VictorJuiz/thesis huggingface dataset:
Neuroimaging functional pain networks in health and disease

Chronic pelvic pain (CPP) is considered a significant public health problem. In the United Kingdom, it has been estimated that 24% of women suffer from CPP. Using neuroimaging, this dissertation aims to characterise the pain experience by examining functional changes in critical pain networks.
I begin by examining the functional correlates of capsaicin-induced central sensitisation in healthy individuals. Most of the results did not reach significance, largely due to the use of early 7T data and small sample sizes. In an exploratory analysis, amygdala - anterior insula connectivity is positively correlated with pain intensity.
The remaining experimental chapters examine mechanisms of pain in women with CPP. I begin by attempting to better characterise this diverse patient population. I demonstrate correlations between measures of the pain experience and psychological scores. Following this, I examine clinically-relevant changes in functional connectivity. I demonstrate that there are potentially different underlying modulatory mechanisms in women with neuropathic components to their pelvic pain. Furthermore, women who experience pain for longer than 24 months have increased functional connectivity between the hippocampus and periaqueductal gray, suggesting pain-related alterations in central circuitry. The final experimental chapters explore surgical and pharmaceutical treatments for CPP and endometriosis; however, due to small sample sizes and nonsignificant findings, limited conclusions can be drawn from the results.
In this dissertation, I found changes in important pain networks that could either represent the maintenance of the pain state or are consequence of the pain itself. These findings may serve as an indicator of underlying central changes that relate to relevant components of the clinical pain experience.

Advisor: Tracey, I
Vincent, K
Exploring mechano-structural processes in osteoarthritis

Articular cartilage is a remarkable tissue with mechanical performance that surpasses engineering standards. Collagen, the most abundant protein in cartilage, plays an important role in this performance. Building on observations of collagen structural changes at the earliest stages of osteoarthritis, we here explore the role of collagen in the disease process. Specifically, we focus on the material properties and organization of collagen fibrils in the cartilage surface, seeking to answer three key questions:
• What are the physical changes to collagen in early osteoarthritis?
• How do physical changes relate to osteoarthritic progression mechanistically?
• Can we detect early, irreversible changes to cartilage intraoperatively to facilitate early treatment?
Ten human tibial plateaus were characterised by atomic force microscopy and Raman spectroscopy, with clinical and histological scoring used for comparison. Minimal changes were found in the collagen molecules themselves, yet a marked increase in intra-fibrillar crosslinking was observed.
A bottom-up numerical model of the collagen fibril network was then implemented to specifically explore the relationship between fibril interactions and mechanics in osteoarthritis. Simulating two different fibril configurations, we established that high connectivity is critical to the resistance to, and recovery from, loading. Osteoarthritis-like bundled configurations were produced by networks with sparse interactions, and identified as a mechanically irreversible stage in disease progression. Coupling the model with experimental results, we argue that the intra-fibril changes appear to link to disease initiation and it is the inter-fibril interactions that drives the disease.
Finally, a pilot study was conducted to explore the potential for quantitative intraoperative imaging to detect irreversible collagen-related changes in the cartilage surface. Based on spectral analysis of the available light from standard arthroscopic equipment, it may be possible to advance arthroscopy from a qualitative to quantitative assessment tool.

Advisor: Brown, C
Gaffney, E
Children of the land and children of the Saint: Heritage, religion, and territoriality in a Brazilian quilombo

This dissertation is looking at quilombo grassroots land and identity politics as they transpire in a compound of Black rural communities in the north of the state of Maranhão, Brazil.
One of the main questions this thesis asks is: How do communities mobilise resources in defence of their territories when formal means of establishing land claims have been exhausted? Based on ethnographic research conducted over fifteen months my analysis delves into strategies employed by peasant groups for the assertion of their collective land ownership. This assertion taps into specific ethno-racial legislation and it is especially directed towards Evangelical Christians, whom the majority of Catholic quilombola residents regard as their territorial and religious antagonists.
This thesis’s broadest argument is that this territorial defence mainly materialises through two streams of action: religious and cultural grassroots activism. It is argued that creative uses and articulations of cultural and religious practices, and the creation of a network of alliances, transpire as the most relevant means of 'informal' community politics.
More specifically, I argue that local ceramic production (intrinsically attached to notions of a 'quilombo heritage') and religious festivities in honour of the local patron saint contribute to the preservation of a specific quilombo territoriality. In the ethnographic context examined, this territoriality is inherently attached to popular Catholicism and notions of quilombola cultural identity. Employing approaches from agrarian, peasant politics, quilombo, and heritage studies, this dissertation seeks to illuminate the dynamic relation between local perceptions of land and territoriality in the 'lands of Santa Teresa'. Overall, this thesis aims at contributing to those studies that explore the diversity and creativity of politics 'from below'.

