VictorJuiz/thesis huggingface dataset:
Categorical post-quantum theories

In this thesis of two Parts, we investigate the application of categorical methods to modelling post-quantum theories.
In Part I we study hyper-decoherence between quantum-like theories. Chapter 1 serves as an introduction to Categorical Probabilistic Theories which combine elements of Categorical Quantum Mechanics and Operational Probabilistic Theories, and to CPM categories which generalise the CPM construction of Selinger to allow for richer group symmetries. In Chapter 2 we study the theory of density hypercubes which exhibits a hyper-decoherence mechanism witnessing quantum theory as an effectful subtheory. We show that this hyper-decoherence process is probabilistic within the theory of density hypercubes and discuss some plausible operational interpretations of this. As a result, we side-step a no-go result regarding the existence of deterministic hyper-decoherence maps, showing that it is nevertheless possible for a post-quantum theory to possess probabilistic hyper-decoherence maps. In Chapter 3 we focus on a particular case of the CPM construction, where the symmetries are generated by the Galois group of a finite field extension. We discuss how to construct probabilistic theories which form towers of decoherence in bijection with the subfields of a Galois extension. These towers generalise the decoherence process of standard quantum theory.
In Part II we study profunctorial methods and their application to spacetime and quantum supermaps. Chapter 4 serves as an introduction to profunctors, promonoidal categories and premonoidal categories, including the enriched version of the latter. Chapter 5 introduces some toy categories of causal curves in spacetime and discusses how we might upgrade the partial monoidal structure of such categories to a total tensor using both pre- and promonoidal categories. Chapter 6 makes this combination of pre- and promonoidal categories more formal, introducing the notion of a pro-effectful category. In the final Chapter 7 we describe how we can use the category of coend optics as a model of quantum combs. We describe the promonoidal structures on this category and their interpretation as horizontal and vertical composition of holes in monoidal categories. We also generalise coend optics to allow for a premonoidal base category, and point towards how the methods of this Chapter might be extended to include arbitrary quantum supermaps.

Keywords: supermaps
profunctors
quantum theory
hyper-decoherence
Advisor: Kissinger, A
Gogioso, S
Immunological and genetic correlates of delayed HIV disease progression in children with perinatally-acquired HIV-1 infection from Harare, Zimbabwe

Understanding the immunological and genetic mechanisms that contribute to HIV-1 disease progression is important in the development of antiviral therapies and vaccines. HIV-1 has evolved to downregulate the cell surface expression of HLA class I in order to avoid the presentation of viral peptides to cytotoxic CD8+ T cells. HLA class I molecules are loaded with antigenic peptides in the endoplasmic reticulum (ER) by the peptide loading complex (PLC), aided by the molecular chaperone protein tapasin. Tapasin promotes the selection of high affinity peptides on HLA class I for presentation to T cells. HLA class I alleles exhibit different dependencies on tapasin for peptide selection and loading. This thesis aimed to investigate the role of tapasin and HLA class I tapasin-dependency in HIV-1 infection. Chapter three describes an association between tapasin-independent HLA class I alleles and slow disease progression in a cohort of children and adolescents with perinatally-acquired HIV-1 infection from Harare, Zimbabwe. Our study then aimed to use the evidence from our clinical data analyses to inform in vitro studies investigating whether HIV-1 interferes with the PLC or tapasin, as has been observed for other viruses. Chapter four describes how HIV-1 downregulates tapasin-dependent HLA class I alleles more efficiently than tapasin-independent alleles. We also show that downregulation of HLA class I by HIV-1 is impeded in PLC knockout cells. Chapter five aimed to assess how HIV-1 affects PLC mRNA and protein expression levels. We show that HIV-1 does not downregulate tapasin, but further experiments are required to interpret the association between HLA class I tapasin-dependency and HIV-1 control. Finally, chapter six describes how tapasin-independent HLA class I alleles are more stably expressed in HIV-1 infection, compared to tapasin-dependent alleles. This thesis provides evidence to show for the first time that HIV-1 may affect tapasin function.

