VictorJuiz/thesis huggingface dataset:
'This cloud had been written upon': Investigating digital editing methods for Anne Bathurst's visionary writing
Keywords: Editorial Theory
Dissenting Christianity
TEI
Manuscript Studies
Textual Innovation
Digital Editions
Feminism
Religion
Philadelphian Society
Mysticism
Anne Bathurst
Radical Theology
Bibliography
17th Century
Literature
IIIF

This dissertation will feature a digital asset, a complete digital edition of Anne Bathurst’s ‘Rhapsodical Mediations’, in addition to an essay detailing the theories behind the digital methods employed in creating this edition as well as an assessment of their results.
This will hone in on the specifics of Anne Bathurst’s manuscript – a historically-significant religious diary which has thus far not been digitised in full – as well as zooming out to the wider implications of what it means to digitise a manuscript which not only contains interesting material features, but, also intensely spiritual content.
The questions at the heart of this dissertation are whether the physical or the mystical can be captured by any pre-existing digital methodology, whether creating a bespoke methodology is worthwhile to this field and whether mystical objects should be digitised at all. After all, how can an interoperable, standardised digital edition be imbued with the mystical essence of visionary writing? – and, how can it meaningfully present the physicality of a manuscript? The mission statement for this project is that an object’s physical existence and digital existence should be intimately interlinked in a creative way, and that this interlinking is a valuable scholarly exercise.
The digital tools involved in this discussion are TEI, IIIF, html, and some AI. In the main, this study will focus on evaluating TEI and other elements which can be interoperable with this widely adopted language. This will be integrated with more traditional humanities scholarship surrounding the physical volume, providence research, the transmission of ‘female knowledge’ in this source material and an exploration of its religious language. This study anticipates that the aforementioned digital methods will further investigations in these areas of study.
The search for CP violation in neutrino oscillations at T2K
Keywords: neutrino oscillation
charge parity violation
CP symmetry
mixing angle

T2K is a long-baseline neutrino oscillation experiment, designed to study the oscillation of a high-intensity muon neutrino beam produced by the J-PARC ac- celerator facility. Neutrinos are detected 295 km downstream of the production point at Super-Kamiokande, a 50 kt water Cherenkov detector capable of differ- entiating between muon neutrino and electron neutrino events. Two beam configurations are possible at T2K, each used to create neutrino beams composed of predominantly neutrinos or anti-neutrinos. Comparisons of the disappearance of muon neutrinos and the appearance of electron neutrinos in the neutrino and anti-neutrino beams are used to measure the neutrino oscillation parameters.
Presented in this thesis are the results of many analyses designed to study various combinations of the Super-Kamiokande oscillation data sets. Analyses considering the antineutrino beam data sets found no substantial evidence for ν ̄e appearance in a ν ̄μ beam or ν ̄μ oscillation inconsistent with observed νμ oscillation. A combined study of all available Super-K oscillation samples measured the CP violating phase δCP and the sine square of the mixing angle θ(13).
This analysis excluded δCP = 0 at the 2σ confidence level under both normal and inverted ordering hypotheses and produced a constraint of -2.978 rad < δCP < -0.467 rad in the normal ordering hypothesis.
Mathematical modelling and transcriptional characterisation of intratumoral regulatory T cell sub-populations
Keywords: mathematical modelling
single cell meta-atlas
LAG3
immunotherapy
CCR8
tumour Tregs

