VictorJuiz/thesis huggingface dataset:
To be a pilgrim: a comparative study of late medieval accounts of pilgrimage from Germany and England to the Holy Land

As a large-scale international cultural phenomenon, the Jerusalem pilgrimage must be approached comparatively. This project compares the pilgrimage accounts of two Germans and two Englishmen who travelled to Jerusalem in the second half of the long fifteenth century. The texts are those of William Wey, (written c.1470), Bernhard von Breydenbach (printed 1486), Arnold von Harff (written 1499) and the Pylgrymage of Sir Richard Guylforde, composed by his anonymous chaplain (printed 1511). Each chapter focuses on a pilgrim, and one of four thematic topics: genre, the religious other, curiosity and print.
This project treats these works as literary texts which can be approached from the perspective of cultural history, rather than as historical sources. The project, therefore, is more a consideration of how the pilgrimage is represented than it is about the events of each pilgrimage, and so it looks at the pilgrimages created in writing. Pilgrimage writings tend to focus on Jerusalem's spiritual significance, rather than its worldly position. In this sense, textual representations of travel to Jerusalem represent something of a disconnect with travel to other physical destinations, and the conceptual space of pilgrimage will be of key significance to this thesis. This has implications for practice as well as writing, and therefore the thesis will address how the writers consider their journeys, as well as the idea of virtual pilgrimage.
The thesis engages with questions of identity, and how it is presented, as well as the authors' relationship with their audiences. This necessitates analysing collective identity, as well as the different audiences for printed and manuscript texts. The most important research question, bringing together these issues, considers whether the authors’ different geographical origins affect their self-presentation and understanding of pilgrimage. This leads to my central contention: that pilgrimage must be portrayed as a single, unified experience.

Advisor: Volfing, A
Moore, H
Sickness, disability, and miracle cures: hagiography in England, c. 700 - c. 1200

This thesis considers how religious literature represented sickness and disability in Anglo- Saxon and post-Conquest England. Based on Gospel accounts of Jesus's healings, narratives of miracle-cures were highly valued within medieval Christian culture. By analysing a selection of miracle-cure narratives from the main period of miracle writing in England, from the age of Bede to the late twelfth century, this project considers the social significance of such stories. All miracle-cures followed the pattern of a spiritual triumph over the material world, but this thesis focuses on how hagiographers represented human experiences of sickness and disabilities.
The first two chapters of this thesis address the conceptual structure of the project. The first explains the two areas of scholarly theory that underpin this thesis. These are the use of narrative sources for historical study; and sociological conceptualisations of bodily difference. The second chapter orientates the case-studies selected for this project in their context. Miracle-cures were recounted in relation to other aspects of the culture of medieval England, most importantly the theology of sainthood and of sin.
The remaining three chapters of the thesis provide detailed thematic analysis of selected miracle-cure narratives. The third chapter asks how the spiritual experience of bodily difference was understood. The next chapter considers the physical understandings of a body that was affected by either sickness or disability, and the links between miracle-cure narratives and contemporary medical theory. The fifth and final chapter addresses the representation of social aspects of sickness and disability in these texts, in particular the moralising rhetoric of such texts in favour of community support.
This thesis concludes with a discussion of how modern Disability Studies and scholarship on medieval culture benefit from interaction with one another.

Keywords: Disability
Saint Swithun
Bede
Saint Cuthbert
Saint Edmund
Miracle Stories
Sickness
Saint AEthelthryth
Thomas Becket
Interaction of anaesthetics with the carotid body glomus cell and the background potassium channel response to hypoxia