Keywords: HLA
AIDS
HIV
Tapasin
immune evasion
Advisor: Rowland-Jones, S
Ferrand, R
Gea-Mallorqui, E
The ecological and the existential: sound and subjectivity in the works of Salvatore Sciarrino and
Helmut Lachenmann

This thesis demonstrates the ways in which sound and sonic procedures represent the Self and its crisis in the works of Salvatore Sciarrinio (b. 1947) and Helmut Lachenmann (b. 1935)—two composers who write music that involves extensive use of extended instrumental and vocal techniques. It also interrogates how the musical representation of the subject reflects the condition of human subjectivity as it was considered in contemporary intellectual discourse. This thesis begins with a conceptualization of the commonality in the musical poetics of the two composers and a theorization of a reception perspective that facilitates a fruitful interpretation of their music—based on the constellational and ecological approaches. The five chapters that follow analyse specific musical techniques in the light of some of their key aesthetic notions, exploring the condition of subjectivity through hermeneutic reading and philosophical reflection. Chapter 2 considers Sciarrinio’s mimetic gestures and the ideas of naturalism and organic music, arguing that Sciarrino’s music calls forth a post-humanist biotic aesthetics that at the same time embraces and negates classical organicism. Chapters 3 and 4 are devoted to two of Sciarrino’s operas. The former explores Luci mie traditrici through the idea of the semanticization of musical form, demonstrating that a Lacanian barred subject underlies the opera’s portrayal of troubled intersubjective relationships. The latter analyses the ecological significance of the multi-dimensional space-time in Lohengrin and revisits Sciarrino’s mimesis through the concept of becoming; it argues that the opera’s representation of a Proteus-like subjectivity enriches Sciarrino’s sonic mimesis. Chapter 5 deals with the relationship between nature and structure in Lachenmann’s musique concrète instrumentale, using the notion of aura to shed light on the way in which a self-reflexive listening subject comes into being in “…zwei Gefühle…”. Chapter 6 probes the entanglement of sound, image, and text in Lachenmann’s Das Mädchen mit den Schwefelhölzern through an investigation of the compositional procedure; the analysis demonstrates that the music’s articulation of a subjective voice is embedded in a sonic procedure that requires the deciphering work of an ideal listener.

Keywords: ecological approach to musical perception
Salvatore Sciarrino
sound
subjectivity
listening
music as existential experience
organicism
ecology of music
Helmut Lachenmann
musical meaning
Advisor: Clarke, E
Cross, J
Acting imperially: race, performance, and cinema in interwar Britain

This thesis explores the role of race, racism, and colonialism in British cinema culture of the 1920s and early 1930s. It argues firstly that silent film performance is received as a racialised element of film form in Britain; race is ‘read’ by British audiences into movements, gestures, and expressions. This is inflected by colonial constructions of racialised bodies and imperial geographies: the intimacies and distances between racialised groups that theorists argue underpin racial difference. Whereas many scholars have demonstrated that interwar British cinema entails performances of class, gender and national identities, this thesis foregrounds the performance of racial identity, often in ways which override or obscure these other social distinctions.
Secondly, it posits that this performance of racial difference informs constructions of taste, decorum, and style in British cinema. Racialised performance determines perceptions of cinema’s effect on the body—of both performers and spectators—and the way it represents and disseminates British cultural and imperial heritage and history. Through performances of race, British filmmakers and critics construct cinema as entertainment, art form, historical record, and colonial educational tool. This thesis takes the reception and production in Britain of four case study genres, the ‘Eastern’, the Limehouse melodrama, the expedition film and the British documentary, to evidence this. Representing different kinds of racialised performance, inflected by the specific settings and forms of racialised encounter depicted in each genre, these case studies raise different aesthetic and political concerns that are all explored through the racialised bodies that take centre stage.