Keywords: land rights
heritage
popular Catholicism
quilombos
Brazil
Advisor: Sarró, R
Ewart, E
Calibration to vanilla and barrier options with the Gyöngy and Brunick--Shreve Markovian projections

In this thesis, we present a novel approach to the calibration of diffusion models to vanilla and barrier options with the Gyöngy and Brunick–Shreve Markovian projection results. Firstly, we derive a forward equation for arbitrage-free barrier option prices in continuous semi-martingale models, in terms of Markovian projections of the stochastic volatility process. This leads to a Dupire-type formula for the coefficient derived by Brunick and Shreve for their mimicking diffusion and can be interpreted as the canonical extension of local volatility for barrier options. Secondly, we treat the problem of long-dated foreign-exchange option pricing and propose a novel and generic calibration technique to vanilla options for four-factor foreign-exchange hybrid local-stochastic volatility models with stochastic short rates. We build upon the particle method introduced by Guyon and Labordère and combine it with new variance reduction techniques in order to accelerate convergence. Finally, we derive the necessary and sufficient condition for the exact calibration to up-and-out call options and provide a step-by-step procedure to calibrate a Brunick–Shreve volatility model, a Heston-type local-stochastic volatility model with local vol-of-vol and a path-dependent local-maximum-stochastic volatility model. While the Brunick–Shreve model is calibrated with our forward PIDE for barriers, both stochastic volatility models require an interesting two-dimensional extension of the particle method. We then derive and prove the self-consistency condition for perfect calibration to barrier options for path-dependent models with stochastic domestic and foreign short rates, where techniques from our previous work can be combined, in order to price accurately long-dated derivatives with barrier feature.

Advisor: Reisinger, C
Musiela, M
Hambly, B
Exploring the mechanisms that underlie the crossmodal correspondences between shapes and tastes

This thesis consists of one theoretical chapter, three experimental chapters, and a final concluding chapter. Eight studies were conducted in total, two of these studies (studies 1-2, Chapter 2) evaluated whether visual aesthetic features (i.e., symmetry, curvature, and the number of elements) influenced how shapes and objects are matched to a valence and to a taste word (i.e., sweet or sour). The evidence reported in Chapter 2 demonstrates that symmetrical / asymmetrical, rounded / angular, and shapes with fewer / more elements are more likely to be matched with a positive / negative valance and to sweetness / sourness. The relationship between valence and shape-taste matching is discussed and challenged. Three different studies (studies 3-7, Chapter 3) analysed whether simple dots and lines that resemble facial features (i.e., eyes and mouth) could be associated with an emotional valence and an emotion, as well as to a specific taste word (i.e., sweet, sour, or bitter). The results reported in Chapter 3 confirm that it is possible to reduce a facial feature to its simplest form (i.e., a line and a dot) and still be associated with a specific valence and emotion. Furthermore, Study 7 demonstrates that dots and lines that resemble eyes and mouths can influence taste expectations (i.e., how sweet, sour, or bitter they predict a product will be). Chapter 4, comprises a short study that provides initial evidence that facial expressions of joy, disgust and anger can influence the perceived intensity of a taste (i.e., sweet, sour, and bitter). The role of embodied cognition in the crossmodal correspondences between shapes and tastes is discussed. Finally, in Chapter 5, the importance of associative learning, the role of evolution in our ability to detect patterns, and embodied cognition are presented as potential mechanisms that explain how it is that shapes are matched to tastes.

Advisor: Spence, C
Sustainability and recycling in fifteenth-century manuscripts

This thesis examines the sustainability of fifteenth-century manuscripts. It analyses the durability of manuscripts, and the ways in which people recycled and reused their books. During the long fifteenth-century (here, 1375-1530), book production in England flourished, driven by increased demand for books. Yet while the fast-developing commercial book trade produced new books in great quantity, significantly, older books were also sustained, recycled and reused.
Although there is awareness within medieval scholarship of recycled manuscript components, such as flyleaves, no sustained study has yet been undertaken into recycled and reused materials in fifteenth-century manuscripts, or into book production’s practices and processes of reuse. In addition, previous book history studies of recycling have focused on the book material reuse that followed the Dissolution. By contrast, this study offers a broader exploration of sustainable practices in fifteenth-century manuscript culture, as well as in-depth analysis of manuscript examples, to argue that book producers made and reused books in sustainable ways.
The introduction outlines key concepts and relevant scholarship, such as studies that follow the material turn, and ecocriticism. The four chapters that follow address sustainability from different angles, focusing primarily on the evidence both in and written on books themselves. Chapter 1 explores the craftsmanship of parchment- making through contemporary recipes and physical evidence in manuscripts. Chapter 2 presents case studies of parchment reused sustainably in books, as off-cuts, quire guards, flyleaves, pastedowns, limp covers, and palimpsests. Chapter 3 surveys spaces reclaimed in books for opportunistic mark-making, in the form of doodles, jottings, and short verses. Chapter 4 presents three surveys of second-hand books and the inscriptions written onto their leaves. A conclusion draws together the findings.
This thesis augments and nuances current scholarship by arguing that fifteenth-century reuse and recycling of book materials were customary aspects of book production and symptomatic of more widespread sustainability in manuscript culture.

