VictorJuiz/thesis huggingface dataset:
Investigations into the effects of neuromodulations on the BOLD-fMRI signal

The blood oxygen level dependent functional MRI (BOLD-fMRI) signal is an indirect measure of the neuronal activity that most BOLD studies are interested in. This thesis uses generative embedding algorithms to investigate some of the challenges and opportunities that this presents for BOLD imaging.
It is standard practice to analyse BOLD signals using general linear models (GLMs) that assume fixed neurovascular coupling. However, this assumption may cause false positive or negative neural activations to be detected if the biological manifestations of brain diseases, disorders and pharmaceutical drugs (termed "neuromodulations") alter this coupling. Generative embedding can help overcome this problem by identifying when a neuromodulation confounds the standard GLM. When applied to anaesthetic neuromodulations found in preclinical imaging data, Fentanyl has the smallest confounding effect and Pentobarbital has the largest, causing extremely significant neural activations to go undetected. Half of the anaesthetics tested caused overestimation of the neuronal activity but the other half caused underestimation. The variability in biological action between anaesthetic modulations in identical brain regions of genetically similar animals highlights the complexity required to comprehensively account for factors confounding neurovascular coupling in GLMs generally. Generative embedding has the potential to augment established algorithms used to compensate for these variations in GLMs without complicating the standard (ANOVA) way of reporting BOLD results.
Neuromodulation of neurovascular coupling can also present opportunities, such as improved diagnosis, monitoring and understanding of brain diseases accompanied by neurovascular uncoupling. Information theory is used to show that the discriminabilities of neurodegenerative-diseased and healthy generative posterior parameter spaces make generative embedding a viable tool for these commercial applications, boasting sensitivity to neurovascular coupling nonlinearities and biological interpretability. The value of hybrid neuroimaging systems over separate neuroimaging technologies is found to be greatest for early-stage neurodegenerative disease.

Keywords: General Linear Modelling
Information Theory
Pre-clinical imaging
Functional Magnetic Resonance Imaging
Anaesthetics
Electroencephalography
fMRI
DCM
Neurovascular coupling
BOLD
EEG
Generative Embedding
Dynamic Causal Modelling
GLM
Blood Oxygen Level Dependent
Advisor: Marchini, J
Woolrich, M
Martin, C
The effect of light elements on metal/silicate partitioning

The accretion of the Earth was marked by the high-pressure segregation of most of its core, accompanied by dissolution of about 10% of one or more “light” elements into the metallic phase. Various light elements have been proposed including S, Si, C and O, with each having an effect on the partitioning behaviour of the trace elements. Metallurgical data indicate that dissolution of even small amounts of light elements in liquid Fe can have profound effects on the activities of some trace components. For instance, significant partitioning of Si into the core of the growing Earth should have affected the observed Mo content of the mantle (Ono-Nakazato et al., 2007).
Here, I use the epsilon model of non-ideal interactions in Fe liquids (ε. I present interaction parameters (ε, derived from 1.5GPa, 1550-1650oC metal-silicate equilibration experiments, for W, Ni, Co and Mo in liquid Fe alloyed with C, and W, Ni, Co, Mo, Cu, Mn, Ag, Sb, Cd, In, Tl, Pb, Ga, Ge, Cr, V and Zn in liquid Fe alloyed with S. Additional epsilon values were taken from the steelmaking sourcebook when necessary.
I used this new data in conjunction with published metal–silicate partitioning results to develop a model of continuous accretion and core segregation taking explicit account of the partitioning of Si (this study) and O (from Ozawa et al., 2008) between metal and silicate and their effects on metal–silicate partitioning of siderophile elements. The best model for explaining the Earth’s formation including the Mo:W ratio of the silicate Earth posits that the Earth’s oxidation state increased in steps from 1 to 6.26% FeO, increasing Si in the Earth’s core and the light elements C and S being added to the planet in the last ~20% of accretion material.

