VictorJuiz/thesis huggingface dataset:
Model-based segmentation methods for analysis of 2d and 3d ultrasound images and sequences

This thesis describes extensions to 2D and 3D model-based segmentation algorithms for the analysis of ultrasound images and sequences.
Starting from a common 2D&plus;t "track-to-last" algorithm, it is shown that the typical method of searching for boundary candidates perpendicular to the model contour is unnecessary if, for each boundary candidate, its corresponding position on the model contour is optimised jointly with the model contour geometry. With this observation, two 2D&plus;t segmentation algorithms, which accurately recover boundary displacements and are capable of segmenting arbitrarily long sequences, are formulated and validated.
Generalising to 3D, subdivision surfaces are shown to be natural choices for continuous model surfaces, and the algorithms necessary for joint optimisation of the correspondences and model surface geometry are described. Three applications of 3D model-based segmentation for ultrasound image analysis are subsequently presented and assessed: skull segmentation for fetal brain image analysis; face segmentation for shape analysis, and single-frame left ventricle (LV) segmentation from echocardiography images for volume measurement. A framework to perform model-based segmentation of multiple 3D sequences - while jointly optimising an underlying linear basis shape model - is subsequently presented for the challenging application of right ventricle (RV) segmentation from 3D&plus;t echocardiography sequences. Finally, an algorithm to automatically select boundary candidates independent of a model surface estimate is described and presented for the task of LV segmentation.
Although motivated by challenges in ultrasound image analysis, the conceptual contributions of this thesis are general and applicable to model-based segmentation problems in many domains. Moreover, the components are modular, enabling straightforward construction of application-specific formulations for new clinical problems as they arise in the future.

Keywords: optimisation
subdivision surfaces
segmentation
Advisor: Noble, J
The passions of power politics: how emotions influence coercive diplomacy

In coercive diplomacy, actors employ the threat of force to get targets to change their behavior. The goal is to achieve the opponent's compliance without waging war. In practice, however, the strategy often falls short-even when coercers enjoy substantial military superiority. This finding inspires the central question of this thesis: What prompts leaders to reject coercive threats from stronger adversaries, and under what conditions do they yield? I argue that target leaders' affective reactions can help to explain why coercive diplomacy succeeds in some cases but not in others. Combining insights from psychology and social constructivism, this thesis presents a theory of emotional choice to analyze how affect enters into target leaders' decision-making. Specifically, it makes the case that preferences are not only socially but also emotionally constructed. The core of the theoretical framework outlines how five key emotions-fear, anger, hope, pride, and humiliation-help to constitute target leaders' preferences. This represents the first attempt to explore how a spectrum of emotions influences leaders' foreign policy decision-making. To test the analytic utility of emotional choice theory, the thesis examines nine major decisions by Nikita Khrushchev during the Cuban missile crisis in 1962 and ten main decisions by Saddam Hussein in the course of the Gulf conflict in 1990-91. The analysis yields mixed results: In the case of about a third of all decisions, the five key emotions exerted only minor effects or no impact at all. Another third of the decisions were influenced by one or more of these emotions to a degree similar to the impact of other factors. In the case of the final third of decisions, however, some of these emotions became the primary forces shaping the construction of preferences. Overall, emotional choice theory has thus advanced our understanding of the target leaders' decision-making in the missile crisis and the Gulf conflict, offering a more comprehensive explanation of why coercive diplomacy succeeded in one case but not in the other.

