VictorJuiz/thesis huggingface dataset:
Passive cavitation mapping for monitoring ultrasound therapy
Keywords: inverse source problem
HIFU
HIFU monitoring
image reconstruction
cavitation

Cavitation is a phenomenon present during many ultrasound therapies, including the thermal ablation of malignant tissue using high intensity focused ultrasound (HIFU). Inertial cavitation, in particular, has been previously shown to result in increased heat deposition and to be associated with broadband noise emissions that can be readily monitored using a passive receiver without interference from the main ultrasound signal. The present work demonstrates how an array of passive receivers can be used to generate maps of cavitation distribution during HIFU exposure, uncovering a new potential method of monitoring HIFU treatment. Using a commercially available ultrasound system (z.one, Zonare, USA), pulse transmission can be switched off and data from 64 elements of an array can be simultaneously acquired to generate passive maps of acoustic source power. For the present work, a 38 mm aperture 5-10 MHz linear array was used, with the 64 elements chosen to span the entire aperture. Theory and simulations were used to show the spatial resolution of the system, the latter showing that the broadband nature of inertial cavitation makes passive maps robust to interference between cavitating bubbles. Passive source mapping was first applied to wire scatterers, demonstrating the ability of the system to resolve broadband sources. With the array transversely placed to the HIFU axis, high-resolution passive maps are generated, and emissions from several cavitating bubbles are resolved. The sensitivity of passive mapping during HIFU exposure is compared with that of an active cavitation detector following exposure. The array was then placed within a rectangular opening in the centre of the HIFU transducer, providing a geometric setup that could be used clinically to monitor HIFU treatment. Cavitation was instigated in continuous and disjoint regions in agar tissue mimicking gel, with the expected regions of cavitation validating the passive maps obtained. Finally, passive maps were generated for samples of ox liver exposed to HIFU. The onset of inertial cavitation as detected by the passive mapping approach was found to provide a much more robust indicator of lesioning than post-exposure B-mode hyperecho, which is in current clinical use. Passive maps based on the broadband component of the received signal were able to localize the lesions both transversely and axially, however cavitation is generally indicated 5 mm prefocal to the lesions. Further work is needed to establish the source of this discrepancy. It is believed that with use of an appropriately designed cavitation detection array, passive mapping will represent a major advance in ultrasound-guided HIFU therapy. Not only can it be utilized in real-time during HIFU exposure, without the need to turn the therapeutic ultrasound field off, but it has also been shown in the context of the present work to provide a strong indicator of successful lesioning and high signal-to-noise compared to conventional B-mode ultrasound techniques.
Methodology for designing megawatt-scale yokeless and segmented armature (YASA) generators for wind turbines
Keywords: direct drive
wind turbine generator
YASA
optimisation
axial flux machine

This thesis develops design methodologies for megawatt(MW)-scale yokeless and segmented armature (YASA) generators for wind turbine applications. The methodologies include the electromagnetic, the structural and the thermal designs of a YASA generator.
The design process starts with developing an analytical method to generate preliminary machine designs for a megawatt-scale YASA generator. This analytical approach considers both electromagnetic and structural aspects of a generator, the parameters of which were obtained and visualised on a design reference map. This new concept of displaying machine parameters is useful for a designer to identify the relationship between them. An optimisation tool using pseudo-weight approach is integrated into the analytical tool to determine a optimum machine design. This is a flexible optimisation tool, allowing the user to give priorities to each objective function. The analytical calculation has reduced the design space for suitable machine candidates to be applied in further finite element analysis (FEM). In finite element analysis of an optimised YASA machine, the electromagnetic performance of a 1 MW YASA generator was produced and verified with analytical and experiment results. This is followed by structural optimisation with finite element method, where a spider wheel with a support ring geometry is applied to the rotor plate. This reduces the structural weight by more than 50% while the structure retain strong stiffness. Finally, the cooling system of the stator of the YASA generator is studied and the cooling channels design is proposed. Simulation results show that the stator of a 1 MW YASA generator can be effectively cooled with forced air.
Modelling microstructural evolution in binary alloys
Keywords: coarsening
Monte Carlo methods
ordering
microstucrures
mean field methods
alloys
modelling
phase separation

