VictorJuiz/thesis huggingface dataset:
Functional genomics of the sepsis response
Keywords: transcriptomics
sepsis
eQTL

Sepsis is defined as a dysregulated immune response to infection causing organ dysfunction, and is a major area of unmet clinical need. Although conventionally considered a unified disease with a common pathway to organ failure and death, substantial clinical and molecular heterogeneity is seen, which has limited efforts to understand pathophysiology and improve therapeutic strategies. Sepsis is associated with global changes in gene expression, and genetic variants are known to affect the response to infection. This thesis therefore uses an integrated functional genomics approach to investigate disease mechanisms and variation in the sepsis response.
Data are presented for 551 patients admitted to intensive care with sepsis due to community acquired pneumonia (CAP) or faecal peritonitis (FP). The sepsis response is explored using genome-wide gene expression and proteomics data, and molecular quantitative trait loci (QTL) are mapped in the context of disease. Comparisons with cardiac surgery patients are performed to identify shared and specific aspects of the host response.
The host transcriptomic response was largely shared across sources of sepsis, although some specificity relating to viral infection and interferon signalling was observed and validated in prospectively recruited patients. Expression-based sepsis response signature (SRS) subgroups previously described in CAP were validated, and were additionally observed in FP. SRS1 is associated with higher early mortality, and shows enrichment of pathways relating to T cell exhaustion, cell death, and endotoxin tolerance. Differences between SRS groups were also observed in the FP plasma proteome. Serial sampling enabled the investigation of temporal changes in gene expression and protein abundance within patients. Lastly, disease-relevant expression QTL were identified, and interactions with source of sepsis and SRS determined, highlighting the potential impact of regulatory variation on the sepsis response.
This thesis demonstrates the benefit of an integrative functional genomics approach to explore heterogeneity in sepsis, and highlights opportunities for patient stratification and personalised medicine.
The state as a moral person and the problem of transgenerational binding
Keywords: intergenerational obligations
sovereignty
constitutions
future generations
moral individualism,
sovereign debt contracts
state personality
moral statism

Modern states are committed to the implicit assumption that one generation has the normative power to bind later generations through laws and contracts. My dissertation explores this assumption through two case studies: constitutions and sovereign debt contracts. I show that in both cases the assumption of transgenerational binding shapes the legal practices and doctrines of modern states. It informs, for instance, the ratification of eternity clauses, the interpretation of constitutions, and the doctrines of sovereign immunity and odious debt.
But although these practices of transgenerational binding are prevalent in modern states, they stand in tension, I argue, with the liberal moral commitments of these states. Liberals are committed to moral individualism, according to which only individual human beings (and some nonhuman animals) are moral persons. Moral individualism, I show, is incompatible with the assumption of transgenerational binding and its accompanying practices and doctrines. By contrast, moral statism, according to which states themselves are moral persons, can easily justify those transgenerational practice. But moral statist justifications are illiberal because they assign states intrinsic moral status above and beyond individual human beings.
I argue that liberals must engage in revisionism whichever theory of political obligation they pick — whether it is a theory of agreement, restitution, justice, reciprocity, or instrumentalism. If liberals assume moral individualism and combine it with any of these theories, they will be forced either to declare some transgenerational practices and doctrines illegitimate or to revise the justification and scope of transgenerational binding in light of instrumentalism. If liberals choose moral statism, they will be able to justify the transgenerational doctrines and practices of constitutions and sovereign debt contracts –– but only at the cost of illiberalism. The dissertation's analysis thus shows that liberals face a trilemma between illegitimacy, instrumentalism, and illiberalism.
'It's need, not greed': needs and values at work in an Italian social cooperative
Keywords: Cooperative
Economic Anthropology
Social enterprise
Third sector
Precarity
Labour

