VictorJuiz/thesis huggingface dataset:
Investigations of the library usage and information needs of clinical medicine and related disciplines

The relationships between medical libraries and the main users of medical information in the teaching hospitals and University departments in Oxford is examined. Systems ideas are used to define the sort of model or picture of the users that a library manager needs in order to provide the appropriate services, and to provide a formal means of incorporating users and their information needs into a management control system. Data were gathered by several methods and combined into a rich picture of the users and their information-seeking behaviour. The systems methodology developed by Checkland at the University of Lancaster was used to test this rich picture and link it with monitoring for library effective- ness. Application of the Checkland methodology was a crucial step which shifted the emphasis of the project from quantitative to conceptual modelling.
The methods of data collection and the results are described as the User Survey. The following techniques were used: questionnaires, semi-structured interviews, direct observation, feedback forms (a critical incident technique), a reference tracing experiment and analysis of existing library records. The data gathered by those methods presented a consistent picture in which the nature of the users' work, ie research or clinical practice, was the dominant influence on information-seeking patterns.
Application of the Checkland methodology and the conceptual models derived from it are described as the Systems Study. This revealed that the formal processes for monitoring and control expected by the conceptual models did not appear in identifiable form in the real world. Further examination showed that a detailed description of the library function was necessary and that this statement could be used to generate performance criteria. In addition, the rich picture from the User Survey was found to be a fair representation of reality. Conclusions for systems thinking, user studies, library managers and medical librarianship are presented.

Advisor: Leggate, P
Shaw, D
Spherically symmetric monopole solutions

Classical gauge theories are studied for spherically symmetric monopole solutions. The Higgs field is taken in the adjoint representation and in the limit of vanishing self-interaction. The equations of motion can be represented by a Lax pair.
Using techniques from group representation theory, explicit solutions are obtained in the case of the principal embedding of the symmetry group SU(2) in the bigger gauge group. The parameters of the solutions can be chosen to give finite fields everywhere, and the large r behaviour of the Higgs field, which determines the symmetry breaking, is discussed. Some low rank groups are studied as examples.
Next, some properties of the non-principal SU(2) embeddings and their classification are discussed. These are then used to obtain more solutions, but the problem has not been solved for the most general case.

Advisor: Heimann, R
The fiction of Franz Nabl in literary context: a re-examination

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.

Keywords: 20th Century Austrian Literature
Franz Nabl
Advisor: Robertson, R
Electronic transport in semiconductors

The first part of this thesis is a study of thermally activated conduction, Hall effect, and Far-Infrared absorption in n-InP. Accurate measurements of threshold energies are deduced from the temperature dependence of these effects, after correction for Fermi level variations, and it is shown that the threshold for electrical conduction is higher than for Hall effect, or cyclotron resonance. An explanation is given in terms of the long range impurity potential fluctuations.
The second part of this thesis presents measurements of the thermopower in heterostructures for the GaInAs - InP, GaInAs - InAlAs, and GaAs - GaAlAs systems, with and without magnetic field, for temperature varying from 2K to 10K. In high magnetic fields, strong oscillations of the thermopower are seen, with the same phase as the Shubnikov - de Haas oscillations in the resistivity, in accordance with theory. The magnitude and temperature dependence of the thermopower are mostly as predicted for the superlattice but those of the heterojunctions disagree with the predictions. A discussion of the cause of this disagreement is given.
In the final part, the value of the relative energy shift between different valleys of the conduction band of a thin film of PbTe grown on BaF2 is obtained. This will be used to obtain the deformation potential of PbTe.

Advisor: Nicholas, R
Dynamics of Feshbach molecule production

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.

Keywords: cold gases
Bose-Einstein condensate
Feshbach molecules
Advisor: Walmsley, I
Regulation and reproductive functions of membrane-bound vesicles secreted by the Drosophila male accessory gland

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.

Keywords: Exosomes
Drosophila
reproduction
cell signalling
Advisor: Wilson, C
Angle and distance geometry problems

Distance geometry problems (DGPs) are concerned with the construction of structures given partial information about distances between vertices. I present a generalisation which I call the angle and distance geometry problem (ADGP), in which partial angle information may be given as well. The work is primarily concerned with the algebraic and theoretical aspects of this problem, although it contains some information on practical applications. The embedding space is typically real three dimensional space for applications such as computer aided design and molecular chemistry, although other embedding spaces are possible. I show that both DGP and ADGP are NP-hard, but that in some sense the ADGP is more expressive than the DGP. To combat the problems of NP-hardness I present some graph theoretic heuristics which may be applied to both DGP and ADGP, and so reduce the time required by general purpose algorithms for their solution. I discuss the general purpose algorithms Cylindrical Algebraic Decomposition and Gröbner bases and their application to this field.
In addition, I present an O(n) parallel algorithm for computing convex hulls in three dimensions, using O(n2) processors connected in a mesh-like topology with no shared memory.

Advisor: McColl, W
McColl, B
Membrane protein mechanotransduction: computational studies and analytics development

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.

