VictorJuiz/thesis huggingface dataset:
Prolegomena to a critical edition of the Chronicle of Matthew of Edessa, with a discussion of computer-aided methods used to edit the text
Keywords: stemmatology
Edessa
computer collation
Armenia
text phylogenetics
Byzantium
Matthew of Edessa
first crusade
text criticism

The Chronicle of Matthew of Edessa is the primary Armenian-language historical source for the eleventh and early twelfth centuries. Matthew was a monk who lived in the ethnically mixed city of Edessa; within his Chronicle, he describes the apogee of independent Armenia, its fall to piecemeal Byzantine annexation, the subsequent loss of Byzantium's eastern territory to the newcomer Saljuq Turks, and the sectarian tension that accompanied the First Crusade. This thesis sets out the methodology adopted for the construction of a critical edition of the text, addresses the approach that Matthew took to the composition of the Chronicle, and gives the edited text of the prophecies attributed to Yovhannēs Kozeṙn and the author's prologues to Books Two and Three of the Chronicle. Chapters 2 and 3 comprise a review of the scholarship to date on the Chronicle, and a discussion of the approach taken to a critical edition of the text. The Chronicle survives in a large number of relatively recently copied manuscripts; it was therefore necessary to devise an approach to text collation and editing that takes full advantage of recent advances in computational methods of philology. I have developed a set of software tools to assist in the task of editing the Chronicle; these tools are useful for the creation of text editions in any language that can be represented through the TEI XML standard. Chapters 4–8 give an examination of the overall framework of Matthew’s Chronicle, and of his interpretation of recent history within that framework. Following a long tradition of the use of prophecy to explain Armenian history, Matthew uses two prophecies attributed to the eleventh-century clerical scholar Yovhannēs Kozeṙn, themselves extended in the twelfth century under the influence of the Apocalypse attributed to Methodius, to frame his argument that both the Byzantine emperors and the Armenian kings had abandoned their responsibility toward the Armenian people. His attitude toward recent history, and particularly toward the Latins of Outremer, may be used to demonstrate that he wrote the Chronicle no later than 1137.
The political economy of the interwar years
Keywords: Economic History
Political Economy

This thesis is a collection of essays on the political economy of the interwar years. It aims to address two of the most prominent and characteristic aspects of the interwar international economy; the break-up of the Gold Standard system and the rise of trade protectionism. I argue that extensions to the franchise are crucial to understanding both of these phenomena. Using evidence based on macro-level panel data analysis, micro-level public opinion surveys as well as numerous qualitative sources, I construct an argument that stresses the importance of these changes in voting rights to economic policy decisions; changes that can help explain the unusual nature of the interwar international economy. The effect of the extended franchise will not be examined in isolation however, with the influence of a number of other important aspects of the political and economic environment also taken into consideration. As arguably the most interesting and novel result of these analyses is the suggested effect of the granting of voting rights to women, the voting preferences of women are examined more closely in an additional chapter using a unique record of women’s voting from Weimar Germany. This allows for the difference between men and women’s actual voting preferences to be explored, something that is usually impossible due to the use of secret ballots. The fact that the separation of votes by gender occurred during one of the most important periods in modern history gives the analysis an even greater significance.
Investigation of expression quantitative trait loci and regulatory genetic variants in primary human immune cells
Keywords: Macrophages
Immune response
Gene expression
Genome-wide association study
monocytes
eQTL
Inflammation
B-cells

The post human genome sequence era has begun to explore various aspects of the functional genome in relation to disease including gene expression, genetic variation and epigenetics. The genetic determinants of common and complex phenotypes are difficult to resolve even though their heritability is recognised. Recent genome-wide association studies (GWAS) for common diseases has identified many new disease susceptibility associated loci. These loci often lie in non-coding regions of the genome and disease associated genetic variants are proposed to act by modulating gene expression.
This thesis investigated genetic variation as determinants of gene expression in the context of the immune system especially focused on the innate immune and inflammatory responses. Different primary human immune cell types were collected from healthy volunteers of European ancestry to achieve this. In order to identify genetic variants associating with gene expression, expression quantitative trait loci (eQTL) mapping was conducted in a cell type specific manner.
The primary dataset (n=288) consists of CD19+ B-cells from the adaptive immune system and CD14+ monocytes from the innate immune system. 78% of the total cis eQTL were found to be cell type specific and include genes relating to their roles in the immune response. Trans eQTL showed greater cell type specificity and include master regulatory eQTL on the LYZ locus at chromosome 12q15 in monocytes and the KLF4 (9p31) in B-cells. The identified eQTL are implicated in association with autoimmune disease susceptibility including inflammatory bowel disease, diabetes and rheumatoid arthritis.
The second analysed dataset (n=64) consists of CD14+ monocytes and macrophages differentiated ex vivo. Macrophages are involved in many inflammatory diseases as well as in the innate immune response. The differential gene expression and eQTL mapping analyses were conducted to investigate macrophages specific gene expression signatures and associations to genetic variants. Macrophage eQTL are involved in signal transduction for the inflammatory response (IL1RN and STAT4) and lipid metabolism (PPARG) with implication for metabolic disease association.
The eQTL analyses using primary immune cell types provide insights into genetic variation in association to gene expression which is involved in autoimmunity and disease susceptibility.
Understanding typhoid disease; a controlled human infection model of typhoid fever
Keywords: typhoid-fever salmonella-Typhi enteric-infection controlled-humnan-infection human-challenge-study