In this thesis morphologies, coarsening mechanisms and kinetics are examined in a systematic way, when phase separation and subsequent microstructural coarsening is modelled using deterministic mean field and stochastic Monte Carlo methods. For the mean field approach a microscopic diffusion equation due to Khachaturyan is employed, and a variation of it with an environment dependent mobility. Monte Carlo simulations are carried out with vacancy and Kawasaki dynamics, and a residence time algorithm is applied in the vacancy case.
In mean field models microstructural evolution results from a direct minimization of a free energy functional, and the mechanism of atomic diffusion does not appear explicitly. In Monte Carlo models, changes in site occupancies are effected by direct exchanges of neighbouring atoms (Kawasaki dynamics), or through vacancy motion. In this thesis the correspondence between mean field and Monte Carlo models in describing phase transformations in binary alloys is examined. Several examples of cases in which these differences between deterministic and stochastic models affect the phase transformation are given, and the underlying differences are analyzed.
It is also investigated how the choice of diffusion mechanism in the Monte Carlo model affects the microstructural evolution. Most Monte Carlo studies have been carried out with Kawasaki dynamics, although in real metals such direct exchanges are very unlikely to occur. It will be shown how the vacancy diffusion mechanism produces a variety of coarsening mechanisms over a range of temperatures, which the Kawasaki dynamics fails to capture. Consequently, kinetics and resulting morphologies, especially at low temperatures, are affected.
Finally, the question of physicality of time scales in mean field and Monte Carlo models is addressed. Often a linear dependence between Monte Carlo time and real physical time is assumed, although there is no rigorous justifcation for this. In mean field models, time is defined through the atomic mobility.By examining the effect of a realistic diffusion mechanism in systems undergoing phase transformation, a critical discussion of time scales in microscopic mean field models and a Monte Carlo model with Kawasaki dynamics is presented.
Bourdieusian political theory and social science: the field of war correspondence 1990-2003
Keywords: practice
field
Bourdieusian political theory
journalism
symbolic system
war correspondence
habitus

This thesis examines the cogency of Bourdieusian political theory and social science on phenomenological, empirical and normative grounds. It investigates whether Bourdieu's philosophy of science leads logically to the political content of Bourdieusian theory, and concludes that the originary determinism which characterises Bourdieu's work is a normative commitment. Rather than characterising that which is bracketed out of Bourdieu's neo-Marxist phenomenology - that is, the level of determination accessible neither to the consciousness of the social agent nor the social scientist - as inherently coercive, the thesis argues that the Bourdieusian modeal can be defended on deontological grounds. Specifically, this entails a deontological acceptance of the cultural value of autonomy and accountability. The tension between these two in turn raises the problem of acceptable levels of exclusion and decontestation, and the thesis concludes that a qualified elitism is defensible and compatible with Boudieusian principles. The thesis incorporates a case study which serves two functions. First, it puts into empirical practice the principles of Bourdieusian philosophy of social science to ascertain what implications and normative commitments are built into Bourdieusian methodology. In this regard it concludes that while it is possible to produce constructive analysis of systematically misrecognised economies, it becomes necessary to delineate the point beyond which positing further levels of coercive determination is counter-productive - and this can only be done according to deontological criteria. Second, it assesses the merit of Bourdieusian sociologies relative to existing accounts of the journalistic field. It concludes that while Bourdieu is excessively dismissive of individual awareness of the conditions of their field, Bourdieusian field analysis produces significant insights into the processes of naturalisation, self-identification, esotericisation and disinterestedness.
On the welfare economics of climate change
Keywords: climate change
pensions
inequality
uncertainty
social choice
computational economics
decision theory

The three constituent chapters of this thesis tackle independent, self-contained research questions, all concerning welfare economics in general and its application to climate change policy in particular.
Climate change is a policy problem for which the costs and benefits are distributed unequally across space and time, as well as one involving a high degree of uncertainty. Therefore, cost-benefit analysis of climate policy ought to be based on a welfare function that is sufficiently sophisticated to incorporate the three dimensions of aggregation: time, risk and space. Chapter 1 is an axiomatic treatment of a stylised model in which all three dimensions appear. The main result is a functional representation of the social welfare function for policy assessment in such situations.
Chapter 2 is a numerical mitigation policy analysis. I modify William Nordhaus' RICE-2010 model by replacing his social welfare function with one that allows for different degrees of inequality aversion along the regional and inter-temporal dimension. I find that, holding the inter-temporal coefficient of inequality aversion fixed, performing the optimisation with a greater degree of regional inequality reduces the optimal carbon tax relative to treating the world as a single aggregate consumer.
In Chapter 3 I analyse climate policy from the point of view of intergenerational transfers. I propose a system of transfers that allows future generations to compensate the current one for its mitigation effort and demonstrate the effects in an OLG model. When the marginal benefit to a - possibly distant - future generation is greater than the cost of compensating the current generation for its abatement effort, a Pareto improvement is possible by a combination of mitigation policy and transfer payments. I show that under very general assumptions the business-as-usual outcome is Pareto dominated by such policies and derive the conditions for the set of climate policies that are not dominated thus.
The sovereignty of the royal portrait in revolutionary and Napoleonic Europe: five case studies surrounding Maria Carolina, Queen of Naples
Keywords: Queen of Naples
death masks
silhouettes
Kingdom of Naples
Antonio Canova
wax portraiture
Maria Carolina
espionage
Napoleonic Wars
caricature
French Revolution
Royal portraits
miniatures
portraiture