This thesis investigates the role anaesthetics play in the depression of the acute hypoxic and hypercapnic ventilatory response. Particular attention is paid to TASK (TWIK related acid sensitive potassium) channels that are known to be sensitive to both hypoxia and the volatile anaesthetics.
After chapters relating to a general introduction and methods, chapter 3 describes studies into the hypoxic and hypercapnic responses of mice with genetic ablation of TASK 1 and/or TASK 3. By using whole animal unrestrained plethysmography, it was demonstrated that any loss of TASK channels resulted in a depression of ventilatory responses to hypoxia and hypercapnia. In isocapnic hypoxia, there is a genotype specific depression by anaesthetics of the remaining AHVR, depending on whether halothane or isoflurane is inspired.
Chapter 4 establishes that propofol depresses the chemosensory responses of carotid body glomus cells. Using ratiometric flurimetry to measure the intracellular calcium concentration in isolated neonatal rat glomus cells, it was demonstrated that propofol depresses the normal cellular response to both hypoxia and hypercapnia. Using pharmacological modulators of GABA and nAChR, and single channel patch clamp electrophysiology of TASK, it is apparent that this depression is independent of these candidate mechanisms.
Chapter 5 describes the effects of the anaesthetic dexmedetomidine at two levels of the hypoxic chemoreflex arc in rodents. Neither isolated rat glomus cells, nor unrestrained mice show significant depression of hypoxic responses when dexmedetomidine is present.
Chapter 6 illustrates the potential role for specific antagonism of TASK channels in stimulating the carotid body. Two TASK channel blockers, A1899 (TASK 1 antagonist) and PK-THPP (TASK 3 antagonist) are shown to cause a significant influx of calcium into isolated glomus cells, and an augmentation in the glomus cell response to hypoxia, which persists in the presence of isoflurane.
Overall, this thesis provides evidence that both TASK 1 and TASK 3 channels are essential for normal hypoxic chemosensitivity. It has extended the knowledge that anaesthetics depress glomus cell chemosensation, by demonstrating that propofol too causes this effect. It also proposes that dexmedetomidine may have greater utility in sparing of ventilatory reflexes. By selectively blocking TASK channels, glomus cells can be stimulated, and exploiting this mechanism would be useful in minimising anaesthetic-induced depression of ventilation.

Keywords: hypoxia
Cohomogeneity one Ricci solitons

In this work we study the cohomogeneity one Ricci soliton equation viewed as a dynamical system. We are particularly interested in the relation between integrability of the associated system and the existence of explicit, closed form solutions of the soliton equation. The contents are organized as follows.
The first chapter is an introduction to Ricci ow and Ricci solitons and their basic properties. We reformulate the rotationally symmetric Ricci soliton equation on &Ropf;n+1 as a system of ODE's following the treatment in [14].
In Chapter 2 we carry out a Painlevé analysis of the previous system. For the steady case, dimensions where n is a perfect square are singled out. The cases n = 4, 9 are particularly distinguished. In the expanding case, only dimension n = 1 is singled out.
In Chapter 3 we reformulate the cohomogeneity one Ricci soliton equation as a Hamiltonian system with constraint. We obtain a conserved quantity for this system and produce explicit formulas for solitons of dimension 5.
In Chapter 4 we introduce the notion of superpotential and use it to produce more explicit formulas for solitons of steady, expanding and shrinking type.
In Chapter 5 we carry out a Painlevé anaylsis of the Hamiltonian corresponding to solitons over warped products of Einstein manifolds with positive scalar curvature. This analysis singles out the cases discussed in the previous chapters. We also carry out an analysis of the Hamiltonian corresponding to the Bérard Bergery ansatz [5]. This analysis singles out a 1-parameter family of solutions.