Regulatory T cells (Tregs) suppress harmful immune responses and help prevent autoimmune reactions. However, high densities of Tregs accumulate in solid tumours and contribute to the suppression of anti-tumor responses. The targeting of intratumoral Tregs via antibody-mediated blockade/depletion is a promising cancer treatment strategy but remains ineffective and induces adverse events. Some of these challenges can be addressed by conducting extensive transcriptional profiling of intratumoral Tregs and quantitatively assessing Treg migration dynamics to identify appropriate therapeutic targets and guide the development of safe and effective Treg-targeting therapeutics.
We hypothesised that tumours harbour resident and transient Tregs with distinct transcriptional and migratory profiles. To test our hypothesis, we used photoconvertible Kaede mice to label and quantify Tregs in MC38 and CT26 tumours. We developed a mathematical model to investigate whether the presence of resident and transient tumour Tregs aligns with the observed data and applied Bayesian parameter estimation to infer the rates of intratumoral Treg migration. In both tumours, we confirmed the presence of resident and transient Tregs and found that Tregs egressed from CT26 tumours to lymphoid tissue to a larger extent than MC38 tumours. Single cell analysis of intratumoral Tregs revealed that resident Tregs upregulate Lag3, Tnfrsf18 and Tnfrsf9. To investigate similarities between murine and human intratumoral Tregs, we constructed Treg meta-atlases using public single cell datasets. In mice, we observed that Lag3 and Ccr8 are unique to tumour Tregs and exhausted CD8 T cells. In humans, CCR8 expression was confined to tumour Tregs whereas LAG3 was mainly expressed on exhausted CD8 T cells.
Collectively, our findings outlined the presence of kinetically and transcriptionally distinct intratumoral Treg subpopulations. Furthermore, our Treg meta-atlases exposed key differences in CCR8 and LAG3 expression between mouse models and humans and supported the potential of CCR8 as a target for depleting human intratumoral Tregs.
Synthesis, structure and magnetism of mixed-anion solids
Keywords: oxide chalcogenides
oxide halide
magnetism
solid-state chemistry
structure-property relationships
mixed-anion solids

This thesis investigates the structure-property relationships in the series of mixed-anion solids Ae2MO2X2Ch2 (Ae = Sr, Ba; M = Co, Ni; X = Cu, Ag; Ch = S, Se), Ae3-xAe’xFe2O5Cu2Ch2 (Ae = Ba, Sr, Ca; Ch = S, Se), and Sr2NiO2Cl2.
A spin-state crossover in the solid solution Sr2NiO2Cu2(Se1-xSx)2 has been observed as a function of composition, with two-dimensional magnetic correlations observed for one sample of high S-content before all sign of magnetic scattering is lost which is accompanied by a clear structural signal suggesting a change from high- to low-spin.
The novel, lithiated Ae2CoO2X2-xLixCh2 (Ae = Sr, Ba; X = Cu, Ag; Ch = S, Se) phases have been synthesised and have similar magnetic ordering to that seen in their non-lithiated analogues. These materials have localised Co2+ moments greater than the spin-only predicted 3 uB, suggesting a large orbital contribution to the moment which is discussed further within the chapter.
Ba3-xSrxFe2O5Cu2Ch2 (x = 1, 2; Ch = S, Se) and BaCa2Fe2O5Cu2S2 both show distinct cation ordering between a larger 12-coordinate site and 8-coordinate site and order antiferromagnetically with moments tilted away from the basal plane as opposed to within the plane when there is only one alkaline earth metal present.
Surface forces and structures in complex electrolytes
Keywords: water-in-salt electrolytes
guanidinium chloride
surface force balance
neutron scattering
ionic liquids
surface forces
denaturants
surfaces

Electrolytes, environments in which ions are free to move, are found throughout the natural and the human-centred world. The biochemistry that allows for life, alongside many of the innovations that make modern life so convenient, rely on the physical chemistry of these substances. Despite this, the behaviours of many complex and high concentration electrolytes are relatively poorly understood. This thesis investigates the forces and structures present in three examples of complex, high concentration electrolytes in order to better the understanding of these fascinating systems.
First, we present measurements of surface forces present in water-in-salt electrolytes, high concentration aqueous electrolytes with potential applications in next generation energy storage devices. We find evidence for a layered structure of aqueous and non-aqueous domains within the confined electrolyte films. These domains are maintained in the bulk liquid, and our analysis of the clustering of the domains suggests consequences for the mechanism of ion transport in water-in-salt electrolytes. We also studied ionic liquids, liquid electrolytes consisting solely of ions. We show that different layered structures can form in ionic liquids confined between surfaces, where the structure adopted depends on the nature of the ions. On studying mixtures of ionic liquids that form different interfacial structures, we find that the mathematical expressions describing the mixtures can be written as a linear combination of the terms describing pure ionic liquids. These results have important implications for the interpretation of correlation lengths within liquid mixtures, and for the optimisation of surface properties by creating liquid mixtures. Finally, we investigate the modifications of surface forces that occur in the presence of the high-concentration protein denaturant guanidinium chloride. We find varying behaviour across a broad concentration range that suggests strong time and concentration dependence in the action of guanidinium chloride at protein surfaces.
Together, the results of this thesis highlight the complexities of high concentration and poorly understood electrolyte solutions, and shed light on their interactions and behaviours. This work will be important in fully understanding the role these complex systems play, both in the devices and conveniences that allow modern life to function, and in the complex chemistries that govern life at a molecular level.
Soft chemistry of layered chalcogenides
Keywords: layered compounds
magnetometry
intercalation
x-ray diffraction
chalcogenides

