VictorJuiz/thesis huggingface dataset:
Quantification of microscopic brain structures using diffusion magnetic resonance

Diffusion-weighted magnetic resonance imaging can be used to estimate microstructural parameters of white matter in the brain. Two complementary techniques are investigated: the use of the temporal diffusion spectrum to explore small length scales and the STEAM technique to probe larger features.
The diffusion spectrum has the potential to be more sensitive to small pores compared to conventional time-dependent diffusion. However, analytical expressions for the diffusion spectrum of particles only exist for simple geometries such as cylinders, which are often used as a model for intra-axonal diffusion. We propose a mathematical model for the extra-axonal space with parameters that are related to the microstructural properties of pore size, tortuosity, and surface-to-volume ratio. Measurements were made with an extra-axonal space phantom to validate the model. Fitted values for the phantom pore size match those from simulation.
We extend the model to include the intra-axonal signal contribution. However, the parameters used to describe the intra- and extra-axonal spaces are related and it is important to remove redundant parameters to avoid overparameterization, which would make the model less robust. We propose analytical expressions to simplify the model. The model was then applied to measurements on fixed corpus callosum, which is a model system consisting of parallel axons. The estimated values of the axon volume fraction and mean and standard deviation of the axon radius distribution are comparable to those found in literature.
Temporal diffusion spectra are useful for measuring the geometric properties of small spaces such as axon radii. However, longer diffusion times accessible using the STEAM sequence are necessary to probe structures with longer diffusion distances such as those parallel to the direction of axons. We used a model from the literature originally developed for use with animal magnetic resonance scanners and simplified it to quantify axial hindrance from data acquired on healthy volunteers in a clinical scanner. The interpretation of axial hindrance, which is a largely unexplored area of research, is discussed.

Keywords: diffusion MRI
extracellular space
extra-axonal space
intra-axonal space
hindered diffusion
diffusion spectrum
magnetic resonance imaging
restricted diffusion
intracellular space
Advisor: Miller, K
Jbabdi, S
Pipe dreams; explaining the energy security policies of Poland, 1990-2007

This thesis seeks to explain Poland’s energy security policies towards Russia in the period from 1990-2007. It is inspired by the puzzle that Poland’s commitments to reduce its dependence on imported oil and gas from Russia have varied considerably during this period. Numerous large-scale projects to enhance energy security have been proposed, abandoned and revisited, all in the absence of a significant change to Poland’s level of dependence on Russia or its exposure to supply risks. This puzzle poses a challenge to conventional approaches to energy security, which tend to explain policies as a function of ‘material’ shifts in the price, supply or demand for fossil fuels. Though these factors are undoubtedly important it is argued that, in the case of Poland, energy security is more affected by domestic decision-making processes than by such material shifts. In particular, the degree and form of intervention in the energy sector by the political executive in Poland is highlighted as a key factor explaining energy security policy output. These interventions in Poland are classified and distinguished according to three types of ‘policy network’ – statist, corporatist and liberal, each of which represented a different outlook on the optimal means for ensuring energy security. These policy networks were embedded within different governments, and their preferences fashioned Poland’s responses to energy security challenges occurring under similar material conditions.

Keywords: energy security
state-business relations
Polish-Russian relations
Poland
political economy of energy
Advisor: Pravda, A
HSV-1 amplicon system for human artificial chromosome formation in human ES/iPS cells and pluripotency induction

Development of safe and efficient approaches for gene delivery in human embryonic stem cells (hESc) and particularly in human induced pluripotent stem (hiPS) cells, which can be derived in a person-specific manner, is considered to be imperative for harnessing their full potential in both the basic and applied research. The aim of this study was to evaluate the potential of human artificial chromosome (HAC) for gene delivery and expression in hESc and hiPS cells. HAC offers many potential advantages including the provision for carrying large genes with corresponding regulatory elements to obtain long-term regulated gene expression. In addition, they can replicate and segregate independently without integration into the host cell genome. To develop HAC in hiPS cells, the first part of the study was aimed at generating hiPS cells utilising the Herpes Simplex Virus (HSV)-1 amplicon system. With the use of EBNA-1/OriP retention elements incorporated into the HSV-1 amplicon vectors, hiPS cells completely free of vector and transgenes sequences were successfully derived from human embryonic fibroblasts. The hiPS cells exhibited proliferation and differentiation potential similar to that of hESc. In the second part of the study, development of HAC in hESc and hiPS cells was assessed by utilising the HSV-1 amplicon system to deliver the HAC DNA. Analysis of the hESc confirmed the presence of functional HAC which replicated the behaviour of the host chromosomes. Additionally, HAC generation did not lead to impairment in the developmental potential and pluripotency of hESc. The hiPS cells supported HAC at low frequency but DNA also integrated into the host chromosomes. The HAC system, therefore, needs further refinements to improve the frequency of HAC formation and reduce the chromosomal integration of HAC constructs in hiPS cells. Overall, these findings provide a simple and safe way of pluripotency induction and genetic modification of pluripotent stem cells using the HSV-1 amplicon system and represent an important advance towards patient specific gene and cell therapy.

