VictorJuiz/thesis huggingface dataset:
Evolution and development of the olfactory neurons in the olfactores clade

In vertebrates, specialised olfactory systems and associated neurons are crucial to sense the outside chemical world. They also play a notable part in reproduction with the role of GnRH-producing neurons, derived from the olfactory placode, in sexual maturation and fertility. Despite the vital importance of these olfactory cell types, our knowledge of their evolutionary origin remains limited. In this work, a comparative approach is undertaken to study the development of olfactory neurons and provide insights into their evolutionary history. Two main organisms are used for comparison: the lamprey Lampetra planeri and the ascidian Ciona intestinalis. These model species are used to investigate the expression, regulation, and function of specific genes to trace olfactory cell type relationships across vertebrates and their chordate relatives. First, the embryonic origin and specification of hypothalamic GnRH secretory neurons in lamprey is examined to develop a pan-vertebrate view of the origin and specification of these crucial neurosecretory cells. The potential association during embryogenesis with the developing olfactory system is investigated and this study provides support for the hypothesis that lamprey hypothalamic GnRH cells do not derive from the nasal placode, despite some specification mechanisms appearing conserved with olfactory-derived GnRH neurons of jawed vertebrates. Second, it is revealed that the palp axial columnar cells (ACCs) of Ciona have homologies with olfactory sensory and secretory neurons of vertebrates. The regulation, expression, and function of MS4A and GnRH genes in the palp ACCs, combined with data from vertebrates, suggest a common evolutionary origin at cell-type level to explain how the olfactory-derived cell types in vertebrates derived from an ACC-like GnRH/chemosensory multifunctional precursor by segregation of functions. Finally, a microfluidic chip for immobilisation and controlled stimulation of Ciona larvae is designed and built to interrogate whether the larva responds to chemical stimuli. The detection by live cell calcium imaging of a CO2-evoked response upon chemical stimulation represents the first experimental evidence that ascidian larva sense chemical cues in their environment and provides a valuable tool for further investigations.

Keywords: development of olfactory neurons
evolution
Advisor: Shimeld, S
Liquid crystal phase-only modulator and optical beam steering system

This thesis describes the development of a new analogue, phase-only liquid crystal (LC) modulator and an LC-based optical beam steering configuration. To begin with, a new and simple method for the rapid and precise measurement of the flexoelectro-optic performance of large tilt-angle chiral nematic LC is presented. These large tilt angle LCs are then employed in the development and demonstration of a flexoelectro-optic LC phase modulator with >2π phase range and sub-millisecond response. It is shown that the voltage-induced rotation of the optic axis is converted into a phase modulation with the aid of a reflective device configuration incorporating a ∼5 μm LC cell, a polarizer, two quarter-wave plates, and a mirror. It is then demonstrated that the mirror and quarter-wave plate can be replaced with a chiral reflector, which improves the robustness of the system.

Based on the reflective phase modulator, two different transmissive phase modulators are considered, which consist of either adding a half-wave plate in between two LC layers when the electric field applied to the two layers is the same or by applying electric fields of opposite polarity, avoiding the need for an additional half-wave plate. Even though those phase modulators can generate 2π phase modulation with sub-millisecond response time, a key disadvantage is that numerous optical components are required. In order to solve this, a LC phase modulator that combines a flexoelectro-optic LC layer, a polymerized reactive mesogen layer and a mirrored substrate is presented, which demonstrates the potential for making next-generation LC on silicon spatial light modulators. In the final part of this thesis, LC phase modulators are combined with LC polarisation gratings to form a novel beam steering for optical communications.

Keywords: integrated device
SLM
fast response
phase modulation
liquid crystal
Advisor: Morris, S
Elston, S
Sex, communism, and videotapes: Polish sexual (r)evolutions, 1956-1989

The thesis investigates the history of state-socialist sexualities in Poland through the lens of visual culture. By focusing on phenomena such as striptease shows, nude photography exhibitions, beauty pageants, and pornographic videotapes, the thesis examines the changing approaches toward nudity and sex in Polish public discourse between 1956 and 1989. Thus, the dissertation seeks to uncover the forgotten history of state-socialist sexual (r)evolutions and engages critically with the scholarship on the global sexual revolution to complicate our understanding of this phenomenon beyond the usual Cold War stereotypes.