Keywords: British cinema
Colonial cinema
Cinema
Interwar Britain
Film history
Race
Performance
British Empire
Advisor: Das, S
Marcus, L
Interactive medical image segmentation - towards integrating human guidance and deep learning

Medical image segmentation is an essential step in many clinical workflows involving diagnostics and patient treatment planning. Deep learning has advanced the field of medical image segmentation, particularly with respect to automating contouring. However, some anatomical structures, such as tumours, are challenging for fully automated methods. When automatic methods fail, manual contouring is required. In such cases, semi-automatic tools can support clinicians in contouring tasks. The objective of this thesis was to leverage clinicians’ expert knowledge when performing segmentation tasks, allowing for interactions along the segmentation workflow and improving deep learning predictions.
In this thesis, a deep learning approach is proposed that produces a 3D segmentation of a structure of interest based on a user-provided input. If trained on a diverse set of structures, state-of-the-art performance was achieved for structures included in the training set. More importantly, the model was also able to generalize and make predictions for unseen structures that were not represented in the training set. Various avenues to guide user interaction and leverage multiple user inputs more effectively were also investigated. These further improved the segmentation performance and demonstrated the ability to accurately segment a broad range of anatomical structures.
An evaluation by clinicians demonstrated that time spent contouring was reduced when using the contextual deep learning tool as compared to conventional contouring tools. This evaluation also revealed that the majority of contouring time is observation time, which is only indirectly affected by the segmentation approach. This suggests, that user interface design and guiding the user’s attention to critical areas can have a large impact on time taken on the contouring task.
Overall, this thesis proposes an interactive deep learning segmentation method, demonstrates its clinical impact, and highlights the potential synergies between clinicians and artificial intelligence.

Advisor: Gooding, MJ
Stride, E
Vallis, K
Electrochemomechanics of lithium metal and alloy anodes for solid-state batteries

The fracture of ceramic solid electrolytes, driven by the plating of lithium within cracks, has been identified as one of the fundamental issues to successfully develop solid-state batteries. Understanding the mechanics of lithium at the nanoscale is therefore essential. In the first experimental chapter, the elastic and plastic properties of lithium are measured by nanoindentation within an electron microscope. Lithium metal samples are characterized by electron backscattered diffraction before and after indentation to understand the dependence of the mechanical properties on crystallographic orientation and determine the stiffness tensor components, moduli, and Poisson’s ratio using a method first proposed by Vlassak and Nix. The measured stiffness tensor components are C11 = 13.3, C12 = 11.2, and C44 = 8.8 GPa. Hardness measurements show a clear size effect with hardness in excess of 100 MPa observed for indent depths below 300 nm, which could contribute toward observed lithium filament propagation.
Lithium alloys have the potential to overcome anode-side challenges in solid state batteries. In the second experimental chapter, lithium-rich magnesium alloys are synthesised and characterised, quantifying the changes in mechanical properties, transport, and surface chemistry that impact electrochemical performance. Increases in hardness, stiffness, adhesion, and creep resistance are quantified by nanoindentation as a function of magnesium content. A decrease in diffusivity is quantified with 6Li pulsed field gradient nuclear magnetic resonance spectroscopy and chronopotentiometry, and an increase in interfacial impedance due to the presence of magnesium is identified with electrochemical impedance spectroscopy which is correlated with x-ray photoelectron spectroscopy data. Throughout, changes in properties are linked to electrochemical performance. This work provides a framework to investigate other lithium alloy systems.
The performance limitations of lithium metal are holding back the development of solid-state cathodes and lithium-free anodes. In the final experimental chapter, indium-lithium alloys are explored as a combined counter and reference electrode for all-solid-state batteries. They enable high current densities without shorting, fast discharge capacity, and high cycle stability. The performance is attributable to very fast diffusion kinetics in the InLi intermetallic, D298KLi =5.8×10−7 cm2s−1. The indium metal phase is essentially ion-blocking, so the performance is tied to the microstructure, which evolves during charge and discharge. A two-layer microstructure is proposed which offers good accessible capacity and good cycle life at high current densities.