This thesis reports the synthesis and characterisation of several new layered chalcogenides. Low temperature intercalation methods have been used to synthesise new metastable materials which retain the general structure of their precursors, but modify their properties.
Chapters 3 and 4 focus on the intercalation chemistry of excitonic insulator candidate Ta2NiSe5 and structurally related compound Ta2NiSe7. Several species can be intercalated into Ta2NiSe5, all cause significant, but similar, rearrangement of the Ta-Ni-Se layers. Conversely, Li intercalation into Ta2NiSe7 is found to be topotactic in nature and highly reversible. High resolution synchrotron XRD data reveals two distinct phases are formed depending on Li content, and neutron diffraction is used to characterise each phase. Electrochemical studies show continuous filling of the Li sites, and are presented as a comparison to the chemical synthesis.
Chapters 5 and 6 of this work explores the manipulation of layered near room temperature ferromagnetic compounds Fe3GeTe2 and Fe5GeTe2, by insertion of Li(NH2) or K into the interlayer spacing. Intercalation into Fe3GeTe2 results in rearrangement of the Fe-Ge-Te layers and an increase in the Curie temperature by approximately 25 K. In contrast, intercalation into Fe5GeTe2 results in no layer rearrangement and very little change to the ferromagnetic behaviour of Fe5GeTe2. The magnetic properties are characterised through SQUID magnetometry, neutron diffraction and Mössbauer spectroscopy on polycrystalline samples.
Pharmacological and structural studies on the hedgehog pathway receptor smoothened
Keywords: cryo-electron microscopy
hedgehog signalling
G protein-coupled receptor
smoothened
drug discovery
structural biology

The Frizzled-class G protein-coupled receptor Smoothened (SMO) is an essential component of the Hedgehog (HH) signalling pathway, which is of paramount importance to developmental processes of bilaterians. Dysregulation of HH signalling has been implicated in multiple pathophysiological processes in adult organisms, such as cancer development. SMO is targeted by multiple anti-cancer drugs, but resistance mutations were reported to decrease inhibitor potency and adverse events force medication discontinuation. While structural and functional studies have furthered our understanding of how SMO is regulated, details of SMO activation mechanisms and the interplay between the multiple SMO ligand-binding sites remain to be further clarified. Furthermore, there is limited information on the mechanisms of downstream signal transduction of vertebrate SMO, which most likely involve the G protein-coupled receptor kinase 2 (GRK2). This thesis describes the work we conducted to contribute to answering these questions, and to the development of next-generation SMO inhibitors. We optimised sample preparation to determine high-resolution structures of inactive SMO from human and fly, and of activated human SMO in complex with the essential downstream pathway component GRK2. Our findings will aid future structural studies on SMO by single particle cryogenic electron microscopy (cryo-EM). Ultimately, these cryo-EM structures will provide insights into the evolutionary divergence of SMO activation mechanisms, and into the mechanisms of vertebrate HH signal transduction. Moreover, we conducted functional characterisation of novel HH pathway inhibitors, which were identified in collaborative projects by high-throughput screening and computational docking. These resulted in the identification of six small molecule series that can inhibit HH signalling, three targeting the SMO extracellular cysteine-rich domain (CRD), and three potentially targeting the transmembrane domain (TMD). The ligands targeting the SMO CRD inhibit vismodegib-resistant mouse SMO-D477G, and are currently undergoing medicinal chemistry optimisation to ultimately enable potential therapeutic applications. Furthermore, these compounds can be used in future structural and functional studies to clarify how SMO selects between different downstream HH pathway effectors.
Cold and controlled ion-radical reactions, relevant to the interstellar medium and outer atmosphere
Keywords: ions
gas phase
radicals
ion trap
cold chemistry