Among the key issues that arise in research of cooperatives are their supposedly hybrid nature and how they are able to balance both social and economic goals. I contend that the concept of ‘needs’ has become an important differentiating factor for the cooperatives I studied in Emilia Romagna. Placing this concept centrally in an analysis of cooperative practice helps to reveal the interplay between various value systems, reaching beyond arguments of the degeneration of cooperatives or the reproduction of dominant models, which both assume a one-way flow of influence. The recent history of the cooperative movement in Italy shows that these institutions have developed along with changing conceptions of need, supported by broader social movements and value systems. The cooperative network is today of central importance, and seen as an egalitarian means to share ideals and drive local innovation. However, my research shows that the instrumentalisation of the concept of ‘need’ also naturalises certain aspects of capitalist practice and has consequences for the enactment of other values within the cooperative. For example, in one cooperative I examined, the focus on meeting the members’ needs for work was important in justifying a decision to merge with another cooperative despite a decision-making process that was seen as less than entirely democratic. This orientation also justified the use of precarious labour, and the need to protect members’ livelihoods helped to justify low pay for internships and municipal job placements, as opposed to furthering the cooperative values of equity and equality. While the cooperative workers desired an element of personal relations, this was sometimes seen to be at odds with the focus on production and the maintenance of jobs. The marketing of more ethical products with reference to their social added value highlighted the central role of individual consumer citizens in bringing about change, which also reinforced divisions within the cooperatives based on who was more or less able to make these choices. In conclusion, I argue that while ‘needs’, like ‘added value’, can unite social and economic concepts of value, this also naturalises certain aspects of capitalist practice, particularly in this case where employment emerges as the primary need to be met. This leads me to suggest that the focus on meeting needs, as opposed to focusing on achieving specific ideals such as democracy and equality, may not be as effective to create alternative practice.
Exact categories, Koszul duality, and derived analytic algebra
Keywords: Koszul Duality
Homotopy Theory
Category Theory
Algebra

Recent work of Bambozzi, Ben-Bassat, and Kremnitzer suggests that derived analytic geometry over a valued field k can be modelled as geometry relative to the quasi-abelian category of Banach spaces, or rather its completion Ind(Bank). In this thesis we develop a robust theory of homotopical algebra in Ch(E) for E any sufficiently 'nice' quasi-abelian, or even exact, category.
Firstly we provide sufficient conditions on weakly idempotent complete exact categories E such that various categories of chain complexes in E are equipped with projective model structures. In particular we show that as soon as E has enough projectives, the category Ch+(E) of bounded below complexes is equipped with a projective model structure. In the case that E also admits all kernels we show that it is also true of Ch≥0(E), and that a generalisation of the Dold-Kan correspondence holds. Supplementing the existence of kernels with a condition on the existence and exactness of certain direct limit functors guarantees that the category of unbounded chain complexes Ch(E) also admits a projective model structure. When E is monoidal we also examine when these model structures are monoidal.
We then develop the homotopy theory of algebras in Ch(E). In particular we show, under very general conditions, that categories of operadic algebras in Ch(E) can be equipped with transferred model structures. Specialising to quasi-abelian categories we prove our main theorem, which is a vast generalisation of Koszul duality. We conclude by defining analytic extensions of the Koszul dual of a Lie algebra in Ind(Bank).
Survival or success? The Kimono retail industry in contemporary Japan
Keywords: Japan
Kimono
Economic Anthropology
Traditional Industries
Clothing

This thesis explores the ways in which the kimono retail industry in contemporary Japanese society is changing in response to the economic crisis of the 1990s and the declining popularity of the kimono as formal wear, leading to falling demand and sales. A central aim of this thesis is to address the lack of academic literature focused on the kimono, particularly economic aspects of the kimono such as the way it is made, sold and consumed. Based on twelve months of ethnographic fieldwork in Aichi prefecture, Kyoto, Tokyo and Yamagata with kimono shop owners, wholesalers, craftspeople, writers, bloggers, designers, government officials and consumers, this thesis explores how a small but influential group that I call the ‘kimono fashion network’ are aiming to change the industry from within by marketing the kimono as fashion and framing the kimono as a lifestyle choice. Their efforts have led to a monumental shift in manufacturing, marketing and selling strategies that have effectively aligned the kimono with global discourses about fashion. This shift has split the kimono retail industry into two camps: those who sell kimono as ceremonial wear for key ritual occasions such as weddings, funerals, tea ceremonies, coming of age ceremonies, graduation and school entrance ceremonies, and those who sell it for fashion. I begin by examining the socio-economic factors that led to falling demand and therefore falling sales in the industry, before exploring how the industry is structured in terms of production and distribution. Finally, I explore how and why the kimono fashion network have gone about changing the industry from within. Adding a different perspective to prevailing understandings of traditional culture in Japan as a vehicle for cultural nationalism, I argue that the contemporary kimono fashion movement has many similiarities with the global phenomenon of lifestyle consumer culture to be found across industrialised nations.
Investigation of topological nodal semimetals through angle-resolved photoemission spectroscopy
Keywords: Fermi arc
Topological Weyl Semimetal
Z2 Invariant
Topological Nodal Line Semimetal
ARPES