Keywords: Metal/Silicate partitioning
Advisor: Wood, B
Shape analysis in mammograms

The number of women diagnosed with the breast cancer continues to rise year on year. Breast cancer is now the most common type of cancer in the UK, with over 55000 cases reported last year. In most cases, mammography is the first step towards diagnosing breast cancer. However, it continues to have many practical limitations as compared to more sophisticated modalities such as MRI. The relatively low cost of mammography, together with the ever increasing risk of women contracting the disease, has led to many developed countries having a breast screening program. These routine breast screens are taken at different points in time and are called temporal mammograms. Currently, a radiologist tends to qualitatively assess temporal mammograms and look for any abnormalities or suspicious regions that might be of a concern. In this thesis, we develop an automatic shape analysis model that can detect and quantify such changes inside the breast. This will not only help in early diagnosis of the disease, which is key to survival, but will potentially aid prognosis and post treatment care.
The core to this thesis is the use of Circular Integral Invariants. We explore its multi-scale properties and use it for image smoothing to reduce image noise and enhance features for segmentation. We implement, modify and enhance a segmentation method which previously has been successfully used to acquire breast regions of interest.
We applied such Integral Invariants for shape description, to be used for shape matching as well as for subdividing shapes into sub-regions and quantifying the differences between two such shapes. We combine boundary information with the information from inside a shape, thus eccentrically transforming shapes before describing their structure. We develop a novel false positives reduction method based on Integral Invariants scale space.
A second aspect of the thesis is the evaluation of and emphasis on the use of breast density maps against the commonly used intensity maps or x-rays. We find density maps sufficient to use in clinical practice. The methods developed in this thesis aim to help clinicians in making diagnostic decision at the point of case. Our shape analysis model is easy to compute, fast and very general in nature that could be deployed in a wide range of applications, beyond mammography.

Keywords: breast density
shape analysis
Breast cancer
computer aided diagnosis
Advisor: Brady, M
The large-scale structure of the universe

In this thesis, several theoretical concepts relating to the large-scale structure of the universe are presented. In particular, various aspects of the hierarchical scenario are investigated. The initial perturbation field and its early evolution are discussed in Chapter 3. Chapter 4 is concerned with two-point correlation functions for galaxies, clusters and super-clusters. In Chapter 5, some effects of using velocity as a distance measure are examined. In particular, it will be argued that caustics in redshift space are an almost inevitable feature of the hierarchical scenario. Chapter 6 concentrates on the possibity that quasar Ly-α absorption lines are redshift caustics.

Advisor: Binney, J
The analysis of offshore foundations subjected to combined loading

This thesis is concerned with four different types of offshore foundations, namely gravity foundations, jack-up foundations, the mudmats for piled jacket structures and caisson foundations for jacket structures. In most applications, these can be idealised as circular rigid foundations. Unlike onshore foundations, offshore foundations are subjected to large horizontal and moment loads. This research used the finite element method to examine the elastic behaviour and stability of circular footings under combined loading. Due to the circular shape of the footings and the combination of vertical, horizontal and moment loads, three dimensional finite element analysis was used. In-depth analyses of the elastic behaviour of circular footings under combined loading (V,H,M) were performed. The vertical stiffness coefficient was investigated using two dimensional axi-symmetric analyses whereas three dimensional analyses were used to examine the other coefficients. Different features of offshore foundations such as footing embedment and cone angle were taken into consideration. Based on the numerical results, a set of empirical expressions for elastic stiffness coefficient was derived. For footing stability calculations, large horizontal or moment loads can cause the footing to lose contact with the soil, or cause the footing to slide relative to the soil. In finite element analyses, this loss of contact and sliding are modelled by interface elements. A new zero-thickness iso-parametric interface element was formulated for both two and three dimensional analyses. An exact close formed solution for integration of the stress-strain relationship (for the two dimensional interface element) was found. The element is then used to explore footing stability. It was shown that by using a yield criteria which allows the interface to behave as either frictional or cohesive interface, depending upon the normal stress, numerical stability is achieved. The footing stability was examined by establishing the bearing capacity envelope. The envelopes for footings on undrained clays were established for surface flat strip footings and for surface flat circular footings. The effects of soil strength varying with depth, cone angle and embedment on the bearing capacity envelope were also investigated.

Keywords: offshore
foundation
Advisor: Houlsby, G
Photocatalytic water splitting by utilising oxide semiconductor materials

This thesis reports the study of metal oxide semiconductors for the application of photoelectrochemical water splitting with a particular emphasis on both anion and cation-doped zinc oxides. A study of the mechanisms of visible light absorption in both anion and cation-doped ZnO semiconductors, the potentials of metal oxide materials modified by impurities as one of the ideal photocatalysts in harvesting solar light has been explored. X-ray photoelectron spectroscopy (XPS) and UV-Vis spectroscopes have been performed to establish the electronic structures of anion and cation-doped ZnO. Aluminium impurities in ZnO thin films reveal the relationship between the bandgap broadening and the so-called Burstein Moss effect. Both cadmium and sulphur dopants were incorporated in ZnO either as powders by the solid state synthesis or as thin films by spray pyrolysis technique. Cadmium and sulphur dopants demonstrate effective electronic bandgap reduction and an increasing absorption of visible light. Furthermore, the incorporation of cadmium and sulphur in ZnO were prepared as photoanodes and evaluated in a custom-built photoelectrochemical workstation for the measurement of photon energy conversion efficiencies.

