VictorJuiz/thesis huggingface dataset:
High resolution microwave spectroscopic studies of hydrates of carboxylic acids

This thesis studies the monohydrate, dihydrate and in some cases, trihydrate of five carboxylic acids, namely acetic acid, propanoic acid, T-difluoroacetic acid, Gdifluoroacetic acid and trifluoacetic acid using the technique of Fourier tranform microwave spectroscopy. The rotational and centrifugal distortion constants of these hydrates were determined with high accuracy. Ab initio calculations were also performed to locate the different conformational minima of the hydrates and to optimize their structures. Comparison of the ab initio predicted rotational and centrifugal distortion constants with the experimentally observed values allows us to determine the structures of the global minimum conformations of the various hydrates without ambiguity.
Hydrogen-bonded ring structures are found to be the predominant feature in all observed hydrates. In this structural arrangement, all the hydrogen bonds formed are located in the same ring, and the cooperativity effect between them significantly strengthens each hydrogen bond, as suggested by the sharp increase of their binding energies in the larger hydrates. The fine and hyperfine splittings observed in the specrum were also successfully analyzed, which allows information on the dynamics of the intramolecular large amplitude tunnelling motions to be extracted explicitly.
In the final part of this thesis, the equilibrium constants for the formation of monohydrates of the different carboxylic acids involved in this thesis, together with that of formic acid whose microwave spectrum has been analyzed elsewhere, were calculated to approximately derive their abundances under typical atmospheric conditions. It was found that about 2% of FMA, ACA and PPA will complex with one H2O molecule to form monohydrates in the low troposphere, while for TFA, the value increases to about 15%, mainly as a result of the larger binding energy of TFA–(H2O) due to fluorination on the end group.

Keywords: high resolution microwave spectroscopy
carboxylic acid
hydrate
ab initio calculation
molecular internal dynamics
structure
Advisor: Howard, B
How and why did MARS facilitate migration control? Understanding the implication of migration and refugee studies (MARS) with the restriction of human mobility by UK state agencies

This thesis makes two related arguments regarding the academic field of migration and refugee studies (MARS) and the control of migration by UK state agencies. The first, and more empirical one, is that the former facilitated the latter: the field’s members provided symbolic, technical, and pedagogic assistance to two non-departmental public bodies in controlling migration. The second, and more theoretical, argument of this thesis is that MARS facilitated migration control because of culture, power, and structure. It is through the field’s implication in the coercion of its human subjects by UK state agencies that MARS academics a) answered their calling, b) assisted class rule as ideologists, and c) separated sacred and profane by policing endogamy.
The introduction describes the existing literature on the relationship between MARS and migration control. The consensus is that the former facilitated the latter. However, these studies fail to provide detailed accounts of the ways in which it did so.
Chapter One defines the elements of my more empirical argument: MARS and migration control. An historical narrative outlines the institutional development of the field since its beginnings in the early 1980s. Then a new model for understanding migration control – i.e., migrant CODAR – is described. Chapter Two uses this model to trace the actor network through which MARS academics facilitated the restriction of their human subjects’ mobility by the UK state agencies of the Advisory Panel on Country Information and the Migration Advisory Committee.
Chapters Three, Four, and Five use Weberian, Marxist, and Durkheimian anthropological approaches (respectively) to explain the implication of MARS and migration control that is described in Chapters One and Two. Finally, the conclusion of the thesis discusses its contributions to both more particular (i.e., the literature surveyed in the introduction on MARS and migration control) and more general (i.e., anthropology) scholarly fields.