Advisor: Wakelin, D
From Hispalis to Ishbiliyya: the ancient port of Seville, from the Roman Empire to the end of the Islamic period (45 BC - AD 1248)

This Thesis focuses on the history and development of the topography, layout, and facilities of the ancient port of Seville, which is located in the lower Guadalquivir River Basin. From a maritime archaeology perspective, it combines terrestrial and maritime archaeological evidence, literary and epigraphic material, as well as palaeo-geomorphological and palaeo-environmental studies. This Thesis is a longue durée or diachronic study ranging between the 1st century BC and the 13th century AD. The Thesis is divided into three main historical periods, and in addition to the port itself, studies the palaeo-geomorphology and palaeo-hydrology of the Guadalquivir River, as well as of the palaeo-climatology of the region during each of these eras.
The first third of the Thesis examines the port of Hispalis during the Roman era. By considering the natural hydrography of the river and the meander of Hispalis, the Thesis proposes a model for the distribution of harbour facilities and their development through the Roman period. Building on this, it becomes possible to assess the extent and scale of these, as well as of the maritime commerce that the Roman port sustained.
The second third of the Thesis focuses on the Late Antique period. Despite the lack of direct archaeological evidence for the port in this era, the Thesis suggests that there was a decline but continuity in the commercial activities in direct connection with the Mediterranean maritime networks. This section also examines the historical events that occurred in Hispalis from the maritime archaeology perspective, arguing that the port was at the core of all these historical episodes because of its geopolitical and strategic importance.
The last third of the Thesis concentrates on the study of the port during the Islamic period. By understanding the extreme changes that occurred in the hydrography and geomorphology of the river in this epoch, the Thesis deciphers the process that led to the progressive siltation of the ancient channel of the river. The study of the archaeological material from the 1981 Plaza Nueva excavation, in combination with other proxies, allows a chronology to be proposed for the demise and subsequent disappearance of the ancient port. The transformation of the meander of the river resulted in the relocation and construction of a new port, which had a prominent role in the maritime history of the world during the centuries that followed.

Keywords: Port
Harbour
Late Antiquity
Islamic
Roman
Seville
Guadalquivir River
Al-Andalus
Advisor: Mango, M
Robinson, D
A qualitative study of teachers’ perspectives regarding the integration of home-school link applications into their practice.

Focus:
As the importance of engaging parents is widely acknowledged by schools and the steep rise in use of home-school link applications within schools, there is a need for research to begin to focus on these home-school link applications. Teachers are now responsible for integrating these applications into their practice. This study focuses of providing these teachers with a voice as they attempt to integrate homes-school link applications into their practice. Furthermore, it to consider the perspectives of teachers who are yet to implement a home-school link application in to hear to aspirations, expectations and concerns regarding the integration these applications.
Research design:
Qualitative semi-structured interviews were selected as the data collection method to answer the proposed research question. 17 interviews were undertaken including a mixture of teacher and SLT members and from a range of schools and year groups. These participants represent two distinct groups, those who were yet to implement a HSLA and those who had already implemented the application. Following the interviews, the data was coded using inductive and deductive coding.
Findings:
This study argues, teachers view the Senior Leadership Team's vision and ethos as a vital factor in the successful integration of a home-school link applications. Furthermore, pressure from the Senior Leadership Team, is the largest pressure teachers experience while using HSLA although those who are yet to implement a home-school link application consider time pressures as a key factor when integrating home-school link application. When teachers consider how they use home-school link applications in their practice, they consistently believed viewing other teacher’s post leads to them developing their practice.