Keywords: mechanosensitive channel of small conductance
mechanosensation
InterQuant
mechanotranduction
E.coli
biochemistry
MscS
molecular dynamics
integral membrane  protein
membrane protein
Bendix
Advisor: Sansom, M
England and the general councils, 1409 - 1563

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.

Keywords: history of political thought
ecclesiastical assemblies
ecclesiology
Advisor: Heal, F
Forrest, I
NMR studies of the dynamics and the folding of hen lysozyme

This thesis describes an investigation into the folding behaviour of hen lysozyme by characterisation of the structure and the dynamics of different conformational states of the protein. The native state, a partially structured state generated by the addition of a cosolvent, trifluoroethanol (TFE), and a highly denatured state of the protein in presence of urea at low pH, have been studied at equilibrium by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. The principal methods utilised in-fchis thesis are the measurement and interpretation of amide hydrogen exchange and 15 N relaxation data.
Amide hydrogen exchange rates from a highly denatured state of hen lysozyme in 8 M urea, at pH 2.0, are well approximated by recent estimates for intrinsic exchange rates from unstructured polypeptides, implying that residual .structures cannot be persistent in this state. In the native protein, by contrast, protection factors are measured to be of the order of 104-108 and can be rationalised by the involvement of amides in secondary structure and burial from the protein surface. Surface accessibility has also been found to be an important determinant of the dynamics of main and sidechain groups monitored by 15N relaxation. For this purpose 15N resonances of native lysozyme were assigned and order parameters derived. The dynamic behaviour was considered in the light of features of the crystal and NMR structures, suggesting that a lack of van der Waals contacts is a major determinant for mobility.
A denatured state of hen lysozyme, formed by addition of TFE cosolvent, has been developed as a model for a partially ordered conformation of the protein. Amide hydrogen exchange measurements show that sites with the highest protection factors, up to 250, are located in stable native-like helices. Near complete assignment of 15N-edited NMR spectra allowed a detailed description of secondary structure in the TFE denatured state. Non-native α-helical structure is present as extensions to the native helices and in a region of the polypeptide which forms part of the β-sheet in the native state. These structures have been shown to be in accord with the helical propensities of the primary sequence.
Preliminary structure calculations suggest that, despite the absence of extensive and persistent tertiary interactions, topological restraints exist in parts of the TFE denatured state, resulting in considerable propensities for native-like arrangements of the secondary structure. Mainchain dynamics determined by 15N relaxation, although increased in magnitude, appear to be related to that of the native state and are dominated by the position of disulphide bonds and by chain hydrophobicity. Thus the structural and the dynamic behaviour of the polypeptide chain in the TFE denatured state could be rationalised, at least in part, by consideration of features of the primary sequence.

Advisor: Dobson, C
Mathematical models of cranial neural crest cell migration

From the developing embryo to the evacuation of football stadiums, the migration and movement of populations of individuals is a vital part of human life. Such movement often occurs in crowded conditions, where the space occupied by each individual impacts on the freedom of others. This thesis aims to analyse and understand the effects of occupied volume (volume exclusion) on the movement of the individual and the population.
We consider, as a motivating system, the rearrangement of individuals required to turn a clump of cells into a functioning embryo. Specifically, we consider the migration of cranial neural crest cells in the developing chick embryo. Working closely with experimental collaborators we construct a hybrid model of the system, consisting of a continuum chemoattractant and individual-based cell description and find that multiple cell phenotypes are required for successful migration. In the crowded environment of the migratory system, volume exclusion is highly important and significantly enhances the speed of cell migration in our model, whilst reducing the numbers of individuals that can enter the domain. The developed model is used to make experimental predictions, that are tested in vivo, using cycles of modelling and experimental work to give greater insight into the biological system.
Our formulated model is computational, and is thus difficult to analyse whilst considering different parameter regimes. The second part of the thesis is driven by the wish to systematically analyse our model. As such, it concentrates on developing new techniques to derive continuum equations from diffusive and chemotactic individual-based and hybrid models in one and two spatial dimensions with the incorporation of volume exclusion. We demonstrate the accuracy of our techniques under different parameter regimes and using different mechanisms of movement. In particular, we show that our derived continuum equations almost always compare better to data averaged over multiple simulations than the equivalent equations without volume exclusion. Thus we establish that volume exclusion has a substantial effect on the evolution of a migrating population.

Keywords: mathematical biology
developmental biology
modelling and simulation of cellular migration
chemotaxis
volume exclusion
Advisor: Maini, P
Baker, R
Some problems on the dynamics of nematic liquid crystals

In this thesis, we consider two problems in the Q-tensor theory of nematic liquid crystals. The first concerns eigenvalue constraints on the Q-tensor order parameter. In particular, by employing a singular potential constructed by Ball and Majumdar, we consider the existence, regularity and "strict physicality" of weak solutions to the Beris-Edwards equations of nemato-hydrodynamics. In the second part of the thesis, we consider a gradient flow of the well-studied Landau-de Gennes energy. We prove some rigorous results on the average long-time statistical behaviour of its solutions, which are in agreement with experimental observations in the condensed matter physics literature.

Keywords: Partial Differential Equations - Liquid Crystals - Condensed Matter Physics
Advisor: Ball, J
Zarnescu, A