Methodologically, this dissertation focuses on the role sexuality played in dominant discourses that attempted to redefine, modernise, and control both male and female bodies. Inspired by Michel Foucault’s approach to the history of sexuality, this thesis focuses on discourse and perceives it as a primary field in which sexuality, norms, and transgressions of norms are constructed and defined.

The dissertation surveys a wide array of sources – from official documents, through articles printed in popular press, up to the first sexualised advertisements. On the one hand, the thesis focuses on the role of communist ideology and official regulations in creating space where new sexual identities could emerge, as well as in limiting their scope. On the other, it also analyses the role consumerist aspirations played in modernising sexual behaviours toward the end of state socialism and how sexuality came to be used as a metaphor to narrate the sense of late state-socialist crisis. In many regards the ‘Eastern’ example teaches us that sexual liberation is not a straightforward and one-dimensional process but, rather, that it can denote quite different things depending on its geographical and social context.

Keywords: state socialism
sexuality
Polish People's Republic
nudism
Poland
gender
history of sexuality
visual culture
communism
pornography
sexual revolution
Advisor: Lebow, K
The diffusion of cyber norms: technospheres, sovereignty, and power

Why have the Chinese and Russian internet sovereignty norms diffused successfully to some countries – thereby undermining the previously dominant US norm of internet freedom – and what are the implications of successful international diffusion of information controls for understandings of sovereignty in International Relations?
Starting in the 1980s, internet freedom swept through the world and soon became the leading global cyber norm. This rise was propelled by US goals of increasing economic power and spreading democracy. Many countries that imported internet technologies, saw the economic benefits of the technologies, but with the import of the internet they also adopted loose market and content regulations. However, in the 2000s, the eruption of protests in the Middle East, Latin America, Africa, and across Asia, powered through internet-connected devices, increased the regime threat perception of authoritarian- leaning leaders. As a result, they started importing technology/techniques associated with internet sovereignty from China and Russia, who had, early-on, built up their information control capabilities. Beijing and Moscow, for their part, have actively promoted internet sovereignty diffusion to geographical areas that they conceived as their spheres of influence – the Commonwealth of Independent States for Russia and the Belt and Road Initiative for China.
This thesis makes several main contributions. It builds a framework to distinguish the three cyber norms it studies: internet freedom, and the Chinese and Russian variants of internet sovereignty. This thesis also devises a neoclassical realist framework of International Relations, which focusses on explanatory variables at the unit level (perception underlying export/import) to explain the international expansion of internet freedom/sovereignty. Additionally, it updates the term of sovereignty to the digital age. Namely, with the diffusion of internet freedom/sovereignty norms, technological spheres of influence emerged, in which the US, China, and Russia have weakened countries’ Westphalian sovereignty and shaped their domestic and interdependence sovereignty.

Keywords: cyber norms
technological spheres of influence
Russia
China
United States
sovereignty
information control
Advisor: Kello, L
Wright, J
Dependency, privilege, and counter-insurgency: a case study of the industrial elite of Hebron in the occupied West Bank

