VictorJuiz/thesis huggingface dataset:
A clinical/immunological neuromyelitis optica association study

Neuromyelitis optica (NMO) and NMO spectrum disorders (NMOSD) are associated with the disease-specific autoantibody aquaporin-4 (AQP4-Ab), which is thought to be pathogenic. Some NMO/NMOSD patients do not have this antibody and may have different clinical and immuno-pathological disease characteristics, but previous clinical NMO/NMOSD studies have been confounded by inclusion of such patients.
To define better the characteristics of AQP4-Ab disease, disease course, outcomes and predictors of disability were investigated in 106 AQP4-Ab positive NMO/NMOSD patients from the UK and Japan. AQP4-Ab positivity conferred a high risk of relapsing disease and substantial disability; age at disease onset and ethnicity were important predictors of disability type. Visual disability was more common in younger patients and those of Afro-Caribbean ethnicity whilst older patients and Caucasian patients were more at risk of motor disability.
To determine whether disease characteristics were influenced by AQP4-Ab binding specificities, the differential binding of patient AQP4-Ab against the two main AQP4 isoforms was investigated. Although the relative binding to the two isoforms differed between patients, there was no association between these differences and clinical features such as relapse type, severity, onset age and ethnicity.
The clinical and in vitro characteristics of AQP4-Ab negative NMO/NMOSD patients were studied. It was shown that these patients represent an aetiologically heterogeneous group. Some have other inflammatory and infectious disorders, some have low levels of AQP4-Ab and a significant proportion have antibodies to myelin oligodendrocyte glycoprotein (MOG-Ab). Others have antibodies that bind to neurons or oligodendrocytes in primary cultures. Attempts to identify novel antigens by immunocapture techniques were made, but were not successful. Patients with MOG-Ab showed differences when compared to those with AQP4-Ab including higher proportion of males, younger age at disease onset and greater likelihood of conus involvement on imaging. Additionally, patients with MOG-Ab appear to have more favourable outcomes, with better improvement from the onset attack and a lower probability of subsequent relapses.
In conclusion, the work in this thesis has shown that AQP4-Ab disease is not synonymous with the term NMO and that seronegative NMO/NMOSD patients represent a clinically and aetiologically heterogeneous group and should therefore be classed separately from those with AQP4-Ab.

Keywords: Neuromyelitis optica
NMO
aquaporin-4
Advisor: Palace, J
Vincent, A
Optical studies of modulation-doped v-groove quantum wires

Experimental studies of optical properties in undoped and modulation-doped v-groove quantum wires (QWR) are presented. The results show good agreement with theoretical predictions.
The investigation of undoped samples demonstrates the successful fabrication of high quality samples with small wire dimensions, exhibiting narrow linewidths and large subband spacings. Calculations from the Schrodinger solver show good agreement with the experimental results. Information about the shape of the confining potential is obtained from magneto-optical measurements where anisotropic shrinkage and binding energies of the excitons are measured. In high excitation power experiments the suppression of the excitonic recombination is observed due to screening and phase space filling. Photoluminescence excitation experiments reveal an inefficient carrier intersubband relaxation.
Extending the optical investigations to modulation-doped samples, the formation of a one-dimensional electron gas can be observed. As a strong indication for this is the presence of a Fermi edge singularity (FES). Furthermore, Poisson-Schrodinger calculations show that the increased electron density in the conduction band leads to modified confinement energies. This was confirmed in magneto photoluminescence (MPL) experiments, where the diamagnetic shift of the luminescence from the first excited state is stronger than in the undoped case, as the state is squeezed further into the corners of the QWR. Recombination of the ground state electrons with different hole states appears as a fine structure in MPL spectra.
Detailed analysis provides clear evidence of the FES. The expected temperature sensitivity of the FES is observed for lattice and electron heating. The FES intensity is also reduced at high excitation powers. The role of hole localisation and subband coupling is discussed. At applied magnetic fields the coupling of bands induces an enhancement of the singularity.
Finally, the behaviour of hot carriers is investigated with time-resolved and electro-photoluminescence measurements. Long luminescence lifetimes indicate that electron-hole separation occurs due to the pinch-off between the QWR and the side quantum well. The field dependence of the electron heating shows quite clearly that LO phonon scattering is the dominant relaxation process at electron temperatures above ~40 K.