Keywords: ZnO
oxide semiconductor
photoelectrochemical cell
band gap
Advisor: Edwards, P
Experimental entanglement distillation of continuous-variable optical states

Entangled photons are ideally suited to the transmission of photonic quantum information. Mitigating the effects of decoherence is fundamental to distributing photonic entanglement across large distances. One such proposal is entanglement distillation, in which operations on a large ensemble of weakly entangled states generate a smaller ensemble of more strongly entangled states.
In this thesis, we experimentally and theoretically analyse various tools required for demonstrating continuous-variable (CV) entanglement distillation, following the proposal by Browne et al., [Phys. Rev. A 67, 062320 (2003)]. Specifically, we propose figures of merit to account for the practical limitations of non-deterministic non-Gaussian operations, and analyse the experimental parameters necessary to optimise them. We develop a source of pulsed two-mode squeezed states, which are the initial states of our entanglement distillation protocol. We use weak-field homodyne detection as a phase-dependent photon counting detector, and demonstrate its utility in conditional state generation. Using these states, we demonstrate sub-binomial light as a tool for benchmarking quantum states. Finally, we applied two-mode weak-field homodyne detection to two entangled states and demonstrate correlations in the photon counting statistics which depend on a joint phase from two independent local oscillators. This setup is sufficient to apply an entanglement witness developed by Puentes et al. [New J. Phys. 12, 033042 (2010)]. Despite encouraging simulations, we do not witness entanglement with this scheme, which we attribute to a noise source unaccounted for in the simulations.
Although we do not demonstrate entanglement distillation outright, the tools we develop to do so represent a general, hybrid approach to CV quantum optics. Developing tools such as phase-resolved projective measurement on two-mode states allows us to probe both the wave and particle nature of entangled light at the single-photon level. Using and expanding these techniques to probe larger quantum systems may prove useful in studies of fundamental physics and quantum enhanced technologies.

Keywords: entanglement
photonics
Quantum optics
Advisor: Walmsley, I
Investigation of non-cholinergic acetylcholinesterase, and related peptides in an in vitro preparation of the substantia nigra

The primary role of acetylcholinesterase (AChE) is hydrolysis of acetylcholine (ACh). However, observations by numerous groups have suggested that AChE may have non-cholinergic functions. Furthermore, developmental roles for AChE and its related enzyme, butyrylcholinesterase (BuChE), which is also capable of ACh hydrolysis, have been postulated.
One line of evidence to support a non-cholinergic role for AChE is the apparent disparity in several brain areas between the distribution of AChE and the cholinergic marker choline acetyltransferase. The substantia nigra (SN), an area of the ventral mesencephalon (VM), which contains the dopaminergic cells that degenerate in Parkinson's disease (PD), is an area that displays such a disparity.
One approach to treating PD involves implantation of embryonic dopaminergic VM cells into the parkinsonian brain. This procedure, known as foetal transplantation, has met with limited success, in part due to degeneration of dopaminergic cells within the donor preparation. It is known that incorporation of trophic factors into the preparation for grafting improves dopaminergic cell survival. It has previously been shown that AChE enhances survival and neurite outgrowth of postnatal dopaminergic cells in organotypic cultures of the VM. The aim of the studies in this thesis was to establish the effects of BuChE and AChE on embryonic dopaminergic neurons in a preparation analogous to that used in the animal model of foetal transplantation as a treatment for PD.
Addition of BuChE and monomeric (G1-) and tetrameric (G4-) forms of AChE enhanced dopaminergic neurite outgrowth. Inhibition of the active site of BuChE and AChE by echothiophate had no effect upon neurite outgrowth or cell survival, demonstrating that the trophic effects of BuChE and AChE on neurite outgrowth were not dependent upon ACh hydrolysis. In contrast, inhibition of the peripheral anionic site (PAS) of AChE by BW284c51 markedly decreased cell survival and neurite outgrowth. The mechanism of action of BW284c51 toxicity was subsequently investigated using a mixture of nicotinic ACh receptor antagonists in order to demonstrate that the chronic toxic effects of BW284c51 were not a consequence of elevated ACh resulting from inhibition of AChE.
Finally, the technique of whole-cell patch-clamp electrophysiology revealed a novel inhibitory effect of BuChE and G1- and G4-AChE on voltage-dependent calcium currents. It was postulated that these actions underlie the trophic effects of BuChE and AChE on embryonic dopaminergic neurons, a suggestion that was supported by the findings that established inhibitors of voltage-dependent calcium currents enhanced dopaminergic neurite outgrowth.
The findings of this thesis are discussed in the context of other studies and are related to both physiological and pathological functions of the central nervous system.