Typhoid disease, caused by infection with S. Typhi, is a significant cause of mortality and morbidity in resource–poor countries. Efforts have been made to generate a new generation of vaccines that are efficacious and can be given to infants, but have been hindered by a poor understanding of the protective immune response to S. Typhi infection, and in particular by the absence of a correlate of protection.
Controlled human infection studies (‘challenge studies’) provide a model for investigating infectious diseases and appraising novel vaccines, including in typhoid disease. This DPhil described the development of a human challenge model of typhoid fever using S
. Typhi Quailes strain administered to healthy adults in a sodium bicarbonate buffer. The careful characterisation and manufactured of the strain is described. Following ingestion of 103 CFU of S. Typhi 55% of participants developed typhoid disease, whilst ingestion of 104 CFU gave a higher attack rate of 65%. At this attack rate vaccine efficacy against human challenge should be demonstrable with a modest sample size. Validity of the model in the appraisal of vaccines was demonstrated using Ty21a, a live, oral, attenuated vaccine. Protective efficacy of Ty21a compared to placebo against challenge was 35%, comparable to that observed in some endemic settings, and the estimated protection in the first year after vaccination in Cochrane meta-analysis.
Clinical, microbiological and humoral immune responses were investigated in participants challenged during model development. Typhoid disease was associated with a high fever in most, but not all participants, and a range of symptoms. Severity of disease was variable, and included asymptomatic bacteraemia, as well as fever and symptoms in participants in whom bacteraemia could not be demonstrated. Typhoid disease was associated with a strong humoral immune response to the flagellin and lipopolysaccharide antigens of S. Typhi but not the Vi polysaccharide capsule. Humoral immune responses were not demonstrated in participants without typhoid fever. There was a dose-response relationship to the clinical, microbiological and humoral responses with participants challenged with 104 CFU having more marked responses than those challenged with 103 CFU. Future success of challenge studies relies on the willing participation of healthy adult volunteers. The motivations for participation, and experiences of participants, were appraised by questionnaire. Whilst financial compensation was an important motivator, it was not the sole motivator. Participants were positive about their experiences, and most would participate again.
Investigation of ultra-wideband wireless communication inside electromagnetically ultra small confined environments
Keywords: ultra wide band
wireless
channel characterization

Ultra-wideband (UWB) communication has been the subject of extensive research in recent years due to its unique capabilities and potential applications, particularly in short-range multiple access wireless communications. However, many important aspects of UWB-based communication systems have not yet been thoroughly investigated. The propagation of UWB signals inside very small enclosed environments is one of the important issues with significant impacts on the future direction, scope, and generally the extent of the success of UWB technology. The objective of this thesis is to obtain a more thorough and comprehensive understanding of ultra-small UWB channels for communication applications and design issues for enhancing the data rate of UWB systems. This works supports the postulation of a high capacity UWB wireless interconnect scheme for communicating devices within conducting enclosures – a wireless “backplane”.
This thesis proposes the use of an Ultra-Wide Bandwidth (UWB) ultra-small scale wireless interconnect scheme for use within electrically small enclosures. Such ultra-small environments (size ≤ 10 wavelengths) are topologically much more complex, being more cluttered, than typical indoor environments (size ≥ 10 wavelengths). The concept is presented through two different scenarios. Firstly, a PC Tower case is presented as a model environment and the work seeks to present the optimum channel performance, where EMI issues are discussed and problem avoidance proposed. Secondly, in order to extrapolate the different results from the study inside the PC, an investigation is carried out using an Aluminium tower case as a more generic model environment. The analysis is based on the behaviour of box modes within a conducting resonator enclosure and the effective communications bandwidth for UWB systems for different sizes and components within.
From these general considerations the research presents theoretical and experimental results from which are derived the communications metrics measured within enclosures. Simulations of the different scenarios are performed using different techniques such as ray tracing and a full wave model, based on CST Microstripes. Empirical data is recorded using a vector network analyser (VNA)-based wideband channel sounding system where channel measurements are carried out in every scenario regarding different aspects such as frequency response and time domain analysis, evaluation of the channel capacity, power delay study and the nature of the environment.
The fiction of Franz Nabl in literary context: a re-examination
Keywords: 20th Century Austrian Literature
Franz Nabl