Advisor: Ryan, J
The mechanisms and effects of modifying attentional biases to threatening information

Patients with both depression and anxiety show an increased tendency to deploy attention towards negative information. Cognitive models of the illnesses predict that these negative attentional biases are causally related to the symptoms of the disorders. Consistent with this, modifying attentional bias using either antidepressant medication or simple, computer based training tasks has previously been associated with altered symptomatology in both non-clinical and clinical populations. The current thesis aimed to investigate the mechanisms by which attentional bias training tasks alter attention. The investigations were conducted within an experimental neuroscience framework which has previously been successfully deployed in studies of antidepressant medication. The thesis then sought to use these initial results to improve the basic understanding of attentional control processes and, ultimately, guide the development of novel treatment strategies. The initial studies of the thesis characterised the behavioural and neural effects of attentional bias training. Behaviourally, a high degree of generalisation of the training effect was found across a range of emotional stimuli. Neurally, training was found to alter activity in a network of prefrontal regions known to be involved in the control of attention. Further analysis, utilising a computational learning model, suggested that the attentional control systems identified in this study could be understood in terms of expectation based processes. These studies therefore indicated that, in contrast to the predominately limbic effects of antidepressant medication, training initially altered the response of frontal control circuitry. The later studies of the thesis investigated possible strategies for extending the use of attentional bias training. Firstly, combining training with antidepressant medication was found to produce an interference effect on emotional memory suggesting that administering both interventions concurrently is likely to erode their cognitive impact. Lastly, attentional bias training was found not to alter attention in patients with bipolar disorder, with the results of the study indicating that standard assessments of attentional bias in this clinical population are likely to be unreliable. Overall, these studies indicate that attentional bias training may be used to alter the top-down control of attention to emotional information and suggest that such effects may interfere with the bottom-up effects of antidepressant drugs. More generally the work demonstrates the utility of using a cognitive-neuroscientific framework to explore the mechanisms and impact of novel therapeutic strategies.

Keywords: cognition
neuroimaging
antidepressants
cognitive bias
Advisor: Harmer, C
Holmes, E
Goodwin, G
Recontextualising Messiaen's early career

This thesis independently re-examines Messiaen's early career and development. It assesses his personal, professional and musical associations with early contemporaries - colleagues, teachers and critics - and places his aesthetic outlook in a wider context.
In his later life, a simplistic mythology of 'difference' grew up around Messiaen; he was perceived as a 'visionary' in a rational age and as a 'simple man of faith' in a complex and secular time. This mythology has given rise to an implicit misconception of Messiaen that places him apart from the main currents of the twentieth century. This misconception is encapsulated by the entry on Messiaen in the second edition of the New Grove Dictionary of Music and Musicians, which begins: 'He was a musician apart'.
In themed essays, I reassess Messiaen's early career by considering in turn several contextual areas. After introducing the wider context, I consider how Messiaen positioned himself biographic-ally and musically in his many writings, focussing on recurring themes (particularly those highlighted by Ernst Kris and Otto Kurz) and drawing on the composer's writings, established or newly discovered, as my main source. Then I examine Messiaen's relationship with his immediate contemporaries and, in particular, the group of fellow musicians with whom he forged his early career. I also discuss the role of Messiaen's first wife, Louise Justine Delbos (better known by her pseudonym Claire Delbos). Subsequently, I go on to explore Messiaen's relation to the French traditions of musical technique and history. Finally, I consider some French aesthetic disputes of the 1930s and examine Messiaen's role in these debates.
Throughout, I challenge the image of the 'musician apart'.

Advisor: Fauser, A
Security and the right to security of person

This thesis inquires into the meaning of the right to security of person. This right is found in many international, regional and domestic human rights instruments. However, academic discourse reveals disagreement about the meaning of the right. The thesis first considers case law from the European Convention on Human Rights, the South African Bill of Rights and the Canadian Charter. The analysis shows that courts too disagree about the meaning of the right to security of person. The thesis then takes a theoretical approach to understanding the meaning of the right. It is argued that the concept of ‘security’ establishes that the right imposes both positive and negative duties but that ‘security’ does not determine which interests are protected by the right. For this, we need consider the meaning of the ‘person’. The notion of personhood as understood in the ‘capabilities approach’ of Amartya Sen and Martha Nussbaum is then introduced. It is suggested that this theory could be used to identify the interests protected by the right. Next, the theoretical developments are applied to the legal context in order to illustrate the variety of interests the right to security of person would protect and the type of duties it would impose. As a result, it is argued that the idea of ‘security of person’ is too broad to form the subject matter of an individual legal right. This raises a question over the relationship between security of person and human rights law. It is proposed that instead of recognising an individual legal right to security of person, human rights law as a whole could be seen as a mechanism to secure the person, the capabilities approach determining what it takes to fulfil a right and thereby secure the person.