A central but understudied aspect of the period following the Oslo peace process in 1993 is the rise of a native Palestinian business elite, which have been playing an important role in the political, economic, and social spheres in the West Bank. This thesis focuses on an important group within the indigenous elite—the industrial elite in Hebron, a governorate that has been under-researched despite constituting the industrial and commercial hub of the West Bank. Informed by a political economy approach, this dissertation critically examines how Hebron’s industrial elite accumulated and concentrated their capital, within a larger context of occupation, de-industrialisation, and absence of a sovereign state.
Drawing on extensive field research, I make three arguments. First, I argue that the development of Hebron’s industrial elite has been driven by dependency relations established by Israel in 1967 and reconfigured following the Oslo accords. I highlight how Hebron’s elite concentrated their capital after Oslo, through business relations with Israeli capitalists and informal linkages with Israeli officers. These alliances, rooted in dependency relations, have represented a network of privileges and have been a necessary condition for business growth after Oslo. Second, I argue that the structure of dependency that has tied the interests of the population to Israel, has been an integral part of Israel’s continuously evolving counter-insurgency strategy, which has sought to co-opt the population and coerce them into acquiescence to ensure stabilisation. Third, through a critical examination of U.S.-led Trade Facilitation Programmes (TFPs), I examine the role of the U.S. in reinforcing capital concentration in Hebron, by distributing privileges to certain actors, while reinforcing dependency relations with Israel. I also reveal how TFPs have recently introduced a new condition for business growth by requiring beneficiary businessmen to become counter-insurgency actors, managing an ‘anti-terror’ infrastructure and a self-surveillance regime under Israel’s control.
Overall, the case study of Hebron’s elite provides a unique prism through which to see the complex assemblage of Israel’s overt and subtle technologies of colonial management. It also contributes to a more critical understanding of elite development in the Global South and provides new insights into the evolving practices of the emerging global security paradigm.

Keywords: trade facilitation projects
dependency theory
strategies of colonial management
economic inequality
counter-insurgency theory
business-state relations
elite formation
processes of capital accumulation and concentration
Advisor: Sánchez-Ancochea, D
Malik, A
Lesbos' other lyricist: studies in Alcaeus

‘Lesbos’ Other Lyricist: Studies in Alcaeus’ argues that Alcaeus is a sophisticated poet. It offers new approaches to and interpretations of his poetry, and provides a re-edition and close reading of Alcaeus frr. 33-57, 59-111.
Part I suggests new approaches to Alcaeus and Greek lyric that emphasise literary interpretation. In contrast to the dominant approaches that treat Alcaeus as a source of historical data or consider his works largely understandable from the context, this study highlights the interpretative benefits of a more varied approach. It therefore goes further than recent works on the literary aspects of Greek lyric by focusing on a single poet and his oeuvre in a thesis-length study, uniting diverse approaches, and asking new questions of old topics. New approaches to the study of epithets, metre, immersion, performance, and history are explored for literary interpretation.
Part II presents a new text, apparatus, and textual and interpretative essays on P.Oxy.1233 and 1234 with their joined fragments (Alcaeus frr. 33-57, 59-111). Focusing on these papyri, which represent a large portion of Alcaeus’ poetic fragments and include a broad range of his poetry, forces confrontation with a mixture of famous and under-studied fragments and enables detailed study of the fragments alongside the methodologies of the first half.
As the first thesis-length study of Alcaeus’ entire corpus for forty years, this project presents a more nuanced view of Alcaeus, provides fresh interpretations of fragments, and suggests new approaches for Alcaeus and Greek lyric more broadly.

Keywords: epithets
papyrology
lesbian poetry
Lesbos
performance
Greek lyric
Alcaeus
ancient history
metre
lyric
Sappho
immersion
Advisor: Hutchinson, G
The making of an alternative religion in late-Meiji Japan (1899-1912): a study of Arai Ōsui (1846-1922)

This paper makes the case for Alternative Religion as an intellectual concept, and uses it to uncover previously overlooked patterns of thought in the late-Meiji and Russo-Japanese War period. It examines Arai Ōsui (1846-1922), an overlooked religious figure, who I argue was vitally influential despite his erasure from our historical knowledge. By using his writing and writings of those interacting with Arai, I make the case for an alternative religious movement operating between the bounds of reli- gious and secular, and East and West bifurcations. This approach elucidates not only Arai’s significance, but also lends reinterpretations of Tanaka Shōzō (1841-1913), and artists Ogiwara Rokuzan (1879-1910) and Takamura Kōtarō (1883-1956) in the early twentieth century.

