VictorJuiz/thesis huggingface dataset:
Density fluctuation measurements with laser scattering

This thesis describes the development and application of a new, non-invasive, diagnostic based on far forward scattering(FFS) of electromagnetic radiation for investigating density fluctuations in fusion research plasmas.
The spatial distribution and phase of the oscillations induced on the profile of a Gaussian laser beam transmitted through a disturbed refractive medium can be predicted in terms of the characteristics of the disturbance, which can in turn be deduced from them. The theory of these interactions is presented with various models of perturbations to account for differing experimental conditions including one developed by the author which takes into account the effect of broadening in the K spectrum of the fluctuations.
Two sets of experiments are discussed in this thesis, both using a FFS apparatus based around a CO2 laser and an array of 12 photoconductive detectors. The first successfully tested the prediction of FFS theory under controlled conditions using a transducer to generate ultrasonic waves in air, and an air jet to produce turbulence. Numerical reconstruction of the scattering structure was achieved under these ideal conditions.
In the second set of experiments, FFS was performed on plasma in the small tokamak TOSCA. Results are presented for density fluctuations with wavenumbers around 2 cm-1 , a bandwidth of several kHz and a relative fluctuation level of 6%. This level is roughly independent of the variation in the mean density and is close to the mixing length level, indicating strong turbulence. The fluctuations are found to be mainly poloidal and follow a v-2 power law. The average phase velocities are around 4.5 km/sec and are slightly larger than the electron diamagnetic drift velocity. The waves are tentatively identified with the electron drift mode. Coherent signals due to long wavelength MHD modes are detected. Results from a Langmuir probe corroborate most of these data.

Advisor: Braithwaite, N
The relationship between type Ia supernovae and their host galaxies

This thesis studies the relationship between type Ia supernovae (SNe Ia) and their host galaxies. The sample consists of 527 SNe Ia with redshift z<0.09 discovered by the Palomar Transient Factory (PTF). We obtained high-quality photometric and spectroscopic data of the host galaxies and determined their stellar mass Mstellar, star formation rate (SFR), gas-phase/stellar metallicity, stellar age and SN offset.
In the first part of the analysis, we compare the SN Ia photometric properties to the host parameters. Strong correlations between the SN Ia light-curve width (stretch) and the host age/mass/metallicity are found: fainter, faster-declining events tend to be hosted by older/massive/metal-rich galaxies. There is also some evidence that redder SNe Ia explode in higher metallicity galaxies. SNe Ia in higher-mass/metallicity galaxies also appear brighter after stretch/colour corrections than their counterparts in lower mass hosts, and the stronger correlation is with gas-phase metallicity suggesting this may be the more important variable. We also compare the host stellar mass distribution to that in galaxy targeted SN surveys and the high-redshift untargeted Supernova Legacy Survey (SNLS). The difference between each stellar mass distribution can be explained by an evolution in the galaxy stellar mass function, coupled with a SN delay-time distribution proportional to t-1. Finally, we found no significant difference in the mass-metallicity relation of our SN Ia hosts compared to field galaxies, suggesting any metallicity effect on the SN Ia rate is small.
In the second part of the analysis, we compare the SN spectral features to the host parameters. We find that SNe Ia with higher Si ii λ6355 velocities tend to explode in more massive galaxies. We study the strength of the high-velocity component of the Ca ii NIR absorption, and find that SNe Ia with a stronger high-velocity component are preferentially hosted by galaxies with a low Mstellar, a blue colour, and a high SFR, and are therefore likely to arise from the youngest progenitor systems. When combined with other studies, our results support the scenario that these high-velocity features are related to an interaction between the SN ejecta and a circumstellar medium (CSM) local to the SN.

Keywords: supernova
distance scale
cosmology
Advisor: Hook, I
Sullivan, M
Dilemmas of regional governance: sub-national territorial politics and river basin management in the USA, France, China, and India

This dissertation identifies and explores the dilemma of regional governance, namely how to address political and economic challenges which occur at the meso-, as opposed to local, national, or international scale. Drawing on a large body of theoretical work on decentralization and federalism, this dissertation addresses the question, how do different institutional arrangements for political, fiscal, and administrative decentralization influence the capacity of political systems to capture regional-scale externalities? It does so by examining the responses of four different political systems, two federal and two unitary, to the problem of capturing economic externalities through River Basin Management (RBM), a quintessential regional issue. RBM outcomes are operationalized in terms of efficacy of capture of both water quality and quantity externalities which occur within inter-jurisdictional river basins.
Through close historical analysis of six paired case studies across the four country cases, the dissertation argues that the capacity of political systems to capture regional-scale externalities depends on the ability of sub-national jurisdictions to pursue localized preferences, which is in this dissertation referred to as sub-national territorial politics. These politics are most prevalent in federal systems, which typically accord sub-national territorial jurisdictions with greater political power and fiscal resources. These political systems feature fewer and weaker regional governance institutions, and generally less effective regional-scale externality capture, than their counterparts.
This dissertation contributes to a growing "sub-national turn" in comparative politics in two ways. First, it identifies the geographically-rooted interests which often shape sub-national actor preferences, particularly with respect to natural resource issues. Second, the dissertation discerns the lack of political incentives for central governments to resolve disputes between sub-national administrative jurisdictions, particularly in the federal systems in which these units are the basis for political representation at the national level.