Advisor: Robson, J
Epidemiology of long-term health outcomes and the response of knee cartilage to bowling biomechanics in elite cricketers

Background: Sport is an important form of physical activity and has been shown to have many health benefits. Cricket is a popular sport in the UK and internationally, but little is known about the short- and long-term health effects of a career in elite cricket. This thesis will describe the long-term physical and mental health of former elite cricketers compared to the general population, explore the association of cricket-related factors with their long-term musculoskeletal health, and evaluate the effect of elite fast bowling on the knee cartilage of current elite fast bowlers.
Methods: A sample of male former elite English cricketers was recruited for a cross-sectional retrospective questionnaire study of the long-term health of former cricketers. Chronic conditions in the former cricketers were compared to a general population sample and cricket-related factors including playing position and injury were tested for their association with musculoskeletal outcomes. A sample of male and female current elite fast bowlers was recruited for a biomechanics and cross-sectional MRI study of their knee cartilage. The knee cartilage was compared between the bowlers’ trailing leg versus the higher loaded leading leg, and was tested for associations with bowling kinematic and kinetic parameters.
Results: The former elite cricketers reported a higher prevalence of osteoarthritis, total hip replacement, total knee replacement, anxiety and depression than the general population sample and a lower prevalence of heart problems than the general population. Injury was the only cricket-related factor analysed to be associated with the musculoskeletal outcomes of joint pain, osteoarthritis, and joint replacement in the former cricketers. The current elite fast bowlers did not demonstrate a statistically significant difference between the compartmental knee cartilage volume in the trailing leg versus the higher loaded leading leg. A clinically significantly greater cartilage volume was found in the lateral tibia compartment of the leading leg than the trailing leg. The lateral tibia cartilage of the leading leg was also found to be significantly associated with the knee flexion/extension moment and abduction/adduction moment at leading leg strike of the bowling action.
Conclusions: This research identifies risks and benefits of a career in elite cricket, providing targets for prevention and resource provision for chronic conditions in current cricketers and cricketers transitioning out of elite cricket. These results also suggest that cartilage may be sensitive to bowling loads in current elite fast bowlers, providing evidence that increased physical activity and loading is associated with increased cartilage volume.

Keywords: Epidemiology
MRI
Osteoarthritis
Biomechanics
Knee
Sport
Cricket
Advisor: Leyland, KM
Newton, J
Arden, N
Task-oriented learning of structured probability distributions

Machine learning models automatically learn from historical data to predict unseen events. Such events are often represented as complex multi-dimensional structures. In many cases there is high uncertainty in the prediction process. Research has developed probabilistic models to capture distributions of complex objects, but their learning objective is often agnostic of the evaluation loss. In this thesis, we address the aforementioned defficiency by designing probabilistic methods for structured object prediction that take into account the task at hand.
First, we consider that the task at hand is explicitly known, but there is ambiguity in the prediction due to an unobserved (latent) variable. We develop a framework for latent structured output prediction that unifies existing empirical risk minimisation methods. We empirically demonstrate that for large and ambiguous latent spaces, performing prediction by minimising the uncertainty in the latent variable provides more accurate results.
Empirical risk minimisation methods predict only a pointwise estimate of the output, however there can be uncertainty on the output value itself. To tackle this deficiency, we introduce a novel type of model to perform probabilistic structured output prediction. Our training objective minimises a dissimilarity coefficient between the data distribution and the model's distribution. This coefficient is defined according to a loss of choice, thereby our objective can be tailored to the task loss. We empirically demonstrate the ability of our model to capture distributions over complex objects.
Finally, we tackle a setting where the task loss is implicitly expressed. Specifically, we consider the case of grouped observations. We propose a new model for learning a representation of the data that decomposes according to the semantics behind this grouping, while allowing efficient test-time inference. We experimentally demonstrate that our model learns a disentangled and controllable representation, leverages grouping information when available, and generalises to unseen observations.

Advisor: Kumar, M
Nowozin, S
Developing biophysical and structural methods for characterisation of small molecule modulators of K2P potassium channels

Biophysical techniques are widely used to determine the structure, function and ligand binding properties of a protein. However, their application to membrane proteins has been limited due to the difficulty of obtaining sufficient purified sample.
In this work, I use such methods to examine the thermostability and ligand binding properties of TREKs, two members of the family of tandem pore domain K+ channels important for the regulation of cellular excitability. Structures of TREK1 and TREK2 are available and thus when combined with such approaches may help guide the design of better ligands.
I first successfully optimised the DSF method using the CPM dye for the detection of TREK ligands and found this to be a viable approach. In addition, direct binding detection methods such as SPR, ITC and Biolayer Interferometry were also investigated.
A test case of 351 compounds derived from an FDA-approved pharmaceutical agent library were then screened against a range of K2P channels using the CPM assay. Several compounds were identified that appeared to thermostabilize the TREKs. These initial hits were further assessed using label-free DSF and functional studies on channel activity. Two compounds, cilnidipine and rimonabant were identified as a novel inhibitor and activator of TREK2 and TREK1 respectively. The findings are significant for the development of potent and selective binders for the TREKs and other membrane proteins, as they identify a viable workflow for identification of binders using biophysical methods.

Advisor: Carpenter, L
Tucker, S
Cawkill, D