This thesis reports the design, construction, and characterisation of a cryogenic linear Paul ion trap chamber. This cryogenic ion trap chamber will be combined with a magnetic guide as a source of radicals, also described in this thesis, for the study of ion–radical reactions under cold and controlled conditions. Ion–radical reactions are important for the chemistry happening in the interstellar medium and in certain regions of Earth’s atmosphere, where both temperature and pressure are low. Despite their importance, there are very few existing methods for studying reactions between ions and radicals at low temperatures.
The new cryogenic linear Paul trap introduced in this thesis is the first such device to incorporate an in-built time-of-flight mass-spectrometer. The design of the apparatus minimizes the temperature at the ion trap region, down to 10K, and ensures that vibrations induced by the cryogenic system do not adversely affect the resolution of the Coulomb crystal images. The constraints of optical access to the trap center for lasers and imaging of Coulomb crystals have been overcome by the implementation of a new optical system based on off-axis parabolic mirrors. We have successfully trapped and imaged Ca+ Coulomb crystals, and work is in preparation to form molecular ions.
Alongside the work on the cryogenic ion trap, the thesis also demonstrates how a magnetic guide can act as a stand-alone source of state and velocity-selected radical species. In this way, a beam of state- and velocity-selected radicals can be filtered from an incoming beam containing a mixture of different species. The magnetic guide therefore provides a source of cold and controlled neutral reactants. Work is underway to combine the two set-ups, facilitating the study of ion–radical reactions.The cryogenic ion trap apparatus presented here is a truly unique apparatus. It will enable us to study reactions involving a range of state selected molecular ions, which, through reactions with velocity- and state-selected radicals from the magnetic guide, can lead to new knowledge on fundamental reaction dynamics and kinetics.
Branchwise-real trees and bisimulations of potentialist systems
Keywords: modal model theory
tree automorphism
branchwise-real tree
rigid
potentialist system
forcing
road space
separable
independence result
Suslin tree
uniform
countable chain condition
first-order Kripke model
Ehrenfeucht-Fraïssé game
Martin’s Axiom
bisimulation
continuous grading

This thesis concerns two topics. The first treats R-trees, which are a certain kind of metric space tree in which every point can be branching. Favre and Jonsson posed the following problem in 2004: can the class of partial orders underlying R-trees be characterised by the fact that every branch is order-isomorphic to a real interval? I first answer this question in the negative, then go on to establish a connection between these trees and traditional set-theoretic trees. This connection is then put to work, answering refinements of Favre and Jonsson's question, yielding several independence results. I next move on to consider the existence of examples of these partial orders without non-trivial automorphisms. I provide constructions of these subject to increasingly strong uniformity conditions. While these constructions all take place in ZFC, they have a strong forcing flavour.
The second topic deals with bisimulations of potentialist systems, which are first-order Kripke models based on embeddings. Given a first-order theory T we can impose a potentialist structure on the class of models of T by taking either all embeddings or all substructure inclusions between models. I show that these two systems are always bisimilar. Next, by connecting with a generalisation of the Ehrenfeucht-Fraïsé game, I show the equivalence of the existence of a bisimulation with elementary equivalence with respect to an infinitary language. Finally, I turn to the question of when a class-sized potentialist system is bisimilar to a set-sized one, providing two different sufficient conditions.
Conceptualising national identity in late twelfth-century chansons de geste composed in French
Keywords: linking national identity to language
chansons  de geste
medieval France
community and memory
creating identities
harnessing digital tools in philology
national identity
emotion
Old French epic
rethinking the notion of an imagined community
medieval French
France and French-ness
mobilizing crusade as memory
producing communities