Keywords: transnational history
Russo-Japanese War
Arai Ōsui
Swedenborgism
alternative religion
Tanaka Shōzō
religion
modern Japan
late-Meiji Japan
Structural studies of pestivirus envelope glycoproteins

Pestiviruses belong to the family Flaviviridae with the most well-known being Bovine Viral Diarrhoea Virus, Border Disease Virus, and Classical Swine Fever Virus affecting cows, sheep, and pigs respectively. These viruses cause a large economic impact especially in the dairy and pig industries. As a result of being enveloped viruses, to enter the cytoplasm and replicate, they must first fuse their membrane with that of the cell’s endosome, in a process which requires a fusion protein. Pestiviruses require two envelope glycoproteins for this step: E2, likely involved with receptor interaction, and E1, likely the fusion protein.
Reported within is the design of over 80 expression constructs, expression testing of 70, large scale production of 16 and the crystallisation of 7. As a result, two x-ray crystallography structures of the ectodomain of a putative pestivirus receptor bovine CD46 were solved. These structures revealed an interesting dimer, like that found in human CD46, although not reported previously. This dimer presents an interesting insight to the potential orientation of CD46 in the cell surface and could potentially play a role in anchoring the virus particles at sites of endocytosis.
This thesis also presents the structure of two novel pestivirus E2 ectodomains from APPV and NRPV. These structures highlight the variety of pestivirus E2 structures and support the finding that E2 is not the fusion protein. Investigations into N-terminal disorder at low pH, such as in the late endosome, revealed that this was not the case for all pestiviruses. The more typical E2 proteins from BVDV, BDV, and CSFV all display evidence of structural changes at low pH while the more atypical pestiviruses APPV and NRPV do not. In addition, an interesting beta-hairpin was revealed towards the N-terminal region of all five E2 proteins which may play a role in receptor interaction.

Keywords: glycoprotein
pestivirus
crystallography
Advisor: Stuart, D
El Omari, K
The Worcester Fragments: a paleographical examination

The Worcester Fragments represent the largest extant collection of polyphonic music from thirteenth-century England, with over a hundred compositions (many of them unica) across more than sixty manuscript fragments. Musicologists have known about the fragments for over a century, but the majority of their attention has been devoted to the remnants of one volume with surviving medieval foliation. Moreover, the tendency has been to conflate the many fragments into one ‘Worcester Repertory’ as though they represent the output of a single scriptorium at one point in time, with the result that the connections between the individual sources and the differences in manuscript production and musical repertory that they represent have been incompletely examined in scholarship.
This thesis seeks to explore how the various manuscripts that make up the Worcester Fragments were originally created, from the preparation of the page to the original phase of copying to later additions in the fourteenth century and beyond, in order to establish a complete history of the Worcester Fragments, from their creation to their demolition and later rediscovery. It might have been titled ‘The Worcester Fragments: A Biography’ for this is not a the study of a codified manuscript that was created at a single point in time, but rather, the story of a number of sources that changed and evolved both in presentation and content, as they passed from maker to user to secondary user to binder and eventually to historian and reconstructer in a long and colourful life of usage. In considering both the history of the transmission of music and the history of the manuscript itself as an object of use and reuse throughout the centuries, a more nuanced understanding of the manuscript is proposed, not as an organised work conceived of and produced in a short period of time, but as a more fluid source, one that has proven to be adaptable, heterogeneously compiled and innovatively updated over time. Through a paleographical and musical re-examination of these various fragmentary sources, the dissertation will propose a new interpretation of the Worcester Fragments, one that separates independently-produced sources by the ‘workshops’ they represent and establishes the chronological timeline in which they were copied. Identifications of compositions will be made, a comprehensive script analysis of the fragments is given here for the first time and both a relatively unknown piece of music and a very famous one will be re-set in a new context of creation and interpretation. Finally, the dissertation will explore the history of the fragments beyond the thirteenth century and re-examine the possibility of a Worcester provenance in the light of the latest discoveries.