Advisor: Dancer, A
Mathematical modelling of the host-virus interaction in chronic HTLV-I infection and its impact on our understanding of viral persistence and pathogenesis

Human T-cell lymphotropic virus type I (HTLV-I) is a persistent human retrovirus characterised by life-long infection and risk of developing one of two major, clinically independent diseases: adult T-cell leukaemia/lymphoma (ATL), an aggressive blood cancer, and HAM/TSP, a progressive neurological and inflammatory disease. Infected individuals typically mount a large, chronically activated CD8+ cytotoxic T-lymphocyte (CTL) response against HTLV-I-infected cells, but ultimately fail to effectively eliminate the virus. Moreover, the identification of determinants to disease manifestation has thus far been elusive.
A central issue in current HTLV-I research is how the virus is able to persist despite strong immune pressure. To explore this issue, we adopt a mathematical modelling approach. Mathematical modelling can help us break apart the complex mechanisms of HTLV-I persistence and identify the underlying principles that govern successful viral propagation in the presence of host immunity. Understanding these interactions is a crucial step on the road to developing effective ways to disrupt the virus life-cycle and may help identify promising new treatment strategies to reduce the severity of HTLV-I infection and minimise the detriment due to associated disease.
The objective of this thesis is to develop a consistent theoretical framework that can help shed light on specific, biologically relevant questions that are of interest to experimentalists and theoretical immunologists trying to understand the complicated host-pathogen dynamics of chronic infection by HTLV-I. In this thesis, we construct a series of mathematical models, each incorporating an increasing level of immunological detail, designed to explore the impact of three biologically significant features that have not been fully considered in previous mathematical models of HTLV-I: (I) the trade-off between proviral latency and activation, (II) the simultaneous expression of viral proteins, and (III) the role of antigenic variability.
The results from investigation of these features in the various models help contribute to our understanding of the dynamics of persistent HTLV-I infection alongside virus-specific host immunity. Although our approach is primarily theoretical in nature, our research is principally driven by a desire to elucidate biologically and clinically relevant phenomena observed in HTLV-I and, for each of the models, we link our results to what is known from experimental observations and discuss their significance in a biologically meaningful context.

Keywords: differential equations and dynamical systems
global asymptotic stability
within-host virus dynamics
infectious disease mathematical modelling
Advisor: Maini, P
Gupta, S
'Trying to have it both ways': John Ashbery and Anglo-American exchange

This dissertation explores John Ashbery's interactions with several generations of English poets, during a period which ranges from the late 1940s to the present day. It seeks to support two principle propositions: that Ashbery's engagements with contemporaneous English poets had a decisive influence on his poetic development; and that Ashbery's own poetic and critical work can be employed to revise our understanding of mid-to-late 20th century English poetry. The dissertation demonstrates that Ashbery's relationships with four English poets—W.H. Auden, F.T. Prince, Lee Harwood and Mark Ford—occurred at significant junctures in, and altered the course of, his poetic development. Ashbery's critical and poetic engagements with these poets, when read together, are shown to constitute an idiosyncratic but coherent re-reading of the English poetry of the past and present. The dissertation addresses the ways in which each poet theorises the difficulties posed, and opportunities afforded, by perceived changes in Anglo-American poetic relations at different points during the 20th century.
Chapter one re-evaluates Ashbery's relationship with Auden. It traces the legacy of Auden's coterie poetics in The Orators for Ashbery and Frank O'Hara, offers a revisionary reading of The Vermont Notebook as a strident response to Auden's late-career conservativism, and reads in depth Ashbery's unpublished, highly ambivalent elegy for him, "If I had My Way, Dear". Chapter Two attends to the extensive correspondence between Ashbery and Prince, argues that Prince's work provided a model for Ashbery's "encrypted" early lyrics addressing his homosexuality, and reads "Clepsydra" as an early elaboration of Ashbery's conception of a reciprocal influential model. Chapter Three examines Lee Harwood's "imitations" of Ashbery, and considers the latter's first critical formation of an English "other tradition" through his association of Harwood with the work of John Clare. Chapter Four portrays Ashbery's relationship with Mark Ford as a successful enactment of reciprocal influence, a form of engagement which allows Ashbery a means to "shake off his own influence" and to retain his status as a "major minor writer".