Keywords: migration and refugee studies
migration control
academics
Advisor: Banks, M
Hybrid ferrocene-based systems

This thesis explores the capacity of sterically and electronically unsaturated boranes to bind substrates of biological and environmental interest, and transduce such binding events into a photo-physical and/or electrochemical response, hence reporting the presence of these substrates.
Chapter three details the synthesis of a range of novel ferrocenyl boranes featuring either a proximal hydrogen-bond donor or a second Lewis acidic centre. These novel boranes were shown to be competent at binding both cyanide and fluoride anions, with the role played by a proximal hydrogen-bond donor or a second Lewis acidic centre in anion binding investigated by both NMR and crystallographic studies.
Chapter four reports the synthesis of novel pyridinyl and related boronic esters, as well as unexpected mixed alkenyl/aryl boranes. The capacity of both types of system to bind fluoride or cyanide anions in solution was investigated by UV-Vis and NMR studies. The photo-physical responses to these anions were also probed, leading to the establishment of both switch-on and switch-off fluorescent responses.
Chapter five extends the knowledge derived from selective anion receptor design and combines this with recent developments in the field of frustrated Lewis pairs (FLPs) to activate, bind and report the presence of nitrous oxide (N2O) molecule. Thus, the syntheses of novel, highly Lewis acidic ferrocenyl boranes that incorporate a high degree of steric loading around the boron centre are reported. The electrochemical and photo-physical response of an FLP system to the presence of N2O was investigated leading to the development of a novel N2O reporting system.

Keywords: sensors
Advisor: Aldridge, S
Analysis of sparse systems

The aim of this thesis is to conduct a general investigation in the field of sparse matrices, to investigate and compare various techniques for handling sparse systems suggested in the literature, to develop some new techniques, and to discuss the feasibility of using sparsity techniques in the solution of overdetermined equations and the eigenvalue problem.

Keywords: graph theory
direct methods
Gaussian elimination
sparse matrices
Advisor: Fox, L
Tewarson, R
Reid, J
Expression and mutagenesis of bacteriorhodopsin an integral membrane protein

Although integral membrane proteins represent nearly a quarter of the genes present in both prokaryotes and eukaryotes, progress in this area of research is often hindered due to the nature of their hydrophobic environment. Elucidating the folding pathway of these proteins is essential to understand many membrane mediated biological processes such as signal transduction, ion transport and chemotaxis.
The wealth of structural and genetic information on bacteriorhodpsin renders it an ideal model system for the study of membrane proteins. Detailed studies however, necessitate efficient methods for its overexpression and purification. Previous expression systems have reported difficulty in obtaining good yields and simple purification procedures.
This thesis investigates a variety of alternative expression and purification systems for the bacterio-opsin gene in Escherichia coli. With sufficient protein, site directed mutagenesis is performed to mutate three proline residues present in the membranous region of bacteriorhodopsin to alanine. The folding kinetics of these mutants is investigated using stopped flow fluorimetry to determine whether proline isomerisation is responsible for a slow step in the folding pathway of bacteriorhodopsin. Comparison of the results with those of the folding kinetics of wild type showed proline isomerisation not to be responsible for the slow step in the pathway. More recent studies have suggested that the slow step may be due to refolding conditions and lateral pressure the lipids impose upon the protein as well as pH.
Separate structural studies using mass spectrometry aimed to study the rates of isotopic exchange of amide and side chain protons in bacteriorhodopsin. Low resolution results obtained using matrix assisted laser desorption ionisation mass spectrometry (MALDI-MS) prompted the investigation of electrospray ionisation mass spectrometry (ESI-MS). Techniques for sample preparation were optimised by investigating a variety of solvent systems and initial deuteration experiments performed.
Phenomenology of exotic hadrons - hybrid mesons and pentaquarks