Nodal semimetals host either degenerate points (Dirac/Weyl points) or lines whose band topology in Brillouin zone can be classified either as trivial (normal nodal semimetals) or non trivial (topological nodal semimetals). This thesis investigates the electronic structure of two different categories of topological nodal semimetals probed by angleresolved photoemission spectroscopy (ARPES):
The first material is Indium Bismuth (InBi). InBi is a semimetal with simple tetragonal structure with P4/nmm space group. This space group is predicted to host protected nodal lines along the perpendicular momentum direction at the high symmetry lines of the Brillouin zone boundary even under strong spin-orbit coupling (SOC) situation. As a semimetal with two heavy elements, InBi is a suitable candidate to test the prediction. The investigation by ARPES demonstrates not only that InBi hosts the nodal line in the presence of strong SOC, it also shows the signature of type-II Dirac crossing along the perpendicular momentum direction from the center of Brillouin zone. However, as the nodal line observed is trivial in nature, there is no exotic drumhead surface states observed in this material. This finding demonstrates that Dirac crossings can be protected in a non-symmorphic space group.
The second material is NbIrTe4 which is a semimetal that breaks inversion symmetry predicted to host only four Weyl points. This simplest configuration is confirmed by the measurement from the top and bottom surface of NbIrTe4 showing only a pair of Fermi arcs each. Furthermore, it is found that the Fermi arc connectivity on the bottom surface experiences re-wiring as it evolves from Weyl points energy to the ARPES Fermi energy level. This change is attributed to the hybridisation between the surface and the bulk states as their projection lie within the vicinity of each other. The finding in this work demonstrates that although Fermi arcs are guaranteed in Weyl semimetals, their shape and connectivity are not protected and may be altered accordingly
A novel human stem cell platform for probing adrenoceptor signaling in iPSC derived cardiomyocytes including those with an adult atrial phenotype
Keywords: Cardiac Physiology
Atrial Cardiomyocytes
Induced Pluripotent Stem Cells
Stem Cells

Scientific research is propelled by two objectives: Understanding and recognizing the essential biology of life, and deciphering this to uncover possible therapeutics in order to improve quality of life as well as relieve pain from disease. The aim of the work described in this thesis was to dissect the fundamental requirements of induced pluripotent stem cells both in pluripotency and differentiation with a particular focus on atrial specificity.
Drug targeting of atrial-specific ion channels has been difficult because of lack of availability of appropriate cardiac cells, and preclinical testing studies have been carried out in non-cardiac cell lines, heterogeneous cardiac populations or animal models that have been unable to accurately represent human cardiomyocyte physiology. Therefore, we sought out to develop a preparation of cardiomyocytes showing an atrial phenotype with adult characteristics from human induced-pluripotent stem cells.
A culture programme involving the use of Gremlin 2 allowed differentiation of cardiomyocytes with an atrial phenotype from human induced-pluripotent stem cells. When these differentiated cultures were dissociated into single myocytes a substantial fraction of cells showed a rod-shaped morphology with a single central nucleus that was broadly similar to that observed in cells isolated from atrial chambers of the heart. Immunolabelling of these myocytes for cardiac proteins (including RyR2 receptors, actinin-2, F-actin) showed striations with a sarcomere spacing of slightly less than 2um. The isolated rod-shaped cells were electrically quiescent unless stimulated to fire action potentials with an amplitude of 100 mV from a resting potential of approximately -70 mV. Proteins expressed included those for IK1, IKur channels. Ca2+ Transients recorded from spontaneously beating cultures showed increases in amplitude in response to stimulation of adrenoceptors (both alpha and beta).
With the aim of identifying key signaling mechanisms in directing cell fate, our new protocol allowed differentiation of human myocytes with an atrial phenotype and adult characteristics that show functional adrenoceptor signaling pathways and are suitable for investigation of drug effects.
Numerical algorithms for the mathematics of information
Keywords: Computational Algebraic Topology
Topological Data Analysis
Numerical Analysis
Compressed sensing
Persistent Homology
Parallel Algorithms
Combinatorial compressed sensing
Expander graphs

This thesis presents a series of algorithmic innovations in Combinatorial Compressed Sensing and Persistent Homology. The unifying strategy across these contributions is in translating structural patterns in the underlying data into specific algorithmic designs in order to achieve: better guarantees in computational complexity, the ability to operate on more complex data, highly efficient parallelisations, or any combination of these.
Gautier, Wilde, and the visual arts: artistic media and movement
Keywords: decadence
aestheticism
Gautier
literature and the visual arts
Wilde