Keywords: river basin management
water resource management
water resource conflict
water resource politics
sub-national politics
Advisor: Bermeo, N
Simulation and control of windfarms

This thesis examines the design of supervisory controllers for windfarms of pitch-controlled wind turbines. The control objectives are the maximisation of the financial income from the generated electricity and the minimisation of the turbines' fatigue damage. The design exploits the wide variations in the ratio of financial income to fatigue damage which are found both spatially across windfarms and as a function of time. The supervisory control strategy makes use of the ability of pitch-controlled turbines to operate with variable power set points; a capability which is rarely exploited in practice.
A windfarm simulation which has been developed for the purposes of testing supervisory controllers is described. It is shown that the simulation is a suitable test-bed for this application. Results are presented which demonstrate how the fatigue damage of a turbine's gearbox and structural components vary as functions of the mean wind-speed, turbulence intensity and power set point, both for isolated turbines and for turbines experiencing wake effects.
A lifetime performance function is proposed and 'ideal' power set point curves are evaluated using a genetic search algorithm. It is shown that significant improvements in performance can be achieved if the operation of the turbines is altered to take account of variable electricity tariffs.
A windfarm control strategy that splits the turbines into interacting and non-interacting categories is found to give good results. Using data generated by the simulation, it is shown that simple cost functions can be developed for non-interacting turbines which, when used in a controller, give performance that is close to the 'ideal'. A similar cost function is applied to a group of three interacting turbines, and it is found that substantial reductions in all measures of total annual fatigue damage are achieved for a small reduction in total annual financial income. The on-line implementation of windfarm supervisory controllers is discussed and the behaviour of a simple hill-climbing algorithm is examined using a simulated group of three interacting turbines.

Keywords: wind turbine
optimisation
supervisory control
fatigue
wind power plant
genetic algorithm
mechanical engineering
control engineering
wind energy
Advisor: Dexter, A
The consequences of international trade price volatility for national income and welfare

The thesis considers the effect of world trade or commodity price volatility on small open economies. It extends the existing literature by including non-tradeable goods and many volatile prices in the model together with consideration of the welfare effects of participation in international risk or capital markets. In addition the thesis systematically addresses the implications of price volatility for resource allocation and presents empirical estimates of the costs and benefits of volatility for a large sample of countries. The most important theme in the analysis is the extent of output flexibility in the face of variable prices. It is shown that price volatility gives rise to high returns to flexibility which suggests that commodity exporting countries should regard price volatility as an opportunity to benefit by being flexible as well as a source of welfare costs. The empirical estimates show that many developing countries have had an inflexible response to changes in world prices over the period 1958-90. Flexibility may improve with the abolition of producer price stabilisation in many countries in the 1980s, a policy reform that is predicted to yield large benefits. These will increase if attempts are also made to improve the functioning of domestic risk and capital markets together with enhanced access to their international equivalents.
Architecture of the HIV-1 glycan shield

In recent years the glycan shield of the HIV-1 envelope spike (Env) has emerged as a potential target for microbicide and vaccine design. The densely packed glycans on its surface include an intrinsic population of under-processed oligomannose structures, and a number of lectins and broadly neutralising antibodies (bnAbs) have been isolated which are reactive to these ‘non-self’ glycan structures. The potential value of these agents in therapeutic or vaccine contexts depends upon the prevalence of their glycan targets in nature and their resilience to sequence mutation. Here the prevalence of oligomannose-type glycans on recombinant gp120 was demonstrated across a panel of isolates, revealing subtle cross clade differences. Alanine scanning of all potential N-glycosylation sites (PNGSs) within a model gp120 demonstrated the overall stability of the oligomannose population, but highlighted regions of glycan clusters where individual glycans act to limit the processing of their neighbours. This was formally demonstrated for the N332 ‘site of vulnerability’, where deletion of nearby glycosylation sites led to altered glycan processing at the N332 site. A panel of N332-dependent bnAbs was screened for their ability to tolerate such changes in glycan processing, with differing results. While some displayed promiscuous binding, others were more sensitive to glycan microheterogeneity. Site-specific glycosylation analysis of the PGT135 epitope revealed that an intolerance of certain glycoforms may explain its limited breadth. While a greater understanding of Env glycan microheterogeneity and bnAb promiscuity is required, these findings reveal insights into the architecture of the HIV-1 glycan shield that suggest it is a conserved and robust target for drug and vaccine design.