This study demonstrates how royal portraiture functioned during the Revolutionary and Napoleonic wars as a vehicle for visualizing and processing the contemporary political upheavals. It does so by considering a notion of the 'sovereignty of the portrait', that is, the semiotic integrity (or precisely the lack thereof) and the material territory of royal portraiture at this historical juncture. Working from an assumption that the precariousness of sovereignty which delineated the Revolutionary and Napoleonic wars goes hand in hand with the precariousness of representation during the same period, it reframes prevailing readings of royal portraiture in the aftermath of the French Revolution by approaching the genre less as one defined by the oneway propagation of a message, and more as a highly unstable intermedial network of representation. This theoretical undertaking is refracted through the figure of Maria Carolina, Queen of Naples (1752-1814), close sister and foil to Queen Marie- Antoinette of France, and who, as de facto ruler of the Kingdom of Naples, physically survived revolution but was twice dethroned and thrice exiled. A diverse ecology of royal portraiture revolving around Maria Carolina is presented across five case studies. Close attention to the materiality of a hyperrealistic wax bust of Maria Carolina reveals how portraiture absorbed the trauma of the French Revolution; Maria Carolina’s correspondence in invisible ink is used as a tool to read a highly distinctive visual language of 'hidden' silhouettes of sovereigns and to explore the in/visibility of exile; a novel reading of Antonio Canova's work for the Neapolitan Bourbons through the lens of contemporary caricature problematizes the binary between ancien régime and parvenue monarchy; and a unique miniature of Maria Carolina offers itself as a material metaphor for post-revolutionary sovereignty. Finally, Maria Carolina’s death mask testifies to how Maria Carolina herself became a relic of the ancien régime.
Genome evolution and epidemiology of human pathogens
Keywords: population genetics
hepatitis C virus
Campylobacter
whole genome sequencing
norovirus
coalescent
evolution

Understanding the transmission dynamics of infectious diseases is important to well-informed public health policy, responsive infection control and individual patient management. The on-going revolution in whole-genome sequencing provides unprecedented resolution for detecting evidence of recent transmission and characterising population-level transmission dynamics. In this thesis, I develop and apply evolutionary approaches to investigating transmission, focusing on three globally important pathogens.
Hepatitis C virus (HCV) is a major cause of liver disease affecting 150 million people and killing 350,000 annually. I conducted a meta-analysis of twentieth-century HCV epidemics, finding that the age of the epidemic can be predicted by genetic diversity. Using the coalescent, I fitted classic susceptible-infected (SI), susceptible-infected-susceptible (SIS) and susceptible-infected-recovered (SIR) epidemiological models. Most epidemics showed signatures of SI dynamics, but three, from Argentina, Hong Kong and Thailand, revealed complex SIR dynamics.
Norovirus is the leading viral cause of diarrhoea, estimated to cost the NHS around £115 million annually. I analysed whole norovirus genomes via a stochastic transmission model, finding that up to 86% of hospital infection was attributable to transmission from another patient in the hospital. In contrast, the rate of new introductions to hospital by infected patients was extremely low (<0.0001%), underlining the importance of ward management during outbreaks.
Campylobacter is the most commonly identified cause of bacterial gastroenteritis worldwide. I developed a zoonotic transmission model based on phylogeography approaches to test whether three strains previously associated with multiple host species were in fact aggregates of strongly host-restricted sub-strains, or genuine generalists. Members of the same strain isolated from different host species were often more closely related than those isolated from the same host species. I estimated 419, 389 and 31 zoonotic transmissions in ST-21, ST-45 and ST-828 respectively, strongly supporting the hypothesis that these strains are adapted to a generalist lifestyle.
Social being and the Navan complex: c.4000BC-c.90BC
Keywords: navan
Northern Ireland
prehistoric
archaelogy

Archaeological records at the Navan site are fragmented and difficult to interpret. This site, in County Armagh, Northern Ireland, features artefacts extending over 4,000 years from the Neolithic period to the Iron Age. This thesis provides a framework for understanding this important material culture. Through an analysis of archaeological theories and specific physical items, links are established among the natural world, culture, and the Navan residents’ understanding of the cosmos. This analysis covers the landscape (e.g. topography), constructed objects (e.g. prehistoric infrastructure such as pools, roads and earthworks), and metaphysical concepts (e.g. sound and time), thus building a holistic picture of how these settlers might have viewed themselves, the physical world around them, and the spiritual world they imagined. While it is not possible to determine definitively these groups’ purposes and motives, the thesis finds clues in the incoherentarchaeological evidence. It explores possible functions for archaeological markers whose significance is not clear.These markers could, for instance, have beenmeans of social separation orceremonial signifiers. Therefore the thesis is both an analysis of a particular site and an investigation into how the archaeological process itself, specifically in a situation of challenging evidence, enables distant worlds to be understood.
Moduli spaces of complexes of sheaves
Keywords: moduli spaces
complexes
sheaves
geometric invariant theory
Harder-Narasimhan stratifications