This thesis challenges previous perceptions about national identity by dissolving the usual boundaries in which literary scholars and critics operate. It contends that the emergence and dynamic reconfiguration of national identity permeates a group of concepts which combine and reformulate themselves within intricate systems of lexical patterns entwined in the text, rather than being confined to a single concept.
Such patterns related to the process of national identity are examined across a corpus of chanson de geste poems taken from the Matter of France which date from around the end of the twelfth century. The corpus comprises Aliscans, La Chanson d’Antioche, La Chanson d’Aspremont, La Chanson des Saisnes and Raoul de Cambrai.
From the beginning of vernacular French literature, terms which one would translate as ‘France’, ‘the French’ and ‘French-ness’ predominantly relate to abstract identity concepts rather than purely geographical ones. The term ‘abstract’ designates lexemes with a shifting, fluid quality which ask for active concretization by a given reader or listener, but also cue his or her concretization in a potentially deliberate way. The analysis thus informs a revised notion of national identity as an imagined community emerging over patterns of language use. The chosen methodology and analytical toolkit opens up a new way of exploring these aspects of the texts.
Chapter 1 explores the question of French national identity at a key juncture in the development of ideas of ‘French-ness’. Chapter 2 investigates how France relates to national identity. This examination includes geographical and political aspects which comprise identity, memory, and territory in the reader’s concretizations of individual instances of language use. Chapter 3 considers who and what is ‘French’ in the corpus and the complexity and non-linearity of the French and ‘French-ness’.
The methodology used in this thesis uses a hybrid approach to textual analysis: data is extracted and then subjected to painstaking philological work, complemented by quantitative analysis in an original way. The interpretation of results is informed by insights from existing scholarship and engages in a productive dialogue with this research, which tends to discuss national identity with respect to much later periods. This dissertation indicates that national identities are already being formed in the late twelfth century.
Punishing mobility: membership, race, and privatization in all-foreign prisons in the United States of America
Keywords: citizenship
deportation
border control
incarceration
race
punishment
privatization

My DPhil thesis examines a set of outsourced, all-foreign prisons operated by the US Federal Bureau of Prisons called Criminal Alien Requirement (CAR) facilities. In operation from 2000 to 2023, these prisons were unique for a series of reasons. First, they were explicitly designed to segregate foreign national offenders from the rest of the Federal prison population. Second, they were the only outsourced prisons within the Federal prison system, and operated under a separate, less-stringent regulatory regime. These all-foreign prisons also disproportionately incarcerated Latino men (89%) in general, and Mexican men (72%) in particular.
This thesis asks what the imbrication of punishment and migration control within all-foreign prisons can tell us about the contemporary nation-state. I develop this argument along three lines. First, I argue that the emergence, operation, and closure of this outsourced all-foreign prison system illustrates the evolving relationship between prisons and migration control. Analysis of the creation of the Criminal Alien Requirement prison system shows us how political leaders imagined a new kind of penal process – what I call the ‘prison-to-deportation pipeline’ – in which deportation became the default result for people without citizenship.
Second, my research demonstrates how outsourced incarceration has become premised on the differential treatment of racialized foreign-national offenders. Criminal Alien Requirement prisons have pioneered a new kind of carceral economy where financial value is extracted from the social and biological reproduction of offenders themselves. I demonstrate how this economic model of incarceration is premised on the differential treatment of non-citizens, and the racialized commodification of illegality.
Finally, my research demonstrates how this system of differential penal treatment produced experiences of abandonment and precarity. These experiences of abandonment defined exclusion from political membership in material and symbolic terms. I argue that paying attention to the ways in which people incarcerated in all-foreign prisons articulated their exclusion offers us a way to begin challenging what Angelica Chazaro calls the ‘criminal alien paradigm’ and uncoupling practices of punishment and migration control.