Advisor: Greenfield, S
Neutron scattering studies of fluorite oxides at high temperatures

The high temperature behaviour of the fluorite oxides UO2, THO2 and Y2O3-stabilised ZrO 2 have been investigated using a variety of neutron scattering techniques. Interest has centred on the cause of the anomalously large enthalpy of UO2 at temperatures above 15OOK, an understanding of which is important in view of its use as a fission reactor fuel. High temperature techniques have been developed which enable the performance of neutron scattering at temperatures up to 3OOOK. Bragg diffraction measurements have shown that a growing fraction of anions vacate their regular sites above 21OOK in UO2 and above 23OOK in ThO2 attaining vacancy concentrations of ~2O% at 29OOK in both materials. Quasielastic scattering investigations have confirmed the occurrence of anion Frenkel disorder in UO2 at high temperatures and have shown that the disorder is of a dynamic nature. Both sets of results may be interpreted in terms of fluctuating, dynamic clusters of vacancies and inter stitials, having lifetimes of a few phonon periods. The elastic constants of UO2, which have been determined up to 293OK from measurements of the long wavelength acoustic phonons, show an increased rate of softening above 24OOK. The zone-centre optic phonons broaden rapidly above 2OOOK in UO2- The full phonon dispersion relation of ThO2, measured at 293K, resembles closely that of UO2. The results provide the first direct, unambiguous evidence of thermally-induced Frenkel disorder in UO2, which is analogous to the disorder observed in the fast-ion phase of the fluorite halides, such as CaF2.
Quasielastic scattering techniques have also been used to study the defect structure of Y 2O 3 -stabilised ZrO 2 between 293K and 2OOOK. Many general features of the scattering observed at room temperature may be explained in terms of nearest neighbour relaxations around oxygen vacancies. The diffuse scattering broadens in energy above 1OOOK, signifying that these clusters of relaxed ions have a finite lifetime of ~5ps at 15OOK. The results have been interpreted in terms of a vacancy hopping model which is consistent with the enhanced conductivity observed in this temperature range.

Advisor: Hutchings, M
al.], M
The political economy of technological change, energy and climate change

This thesis sets out to explore some of the key dimensions in the process of socio-technological change inherent in the shift to a low carbon economy. This is done in two parts, the first focusing on theory, the second, empirical case studies. Out of the diversity of interactions between actors, technologies, and policies surrounding this process, one key question emerges: can societies really shift the structure of their economies so fundamentally to achieve a low carbon future within a reasonable timeframe? Chapter One develops an integrated approach to economic and political change to interrogate this question. This synthesizes a review of literature (Part One) examining the role of technology within some of the main theories of economic change in the social sciences. Two broad paradigms are distinguished. First, a paradigm based around the notion of equilibrium, notably the standard welfare approach of neoclassical economics; and secondly, an evolutionary paradigm, which views the economy as a complex adaptive system – such as exemplified by theories of path dependency. This theoretical background provides a broad narrative to frame and inform Part Two of the thesis. First in Chapter Four, socio-technical change is investigated in the context of the diffusion of energy efficient lighting in Germany. This study investigates the relationships between human behaviour and attitudes, lamp technology and the evolving nature of institutions, to provide a framework with which to consider the contentious issue of individual freedom versus government control in the politics of change to lower-carbon emissions. In Chapter Five, the case for the creation of a market for CO2 pollution permits is developed. In making this case, the strengths and weaknesses of emissions trading are compared and contrasted with other policy instruments and the broader political economy of the various policy options discussed. Chapter 6 builds on this to examine the political economy of implementing an emissions trading scheme in Australia and the impact the Kyoto Protocol has had on domestic politics and GHG mitigation. Chapter Seven continues with the theme of building ‘a political ecology of the state’ by investigating the politics and economics of greenhouse gas mitigation in Russia. Finally, Chapter Eight recapitulates the aims, nature and conclusions of this research and draws out its implications for policy as well as mapping out some areas for further research. In particular, the need to bring a greater sense of politics back into the study of the economy is highlighted as a vital part of building a renewed, more sustainable economic paradigm in the wake of the financial crisis and, as a way of strengthening the connection between social values and market outcomes.

Keywords: economics
climate change
politics
Technology
energy
Advisor: Clark, G