Keywords: gp120
glycosylation
broadly neutralising antibodies
vaccines
HIV
Advisor: Crispin, M
Wormald, M
The biosynthesis of β-lactams

This thesis reports the work done on two research projects which were carried out independently of each other but converge on the central theme of β-lactam biosynthesis. Chapter 1 provides an overview of biosynthesis in secondary metabolism, with special emphasis on current knowledge about the β-lactams.
The first project, covered from Chapters 2 to 5, was part of our group's continuing effort to understand the structure and mechanism of Ring Expandase-Hydroxylase (REXH), an enzyme involved in the biosynthesis of cephalosporin C in Cephalosporium acremonium. REXH is a bifunctional enzyme, converting penicillin N to DAOC and thence to DAC.
[diagram omitted from transcription]
Chapter 3 discusses the investigation of purification protocols for native REXH and soluble recombinant REXH, as well as an improved refolding method for recombinant REXH expressed as inclusion bodies. Chapter 4 describes two new alternative substrates for REXH, viz. carba-DAOC and DAC, whilst the y-lactam analogue of penicillin N was not found to be a substrate for REXH. Chapter 5 summarises some structural investigations of REXH employing methods such as electrospray mass spectrometry, selective proteolysis and inhibition kinetics.
[diagram omitted from transcription]
The second project, covered from Chapters 6 to 9, represents the first biosynthetic studies on valclavam, an antifungal produced by Streptomyces antibioticus. Valclavam belongs to the family of clavams which includes clavulanic acid as its most well studied member.
[diagram omitted from transcription]
Chapter 7 details the development of methods for the bioassay, fermentation and isolation of valclavam. It also describes the isolation of a stable degradation fragment of valclavam which led to the revision of the structures of valclavam and Tü 1718B (another metabolite from the same organism). Chapter 8 gives an account of the whole-cell feeding experiments which strongly suggest that the primary metabolic precursors for valclavam are L-valine, L-arginine, L-methionine and glycerol. Chapter 9 reports the discovery of two enzymic activities, belonging to those of clavaminic acid synthase and proclavaminic acid amidino hydrolase, which are likely to be involved in the biosynthesis of valclavam. Together, the results of Chapters 8 and 9 point to an extensive overlap between the clavulanic acid pathway in Streptomyces clavuligerus and the valclavam pathway in Streptomyces antibioticus.

Advisor: Schofield, C
Studying the brain mechanisms of dyspnoea with functional magnetic resonance imaging

Dyspnoea (breathlessness) is a debilitating, often poorly controlled, symptom of cardiopulmonary, neurovascular and psychological disorders. This thesis develops the necessary methodology to dissociate aspects of the acute dyspnoea experience using functional magnetic resonance imaging (FMRI) in healthy volunteers. The neuronal mechanisms underlying dyspnoea anticipation, its perceived intensity and unpleasantness and the modulation of these mechanisms by the opioid remifentanil were explored.
We investigated the subjective perception of respiratory loading, a commonly used dyspnoea stimulus, and its potential systematic confounds on FMRI due to cerebral blood flow changes. Investigation of the perception of respiratory loading at different levels of hypercapnia (increased end-tidal CO2) showed that hypercapnia should be kept to a minimum to avoid increased baseline respiratory unpleasantness whilst maintaining the stable arterial CO2 (isocapnia) beneficial for FMRI analysis. Investigation of the effects of respiratory loading (± 9 cmH2O) on cerebral blood flow showed that systematic confounds of respiratory loading on perfusion-based neuroimaging data were small (~5%) and did not significantly alter neural activation in response to visual stimulation.
Isocapnic respiratory loading during a classical fear-conditioning paradigm during FMRI was used to investigate dyspnoea anticipation, and dissociate the intensity and unpleasantness of acute dyspnoea by modulating unpleasantness with remifentanil. Differential neural networks were found to be involved in perceived intensity (thalamus, insula, somatosensory cortex) and unpleasantness (hippocampus, medial prefrontal cortex). Remifentanil reduced respiratory unpleasantness without affecting the perceived intensity and differentially reduced brain activity during both dyspnoea anticipation and perception.
This thesis showed the potential of isocapnic respiratory loading for the study of dyspnoea with FMRI. This stimulus revealed, for the first time, brain activation for dyspnoea anticipation, perceived intensity and unpleasantness. The opioid-sensitive nature of the anticipation and unpleasantness of dyspnoea provides brain targets for future research and might facilitate more effective dyspnoea palliation.

