VictorJuiz/thesis huggingface dataset:
Efficient numerical methods for ultrasound elastography
Keywords: soft tissue
ultrasound
algorithm
modeling
elastography

In this thesis, two algorithms are introduced for use in ultrasound elastography. Ultrasound elastography is a technique developed in the last 20 years by which anomalous regions in soft tissue are located and diagnosed without the need for biopsy. Due to this, the relativity cheap cost of ultrasound imaging and the high level of accuracy in the methods, ultrasound elastography methods have shown great potential for the diagnosis of cancer in soft tissues. The algorithms introduced in this thesis represent an advance in this field.
The first algorithm is a two-step iteration procedure consisting of two minimization problems - displacement estimation and elastic parameter calculation that allow for diagnosis of any anomalous regions within soft tissue. The algorithm represents an improvement on existing methods in several ways. A weighting factor is introduced for each different point in the tissue dependent on the confidence in the accuracy of the data at that point, an exponential substitution is made for the elasticity modulus, an adjoint method is used for efficient calculation of the gradient vector and a total variation regularization technique is used. Most importantly, an adaptive mesh refinement strategy is introduced that allows highly efficient calculation of the elasticity distribution of the tissue though using a number of degrees of freedom several orders lower than methods that use a uniform mesh refinement strategy. Results are presented that show the algorithm is robust even in the presence of significant noise and that it can locate a tumour of 4mm in diameter within a 5cm square region of tissue. Also, the algorithm is extended into 3 dimensions and results are presented that show that it can calculate a 3 dimensional elasticity distribution efficiently. This extension into 3-d is a significant advance in the field.
The second algorithm is a one-step algorithm that seeks to combine the two problems of elasticity distribution and displacement calculation into one. As in the two-step algorithm, a weighting factor, exponential substitution for the elasticity parameter, adjoint method for calculation of the gradient vector, total variation regularization and adaptive mesh refinement strategy are incorporated. Results are presented that show that this original approach can locate tumours of varying sizes and shapes in the presence of varying levels of added artificial noise and that it can determine the presence of a tumour in images taken from breast tissue in vivo.
Toward a divinised poetics: God, self, and poeisis in W. B. Yeats, David Jones, and T. S. Eliot
Keywords: barth
eliot
quartets
yoga
modernism
religion
poetics
theology
tantra
poetry
jones
yeats
anathemata
theosophy

This thesis examines the traces of theological and broader religious discourses in selected works of three major twentieth-century poets. Each of the texts examined in this thesis encodes within its poetics a distinct, theologically derived conception of the ontological status of the self in relation to the Absolute. Yeats primarily envisions the relation as one of essential identity, Jones regards it as defined by alterity, and Eliot depicts it as dialectical and paradoxical.
Critics have underestimated the impact on Yeats’s late work of his final and most sustained engagement with Indic traditions, which issued from his friendship and collaboration with Shri Purohit Swami. Though Yeats projected Theosophical notions on the Indic texts and traditions he studied with Purohit, he successfully incorporated principles of Classical Yoga and Tantra into his later poetry. Much of Yeats’s late poetics reflects his struggle to situate the individuated self ontologically in light of traditions that devalue that self in favor of an impersonal, cosmic subjectivity.
David Jones’s The Anathemata encodes a religious position opposed to that of Yeats. For Jones, a devout Roman Catholic committed to the bodily, God is Wholly Other. The self is fallen and circumscribed, and must connect with the divine chiefly through the mediation of the sacraments. In The Anathemata, the poet functions as a kind of lay priest attempting sacramentally to recuperate sacred signs. Because, according to Jones’s exoteric theology, the self must love God through fellow creatures, The Anathemata is not only circular, forming a verbal templum around the Cross; it is also built of massive, rich elaborations of creaturely detail, including highly embroidered and historicized voices and discourses.
Critics have long noted the influence of Christian mystical texts on Eliot’s Four Quartets, but some have also detected a countercurrent within the later three Quartets, one that resists the timeless even as the poem valorizes transcending time. This tension, central to Four Quartets, reflects Eliot’s engagement with the dialectical theology of Karl Barth. Eliot’s deployment of paradox and negation does not merely echo the apophatic theology of the mystical texts that figure in the poem; it also reflects the discursive strategies of Barth’s theology. The self in Four Quartets is dialectical and paradoxical: suspended between time and eternity, it can transcend its own finitude only by embracing it.
Modernism and the politics of time: time and history in the work of H. G. Wells, D. H. Lawrence and Virginia Woolf
Keywords: time
Modernism
narrative
H. G. Wells
D. H. Lawrence
history
Virginia Woolf