Keywords: Human embryonic stem cells (hESc)
induced pluripotent stem cells (iPS)
Herpes Simplex Virus (HSV)-1 amplicon system
Human artificial chromosomes (HAC)
gene therapy
gene delivery
Advisor: Monaco, Z
Mapping and understanding the distributions of potential vector mosquitoes in the UK: New methods and applications

A number of emerging vector-borne diseases have the potential to be transmitted in the UK by native mosquitoes. Human infection by some of these diseases requires the presence of communities of multiple vector mosquito species. Mitigating the risk posed by these diseases requires an understanding of the spatial distributions of the UK mosquito fauna. Little empirical data is available from which to determine the distributions of mosquito species in the UK. Identifying areas at risk from mosquito-borne disease therefore requires statistical modelling to investigate and predict mosquito distributions.
This thesis investigates the distributions of potential vector mosquitoes in the UK at landscape to national scales. A number of new methodological approaches for species distri- bution modelling are developed. These methods are then used to map and understand the distributions of mosquito communities with the potential to transmit diseases to humans.
Chapter 2 reports the establishment of substantial populations of the West Nile virus (WNV) vector mosquito Culex modestus in wetlands in southern England. This represents a drastic shift in the species’ known range and an increase in the risk of WNV transmission where Cx. modestus is present.
Chapter 3 develops and applies a new species interaction distribution model which identifies fish and ditch shrimp of the genus Palaemonetes as predators which may restrict the distribution of the potential WNV vector community in these wetlands.
Chapter 4 develops a number of methods to make robust predictions of the probability of presence of a species from presence-only data, by eliciting and applying estimates of the species’ prevalence.
Chapter 5 introduces a new Bayesian species distribution modelling approach which outperforms existing methods and has number of useful features for dealing with poor- quality data.
Chapter 6 applies methods developed in the previous two chapters to produce the first high-resolution distribution maps of potential vector mosquitoes in the UK. These maps identify several wetland areas where vector communities exist which could maintain WNV transmission in birds and transmit it to humans.
This thesis makes significant contributions to our understanding of the distributions of UK mosquito species. It also provides methods for species distribution modelling which could be widely applied in ecology and epidemiology.

Keywords: Bayesian
presence-only
Emerging infectious diseases
ecology
Community ecology
West Nile fever
Gaussian process
species distribution modles
statistics
mosquito
Advisor: Rogers, D
Purse, BV
Nunn, MA
Structural studies of immunoglobulin molecules the Fv fragment of mouse myeloma protein M315

The antibody is the main weapon in the body's defence against invading foreign materials. The different functions of the antibody molecule are performed by different parts of the structure. Some of these regions can be isolated in the form of enzymically-cleaved fragments. The Fv fragment, consisting of the variable regions of the light and heavy chains of the molecule, is the site of binding of the foreign antigen to which the antibody is specific.
Protein M315, a mouse myeloma protein, has an affinity for small molecules containing dinitrophenyl groups, comparable to that of a true antibody for its antigen. It is thus a particularly appropriate tool for examining antigen-antibody interactions.
The genetic mechanism of how the very large repertoire of antigenbinding specificities of antibodies arises in an organism has puzzled iiranunologists in the past. Recently, some progress on discovering this mechanism has been made, and some of the observations which have been reported and theories which have been proposed are reviewed.
The Fv fragment, which contains the antigen-binding site of the immunoglobulin, has been isolated from M315, and crystallized. The 6A* resolution data were measured on the four-circle diffractometer, and those to 2.7Å resolution by rotation photography. Phases were found by the method of isomorphous replacement with two heavy-atom compounds. The determination and refinement of the positions and extent of heavy-atom binding, are described. Electron density maps were calculated initially to 6Å and finally to 4.5Å resolution.
The 4.5Å resolution electron density map shows two complete Fv fragments in the asymmetric unit. The interactions between the VH and VL subunits are very close. However, the two molecules are oriented quite differently in the unit cell.
An initial examination of the binding of a small hapten, dinitroaniline, has been made. Crystals which were isomorphous with the native ones, 'were grown of Fv in the presence of the hapten. Preliminary indications are that the two crystallographically independent molecules may have different binding properties.
The directions in which the project may proceed, including the extension of the resolution and the assignment of atomic coordinates, are discussed.