Keywords: medieval musicology
medieval music
polyphony
paleography
codicology
medieval manuscript
scribe
Targeted treatment approaches and pathogenicity of antibody subclasses in MuSK-myasthenia gravis

Muscle Specific Kinase myasthenia gravis (MuSK-MG) is an autoimmune disease that impairs neuromuscular transmission leading to muscle fatigability. No targeted medications are currently available, and non-specific immunotherapies are required. MuSK initiates a phosphorylation cascade regulating the clustering of acetylcholine receptors (AChRs) at the neuromuscular junction (NMJ). SH2 domain-containing phosphatase (SHP2) negatively regulates the pathway inhibiting MuSK activation. In MuSK-MG, monovalent IgG4 autoantibodies block MuSK phosphorylation dispersing AChR clusters. The role of the smaller population of divalent MuSK IgG1, 2 and 3 antibodies is still undefined. The aims of the study were a) to test in vitro and in vivo SHP2 inhibition by NSC-87877 evaluating its efficacy in counteracting the effects of MuSK-Abs; b) to investigate the pathogenic contribution of MuSK IgG1-3-Abs.
Protein phosphorylation and AChR clustering were studied in different cell lines exposed to NSC-87877, and to either patients’ purified MuSK-Ab subclasses or anti-MuSK monoclonals. NSC-87877 was tested for safety and efficacy in wild-type mice and a model of AChR deficiency syndrome. Effects of MuSK IgG1-3 were evaluated on impairment of the MuSK-Lrp4 interaction required for MuSK activation, and on the cytoskeleton activation necessary for cluster maturation. RNA transcriptomic analysis was performed to look for changes in intracellular pathways.
In vitro, NSC-87877 increased MuSK phosphorylation protecting AChR clusters from dispersal in the presence of all MuSK-Ab subclasses. Functional MUSK was required for the effectiveness of the drug. In vivo, no side effects were observed but the available genetice myasthenic syndrome models did not improve. Divalent MuSK antibodies activated the phosphorylation cascade but failed to sustain cluster maturation, impairing MuSK-Lrp4 interaction and cytoskeleton rearrangements. Transcriptomic analysis did not detect specific changes that could inform on the mechanisms. In conclusion, SHP2 inhibition showed promising results in vitro, although more studies are needed in vivo to evaluate its potential effectiveness. Although the exact mechanisms of MuSK IgG1-3 antibodies were not identified, the work in this thesis confirms their potential pathogenic role in MuSK-MG that requires further investigation.

Keywords: autoimmune
neuromuscular junction
myasthenia
MuSK
IgG subclasses
Advisor: Beeson, D
Cossins, J
Webster, R
On neural differential equations

The conjoining of dynamical systems and deep learning has become a topic of great interest. In particular, neural differential equations (NDEs) demonstrate that neural networks and differential equation are two sides of the same coin. Traditional parameterised differential equations are a special case. Many popular neural network architectures, such as residual networks and recurrent networks, are discretisations.
NDEs are suitable for tackling generative problems, dynamical systems, and time series (particularly in physics, finance, ...) and are thus of interest to both modern machine learning and traditional mathematical modelling. NDEs offer high-capacity function approximation, strong priors on model space, the ability to handle irregular data, memory efficiency, and a wealth of available theory on both sides.
This doctoral thesis provides an in-depth survey of the field.
Topics include: neural ordinary differential equations (e.g. for hybrid neural/mechanistic modelling of physical systems); neural controlled differential equations (e.g. for learning functions of irregular time series); and neural stochastic differential equations (e.g. to produce generative models capable of representing complex stochastic dynamics, or sampling from complex high-dimensional distributions).
Further topics include: numerical methods for NDEs (e.g. reversible differential equations solvers, backpropagation through differential equations, Brownian reconstruction); symbolic regression for dynamical systems (e.g. via regularised evolution); and deep implicit models (e.g. deep equilibrium models, differentiable optimisation).
We anticipate this thesis will be of interest to anyone interested in the marriage of deep learning with dynamical systems, and hope it will provide a useful reference for the current state of the art.

Keywords: neural differential equation
neural controlled differential equation
neural stochastic differential equation
neural ordinary differential equation
Advisor: Lyons, T