Keywords: coercive diplomacy
emotions
Advisor: Khong, Y
The place-name evidence for a routeway network in early Medieval England

Evidence for routes in use in the early medieval period from documents and excavations is fragmentary, and from maps is nil, but place-names help to fill the gap. Known early roads, travellers and possible origins of place-names are considered before detailed examination of the place-names that consistently occur by routeways. Ways of measuring proximity of named settlements to routeways, including the chi-squared test and dispersion graphs, are described.
The place-names are considered in detail. The road terms strǣt and weg yielded useful information; pæth and stīg did not. Gewæd and gelād indicated difficult crossings; ford was too ubiquitous to be useful. Facilities available were indicated by mere-tūn and byden-welle (water supply); strǣt-tūn and calde-cot but not Coldharbour (lodgings); mōr-tūn and mersc-tūn (fodder); dræg-tun and dræg-cot (aid to travellers in difficulty); grǣfe-tūn (pay-load). Ōra and ofer, round-shouldered ridges, were used as 'signposts' at significant points on roads and waterways to indicate, inter alia, harbour entrances, cross roads and mineral deposits. Cumb-tūn, denu-tūn, ceaster and wīc-hām were easily recognised and helped travellers to identify their whereabouts. Seaways and rivers in use were highlighted by the use of port, hȳth, ēa-tūn and lād
A series of these indicative names occurring along a route, usually Roman, suggests that the route was in use. Certain saltways, Gough (c. 1360) and Ogilby (1675) routes and a few others were also highlighted. Findings are summarised on the end-paper map.
As a check on the results, coin-find distributions for the early eighth century and late tenth/ early eleventh century were mapped against route-ways. Routes in use from placename and coin evidence were broadly similar. Evidence from pottery scatters was difficult to assemble, and gave poorer results. The evolution of the naming system is discussed. The consistent way that widely occurring landforms and habitation types were named throughout England enables the mapping of an early medieval routeway network using place-name evidence. The appendices list and map each corpus.

Advisor: Blair, J
The lawmaking of national parliaments: rethinking Europeanisation patterns

National parliaments are frequently labelled as the ‘victims’ of European integration and the EU is accused of causing the erosion of parliamentary democracy. This thesis reviews these claims by examining the influence of the European Union on national parliaments in their lawmaking capacity. The Europeanisation of legislatures is analysed at the level of the transformation of their competence as domestic lawmakers and ‘European players’ (Europeanisation of competence) and at the level of institutional and procedural adaptation (institutional Europeanisation). In this way, the thesis addresses some of the major cleavages causing disagreement between the proponents and opponents of the disempowerment of national parliaments. It is argued that the EU brings not only restrictions, but also benefits to the legislative activities of national representative institutions; and, in fact, the strengthening or weakening pattern of Europeanisation largely depends on parliamentary capacity and willingness to adapt. The study not only assesses the pattern of EU influence on the national parliaments of its Member States, but also examines whether similar processes can be identified in non-Member States. The analysis regarding non-Member States looks beyond the examples that are typically assessed by Europeanisation studies (e.g. the EEA, the EFTA and the candidate countries) and instead focuses on the case of Ukraine. The latter represents the Eastern neighbours of the EU that lack creditable membership prospects and would therefore be expected to demonstrate a weaker (if any) impact of the EU on its parliament. By building the links between the processes of Europeanisation within the EU and ‘far beyond’ its borders, this thesis aims to prove that the ‘de-parliamentarisation vs. re-parliamentarisation’ discussion is of much wider geographical relevance than it might appear at first sight.

Keywords: the European Union
lawmaking
Barroso initiative
de-parliamentarisation
EU lawmaking
acquis communautaire
legislative process
subsidiarity
Europeanisation
Treaty of Lisbon
Europeanization
approximation of laws
national parliaments
national legislatures
COSAC
parliamentary scrutiny
EU legislative process
parliamentary democracy
European integration
Advisor: Ziegler, K
Autoduality of the Hitchin system and the geometric Langlands programme