Keywords: battery
nanoindentation
solid state
lithium
alloy
Advisor: Pasta, M
Reach for the sky: A typology of angelic discourse and its liturgical impact within the Yaḥad.

And God said, 'Let there be lights in the firmament of the heaven to divide the day from the night; and let them be for signs, and for seasons, and for days, and years...'(Genesis 1:14).
Time was created and a method for determining a calendar was invented. In creation, God gives us time and space, a separation of the heavenly and the earthly, and a Sabbath day on with which to worship God. Yet God also transcends time and space, being both the beginning and the end - 'the alpha and omega' - the past, the present and the future all at once. What if humans also had that ability: a way of being connected with the past, present and future; an intellectual transcendence of the earthly into the heavenly?
This thesis uses spatial theory to analyse the angelic and priestly discourse of the Songs of the Sabbath Sacrifice (Shirot), and its liturgical impact within the Yaḥad. Firstly, scriptural tropes and themes are investigated to show how these are later incorporated into the development of the Shirot and the inter-relationship between God, divine beings and humanity. Secondly, the placement of the Shirot within the liturgical calendar at Qumran is analysed. Thirdly, spatial theory is used to investigate the text of the Shirot, focussing on the heavenly hierarchy of angelic beings and their function within the priestly ministry of worship in heaven. Finally, the connection between angelic beings and the earthly community using the Shirot is scrutinised. The question of 'what does it mean to be a member of the Yaḥad?' is addressed, before investigating the formation or transformation of the use of communal liturgy like the Shirot, in order to understand to what extent liturgical worship like the Shirot contributed to the formation of identity and self within the Yaḥad's quest for perfection.

Keywords: Dead Sea Scrolls
Songs of the Sabbath Sacrifice
Worship
Yaḥad
Angelology
Jubilees
Calendar
Space
Liturgy
Self
Fire
Advisor: Najman, H
The careers of Roger and Robert Morris, architects

This thesis is concerned with an examination of the life and work of the mid eighteenth century architect Roger Morris and his kinsman, the Palladian theorist and surveyor Robert Morris.
Roger Morris was one of the pioneers of the Palladian movement in England. Owing to the paucity of drawings and other documentary evidence associated with him, however, Morris has frequently been overshadowed and neglected in favour of more fully documented architects such as Campbell and Kent, and particularly his patron and architectural collaborator, the 9th Earl of Pembroke. This work attempts to establish Morris as a leading architect of the period: uniquely skilled in carpentry and bricklaying as well as in the field of architectural design, by the late 1720s Morris was already the principal architect of the circle of the Prince of Wales (George II after 1727), a group which provided Morris with the bulk of his practice. At the same time Morris continued to exercise his skills as a craftsman. This thesis attempts to determine the extent of his practice - clarifying his authorship of attributed buildings where possible - and to trace the financial and social success commensurate with his professional progress. It also defines his unique architectural style, an unusually eclectic combination of standard English Neopalladianism and elements of Baroque, Neoclassicism and Gothic.
Robert Morris was the first theorist of the Palladian movement in Britain and, as such, became a considerable influence on subsequent architects both in Britain and in America. Having trained as a joiner, he studied architecture with Roger Morris, whose buildings became a major influence on his writings. This work delineates his use of contemporary, Renaissance and Antique artistic theory to form a consistent system embracing architectural form, proportion and siting unique in British architecture. Additionally, the extent of Robert Morris’ surveying, designing and literary activities is defined, where sources permit.