In nineteenth-century literary studies and histories, Théophile Gautier (1811-1872) is still largely remembered as the instigator of the doctrine of Art for Art’s Sake, mostly because of his novel Mademoiselle de Maupin (1835) and its controversial preface. This recognition is usually accompanied by a retrospective appreciation of Gautier’s work in light of the more famous authors who succeeded him and developed some of the precepts of the doctrine, such as Baudelaire.
This thesis is a comparative study of Gautier and Oscar Wilde (1854-1900) as the two main exponents of the doctrine of Art for Art’s Sake respectively in France and Britain. While comparisons between Gautier and Baudelaire have tended to highlight the superiority of the latter, a comparison with Wilde allows Gautier to be seen and understood in his own terms, and simultaneously casts a new light on Wilde’s contribution to the development of the doctrine. My study is the first to examine the works of the two authors comparatively from the vantage point of their aesthetic theories.
I argue that in order better to assess their contribution, it is necessary to start with an analysis of their experimentations with literary form. The overall aim of the thesis is to re-evaluate their fictional works which, as a result of their commitment to the doctrine, are often seen as lacking in depth and content, and as being too descriptive and decorative. The central argument is that the very decorative form of their works should be seen as the starting point of an ambitious reflection on literature, its aims and its relation to other artistic media, the visual arts in particular.
The differential Europeanisation of Central and Eastern Europe, 1989-2000: a constructivist study of the foreign policy identities of Poland, Bulgaria and Russia
Keywords: Russia
Ideas
International and domestic factors
Constructivism
Foreign Policy
Interests
Interpretivism
Poland
Realism
Europeanisation
Social Psychology
Bulgaria
Identities

The thesis addresses the puzzle of the differential integration of former communist states in the Euro-Atlantic community of nations between 1989 and 2000. Notwithstanding the predominant universalist-rationalist assumption that the adoption of an institutional-administrative blueprint for reform could lead to convergence between East and West, countries such as Poland, Bulgaria and Russia did not converge similarly (or at all) on the West European normative model and framework of international relations.
To account for this divergence, the thesis examines the impact of the culturally-historically informed, Polish, Bulgarian and Russian identities and conceptions of 'Europe' (as opposed to the formal-institutional transition from one system to another) on the process of foreign policy transformation. The doctoral research employs Constructivism, Social Psychological insights and an interpretivist methodology, drawing on 75 elite interviews.
The main argument states that differential Europeanisation can be understood on the basis of differentiated levels of inclusion and establishment of relations of mutual recognition and belongingness – ¬substantiated by a differentiated extent of ideational affinity (i.e., normative compatibility), which are (re)enacted in the interactive, mutually constitutive process of identification between Self and Other (i.e., between Poland, Bulgaria and Russia and (Western) Europe). Three propositions of 'thick', 'ambivalent' and 'thin' Europeanisation are derived from the argument (whereby the comparative benchmark of Europeanisation is an ideal-typical model of European-ness).
Key contributions focus on the development of a refined Constructivist theory and a systematic empirical comparison of Polish, Bulgarian and Russian foreign policy identities. Also, the study’s conclusions reinvigorate and reconfirm the importance of the continuity (rather than just constant flux) of culturally-historically shaped patterns of group self-understandings and sub-regional identifications as well as Constructivism’s greater plausibility in accounting for the research puzzle than (Neoclassical) Realism through the stipulation of a mutually constitutive relationship between international and domestic factors and between ideational and interest-based considerations.
Women in British Nonconformity, circa 1880-1920, with special reference to the Society of Friends, Baptist Union and Salvation Army
Keywords: Salvation
Baptist
Society
Union
Friends
church
churches
Quaker
Nonconformity
army
Protestants
women
British
Dissenters
Quakers

The reclamation and analysis of women's experiences within three Nonconformist denominations is the focus of this thesis. The first chapter places each denomination in its social and theological context, and describes its governing structures. The bulk of the thesis is devoted to situating women within this context and examining the ways in which women sought representation within male-dominated governing structures.
Chapter two examines the conflict between Friends' egalitarian theology and women's lack of governing power. Although women Friends gained access to the governing body of the Society, the issue of equality remained problematic. The chapter finishes with a discussion of the Society's split over women's suffrage. The Baptist Zenana Mission is the focus of the third chapter. Zenana missionaries claimed spiritual and imperial authority over "native" women and used the languages of separate spheres to carve out a vocation for single women in keeping with denominational norms. In so doing, they marginalised the work done by missionary wives. The fourth chapter begins with an examination of the life and theology of Catherine Booth, whose contribution to the Salvation Army is often neglected. Catherine advocated women's ministry in terms that validated both "women's work for women" and public preaching. This chapter looks at the appeal of officership for women, especially the empowering experiences of salvation and holiness, and charts the growth of the Women's Social Work. Despite the Army's egalitarian theology, conflict was felt by women officers who struggled to combine corps and family duties.
The final chapter briefly examines idealised representations of women to conclude that their defining power, while significant, was by no means hegemonic.