we have studied how ageing shapes the transcriptome of the memory T cell compartment utilising publicly available single cell transcriptomic datasets with a view to investigate if recovering from a severe case of COVID-19 shares biological processes with ageing in the context of the memory T cell compartment of a healthy donor cohort.
Our study of the HSC compartment has shown that a computationally defined HSC populations exhibiting the gene expression patterns associated with platelet bias in murine HSCs can be identified in healthy human males. The previously identified HSC population is enriched in old individuals. Moreover, this population exhibited the transcriptomic features associated with previously documented HSC populations with high self-renewal capacity and quiescence. With ageing there were no major shifts in which pathways were upregulated or downregulated, but more of an accentuation of the transcriptomic programmes already present at younger ages.
An ageing-associated inflammatory gene expression signature was identified at the level of the memory T cell compartment of the studied healthy human cohort. Known signalling pathways and gene families associated with ageing in the T cell compartment such as IL-10 signalling were associated with this signature as well as novel ones such as the aminoacyl-tRNA synthetases. By leveraging a machine learning-based methodology, it was shown that at the level of the memory T cell compartment, the most important biological processes that are shared between ageing and recovering from COVID-19 are IL-10 signalling and BAX-mediated apoptosis.
The potential functional implications of the ageing associated observations made in the human HSC and memory T cell compartments remain open questions that could potentially allow us to understand what are the signals that determine fate specifications in HSCs and the long-term deleterious effects of experiencing a respiratory viral infection on the functionality of the adaptive immune system.

Advisor: Vyas, P
Nerlov, C
The Ministry of Health, 1919-1929 : ideas and practice in a government department

The subject of the thesis is the Ministry of Health's first decade. The chapters may be separated into three loosely related parts. After an introduction setting out the scope of the study, the first part - composed of two chapters - concerns itself with the Ministry's origins and the early months of its existence. ts departmental antecedents are identified and their administrative cultures defined. The impact of the Report of the Machinery of Government Committee, 1918 (Cd. 9230) on thinking about the Ministry's organisation is assessed. The actual arrangement of the department's permanent staff is dealt with in the second chapter, the latter section of which charts the ways that changes in the department's operation reflect changes in Civil servants' views about their bureaucratic function. Particular attention is paid to the Ministry's first permanent secretary, Sir Robert Morant; to the relations of the lay and administrative classes; and to the attitudes and thinking of Sir Arthur Robinson, Morant's successor.
The second part is a political biography of Neville Chamberlain, thrice Minister of Health and from 1924 to 1929 the sixth incumbent. t considers the elements in his family back- ground and in his career that fitted him for this ministerial position; and it examines his work practices and relations with official advisers.
The subject of the third part - the last two chapters - is the condition of local government in the 1920s as perceived by various officials and members of government enquiries. It discusses the work of the Royal Commission on Local Government, 1923-29 and the drafting of the Local Government Act of 1929.
The thesis is completed by a conclusion and by four appendices. The first two list the Ministers of Health and their principal officials in the interwar period. The others provide details of the careers, hierarchy, and Salary scales of the department's permanent staff. There is an extensive bibliography.

Keywords: Great Britain
Public health administration
Ministry of Health
twentieth century
20th century
government
Advisor: Harris, J
Vox legati vox rei publicae

Relying on prior work in the incorporation of sociolinguistic concepts of 'impoliteness' into studies of international relations and diplomacy, this thesis utilises mixed qualitative and quantitative methods to comprehensively analyse speeches delivered by representatives of the People's Republic of China at plenary sessions of the United Nations General Assembly. In adjudging between plausible explanations contained in the literature for the actions at multilateral international institutions, this thesis finds a complex relationship between deployment of undiplomatic language at multilateral fora and a state's relationship with a putative international order. Findings strongly supported include rising power trends, core interests defence, and naming-and-shaming socialisation.