This thesis argues for a revised understanding of time in modernist literature. It challenges the longstanding critical tradition that has used the French philosopher Henri Bergson's distinction between clock-time and durée to explicate time in the modernist novel. To do so, it replaces Stephen Kern's influential understanding of modernity as characterized by the solidification of a homogenous clock-time, with Peter Osborne’s notion of modernity as structured by a competing range of temporalizations of history.
The following chapters then read the fictional and historical writings of H. G. Wells, D. H. Lawrence and Virginia Woolf alongside such a conception of modernity, and show that all these writers explored different versions of historical time. Wells explored geological time in The Time Machine (1895) and An Outline of History (1920), Lawrence adapted Friedrich Nietzsche's thought of eternal recurrence in Women in Love (1920), Movements in European History (1921) and Lady Chatterley's Lover (1928), and Woolf imagined an aeviternal historical continuity and a phenomenological historical time in Between the Acts (1941).
By addressing historical time, this thesis enables a reassessment of the politics of modernist time. It challenges the view that the purported modernist exploration of a Bergsonian private time constitutes an asocial and ahistorical retreat from the political. Rather, by transferring Osborne's notion of a 'politics of time' to the literary sphere, this study argues that the competing configurations of politically-charged historical time in literary modernism, form the analogue of the competing versions of such a time within modernity, emblematized by the contrasting accounts of historical time of Martin Heidegger and Walter Benjamin.
'The burglar's mate'? How London's probation officers persuaded magistrates in Social Enquiry Reports, 1958-72
Keywords: 1960s
probation
gender
Crime

A clash of generations occurred in the 1960s Probation Service when increasing numbers of university graduates entered the profession. They have been described as permissive by historians because they prioritised the welfare of the offender. This was in contrast to their older, and relatively untrained, colleagues for whom a reform project was premised on the disciplining of character. Due to a lack of sources, however, it remains unclear how these two generations differed in their attempts to persuade magistrates over sentencing outcomes. Fortuitously, a rare cache of over 2,000 Social Enquiry Reports (SERs) survives in the records of the City’s Justice Rooms. Written by probation officers from across the Metropolitan London area, the reports represent a cross section of the capital’s diverse population. Using a number of techniques including oral and secondary sources, this thesis identifies members of both generations and examines the way that they persuaded magistrates. Sorting the SERs into types of offender, the thesis shows that both generations ultimately persuaded magistrates by subtly indicating in reports whether or not the offender and their families conformed to conventional gender norms. The main reason why SERs by the permissive university graduates closely resembled those written by their older colleagues was due to their common perception of magistrates as being socially conservative. Regardless of how liberal or not Britain became in the sixties, the courtroom was not considered to be a place where a rethink of morality had occurred. The university graduates therefore invoked normative character ideals in SERs because they believed it was likely to be the best way to achieve the desired outcome in court. Finally, as responses to offending were shaped by gender ideologies rather than the nature of the offence or previous convictions, the concept of the probation officer as ‘the burglar’s mate’ is rendered problematic.
The analysis of offshore foundations subjected to combined loading
Keywords: foundation
offshore

Shallow offshore foundations, which achieve their stability through the foundation bearing on the seabed, can in most applications be idealised as large rigid circular footings subjected to vertical, horizontal and moment loading. A small strain linear-elastic perfectly-plastic three- dimensional finite element program was developed to analyse this combined loading problem. The selection of a suitable three-dimensional finite element for accurate and computationally efficient analysis was based on the element's ability to model incompressible soil conditions, using exact numerical integration. A new approach for evaluating element suitability is developed and is quantified in terms of the parameter free degrees-of-freedom (equal to the degrees-of-freedom minus the incompressibility constraints). The tetrahedron family of three- dimensional elements is found to be in general more suitable and computationally efficient than the Serendipity and Lagrangian cube families. The 20-node quadratic strain tetrahedron is adopted for all analyses presented in this thesis. For combined loading, most of the available elastic analytical solutions are for rigid circular footings placed at the surface. Finite element analyses reveal certain inadequacies in some of these solutions. The elastic numerical analyses also examine the effect of footing embedment for three cases of embedment geometry. This demonstrates that the increase in footing stiffness (reduction in displacement) due to embedment for horizontal and moment loading is developed at shallower depths, and has a greater magnitude, than for vertical loading. The stability of a rough rigid circular footing placed on the surface of an undrained clay is examined. Zero thickness interface elements, despite experiencing some numerical instability problems, were found to model the footing-soil interaction better than conventional continuum elements. However, application of interface elements to footings which can lose contact with the soil, under moment loading conditions, resulted in numerical instability of the solution. A simpler model was therefore used to define the shape of the three-dimensional failure envelope at high vertical load. Comparisons with the semi-empirical inclination factors of bearing capacity solutions are included.
The structural basis of immune receptor signalling
Keywords: protein disorder
cancer vaccine
Melan-A
tumour immunology
TCR
T cell receptor
TLR
toll-like receptor
MHC