This thesis is concerned with the study of the geometry and derived categories associated to the moduli problems of local systems and Higgs bundles in positive characteristic. As a cornerstone of our investigation, we establish a local system analogue of the BNR correspondence for Higgs bundles. This result (Proposition 4.3.1) relates flat connections to certain modules of an Azumaya algebra on the family of spectral curves. We prove properness over the semistable locus of the Hitchin map for local systems introduced by Laszlo–Pauly (Theorem 4.4.1). Moreover, we show that with respect to this Hitchin map, the moduli stack of local systems is étale locally equivalent to the moduli stack of Higgs bundles (Theorem 4.6.3) (with or without stability conditions). Subsequently, we study two-dimensional examples of moduli spaces of parabolic Higgs bundles and local systems (Theorem 5.2.1), given by equivariant Hilbert schemes of cotangent bundles of elliptic curves. Furthermore, the Hilbert schemes of points of these surfaces are equivalent to moduli spaces of parabolic Higgs bundles, respectively local systems (Theorem 5.3.1). The proof for local systems in positive characteristic relies on the properness results for the Hitchin fibration established earlier. The Autoduality Conjecture of Donagi–Pantev follows from Bridgeland–King–Reid’s McKay equivalence in these examples. The last chapter of this thesis is concerned with the con- struction of derived equivalences, resembling a Geometric Langlands Correspondence in positive characteristic, generalizing work of Bezrukavnikov–Braverman. Away from finitely many primes, we show that over the locus of integral spectral curves, the derived category of coherent sheaves on the stack of local systems is equivalent to a derived category of coherent D-modules on the stack of vector bundles. We conclude by establishing the Hecke eigenproperty of Arinkin’s autoduality and thereby of the Geometric Langlands equivalence in positive characteristic.

Keywords: Geometric Langlands
Hilbert schemes
Higgs bundles
Advisor: Hausel, T
The separation of signals and background in a nucleon decay experiment

Two aspects of the problems encountered in searching for nucleon decay in the Soudan 2 detector are discussed.
The types of event which are expected are discussed. The most common are Induced by gamma rays from the naturally occurring radioactive isotopes in the cavern rock. A calculation has been developed to predict the rates of such events in the detector and the results agree well when compared with measurements made underground. Some radioactive events cause Compton scattering in the wireplane region of the detector and prohibit the use of a simple multiplicity trigger. Such events have been studied. An electronic trigger system has been designed which will achieve a factor of 103 rejection of these events while remaining efficient for even the most difficult modes of proton decay (75% for p -> K +V ). It is predicted that radioactive triggers will occur at less than 3Hz when the full detector is operating.
The neutrino induced background to proton decay has been simulated. The neutrino flux at the detector caused by cosmic ray induced showers in the atmosphere has been predicted. A comprehensive low energy (0.2 GeV to 20 GeV) Monte-Carlo neutrino event generator has been developed as a tool for background studies to proton decay. The Teinteraction of proton decay or neutrino interaction products in the parent nucleus is discussed. It is found that these reinteractions are quite probable, except for K⁺ and K° particles. Data from a low energy neutrino beam experiment has been studied and it is deduced that in some cases, the events seen in the detector will contain visible tracks associated with the disintegration of the parent nucleus. A background estimate for the mode p ➝ K+V from the neutrino interaction Vn ➝ μ~p is presented.

Advisor: Cobb, J
Molecular biophysics of strong DNA bending and the RecQ DNA helicase