This thesis is concerned with the properties of two classes of exotic hadron: hy- brid mesons, in which an excitation of the gluonic field causes distinction from the conventional mesons and can give rise to JPC quantum numbers not available to a qq̄ state; and pentaquarks, where the usual baryonic qqq structure is supplemented by a qq̄ pair, potentially giving the state an exotic flavour structure.
In the hybrid meson sector, we work within the flux-tube model and extend upon an observation made by Isgur that the oscillations of the flux-tube can have dynamical effects upon the quarks living on the ends of the tube. We reverse the logic by allowing oscillations of the quarks caused by interactions with currents to excite modes in the flux-tube and hence hybrid mesons.
Electromagnetic, weak and pionic currents are all applied, allowing us to make predictions about the radiative and hadronic decays of hybrid mesons and their production rates in exclusive hadronic decays of the B-meson. Such predictions are of interest to past, present and future experiments at E852, the B-factories and Jefferson Lab.
In light of the possible observation of a pentaquark state, the Θ+ , we investigate some phenomenological consequences of certain models proposed to describe this state and attempt to justify one such model within a quark model framework.
Jaffe and Wilczek's model for pentaquarks predicts in addition to the 10 [note: with a horizontal line above] with JP=½ , a 10 [note: with a horizontal line above] with JP=3/2+, the multiplets being initially degenerate. Within a dynamical model we are able to calculate the spin-orbit splitting between them and find it to not be large.
We also consider the effect of a near degenerate 8 on the states in a pentaquark 10 [note: with a horizontal line above] , outlining a set of characteristic decay systematics that may be used in the search for non-flavour-exotic pentaquarks.
In a constituent quark model with colour-spin interactions it is found to be possible to accommodate a Jaffe-Wilczek-like Θ+ with a rather low mass, while simultaneously describing the Δ-N splitting.

Advisor: Close, F
Social and environmental determinants of changing distribution and incidence of tick-borne encephalitis in Western Europe

In Western Europe the incidence of tick-borne encephalitis (TBE) has increased over the last 30 years, coupled with changes in distribution. Modifications in the TBE enzootic cycle, through a combination of changes in temperature, vertebrate abundance and habitat suitability may have increased the risk of TBE in recent years. In Switzerland, analysis using satellite-derived climate data demonstrated that the environment of areas with TBE since the 1980s and areas that recently became endemic for TBE have become more similar between 2001 and 2009. This was coupled with an increase in April, May and June temperature, which could have affected the tick population and/or human exposure to ticks. Deer and boar abundance also changed in some cantons. In Germany, spatio-temporal modelling demonstrated the importance of temperature, vertebrate abundance and unemployment in the incidence and distribution of TBE between 2001 and 2009. Changes in TBE reporting, April, May and June temperature, vertebrate abundance and pesticide use may have contributed to increases in TBE in 1992 and 2001.
Human exposure patterns, however, appear to be as important as the enzootic cycle in shaping the incidence of TBE, not only in determining the overall trend but also in interacting with the weekly, seasonal and yearly patterns of tick hazard to give the observed incidence. In Switzerland, in weeks with warm, sunny weather, human exposure to ticks is promoted and short-term increases in tick bites are seen. Human outdoor activity also shifts the seasonal pattern of tick bites, when compared with tick questing. There was no apparent increase in time spent in outdoor activities between the 1990s and 2000s in Italy, Germany and Austria, but survey data demonstrated that walking and hiking were already popular activities across Europe by the 1990s. The popularity of mushroom and berry foraging as a source of income in Latvia, Lithuania and Poland, coupled with the expense of vaccination, provide an inverse link between economic wellbeing and TBE risk. Correspondingly, in 2009, the economic recession was associated with an increase with TBE in these three countries.

Keywords: tick-borne diseases
tick-borne encephalitis
public health
infectious disease
epidemiology
Advisor: Randolph, S
Rogers, D
On the stochastic modelling of reaction-diffusion processes

Traditionally, the law of mass action has been used to deterministically model chemical reactions. There are, however, fundamental limitations to this approach when the number of molecules involved in the reactions is small. This is often the case in biological cells, and many authors have reported that deterministic models do not adequately describe processes such as gene expression. This dissertation shows circumstances in which stochastic simulation describes non-linear reactions more accurately than deterministic models. Exact stochastic algorithms due to Gillespie and Gibson-Bruck, based on the chemical master equation, are introduced. A compartment based model is described and analysed for reaction-diffusion systems with low copy numbers of molecules. Finally, this approach is used to produce Turing patterns that may be useful in describing pattern formation in developmental biology.
Comparative studies on the citric acid cycle in muscle