This thesis re-evaluates the work of the neglected Austrian novelist Franz Nabl. Nabl’s reputation has long been overshadowed by the prestige of Jung-Wien, denigrated by inaccurate association with the Heimatroman, and even unjustly tarnished by his appropriation during National Socialism. My work aims to correct these misconceptions, demonstrating that his best fiction merits rehabilitation not only in its own right, but also for the important questions it raises about conventional narratives of Austrian literary history. Structured chronologically, the five chapters of this thesis provide fresh analyses of Nabl’s texts, many of which have previously received only scant scholarly attention. These close readings are located in a range of relevant literary-historical and cultural contexts, illustrating that Nabl’s writing not only belongs in surprising literary company, but also that his works fit into important, yet often overlooked patterns in Austrian literary history which are often obscured by a tradition of criticism which values ‘modernism’ over ‘realism’, and privileges the aesthetically progressive over the apparently conservative.
The first chapter investigates Nabl’s earliest fiction in the literary and cultural context of fin-de-siècle Vienna, revealing unexpected connections between Nabl and acknowledged modernists, such as Schnitzler and Kafka. The second and third chapters engage with Nabl’s novels, Ödhof and Das Grab des Lebendigen, establishing his status as a significant critical realist within a long tradition of Austrian works exploring unhappy family life. The fourth chapter focuses on the misleading view of Nabl as a regionalist, demonstrating that, while not all Heimat novels deserve critical condemnation, Nabl’s narratives of rural life invoke the conventions of the Heimatroman only to disappoint them. In the last chapter, I explore Nabl’s complicated relationship to National Socialism, showing that, although his involvements with the Nazis were ill-judged, Nabl was not committed to their politics and wrote only politically innocuous fiction during the regime.
Dynamics of Feshbach molecule production
Keywords: cold gases
Bose-Einstein condensate
Feshbach molecules

The variation of a magnetic field in the vicinity of a zero-energy resonance allows highly vibrationally excited molecules (‘Feshbach molecules’) to be produced from an ultracold atomic gas. In this thesis, we study the dynamics of this process. We begin by studying the dissociation of Feshbach molecules, showing that in the limit of a sudden jump the shape of the spectrum of dissociated atoms can act as a probe of the zero-energy resonance. For some resonances, such jumps are within reach of current experiments. We also study the intermediate region between sudden jumps and asymptotically wide, linear ramps. It is shown from a precise derivation how the latter limit leads to a universal spectrum with a shape independent of the implementation of the two-body physics, provided that the near-resonant scattering properties are correctly modelled. We then turn to the dynamics of Feshbach molecule production from thermal and condensed gases. Our microscopic quantum dynamics approach includes the exact twobody evolution as an input to the many-body calculations. We show that in the long-time limit, and the Markov limit for the interactions, the non-Markovian Boltzmann equation (NMBE) we derive for the one-body density matrix reduces to the normal Boltzmann equation. In the limit of short times and small depletion of the atomic gas, the molecule production efficiency can be calculated by thermally averaging the two-body transition probability density. This thermal averaging technique is applied to studies of the formation of Feshbach molecules using a magnetic field modulation that is near-resonant with the molecular bound state energy. The continuum is shown to have a significant effect on both the dynamics and efficiency of this process. We examine the dependence of the molecule production efficiency on the duration, amplitude and frequency of the modulation, as well as the temperature and density of the gas. This method of producing molecules is effective for a wide range of bound state energies, but requires sufficient variation of the two-body energy levels with magnetic field. Lastly, we implement the NMBE for the case of a fast linear ramp across a Feshbach resonance. The solution of this equation is made feasible by including a large part of the required computation in the kernel, which is calculated in advance. The NMBE allows predictions of the molecule production efficiency which go beyond the thermal averaging technique by accounting for the depletion and rethermalisation of the continuum. In the limit of small depletions, the two approaches give the same results. As the depletion increases, the two approaches differ due to many-body effects limiting the maximum possible molecule production efficiency. We have observed this in our simulations by considering higher-density gases. We have therefore shown the suitability and practicability of this beyond mean-field approach for application to further problems in the production of Feshbach molecules from ultracold gases.
Regulation and reproductive functions of membrane-bound vesicles secreted by the Drosophila male accessory gland
Keywords: Exosomes
Drosophila
reproduction
cell signalling