This thesis is on moduli spaces of complexes of sheaves and diagrams of such moduli spaces. The objects in these diagrams are constructed as geometric invariant theory quotients and the points in these quotients correspond to certain equivalence classes of complexes. The morphisms in these diagrams are constructed by taking direct sums with acyclic complexes. We then study the colimit of such a diagram and in particular are interested in studying the images of quasi-isomorphic complexes in the colimit.
As part of this thesis we construct categorical quotients of a group action on unstable strata appearing in a stratification associated to a complex projective scheme with a reductive group action linearised by an ample line bundle. We study this stratification for a closed subscheme of a quot scheme parametrising quotient sheaves over a complex projective scheme and relate the Harder-Narasimhan types of unstable sheaves with the unstable strata in the associated stratification. We also study the stratification of a parameter space for complexes with respect to a linearisation determined by certain stability parameters and show that a similar result holds in this case.
The objects in these diagrams are indexed by different Harder-Narasimhan types for complexes and are quotients of parameter schemes for complexes of this fixed Harder-Narasimhan type. This quotient is given by a choice of linearisation of the action and so the diagrams depend on these choices. We conjecture that these choices can be made so that for any quasi-isomorphism between complexes representing points in this diagram both complexes are identified in the colimit of this diagram.
Regulation of CRAC channels and agonist-induced Ca2+ signals
Keywords: Store-operated Calcium Channels
Calcium ions

Calcium ions (Ca2+) are extremely important intracellular messengers, activating a plethora of cellular processes. Growing evidence now points to a major role for the local Ca2+ signal in driving specific cellular responses. The simplest and most fundamental local Ca2+ signal is the Ca2+ microdomain, which rapidly forms when Ca2+ permeable ion channels open. In non-excitable cells the dominant Ca2+ entry channels are store-operated Ca2+ channels (SOCCs). The best characterised is the Ca2+ release activated Ca2+ (CRAC) channel. How local Ca2+ entry through CRAC channels impacts on channel function however is unclear. I have investigated the interaction between the Ca2+ binding protein calmodulin and CRAC channel activity and subsequent agonist-induced Ca2+ signals. Furthermore, I have investigated a role for mitofusin 2 (a protein that is known to tether the ER and mitochondria) on these Ca2+ signals.
Using three different calmodulin mutant constructs with alterations to their Ca2+ binding sensitivities, I have shown that calmodulin facilitates CRAC channel dependent Ca2+ entry and maintains agonist-induced cytosolic Ca2+ oscillations in a lobe-specific manner. Calmodulin has four Ca2+ binding sites, two on the N-lobe and two on the C-lobe. I found a dominant negative calmodulin mutant (CAM4M, where all four binding sites had been mutated), or one where the C-lobe could not bind Ca2+ (CAM2C), impaired both Ca2+ influx through CRAC channels and maintenance of cytosolic Ca2+ oscillations. In contrast, a Ca2+-insensitive N-lobe mutant had little effect, (CAM2N). Knockdown of the mitochondrial Ca2+ uniporter regulator (MICU1) or mitochondrial membrane depolarization had similar effects to those seen with CAM4M or CAM2C, suggesting that at least in part, the action of calmodulin was through regulation of mitochondrial Ca2+ dynamics. This was confirmed by directly measuring the mitochondrial matrix Ca2+ concentration in intact RBL-1 cells using the mitochondrial targeted, fluorescent protein, pericam. Both CAM4M and disruption of mitochondrial Ca2+ buffering impaired agonist-induced mitochondrial Ca2+ uptake, suggesting that the modulation of CRAC channels occurred through Ca2+-calmodulin facilitation of mitochondrial Ca2+ uptake. Using a mutant Orai1 (A73E) that cannot bind calmodulin, I have shown that calmodulin tethered to the CRAC channel provides a major source of calmodulin for effective mitochondrial Ca2+ uptake. Physiological relevance of my proposed pathway was provided from experiments where I showed knockdown of MICU1 impaired agonist-induced CRAC channel dependent NFAT-1-driven gene expression. In addition, I establish a crucial role for mitochondrial MFN2 and presumably its ability to properly link the mitochondria and ER in the control of CRAC channels and agonist-induced Ca2+ signals.