Advisor: Bush, R
Computer vision and machine learning for microscopy image analysis

This thesis presents methods that address three fundamental tasks in the field of microscopy image analysis: detection of instances of an object, counting instances of an object when individual detection is not possible, and exploration of large datasets of microscopy images. We address these areas while strongly considering the constraints related to the usability and flexibility of a real practice. Through the use of computer vision and machine learning, we aim to deal with minimalistic user annotations, interactivity and intuitive data visualization.
Firstly, a novel framework is presented to detect all the instances of an object of interest in microscopy images, where they may be partially overlapping and clustered. To this end, a tree-structured discrete graphical model is introduced, that is used to select and label a set of non-overlapping candidate regions in the microscopy image by a global optimization of a classification score. Additionally, it is shown how to learn, from the images, the generation of a surface that can improve the collection of the candidate regions. The learning for the object model and optimal surface only require simplistic annotations -- a dot on each instance of the object.
Secondly, it is considered the scenario where individual instances of an object may not be discernible due to extreme overlap, but the count of instances over regions of interest is still useful quantitative information. A novel object density estimation approach is proposed, which is also trained from simple dot-annotations, and achieves a similar accuracy to current state-of-the-art methods while being considerably faster to train. The application to counting in time-lapse microscopy sequences is illustrated. Moreover, by taking advantage of the possibility to learn on-the-fly from simple annotations, an interactive counting system is developed which allows a user to quickly obtain object counts on simple cases, or to bootstrap dataset annotations for more complex scenarios.
Finally, the exploration of microscopy datasets coming from large exploratory studies is considered. An unsupervised pipeline is proposed, which allows the discovery and visualization of the effect of external perturbations such as drugs over a target of interest (e.g. a cell protein). This framework enables a user to perform large scale image-dataset exploration in an intuitive way using a novel 2D visualization tool.

Advisor: Noble, A
Lempitsky, V
Zisserman, A
Flexure and rheology of Pacific oceanic lithosphere

The idea of a rigid lithosphere that supports loads through flexural isostasy was first postulated in the late 19th century. Since then, there has been much effort to investigate the spatial and temporal variation of the lithosphere’s flexural rigidity, and to understand how these variations are linked to its rheology. In this thesis, flexural modelling is used to first re-assess the variation in the rigidity of oceanic lithosphere with its age at the time of loading, and then to constrain mantle rheology by testing the predictions of laboratory-derived flow laws.
A broken elastic plate model was used to model trench-normal, ensemble-averaged profiles of satellite-derived gravity at the trench-outer rise system of circum-Pacific subduction zones, where an inverse procedure was used to find the best-fit Te and loading conditions. The results show a first-order increase in Te with plate age, which is best fit by the depth to the 400 ± 35 °C plate-cooling isotherm. Fits to the observed gravity are significantly improved by an elastic plate that weakens landward of the outer rise, which suggests that bending-induced plate weakening is a ubiquitous feature of circum-Pacific subduction zones.
Two methods were used to constrain mantle rheology. In the first, the Te derived by modelling flexural observations was compared to the Te predicted by laboratory-derived yield strength envelopes. In the second, flexural observations were modelled using elastic-plastic plates with laboratory-derived, depth-dependent yield strength. The results show that flow laws for low-temperature plasticity of dry olivine provide a good fit to the observations at circum-Pacific subduction zones, but are much too strong to fit observations of flexure in the Hawaiian Islands region. We suggest that this discrepancy can be explained by differences in the timescale of loading combined with moderate thermal rejuvenation of the Hawaiian lithosphere.