This work investigates the mechanisms of binding of T cell receptors (TCRs) to Class I MHC-peptide complexes (pMHC). The structure of a TCR specific for the Melan-A tumour antigen bound to its cognate pMHC was solved to a resolution of 2.5 Å which gives insight into how this TCR could be mutated to optimize binding and subsequently used as a cancer vaccine. Detailed sequence and geometric analyses of all currently available structures of Class I TCR-pMHC complexes revealed that TCRs can bind to pMHC with a range of orientations, yet always focus on the central portion of the peptide and use a specific subset of six residues on the MHC helices for binding. The most striking finding was the use of aromatic residues in the TCR CDR loops to bind to residue Q155 on the MHC α2 helix. Attempts were also made to express and purify Toll-like receptors (TLRs) with the aim of solving one or more of these structures. However, despite testing of over 50 different constructs from 12 different TLRs or associated proteins, insufficient soluble protein expression was obtained for crystallization trials. Finally, a protein disorder prediction tool was developed to aid construct design for structural biology studies and improve the chances of obtaining protein crystals. This tool is based on a novel type of neural network and blind tests comparing it to 8 other disorder prediction tools showed it is one of the best in the field. It is freely available at www.strubi.ox.ac.uk/RONN. Analysis of large datasets revealed that the position of order/disorder transitions is quite precisely defined in amino-acid sequences and that transition regions have an amino acid composition distinct from that of bulk ordered and disordered sequences. There is a steady decrease in order-promoting residues on the ordered side of boundaries as well as a weak sequence signal, both of which signify the approaching disorder and may prove useful for improving existing disorder prediction tools.
Rhetoric or reality?: victims' enforcement mechanisms in England and Wales and the United States
Keywords: enforcement
victims
rights

Recent policies in England and Wales and the United States have recognised for the first time enforcement mechanisms for victims of crime under the Crime Victims’ Rights Act (CVRA) in the United States as well the Code of Practice for Victims of Crime in England and Wales (the Code). Although very different from one another, these policies ostensibly aimed to provide a stronger commitment to victims’ rights, by recognising an accessible, timely and impartial process that recognises accountability and provides individual remedies in cases of breaches.
This thesis engages in a careful in-depth analysis of these mechanisms and their implementation based on elite qualitative interviews, case law analysis and a multidisciplinary examination of the relevant literature. It argues that on the whole, these mechanisms have presented a number of limitations, and thus in many respects cannot and have not delivered accessible, and timely means to respond to victims’ rights breaches. Most importantly, it demonstrates that for certain types of breaches and in certain contextual settings, these mechanisms have recognised only limited or no redress at all for breaches. This research takes the available victims’ literature further by arguing that many of these promises have been closer to rhetoric than reality and providing a more nuanced portrait of the substantial difficulties and limitations that relate to these enforcement mechanisms. In effect, these limitations can be understood in light of the nature and structural components of these selected mechanisms, as well as the ways they have been implemented by the main actors involved in these processes and the different contexts under which the different types of breaches take place.
Finally, despite their limitations, when compared to one another, each mechanism can be considered a better option for access, timeliness and redress – depending on context and the type of breach. Following from this analysis, a complementary approach is developed which can facilitate and increase opportunity for redress for a wider range of situations. It is important to bear in mind however the limits of the complementary approach; namely, that it only includes elements inspired from the two mechanisms examined in this thesis and that there are several limitations that relate to transplants and policy transfers.
Towards a knowledge management methodology for articulating the role of hidden knowledges
Keywords: ethnography
tacit knowledge
pattern languages
knowledge management systems
knowledge management
ethnomethodology

Knowledge Management Systems are deployed in organisations of all sizes to support the coordination and control of a range of intellectual assets, and the low cost infrastructures made available by the shift to ‘cloud computing’ looks to only increase the speed and pervasiveness of this move. However, their implementation has not been without its problems, and the development of novel interventions capable of supporting the mundane work of everyday organisational settings has ultimately been limited. A common source of trouble for those formulating such systems is said to be that some proportion of the knowledge held by a setting’s members is hidden from the undirected view of both The Organisation and its analysts - typically characterised as a tacit knowledge - and can therefore go unnoticed during the design and deployment of new technologies. Notwithstanding its utility, overuse of this characterisation has resulted in the inappropriate labelling of a disparate assortment of phenomena, some of which might be more appropriately re-specified as ‘hidden knowledges’: a standpoint which seeks to acknowledge their unspoken character without making any unwarranted claims regarding their cognitive status. Approaches which focus on the situated and contingent properties of the actual work carried out by a setting’s members - such as ethnomethodologically informed ethnography - have shown significant promise as a mechanism for transforming the role played by members’ practices into an explicit topic of study. Specifically they have proven particularly adept at noticing those aspects of members’ work that might ordinarily be hidden from an undirected view, such as the methodic procedures through which we can sometimes mean more than we can say in-just-so-many-words. Here - within the context of gathering the requirements for new Knowledge Management Systems to support the reuse of existing knowledge - the findings from the application of just such an approach are presented in the form of a Pattern Language for Knowledge Management Systems: a descriptive device that lends itself to articulating the role that such hidden knowledges are playing in everyday work settings. By combining these three facets, this work shows that it is possible to take a more meaningful approach towards noticing those knowledges which might ordinarily be hidden from view, and apply our new understanding of them to the design of Knowledge Management Systems that actively engage with the knowledgeable work of a setting’s members.
Adrenergic regulation of regional fat metabolism
Keywords: fatty acid trafficking
catecholamines
adipose tissue