Keywords: Foreign policy
Socialisation
China
Diplomacy
Politeness theory
Mixed methods
Undiplomatic language
International relations
Sixteenth-century intabulation processes and their relationship to the formation and understanding of Sweelinck's keyboard style

This study assesses the nature of sixteenth-century intabulation processes. Rather than being merely techniques of arrangement they are part of the imitatio tradition which is central to the musical language of sixteenth-century Continental polyphonic composition. M.A. Cavazzoni's music shows an understanding of the modal procedures and cadential structures of Renaissance vocal polyphony. Ornamentation and figuration are subject to a more fundamental underlying structure of periodic imitation, as they are in intabulation. In the music of Girolamo Cavazzoni the structures of a plainchant melody - its cadences and modal characteristics - are reworked by the keyboard composer into a polyphonic imitative piece. Intabulation processes from Spanish and Italian sources of the late sixteenth century show that an overall periodic imitative structure and the elaboration of cadence is more important to the Continental keyboard composer than “idiomatic" figuration itself.
Chapters 4 and 5 confirm the Continental background to Sweelinck's music which can be seen in his vocal music. John Bull's "late" style responds to Continental concerns for imitatio. This suggests the reverse of the widely held view that English keyboard music influenced that of the Continent in the early decades of the seventeenth century. Figuration patterns are an unreliable guide to underlying compositional processes. Sweelinck's keyboard music is influenced by intabulation processes. Even the toccata, the texture of which grows from a polyphonic reworking of the psalm tone, can be seen as part of the same tradition as the intabulation. The English fantasia style is based on the development of small-scale patterns whereas periodic imitation dominates Sweelinck's musical thought. Figuration patterns are of secondary importance. The study concludes that Sweelinck's music is part of the Continental imitatio tradition and that the influence of the English virginalists on his style is negligible.

Keywords: intabulation
16th-century
Sixteenth-century
keyboard instrument music
keyboard music
musical style
arrangement
Sweelinck
Advisor: Harper, J
Caldwell, J
The popularity and influence of Spohr in England

The popularity and influence of Louis Spohr have been misunderstood or ignored by musical historians of the present century. In a few cases there has been an uneasy recognition that he occupied a more prominent position in the eyes of contemporaries than the current neglect of his music might suggest, but no modern scholar has attempted a detailed examination of the attitudes which obtained towards him during his lifetime or an adequate investigation of the elements of his style and its influence on other composers. There are strong grounds for believing that the well documented admiration of many of the most important of his younger German contemporaries was not without its fruits in their music.
This thesis attempts to establish the extent and nature of his impact in England. In all previous studies of English music during these years (1820- 1860) Spohr has not warranted more than a few generally dismissive sentences; from the evidence presented it will be clear that not only is this an inadequate account of his importance as a composer, but also a gross distortion of our understanding. of the English musical scene at that time. Looking at English music from the central or near central position which Spohr occupied in the 1830's and 1840's reveals much about the development of taste and sheds light upon trends and opinions which are otherwise imperfectly understood. The fact that Spohr's music was believed by many to represent the stoutest bulwark of good taste and seriousness of purpose in contemporary music during that period is of prime importance. Much light is also thrown on musical journalism and the camps into which it was divided, though more questions are raised than can possibly be answered adequately in the space available.
Chapters 1 to 6 attempt a detailed reconstruction of shifting attitudes towards Spohr between 1820 and his death in 1859 and relate them to general trends in the English musical world. Chapter 7 traces the stages by which his reputation declined. Chapter 8 considers his style and its origins. And Chapter 9 examines his influence on English composers. Appendix A examines the career of Edward Taylor. Appendix B lists all performances of his music in England between 1820 and 1859 which it has been possible to trace. Appendix C lists English publications of Spohr's works reviewed in periodicals from 1820- 1833. The periodicals section of the bibliography makes a tentative identification of musical critics together with the dates at which they were writing for particular journals.