Membrane-bound vesicle secretion provides a novel intercellular communication mechanism, whose roles and regulation remain poorly characterised, particularly in vivo. I have identified two classes of lipid-containing, vesicle-like structures secreted into seminal fluid by epithelial cells of the Drosophila male accessory gland (AG). Exosomes, one class of membrane-bound vesicle formed inside late endosomal multivesicular bodies, are specifically secreted by secondary cells (SCs). The unusual cell biology of SCs allowed me to develop a powerful new high resolution in vivo system to characterise the mechanisms underlying intracellular membrane trafficking events underlying exosome biogenesis using real-time live imaging. I characterise how specific ESCRTs (endosomal sorting complexes required for transport) control SC exosome biogenesis, and identify a novel role for BMP signalling in regulating endolysosomal trafficking events necessary for exosome secretion. I also identify roles for epidermal growth factor receptor (EGFR) and phosphatidylinositide 3-kinase (PI3K) signalling in exosome biogenesis. Importantly, SC exosomes are transferred to females during mating. Here, they fuse with sperm, mirroring in vitro interactions between human prostate exosomes and sperm, and interact with the female reproductive tract epithelium. Blocking SC exosome production specifically suppresses post-mating effects on female receptivity to remating, demonstrating that exosomes have an important reproductive signalling function in vivo, directly or indirectly reprogramming female cells. Finally, I show that main cells, the major epithelial AG cell type, shed lipid-containing microvesicle-like structures from their apical surface. Remarkably, these vesicles carry the seminal peptide, sex peptide, into females during mating and also contribute to the anterior mating plug. In summary, my data reveal previously unsuspected roles for exosomes and microvesicles in Drosophila reproduction that may be evolutionarily conserved. Since these vesicles mediate physiological processes previously thought to involve soluble peptides, my work suggests that current models explaining male reprogramming of female behaviours in flies and higher organisms need substantial revision.
Membrane protein mechanotransduction: computational studies and analytics development
Keywords: mechanosensitive channel of small conductance
mechanosensation
InterQuant
mechanotranduction
E.coli
biochemistry
MscS
molecular dynamics
integral membrane  protein
membrane protein
Bendix

Membrane protein mechanotransduction is the altered function of an integral membrane protein in response to mechanical force. Such mechanosensors are found in all kingdoms of life, and increasing numbers of membrane proteins have been found to exhibit mechanosensitivity. How they mechanotransduce is an active research area and the topic of this thesis.
The methodology employed is classical molecular dynamics (MD) simulations. MD systems are complex, and two programs were developed to reduce this apparent complexity in terms of both visual abstraction and statistical analysis. Bendix detects and visualises helices as cylinders that follow the helix axis, and quantifies helix distortion. The functionality of Bendix is demonstrated on the symporter Mhp1, where a state is identified that had hitherto only been proposed. InterQuant tracks, categorises and orders proximity between parts of an MD system. Results from multiple systems are statistically interrogated for reproducibility and significant differences at the resolution of protein chains, residues or atoms.
Using these tools, the interaction between membrane and the Escherichia coli mechanosensitive channel of small conductance, MscS, is investigated. Results are presented for crystal structures captured in different states, one of which features electron density proposed to be lipid. MD results supports this hypothesis, and identify differential lipid interaction between closed and open states. It is concluded that propensity for lipid to leave for membrane bulk drives MscS state stability.
In a subsequent study, MscS is opened by membrane surface tension for the first time in an MD setup. The gating mechanism of MscS is explored in terms of both membrane and protein deformation in response to membrane stretch. Using novel tension methodology and the longest MD simulations of MscS performed to date, a molecular basis for the Dashpot gating mechanism is proposed. Lipid emerges as an active structural element with the capacity to augment protein structure in the protein structure-function paradigm.
England and the general councils, 1409 - 1563
Keywords: history of political thought
ecclesiastical assemblies
ecclesiology

My doctoral thesis examines the intellectual and political relationship between England and the general councils of the Church from the Council of Pisa until the Council of Trent. It illuminates the hitherto unexplored features of the revolution that was the end of universal papal authority. With the transfer of spiritual authority to Henry VIII, the heads of England’s Protestant regimes inherited the papacy’s distrust of the general council, which had the potential to interfere with the course of the reformation in England.
At the same time, the thesis examines the changing nature of public commitment to universal decision-making in the Church in the face of resistance by hierarchs (papal or royal). It finds a widespread support for the general council over the period, but also a plurality of views about how conciliar government could be reconciled with monarchical rule in the Church. In the fifteenth century, conciliarism had to contend with the suspicions of those who wished to shore up the Church hierarchy against Wycliffite attacks. In the sixteenth century, there was still competition between the establishment’s defence of an hierarchical Church, directed by the monarchy, and theories which stressed the importance of conciliar government. These arguments took different shapes when used by popular rebels in favour of traditional religion grounded on conciliar consent, or by Protestants in favour of synodal government by the godly. But they were both outcomes of enduring instabilities in the ideology of Church government, which had their roots in the fifteenth century.