Muscles throughout the animal kingdom vary widely in physiological function and metabolic characteristics. The citric acid cycle (or TCA cycle) plays a very important role in energy production in muscle. However there exists no simple means of estimating the quantitative significance of the TCA cycle in different muscles from animals across the animal kingdom.
The measurement of maximum catalytic activities of some enzymes may provide a reasonably rapid method for the indication of the maximum flux through metabolic pathways. However, only some'key 1 enzymes can play this role of 'rate-indicator'. These enzymes must catalyse reactions which are far displaced from equilibrium in vivo, and which are externally regulated. The theory behind this experimental approach to the regulation of metabolism is explained in Chapter One. The maximum activities in vitro of these 'rate-indicator' enzymes must also be tested against measured maximum rates of operation of the metabolic pathway in which they occur.
Using the above criteria, the work in this thesis demonstrates that 2- oxoglutarate dehydrogenase can be used as an indicator of maximum flux through the TCA cycle in muscles from vertebrates and invetebrates, and that pyruvate dehydrogenase can be similarly used for pyruvate oxidation in vertebrate muscles (Chapter Four). The investigations into the optimal conditions for extraction and assay of these enzymes are discussed in Chapter Three.
A comparative survey of the maximum catalytic activities in vitro of 2-oxoglutarate dehydrogenase and pyruvate dehydrogenase in muscles throughout the animal kingdom was carried out. Knowledge of the quantitative nature of the TCA cycle enabled the physiological function and metabolic characteristics of these muscles to be discussed in detail (Chapters Four and Five).

Advisor: Newsholme, E
The dialogues of the Cyropaedia

This thesis is an examination of the dialogues of Xenophon's Cyropaedia. Chapter I opens with a brief introduction to the Cyr. - its genre, date, epilogue and place in modern scholarship. The second half of the chapter is devoted to an overall survey of the work's dialogues. The dialogues are listed and divided into seven main categories; various formal features of the dialogues - their length, number of speakers, presence of an audience, dramatic background etc. - are noted.
The second chapter deals with the "Socratic" or didactic dialogues of the Cyr. These conversations are first compared to Xenophon's actual Socratic dialogues, particularly those of the Memorabilia, and are shown to have several of the same characteristics: a leading didactic figure, discussion of ethical questions, the use of analogies and a series of brief questions and replies etc. A detailed commentary on the "Socratic" dialogues of the Cyr. follows; some of these dialogues are seen to be livelier and more dialectical than Xenophon's genuine Socratic conversations and his hero Cyrus is not always assigned the role of teacher.
Symposium dialogues are the subject of the third chapter. These conversations are shown to have several features or themes in common, such as a blend of serious and light conversation, a discussion of poverty and wealth, a love interest and rivalry among the guests. The symposia of the Cyr. are compared to earlier literary symposia, including those of Plato and Xenophon, and some of the more Persian features of these parties are pointed out.
Chapter IV deals with the novelle or colourful tales of the Cyr. - the stories of Croesus, Panthea, Gobryas and Gadatas. The characters and plots of these stories are found to have much in common with the novelle of Ctesias and Herodotus. Nonetheless, it is argued in a detailed commentary on these dialogues that Xenophon displays considerable skill and originality in the telling of these tales.
The fifth chapter is a brief commentary on the remaining categories of dialogues: short or anecdotal conversations, negotiation, planning and information dialogues. These dialogues are compared to similar conversations in other works by Xenophon.
Finally, there are three appendices. The first questions whether Cyrus is portrayed as an ideal hero even after the conquest of Babylon, and the second discusses the problem of Persian sources in the Cyr. The third appendix is a list of the speeches of the Cyr.
An archaeobotanical analysis of Silchester and the wider region across the late Iron Age - Roman transition