Advisor: Phillips, D
The role of dissociation in the development and maintenance of post-traumatic stress disorder

The aim of this thesis was to investigate psychological factors influencing the development and maintenance of post-traumatic symptoms, with particular attention to the role of dissociation. The concept of dissociation is at present not well understood, and a secondary aim of this thesis was to clarify its meaning and structure and enable its assessment.
Chapter 2 reports the development and testing of a questionnaire measuring trait dissociation, and the factor analysis of this questionnaire into seven sub-factors with low to medium intercorrelations, along with an analysis of the reliability and validity of this questionnaire, which was used in the subsequent studies.
Chapters 3 and 4 consist of experimental studies investigating the relationship between dissociation and later intrusive memories using a videotape of scenes from road traffic accidents as a stimulus. The first study attempted to manipulate dissociation, while the second used extreme scorers on the trait dissociation questionnaire. The manipulation of dissociation proved difficult, but both studies showed a relationship between dissociation and later intrusions.
Chapters 6 and 7 report on two prospective clinical studies following road traffic accident victims over the first six months following their accident, and investigates the role of dissociation and other psychological factors in the development of post-traumatic symptoms. Both state and trait dissociation, and the emotional numbing subfactor of dissociation in particular, predict the later development and maintenance of other post-traumatic symptoms. Persistent dissociation was more predictive of later symptoms than dissociation in the first few days after the accident.
These results are discussed in relation to current thinking about the concept of dissociation and the DSM diagnoses of post-traumatic stress disorder and acute stress disorder. In particular it seems useful to distinguish between components of dissociation in terms of their relationship to PTSD. Possible future research and clinical implications are also addressed.
Quantum models of space-time based on recoupling theory

Models of geometry that are intrinsically quantum-mechanical in nature arise from the recoupling theory of space-time symmetry groups. Roger Penrose constructed such a model from SU(2) recoupling in his theory of spin networks; he showed that spin measurements in a classical limit are necessarily consistent with a three-dimensional Euclidian vector space. T. Regge and G. Ponzano expressed the semi-classical limit of this spin model in a form resembling a path integral of the Einstein-Hilbert action in three Euclidian dimensions. This thesis gives new proofs of the Penrose spin geometry theorem and of the Regge-Ponzano decomposition theorem. We then consider how to generalize these two approaches to other groups that give rise to new models of quantum geometries. In particular, we show how to construct quantum models of four-dimensional relativistic space-time from the re-coupling theory of the Poincare group.

Keywords: penrose
racah
spin networks
quantum
relativity
groups
geometry
poincare group
regge
ponzano
recoupling
Advisor: Penrose, R
Model free optimisation in risk management

Following the financial crisis of 2008, the need for more robust techniques to quantify the capital charge for risk management has become a pressing problem. Under Basel II/III, banks are allowed to calculate the capital charge using internally developed models subject to regulatory approval. An interesting problem for the regulator is to compare the resulting figures against the required capital under worst case scenarios. The existing literature on the latter problem, which is based on the marginal problem, assumes that no a-priori information is known about the dependencies of contributing risks. These problems are linear optimisation problems over a constrained set of probability measures, discretisation of which leads to large scale LPs. But this approach is very conservative and cannot be implemented robustly in practice, due to the scarcity of historical data. In our approach, we take a less conservative strategy by incorporating dependence information contained in the data in a form that still leads to LPs, an important feature of such problems due to their high dimensionality. Conceptually, our model is the discretisation of an infinite dimensional linear optimisation problem over a set of probability measures. For some specific cases we can prove strong duality, opening up the approach of discretising the dual instead of the primal. This approach is preferable, as it yields better numerical results. In this work we also apply our model to model-free path-dependent option pricing. Use of delayed column generation techniques allows us to solve problems several orders of magnitude larger than via the standard simplex algorithm. For high-dimensional LPs we also implement Nesterov's smoothing technique to solve the problems.