Keywords: capabilities approach
human rights
security
right to security
personhood
socio-economic rights
Advisor: Galligan, D
Lazarus, L
Modernising tradition: the architectural thought of Giles Gilbert Scott (1880-1960)

The architect Giles Gilbert Scott (1880 – 1960) designed the red telephone kiosk, Liverpool Anglican Cathedral, Battersea Power Station, and the House of Commons Chamber amongst other major projects. Yet this thesis is the first scholarly study of his work as a theorist and practitioner. Scott’s ideas provide a window into how architects, critics, and clients of his generation thought about architecture, helping us to understand the design of the interwar period in a way that the backward projection of our own intellectual frameworks cannot do. Often relegated to a minor place in architectural histories, in his time Scott was one of the best known architects in the world, author of numerous iconic structures and widely influential. By returning him to a prominent place in the narrative, the thesis reveals a world in which so-called traditionalists and modernists were concerned with the exploration of common themes – the social role of the architect, the psychological effect of buildings, the nature of construction and tradition. The first two chapters explore Scott’s ideas about history and architectural context by investigating his work at Oxford and Cambridge. The third chapter focuses on his church work as a way of understanding his ideas about tradition and the role of psychology in architecture. The fourth chapter explores the ways that he gave meaning to his designs using rhetoric and planning. Set against the backdrop of the postwar decline of his reputation, the final chapter examines the legacy of his architectural theories. By returning Scott to the historical narrative, our understanding of interwar architecture is greatly broadened. And by expanding our knowledge of the least understood era of twentieth century architecture, we come to better understand how modern architecture as we know it was forged.

Keywords: Giles Gilbert Scott
Advisor: Tyack, G
Whyte, W
Wright, A
Quantitative dopamine imaging in humans using magnetic resonance and positron emission tomography

Dopamine is an important neurotransmitter that is involved in several human functions such as reward, cognition, emotions and movement. Abnormalities of the neurotransmitter itself, or the dopamine receptors through which it exerts its actions, contribute to a wide range of psychiatric and neurological disorders such as Parkinson’s disease and schizophrenia. Thus far, despite the great interest and extensive research, the exact role of dopamine and the causalities of dopamine related disorders are not fully understood.
Here we have developed multimodal imaging methods, to investigate the release of dopamine and the distribution of the dopamine D2-like receptor family in-vivo in healthy humans. We use the [11C]PHNO PET ligand, which enables exploration of dopamine-related parameters in striatal regions, and for the first time in extrastriatal regions, that are known to be associated with distinctive functions and disorders. Our methods involve robust approaches for the manual and automated delineation of these brain regions, in terms of structural and functional organisation, using information from structural and diffusion MRI images. These data have been combined with [11C]PHNO PET data for quantitative dopamine imaging.
Our investigation has revealed the distribution and the relative density of the D3R and D2R sites of the dopamine D2-like receptor family, in healthy humans. In addition, we have demonstrated that the release of dopamine has a functional rather than a structural specificity and that the relative densities of the D3R and D2R sites do not drive this specificity. We have also shown that the dopamine D3R receptor is primarily distributed in regions that have a central role in reward and addiction. A finding that supports theories that assigns a primarily limbic role to the D3R.

Keywords: PET
anatomy
Pallidum
Dopamine Receptor
Substantia nigra
DTI
Positron Emission Tomography
Dopamine
MRI
Basal ganglia
Striatum
Magnetic resonance imaging
Brain
Regions of Interest
Diffusion weighted imaging
Advisor: Gunn, R
Mark, J
Applications of optical-feedback cavity-enhanced absorption spectroscopy

This thesis presents two contrasting implementations of the optical-feedback cavity-enhanced absorption spectroscopy (OF-CEAS) technique. OF-CEAS com- bines passive optical-feedback locking of semiconductor lasers with cavity-enhanced absorption spectroscopy, and is well suited to sensitive detection of pressure- broadened trace gases. Chapters 1 and 2 set the work in this thesis in context, by describing the theory and discussing the motivations behind trace gas sensing by tuneable laser spectroscopy in the near- and mid-IR.
Chapter 3 reviews the theory of OF-CEAS, prior to presenting the results of an experimental implementation based on a near-IR DFB diode laser setup following the traditional V-cavity methodology to spatially decouple the optical- feedback beam from the direct back reflection. The capabilities of the system are demonstrated by accurate determination of a self-broadened half-width at half- maximum of a CO 2 transition, and by detection of acetylene in a car exhaust sample.
Chapter 4 describes the design and implementation of the linear cavity method- ology for QCL OF-CEAS, which is the significant contribution of this work. Successful OF-CEAS locking with the linear cavity is shown for two different DFB-QCLs, with close operating wavelengths (5.5 and 5.2 µm) but quite different operating powers and facet size. Chapter 5 presents quantitative spectroscopic results from the linear cavity OF-CEAS instrument, using both lasers. Spec- troscopy on mixes of N 2 O and NO returned sensitivities, quantified by the α min , of 2.7 × 10 −8 cm −1 in 1 s at 0.28 atm and 2.4 × 10 −8 cm −1 in 1 s at 0.19 atm respectively. Limited by etalon fringing on the baseline, the α min compared well with those obtained with V-cavity QCL OF-CEAS instruments. The temporal stability was investigated by Allan variance calculations and the best minimum detectable concentrations for the linear QCL OF-CEAS instrument were 32 ppm for N 2 O (35 s) and 5 ppb for NO (2 s). For NO, this detection limit compares favourably with other mid-IR QCL-based NO sensors, and is sufficient for mon- itoring NO in polluted urban environments. With the Maxion DFB-QCL, mon- itoring of NO in air outside the laboratory was attempted, and an air sample drying system benchmarked. Although this experiment proved unsuccessful, it was possible detect trace amounts of NO desorbing from the walls of the gas cell. Over the course of one hour the concentration rose from 3.8 ± 0.7 ppb to 28.4 ± 0.2 ppb, leading to a rate of desorption of 6.76 ± 0.01 × 10 −3 ppb s −1 . The sensitivity (α min ) of these spectra was 7.0 × 10 −9 cm −1 in 1 s, improved due to the higher mirror reflectivity at the lasing wavelength of the Maxion DFB-QCL, although still limited by etalon fringing.