Molecular biophysics is a rapidly evolving field aimed at the physics-based investigation of the biomolecular processes that enable life. In this thesis, we explore two such processes: the thermodynamics of DNA bending, and the mechanism of the RecQ DNA helicase. A computational approach using a coarse-grained model of DNA is employed for the former; an experimental approach relying heavily on single-molecule fluorescence for the latter.
There is much interest in understanding the physics of DNA bending, due to both its biological role in genome regulation and its relevance to nanotechnology. Small DNA bending fluctuations are well described by existing models; however, there is less consensus on what happens at larger bending fluctuations. A coarse-grained simulation is used to fully characterize the thermodynamics and mechanics of duplex DNA bending. We then use this newfound insight to harmonize experimental results between four distinct experimental systems: a 'molecular vise', DNA cyclization, DNA minicircles and a 'strained duplex'. We find that a specific structural defect present at large bending fluctuations, a 'kink', is responsible for the deviation from existing theory at lengths below about 80 base pairs.
The RecQ DNA helicase is also of much biological and clinical interest, owing to its essential role in genome integrity via replication, recombination and repair. In humans, heritable defects in the RecQ helicases manifest clinically as premature aging and a greatly elevated cancer risk, in disorders such as Werner and Bloom syndromes. Unfortunately, the mechanism by which the RecQ helicase processes DNA remains poorly understood. Although several models have been proposed to describe the mechanics of helicases based on biochemical and structural data, ensemble experiments have been unable to address some of the more nuanced questions of helicase function. We prepare novel substrates to probe the mechanism of the RecQ helicase via single-molecule fluorescence, exploring DNA binding, translocation and unwinding. Using this insight, we propose a model for RecQ helicase activity.

Keywords: Molecular simulation
DNA minicircles
Monte Carlo simulation
Fluorescence Resonance Energy Transfer (FRET)
Supercoiling
Computer simulations
Helicase
Molecular dynamics
RecQ
DNA cyclization
DNA
DNA bending
Biophysics
Single molecules
Advisor: Doye, J
Louis, A
Motion correction for functional magnetic resonance images

This work addresses the distortions in Functional Magnetic Resonance Images (FMRI) caused by subject motion. FMRI is a non-invasive technique which shows great promise in providing researchers and clinicians with neurological information both about healthy subjects and clinical patients by mapping functional activation within the brain using Echo Planar Imaging (EPI). If reliable information is to be obtained from these images, motion correction must be carried out in order to remove or suppress the artefacts arising from subject movement. This work begins by using exploratory data techniques to describe these artefacts so that they can be characterised according to their origin and spatio-temporal manifestation.
Based on testing of the accuracy and consistency of existing rigid-body motion correction methods on FMRI data, a new registration algorithm Motion Correction using the FMRIB Linear Image Registration Tool (MCFLIRT) has been developed. It is shown that while MCFLIRT is both more accurate and more robust than previous methods, rigid-body registration schemes in general cannot completely remove the distortions associated with motion and so subsequent analysis of the images may still be inaccurate. Furthermore, it is demonstrated that failure to use a sufficiently detailed model of subject motion in FMRI can in fact lead to degradation of the images through the use of existing motion correction algorithms. Based on these findings, alternative schemes including non-rigid registration and adaptive real-time methods are evaluated.
Leading on from this investigation, a framework for Temporally-Integrated Geometric EPI Realignment (TIGER), incorporating both spatial and temporal information about the images, is proposed. An implementation based on this novel modality-specific model is developed and tested against existing rigid-body registration methods. Results show that this new approach is able to achieve significantly more accurate results than previous methods. The quality of correction provided by this new approach brings more subtle artefacts in the data to the fore, suggesting a number of avenues of further research in this area. These are outlined in the final chapter of the thesis.

Advisor: Brady, M
Jenkinson, M
Sir Mike Brady and Dr. Mark Jenkinson
Hydrogen-bonding motifs for non-covalent synthesis

This work describes the design and synthesis of a set of four organic molecules that are intended to hydrogen-bond to each other in a pairwise manner. The four hydrogen-bonding units, termed ‘A’, ‘B’, ‘C’ and ‘D’, when placed in solution together, are designed so that A binds only to B, and C binds only to D. Each unit does not bind to itself, nor to either of the other two units to which binding is not intended. For example, A binds to B, but not to A, C, or D. Each unit contains an array of four hydrogen-bonds for strong binding to its partner, is designed to be as rigid as possible, as non-tautomeric as possible, and utilises a staggered non-symmetrical architecture.
Of the four intended compounds, three were successfully synthesised (A, B and D). Units B and D were soluble in CDCl3, but Unit A was not. Therefore, the design and synthesis of Unit A was amended, and two variants of Unit A that are both soluble in CDCl3 were successfully synthesised.
1H NMR binding experiments were performed between Unit B and each of the two variants of Unit A. Their binding behaviour was described. A binding constant could not be calculated because the units did not bind in a 1:1 fashion.