Introduction: An increased gluteofemoral adipose tissue (AT) mass is associated with a protective cardiovascular and metabolic risk profile, and effective fatty acid retention in femoral AT has been proposed as a possible mechanism. Catecholamines are important regulators of AT lipolysis and blood flow (ATBF). The aim of the thesis was to investigate regional differences in the adrenergic regulation of fatty acid release and ATBF between abdominal and femoral AT in vivo. Furthermore, in vivo regional fatty acid trafficking was studied in a physiological setting over 24 h.
Methods: Regional fatty acid trafficking, along with the measurement of ATBF, was studied with the arterio-venous difference technique and stable isotope tracers in healthy volunteers. Adrenergic agonists (isoprenaline, adrenaline) were infused either locally by microinfusion, or systemically. Local microinfusion of adrenoreceptor antagonists (propranolol, phentolamine) was used to characterize specific adrenoreceptor subtype effects. The trafficking of dietary fatty acids was studied over a 24 h period involving three meals containing stable isotope-labelled fatty acids along with intravenous infusions of another labelled fatty acid.
Results: Femoral ATBF and lipolysis was less responsive to adrenergic stimulation with adrenaline compared to abdominal AT. This was due to increased femoral α-adrenoreceptor responsiveness. When studied over 24 h, femoral AT showed a lower lipolysis rate compared to abdominal AT, while dietary fatty acids were extracted more avidly by abdominal AT. Uptake of non-dietary fatty acids (derived from very-low-density lipoproteins or unbound non-esterified fatty acids) was comparable between abdominal and femoral AT.
Conclusion: There are fundamental differences in response to adrenergic stimuli between abdominal and gluteofemoral tissues and the ability of femoral AT to trap non-dietary fatty acids may provide protection of other tissues from ectopic fatty acid deposition.
A laser based straightness monitor for a prototype automated linear collider tunnel surveying system
Keywords: ILC
least squares minimisation
network reconstruction
tunnel surveying
linear collider
laser straightness monitor
straightness monitor
accelerator alignment
laser beam spot fitting

For precise measurement of new TeV-scale physics and precision studies of the Higgs Boson, a new lepton collider is required. To enable meaningful analysis, a centre of mass energy of 500GeV and luminosity of 1034cm-2s-1 is needed. The planned 31km long International Linear Collider is capable of meeting these targets, requiring a final emittance of 10 micro-radians horizontally and 35nmrad vertically. To achieve these demanding emittance values, the accelerator components in the main linacs must be aligned against an accurately mapped network of reference markers along the entire tunnel. An automated system could map this tunnel network quickly, accurately, safely and repeatedly; the Linear Collider Alignment and Survey (LiCAS) Rapid Tunnel Reference Surveyor (RTRS) is a working prototype of such a system.
The LiCAS RTRS is a train of measurement units that accurately locate regularly spaced retro-reflector markers using Frequency Scanning Interferometry (FSI). The unit locations with respect to each other are precisely reconstructed using a Laser Straightness Monitor (LSM) and tilt sensor system, along with a system of internal FSI lines. The design, commissioning, practical usage, calibration, and reconstruction performance of the LSM is addressed in this work.
The commissioned RTRS is described and the properties of the LSM components are investigated in detail. A method of finding the position of laser beam spots on the LSM cameras is developed, along with a process of combining individual spot positions into a more robust measurement compatible with the data from other sub-systems. Laser beam propagation along the LSM is modelled and a robust method of reconstructing CCD beam spot position measurements into positions and orientations of the LSM units is described. A method of calibrating LSM units using an external witness system is presented, along with a way of using the overdetermined nature of the LSM to improve calibration constant errors by including data taken from unwitnessed runs.
The reconstruction uncertainty, inclusive of both statistical and systematic effects, of the LSM system is found to be of 5.8 microns × 5.3 microns in lateral translations and 27.6 microradians × 34.1 microradians in rotations perpendicular to the beam, with an uncertainty of 51.1 microradians in rotations around the beam coming from a tilt-sensor arrangement.