Keywords: popularity
England
Spohr
nineteenth century
influence
music
19th century
English music
Louis Spohr
Validation of flow simulation model using particle image velocimetry data and dimensionality reduction techniques

In-cylinder air motion has a profound influence on the mixture preparation and subsequent combustion in the internal combustion engines. The particle image velocimetry (PIV) technique provides a quantitative tool to measure the in-cylinder air velocity with high spatial and temporal resolution. Additionally, the in-cylinder flow velocity field can also be simulated by computational fluid dynamics (CFD) tools, of which the Reynolds averaged Navier-Stokes (RANS) method predicts the overall flow structures with acceptable accuracy and affordable computational cost for widespread industrial applications. In order to provide a more accurate and robust prediction, the simulation results need to be validated against the experimental measurements. In this thesis, the crank-angle resolved in-cylinder air flow fields were measured using the PIV technique in multiple planes of a near-production optical engine under different working conditions for a few hundreds of consecutive cycles. The measured flow fields show a high consistency over multiple measurement planes and across different test runs, and hence they can be used to validate the flow simulation model. Vector field comparison metrics were used to compare the measured and the simulated flow fields, and to identify the regions of interest and differences in flow characteristics. Due to the nature of averaging physical parameters in RANS, its validation against experimental results obtained by particle image velocimetry (PIV) requires consideration of how best to average or filter the measured turbulent flows. During the validation process, it was found that the use of the conventional PIV ensemble mean flow field may lead to biased conclusions in some cases. Therefore, two dimensionality reduction techniques, namely the proper orthogonal decomposition (POD) and the kernel principal component analysis (KPCA), were used to preserve the large-scale cycle-to-cycle variations while filtering out the small-scale turbulent fluctuations in experimental measurements, and hence enabled a fair comparison to the RANS simulations. Recommendations are made on how to provide an appropriate validation between measured data and simulation results in highly fluctuating flow fields such as the in-cylinder air motion.

Keywords: kernel principal component analysis
particle image velocimetry
proper orthogonal decomposition
Advisor: Stone, R
Williams, B
Role extraction, dynamics, and optimisation on networks

Understanding the relationships between products is an important problem in industry, where two central concepts are complements and substitutes. Complementary products are sold separately but used together, each creating a demand for the other, while substitute products can be used in place of each other, each taking a demand from the other. Hence, such two competing product relationships are also essential in further understanding how the demand change of some products transforms into the change of the whole range of products.
To start with, we capture the information in the sales transaction data through a bipartite network representation, then products of the two competing relationships can be characterised as certain roles in the network. For this reason, the identification of the nature of a relationship between products is directly related to the more general problem of role extraction in network science. Targeting at extracting the two specific roles, we propose a novel customised data-driven role extraction method. With the product relationships, we can consider unipartite networks only of products, and then the change of demand can be modelled as dynamics on top of such networks. Further, the associated decision making can be formulated as optimisation problems with appropriate objectives. In this thesis, we consider the one that is closely related to viral marketing, where we aim to maximise the overall revenue through putting a small range of products on promotion. We model the dynamic of demand changes as information propagating through the network, and the overall change as the influence on each node, thus the problem is then a variant of the influence maximisation, where our objective is a (price-)weighted sum of the influence. Accordingly, we propose a novel class of information propagation model for demand dynamics, unifying the mechanisms underlying the classic models, and a general framework for the associated influence maximisation problem, from simple networks of a single relation to signed networks of two competing relations.
Although inspired by the retail industry, the proposed role extraction method can be applied to other contexts, including trading networks, ecological systems and social networks, where both the identification of cooperative and competitive relations are of interest. Further, the proposed information propagation model and influence maximisation framework are also applicable to more general dynamical processes on either simple or signed networks, including social networks with trust-distrust relationships and brain networks with positive-negative functional connections.

Keywords: Influence maximisation
Role extraction
Information propagation
Complementary and substitute relationships
Networks
Advisor: Lambiotte, R
Wallis, A
Lautz, S