Keywords: chemistry
supramolecular
hydrogen-bond
synthesis
Advisor: Anderson, E
The origins, development and meaning of the figure Urizen in the poetry, prophecies and graphic art of William Blake

The thesis examines Urizen in relation to Blake's intellectual, religious and artistic background.
The ideas of jealousy, possessiveness and the cruelties of Kings and Priests are already present in early Blake. These various kinds of restriction contribute to the notion of the 'bounded', the sources of which are traced to empirical philosophy, though it has a very wide reference in Blake. It is central to the meaning of Urizen, whose name probably derives from a Greek verb meaning 'to bound, limit'.
But Blake also believed in firm outline. Is this not a limit? The difference between the two notions of 'bound' is examined, with reference to the Neoplatonists: the contrast is very close to that between the 'mechanic'and the 'organic'.
Urizen develops in relationship with his antagonists, Ore and, more subtly, the Bard. Ore and Urizen are both described in terms of the serpent and Satanic imagery, which suggests that they are part of the same malaise. The Bard looks like Urizen, for the Priest derives from the Poet, as Blake would have learned from contemporary primitivist writers. Urizen, like the Priest, abstracts the Infinite from the world of Forms. The sources of this idea are to be found in Fludd and the Gnostics.
The Ore-cycle finds its fullest expression in Vala. Blake may have thought of Urizen and Ore as the opposed poles of the cycle of Melancholy and Mania: Urizen owes much to the iconography of Saturn and Melancholy.
It is this cycle of alternating and divided Reason and Energy which Blake now thinks the true evil: Satan the Selfhood. There are many alchemical sources for a divided Satan, such as we see in the guises of Urizen and Luvah in Illustrations of the Book of Job. But Blake also comes to value the qualities of a redeemed Urizen, who had always had the grandeur of the Creator about him. The Priest may become the Bard again, as in the Job illustrations; or to put it another way: the 'bounded' may become Living Form.
The growth and distribution of the Latter Saint Church [sic] in Wales, 1840-1860

The growth and distribution of the Latter Day Saint Church between 1840 and 1860 is an aspect of Welsh history and geography which has received little attention. Studies of Mormonism in Wales have tended to focus on the general history of the church, or on spirituality and eschatology, with only little reference to the society in which it developed.
This study examines Mormonism in Wales as part of a radical Christian movement which arose among the working class of Britain. This movement developed alongside the radical movement in Britain, and is typified by Christian Chartism. Radical Christianity can be characterized as anti-clerical, anti-creedal, Arminian, and, sometimes chiliastic. It was marked by the view that Christianity and communism were compatible, and that Christianity, rather than being a passive means of coping with social conditions, could provide a powerful ideology with which to bolster secular attempts at reform.
As a means of establishing the radical nature of Mormonism and the basis of its appeal to a portion of the Welsh proletariat, Mormonism is examined in its American context. The social climate in which its doctrines originated is discussed, with reference to the characteristics of radical Christianity noted above. These include: doctrines concerning the priesthood; salvation; the United Order, which provided the basis of Mormon communism; and the progression of men to godhood.
Finally, Mormonism is examined in relation to Nonconformity, to Welsh society in general, and to a growing radical, national identity among the Welsh. The distribution of Mormon congregations is discussed in relation to denominationalism throughout Wales, with the purpose of explaining a primarily urban-industrial distribution, concentrated in the valleys of Monmouthshire and eastern Glamorgan.
The thesis concludes with a review of methods of diffusion, followed by a discussion of reasons for Mormonism's decline in the 1850s and 1860s.

Advisor: Harvey, D