The separation of agricultural practice from urban communities has long been understood as a key defining feature of urban societies. This thesis investigates the relationship between developments in agriculture and urbanisation in Late Iron Age and Roman Britain. The Late Iron Age period saw the rise of oppida, characterised by extensive dyke systems, the presence of elites and imported material culture. Three models of the agricultural basis of oppida are currently available: agricultural innovations, surplus production, and non-arable settlements. These three models have been evaluated through three methods: the analysis of charred, waterlogged and mineralised plant remains from Silchester, an oppidum and civitas capital in southern Britain; the quantitative analysis of secondary archaeobotanical data from the regional area of the Hampshire Downs and the Thames Valley; and the synthesis of archaeobotanical evidence for food and agriculture at oppida and Roman towns in Britain.
Key findings are that spelt wheat and barley were cultivated at Late Iron Age Silchester in combination with a new crop (flax), new management techniques (hay meadows) and the consumption of new plant foods (olives, celery and coriander). Following the establishment of the Roman civitas capital, the agricultural basis continued unchanged for several decades before a re-organisation c. AD70/80, whereby crop-processing ceased within Silchester. The regional crop-processing and weed ecology analysis shows that arable farming was conducted at Silchester, and that large-scale handling of cereals was not occurring unlike at earlier hillforts, and later towns. The evidence for animal stabling, flax cultivation, haymaking, and new plant foods from Silchester are interpreted as representing the coalescence of a rural population, developing new farming techniques to cope with the nucleated population, and therefore supportive of internal models of oppida development.

Keywords: Iron Age Britain
Roman Britain
Archaeobotany; Agriculture
Advisor: Robinson, M
Molecular mechanisms of OXR1 function

By 2040, the World Health Organization expects neurodegenerative diseases, such as Alzheimer’s disease, amyotrophic lateral sclerosis (ALS), and Parkinson’s disease, to surpass cancer as the second most common cause of death worldwide. Currently, only treatments for symptoms of these diseases are available. Thus, research is critical to alleviate this public health burden by elucidating the pathogenic processes and developing novel therapies. While exact mechanisms by which these heterogeneous neuropathological conditions become manifest in patients remain unclear, growing evidence suggests that oxidative stress (OS) makes a significant contribution to neuronal dysfunction and apoptosis in all major neurodegenerative diseases. Recently, the gene oxidation resistance 1 (Oxr1) has emerged as a critical regulator of neuronal survival in response to OS. Oxr1 is expressed throughout the central nervous system, and its highly conserved TLDc domain protects neurons from oxidative damage through an unknown mechanism.
This thesis aimed to define mechanisms by which Oxr1 confers neuronal sensitivity to OS, and to determine its role in neurodegenerative diseases. I found that Oxr1 mediates cytoplasmic localization of ALS-associated proteins Fused in Sarcoma (FUS) and transactive response DNA binding protein 43 kDa (TDP-43) through a TLDc domain- and arginine methylation-dependent pathway. Next, I investigated in vivo neuroprotective functions of Oxr1, and demonstrated that neuronal Oxr1 over-expression extends survival and ameliorates behavioural dysfunction and pathology of an ALS mouse model. In particular, neuronal Oxr1 over-expression strikingly delays neuroinflammation during ALS pathogenesis. Finally, I characterised a mouse model that specifically deletes Oxr1 from motor neurons. While loss of Oxr1 in ChAT-positive motor neurons does not cause overt neurodegeneration in the spinal cord, constitutive loss of Oxr1 leads to neuroinflammation in the cerebellum and spinal cord. Taken together, these studies illuminate functions of Oxr1 in the complex antioxidant defence network and present implications for future therapeutic strategies.

Keywords: Oxr1
mouse models
oxidative stress
oxidation resistance 1
Amyotrophic lateral sclerosis
Neurodegeneration
inflammation
Motor Neurone disease
Advisor: Davies, K