Keywords: Robert Morris
architects
Great Britain
18th century
careers
Roger Morris
eighteenth century
Rebuilding a superenhancer to investigate the additive and synergistic effects of its individual components

Superenhancers are clusters of putative enhancers, densely occupied by histone 3 lysine 27 acetylation, transcription factors, and coactivators such as the mediator complex. There is a tendency for superenhancers to regulate key cell-type-specific genes, and their dysregulation is often associated with disease. It remains unclear whether superenhancer constituent elements work independently or collaboratively and whether they have distinct roles in activating expression of their cognate genes. During my DPhil, I address these two questions by studying a model mammalian superenhancer at the mouse α-globin locus, active exclusively in erythroid cells. I sought to determine how the five constituents (R1, R2, R3, Rm, R4) of the mouse αglobin superenhancer exert control over α-globin gene expression during erythropoiesis. Firstly, I tested the sufficiency of the previously described strongest αglobin superenhancer constituent (R2) to independently activate α-globin expression; this entailed characterising, in detail, a mouse model in which the other four α-globin superenhancer elements have been removed from the native locus. Surprisingly, I show that this strong enhancer is incapable of driving the expected level of expression, independently. Secondly, following synthetic biology and genome editing techniques in mouse Embryonic Stem Cells (mESCs), I rebuilt the native α-globin superenhancer in all informative combinations, starting from an enhancer-less baseline in which all five constituents have been removed. Examination of molecular phenotypes of erythroid cells derived from the engineered mESCs revealed a complex relationship between inequivalent constituents which cooperate in additive, synergistic, and redundant fashions. I also uncovered a novel class of regulatory element within the αglobin superenhancer, which I named facilitators. Unlike canonical enhancers (R1, R2), facilitators (R3, Rm, R4) have no intrinsic enhancer activity. However, they are necessary to potentiate canonical enhancers, in order to attain optimal levels of target gene expression. Lastly, by comparing the impact of the three facilitators on gene expression, I discovered a functional hierarchy that seems to be position-dependent. Ultimately, I have rigorously dissected the α-globin superenhancer and described a new class of regulatory element, which I named facilitators, that were previously mistaken for weak enhancers. Furthermore, I unravelled a necessary mode of cooperation manifested between two types of superenhancer constituent elements, canonical enhancers and facilitators, highlighting an emergent property of a superenhancer.

Advisor: Kassouf, M
Higgs, D
The last modernist wave: a metamodernist approach to Greek literature of the 1960s

This thesis discusses the peculiar cultural landscape of Greece in the ‘long 1960s,’ arguing that this period, extending from around 1956 to 1974, constitute a case of metamodernism. Metamodernism, defined as a structure of feeling, emerges from the interplay between established modernist figures and emerging intellectuals, set against a backdrop of intense political instability and rapid economic growth.
The thesis consists of four chapters. Chapter One delves into the cultural production of the Greek 1960s, eliciting in the intellectual debates the ‘condition of the boundary,’ an affect linked to a diffused sense of crisis stemming from societal and cultural transformations. These elements converge in metamodernism, adopted from English Studies and retroactively adapted for the Greek long 1960s. The next three chapters examine four literary works that engage with classical mythology, a hallmark of modernism, and used in this thesis as a catalyst for discussing broader issues regarding metamodernism and the Greek 1960s. Chapter Two examines Yannis Ritsos’s Τέταρτη διάσταση, exploring the role of the boundary-affect in the collection’s development and reinterpreting the concept of the ‘fourth dimension’ as a Bergsonian durée. Chapter Three centres on Stelios Xefloudas’s novel Οδυσσέας challenging the conventional use of the mythical method and delving into the violent cyclicality of history through Walter Benjamin's historiosophy. The final chapter explores Margarita Liberaki’s screenplay for Jules Dassin’s film Phaedra and her later play Το μυστικό κρεβάτι ή Τηλέγονος, problematising the question of Greekness from the standpoint of diasporic subjects and through a feminist lens, underscoring the performative nature of national identity and the transformation of the desire for nostos, shifting from the diaspora to Greece itself.
The major contribution of the thesis is the re-evaluation of the relationship between Greek modernism and the 1960s, as well as the more localised contribution to the contemporary theorisations of metamodernism, revealing its flexibility and productivity.

Keywords: modern Greek literature
Margarita Liberaki
metamodernism
sixties
Giannis Ritsos
Stelios Xephloudas
classical reception
Advisor: Papanikolaou, D