Keywords: PHYSICAL CHEMISTRY
SPECTROSCOPY
LASERS
Advisor: Ritchie, G
Colloidal interfaces in confinement

A fluid-fluid demixing colloid-polymer system provides us with an opportunity to study interfacial phenomena that cannot be observed in molecular systems due to unfavourable length and timescales. We develop such a system compatible with cells of varying dimensions, allowing us to investigate confined interfacial behaviour in real space using Confocal Scanning Laser Microscopy.
The degree to which a system is affected by the sedimentation-diffusion gradient is dependent on the ratio of the suspension height to the gravitational length of the colloids. We illustrate that we may control the distance of our interface to the critical point by altering the suspension height, determining the importance of the gravitational field. Furthermore, the timescale on which the sedimentation- diffusion gradient is established is considerably longer than that of initial fluid-fluid demixing. We show that after the formation of the macroscopic interface, the system passes through a series of local mechanical equilibria on the way to achieving full equilibrium. Should the system be of sufficient height, it will pass through the gas-liquid critical point opening up new ways to study critical phenomena.
The time and length scales of the fluid-fluid demixing of our system may be manipulated by altering the density and viscosity of our solvent. We exploit a slowed phase separation process to study the interplay between demixing and wetting phenomena of systems in the vicinity of a single wetting surface, and confined between two parallel plates. We demonstrate that the presence of a surface strongly affects the morphology of phase separation. The growth of the wetting layer is determined by the demixing regime of the system, and may be accelerated by hydrodynamics. The additional restriction by a second surface limits the lengthscale of coarsening domains and may further alter the mechanism of wetting layer growth.

Keywords: interfacial phenomena
wetting
colloids
phase separation
Advisor: Aarts, D
The origin, nature and distribution of gypsum crusts in deserts

All the warm deserts of the world exhibit gypsum crusts in favourable localities, generally areas with a source of gypsum and less than 250 mm of rainfall annually. The features, comprising loose powdery or cemented crystalline accumulations of calcium sulphate dihydrate, are found at the surface or within the uppermost 10 m of regolith. Thicknesses vary from a few millimetres to several metres and purities range from about 15% to nearly 100% gypsum.
A review of the literature on gypsum soils and crusts reveals that the classification of types requires both standardizing and simplifying. A preliminary classification of crusts into three types can be made on the basis of structural and stratigraphic characteristics of examples from southern Tunisia and the Central Namib Desert. The types consist of subaerial aqueous evaporites, two subsurface and three surface forms. Detailed physical and chemical analyses justify a broadly similar genetic classification though one subsurface form is believed to be a primary pedogenic type of which the surface forms represent relics at various stages of solutional deterioration.
Examples of subaerial aqueous evaporites are all products of shallow-water sedimentation in seasonally flooded chotts and sabkhas. The non-pedogenic subsurface type, croûte de nappe, is produced by displacive crystallization at the surface of a fluctuating water table. Gypsum precipitation results from either evaporation or mixing of saline waters causing saturation with respect to gypsum. Surface gypsum crusts are subsurface illuvial accretions exposed by erosion of overlying material. The gypsum is derived from solution of surface aeolian, atmospheric, colluvial or alluvial deposits by meteoric waters which percolate into the upper soil zone replenishing the antecedent soil moisture deficit. Subsurface accumulation results from displacive crystallization at host sediment grain contacts when gypsum saturated soil moisture evaporates.