Keywords: dyspnoea
neuroimaging
perception
FMRI
psychology
Advisor: Pattinson, K
Farmery, A
Power functions and exponentials in o-minimal expansions of fields

The principal focus of this thesis is the study of the real numbers regarded as a structure endowed with its usual addition and multiplication and the operations of raising to real powers. For our first main result we prove that any statement in the language of this structure is equivalent to an existential statement, and furthermore that this existential statement can be chosen independently of the concrete interpretations of the real power functions in the statement; i.e. one existential statement will work for any choice of real power functions. This result we call uniform model completeness. For the second main result we introduce the first order theory of raising to an infinite power, which can be seen as the theory of a class of real closed fields, each expanded by a power function with infinite exponent. We note that it follows from the first main theorem that this theory is model-complete, furthermore we prove that it is decidable if and only if the theory of the real field with the exponential function is decidable. For the final main theorem we consider the problem of expanding an arbitrary o-minimal expansion of a field by a non-trivial exponential function whilst preserving o-minimality. We show that this can be done under the assumption that the structure already defines exponentiation on a bounded interval, and a further assumption about the prime model of the structure.

Keywords: real numbers
power function
model completeness
exponentiation
o-minimal
decidability
Advisor: Wilkie, A
X-ray analysis of biological macromolecules

The work described in this thesis relates to two topics: the crystallography of the enzyme α-glucan phosphorylase extracted from rabbit muscle, and the development of a photographic data collection system using a rotation camera.
Crystals of phosphorylase in the a and b forms were obtained with the spacegroup P21. These crystals have the phosphorylase tetramer, molecular weight 400,000 daltons, as the asymmetric unit and, therefore, the structure determination using them presents a considerable crystallographic problem. The crystals were also grown in the presence of methyl mercury chloride thereby producing a potential heavy atom derivative. A small amount of work was carried out on these crystals before another crystal form of phosphorylase b was discovered.
This second crystal form has the space group P41212 (or P43212) and has the phosphorylase monomer, molecular weight 100,000 daltons, as the asymmetric unit. Although the unit cell volume of these tetragonal crystals is slightly larger than that of the monoclinic crystals, the spacegroup symmetry reduces the number of unique reflections by a factor of approximately 4; hence these crystals are potentially more useful for a structure determination. The tetragonal crystals grow most readily in the presence of inosine monophosphate, and will not grow at all in the presence of adenosine monophosphate.
A search for isomorphous heavy atom derivatives of these tetragonal crystals has been conducted with a limited amount of success. Diffusion of platinum, in the form of the platinum diamino-dichloride ion, into the native crystals yields a single site derivative of high occupancy. Various methods of data collection were considered before 6Å data sets were collected on the four circle diffractometer for the native and 4 potential heavy atom derivatives. The method of data collection and data processing are discussed in this thesis and the results given.
A rotation camera had been built in the laboratory by Mr. M. Pickford and Mr. J. Marsh to a design by Dr. D.I. Brown. The camera was intended for use with crystals which had large unit cells. Testing and further development of this camera was carried out, and is described in this thesis. The films from the rotation camera are processed using a Photoscan P1000 Microdensitometer which produces digital images of the films on magnetic tapes. The development of computer programmes to predict the positions of reflections on rotation films and to calculate their integrated intensities using the microdensitometer output tapes is described. An outline of rotation camera geometry is also given.
A series of rotation photographs was. taken with a crystal of lysozyme on the camera in order to check the computer pro- grammes. The first results of these checks were very encouraging. Some initial experiments using a tetragonal phosphorylase b crystal on the camera were carried out with encouraging results.
Reinterpreting environmental scarcity and conflict

The thesis explores links between resources and conflict in contemporary Somalia. The central research questions were: Why did a society which is believed to be resilient and adaptive to its harsh environment become vulnerable? To what extent did environmental factors contribute to the emergence of conflict? How can natural resource scarcity and abundance be related to the existence of, or potential for, violent conflict, bearing in mind the historical, political, economic and cultural context of conflict? Can other determining factors such as power-relations, access to trade, or clan affiliation be linked to lower economic, institutional, and social performance and associated with higher levels of violent conflict? If a link can be made, this will help to forecast where conflict might take place. Because Somalia is largely an arid country, highly susceptible to natural disasters, and because its people have been victims of severe famine in recent decades, my starting point for this research was to investigate literature on the supposed environmental causes of conflict. Analysis of the literature which links environmental degradation and scarcity to state-collapse or civil war suggested, however, that such linkages are problematic. I argue instead that people engage in violent conflict in Somalia because they struggle to establish control over valuable resources. These resources are likely to be renewables, such as cash crops in the form of plantations in riverine areas, cereals in the Bay region, and charcoal in the coastal region of Brawa. Conflict arose over the struggle to monopolise these resources, and over the distribution of profits. Clan leaders sought to expand a source of 'tax' revenue by controlling trade networks, seaports and airports. This general approach may explain why southern Somalia has experienced continuous insecurity over the past decade.

Advisor: Professor William Beinart, D