Advisor: Watts, A
The class I human leukocyte antigen in immune control and intra-host evolution of HIV-1

The CD8+ T (CTL) cell response is an important component of the immune response to HIV-1 infection. Presentation of peptides by the human leukocyte antigen (HLA) class I is key in directing that response. HLA-B*27:05 and HLA-B*57:01 have been consistently associated with immune control of HIV. To gain novel insights into the determinants of an effective CTL response mediated by these alleles, this work investigated cases of HIV disease control and progression in HLA-B*27:05 and B*57:01-expressing subjects. These subjects were either infected with clades of HIV infrequently found in combination with these alleles (C clade in HLA-B*27:05, and CRF01_AE clade in HLA-B*27:05/B*57:01) and/or represented the rare scenario of dual expression of both alleles. Transmission pair studies, viral replicative capacity assays and full-length ultra-deep sequencing were used to characterise CTL-mediated intra-host viral evolution, viral fitness and their effect on disease outcome.
In the context of HLA-B*27:05 expression, this work demonstrated that the patterns of CTL immune escape and the associated viral fitness are considerably different in C clade compared to B clade HIV infection. This work also showed that rapid intra-host viral evolution and selection of escape may lead to disease progression despite expression of both favourable HLA class I alleles. The critical role of the Gag-specific CTL response in maintaining disease control, despite applying an unbiased genome-wide approach to detecting viral evolution, was demonstrated.
This work has described the interactions between expression of HLA-B*27:05 and/or HLA-B*57:01, intra-host viral evolution and HIV disease progression, contributing to our understanding of CTL-mediated immune control. This is an important approach for elucidating correlates of protective immunity against HIV infection that may inform the design of intervention strategies.

Advisor: Goulder, P
Matthews, P
The association between impaired fetal growth and neurodevelopment in childhood

Impaired fetal growth is associated with an increased risk of negative neurodevelopmental outcomes. The majority of research to date, however, has relied on birth weight as an index of fetal growth impairment. Furthermore, few studies have included samples from low- and middle-income countries (LMICs). The objective of this thesis was to examine the association between impaired fetal growth, using a range of birth indices, and neurodevelopment in childhood.
A systematic review showed that cognitive development and attention are two domains particularly affected by impaired fetal growth and thus was the focus of this thesis. Cognitive development and attention were assessed in three large, prospective birth cohorts drawn from high-, middle- and low-income countries: Pelotas (Brazil) 2004 (N=3579), ALSPAC (UK) (N=7354) and INTERGROWTH-21st (UK, Italy, Brazil, India and Kenya) (N=1073). INTERGROWTH-21st only enrolled low-risk mothers, whereas Pelotas and ALSPAC were not selective. In all three cohorts, indices of birth weight, stunting, wasting and asymmetry were collected at birth. Attention was assessed using subscales of the Child Behaviour Checklist or the Strengths and Difficulties Questionnaire; and cognition was assessed using the Wechsler Preschool and Primary Scales of Intelligence-Revised or INTERGROWTH-21st Neurodevelopmental Assessment (INTER-NDA). Each cohort measured these outcomes at one time point (range = 2-6 years of age). As part of this thesis the INTER-NDA was validated against the Bayley Scales of Infant Development.
Associations between birth anthropometric indices and both cognitive and attention outcomes were assessed using hierarchical ordinal logistic regression. Attention impairment was associated with stunted birth length (BL) but only in females (OR=1.21-1.69, p<.05), across cohorts drawn from high-, middle- and low-income countries. In contrast, cognitive impairment was associated with stunted head circumference (HC) and low ponderal index (PI) in both sexes, although predominantly in LMIC settings (HC: OR=1.73-1.91, p<.05; PI: OR=1.46-4.91, p<.05).
Identification of a female-specific association between stunted BL and poor attention across cohorts from different settings, suggests the association is robust to differential confounding effects. In contrast, the stronger association in LMICs between cognitive impairment and stunted HC and low PI suggests confounding structures (e.g. maternal and neonatal health care) may modify the effect of fetal growth on cognitive development. Birth indices (specifically BL, HC and PI) may be particularly helpful in identifying children at risk of neurodevelopmental impairment for early intervention.

Keywords: neurodevelopment
cognitive development
anthropometry
fetal growth
attention development
Advisor: Stein, A
Fernandes, M