Keywords: Model Free Option Pricing
Quantitative Risk Management
Infinite Dimensional Optimisation
Model Free Optimisation
Advisor: Raphael, H
The facultative endosymbionts of grain aphids and the horizontal transfer of ecologically important traits

Insects are often infected with facultative endosymbiotic bacteria, which can have a range of important ecological effects. The grain aphid, Sitobion avenae, harbours diverse facultative symbionts, which suggests their importance in grain aphid biology.
This thesis attempts to explain the ecological roles of the facultative endosymbionts in S. avenae. It also examines the question of whether the horizontal transmission of symbionts between aphid clones and species can be important for shaping the ecology and evolution of multi-species aphid communities. Novel techniques developed for research with the grain aphid study system are presented.
Grain aphid clones vary in their tolerance to low temperatures, but this trait is not affected by their facultative endosymbionts.
Strains of a symbiont Hamiltonella defensa do not protect grain aphids from hymenopterous parasitoids, regardless of the host genotype. However, experienced parasitoid females preferentially oviposit in aphids which do not harbour symbionts.
Comparison of the fitness consequences of infection with the same Hamiltonella strains in their original and in novel grain aphid host clones reveal no consistent differences.
Symbiont strains establish easily following artificial transfer between clones of the grain aphid, but the symbionts transferred from other aphid species form less stable infections. Hamiltonella strains do not affect the fecundity of their grain aphid host clones regardless of their host species of origin, but also do not generally confer protection against parasitoids.
There are no clear patterns in the distribution of parasitoid-resistant phenotypes across phylogenetic trees of Hamiltonella and its bacteriophage APSE.
Strains of four unrelated species of endosymbionts, Rickettsia, Spiroplasma, Rickettsiella and Regiella, confer the same pathogen-resistant phenotype to a single pea aphid clone. The same symbiont strains can confer resistance to clones of two different aphid species. Some strains in multiple infections may compensate for the costs of infections with other symbionts.
The importance of these results for understanding the ecological and evolutionary role of facultative endosymbionts in aphids and other insects are discussed, and directions for further research are proposed.

Keywords: parasitoid
facultative endosymbiotic bacteria
insect
aphid
symbiosis
mutualism
Advisor: Godfray, C
Ferrari, J
Tent-maps, two-point sets, and the self-Tietze property

This thesis discusses three distinct topics.
A topological space X is said to be self-Tietze if for every closed C ⊂ X, every continuous f : C &rightarrow; X admits a continuous extension F : X &rightarrow; X. We show that every disconnected, self-Tietze space is ultranormal. The Tychonoff Plank is an example of a compact self-Tietze space which is not completely normal, and we establish that a completely normal, zerodimensional, homogeneous space need not be self-Tietze.
A subset of the plane is a two-point set if it meets every straight line in exactly two points. We show that a two-point set cannot contain a dense Gδ subset of an arc. We also show that the complement of a two-point set is necessarily path-connected. Finally, we construct a zero-dimensional subset of the plane of which the complement is simply-connected.
For ⋋ ∈ ℝ, the tent-map with slope ⋋ is the function f : [0, 1] &rightarrow; ℝ such that f(x) = ⋋x for x &leq; ½ and f(x) = ⋋(1 - x) for x &geq; ½. Properties of w-limit sets of tent-maps, i.e. sets of the form
⋂
n∈ℕ
_________________
{ fn + k (x) | k ∈ ℕ }
for x ∈ [0, 1], are examined, and an example of a tent-map and a closed, invariant, nonempty, internally chain transitive subset of [0, 1] which is not an w-limit set is given.

Keywords: tent-map
two-point set
retractifiable
self-Tietze
Advisor: Knight, R
Collins, P
I am what I consume

This thesis employs interpretive research via ethnographic fieldwork to explore the complex relationship between the postmodern self and consumption symbolism. In postmodernity, where society becomes more global but simultaneously decentred, pastiche-like and hyperreal, the self is encountering a number of dilemmas propelled by the looming threat of personal meaninglessness. In order to attain a sense of existence, the self appears to seek the meaningfulness of life from and through symbolic consumption. Indeed, postmodernity is primarily a consumer culture where consumption is central to the meaningful practice of our everyday life. The postmodern self makes consumption choices not only from the products' utilities but also from their symbolic meanings, the function of which operates in two directions: outward in constructing the social world, social-symbolism; and inward in constructing our self-identity, self-symbolism.
To understand these phenomena, ethnographic fieldwork of four distinctive groups - a group of male femaling transgenders, a group of young nouveaux riches, a group of young extremist Buddhists and a group of young provincial women - are conducted in Bangkok, Thailand. Principally, the research explores how the informants employ everyday consumption symbolically in their self-creation processes. It also examines how the informants appropriate symbolic meanings through and from their lived and mediated experiences, and incorporate these meanings into their symbolic self-projects by means of everyday consumption. Moreover, it observes how the informants negotiate their self-social symbolism through the process of self-others identification within their friendship groups. The interpretations unfold a number of surprising outcomes which provide insight into the informants' self-projects and their consumption experiences. To conceptualise the interpretations, a model - Consumption Symbolism and the Harmonising Self - is proposed.