VictorJuiz/thesis huggingface dataset:
Mental symptoms in the Akkadian diagnostic handbook: a study of patterns in the description of depression, anxiety, and madness

This study is concerned with reconstructing patterns in the description of mental distress, disturbance, and disorder in diagnostic descriptions from medical texts recorded in Akkadian from the first millennium BCE. In the service of this aim, the study also offers a theoretical framework for the approach to mental disorder in Akkadian medical diagnostic texts. With a few exceptions, previous studies of mental disorder in the Akkadian medical tradition have relied in large part on the method of retrospective diagnosis, which, for reasons to be set out, can be a problematic methodology. This study offers an alternative framework that defines objects of inquiry that can be meaningfully applied to the Akkadian sources. This framework incorporates principles from the fields of the history, philosophy, and anthropology of medicine and takes into account the type of information recorded in the Akkadian medical diagnostic texts. Organised around three core symptoms of ašuštu "Depression", ḫ&imacr;p libbi "Heartbreak", and ṭ&emacr;mu šanû/nak&amacr;ru "The mind alters/changes", this study investigates the occurrences of these terms and expressions in the Diagnostic Handbook to determine an initial repertoire of symptoms that recur with these. These recurring symptoms are taken to reflect patterns in the description of mental symptoms and are supplemented with medical therapeutic texts, especially those for ghost- and witchcraft-induced illness. Mental symptoms organised with the core symptoms of this study are primarily expressed through the paradigms of change and somatisation. The recurrence of these patterns reveals native paradigms in the expression of mental symptoms that can be explained with intercultural parallels and that begin to reveal the ways in which disorders with a strong cognitive and affective component were made comprehensible in a clinical context.

Advisor: Dahl, J
Investigating mechanisms of transcriptional interference in Schizosaccharomyces pombe

Eukaryotic cells transcribe a vast array of non-coding RNAs, most of which have not been assigned a functional role. The work presented here reveals a novel mechanism of transcriptional repression that is mediated by the non-coding RNA prt (pho1-repressing transcript). The prt transcript is shown to recruit a histone deacetylase, Clr3, to repress pho1. This gene encodes a secreted acid phosphatase essential for phosphate acquisition in fission yeast. In the presence of phosphate, prt is produced from an upstream promoter and leads to silencing of pho1. Thus far, this has been explained by prt transcription leading to deposition of repressive methylation over the locus. However, this explanation is known to be incomplete since deletion of the only known histone methyltransferase does not lead to pho1 induction comparable to deletion of the prt promoter. This suggests that another mechanism must be involved in mediating transcriptional interference via non-coding transcription.
In the present study the putative ncRNA-binding protein Seb1, together with the chromatin modifying complex SHREC, is demonstrated to associate with prt to elicit silencing of pho1 by a mechanism that is independent of H3K9 methylation and instead relies on deacetylase activity provided by the Clr3 component of SHREC. These data reveal a previously uncharacterised layer of ncRNA-mediated gene regulation and provide important conceptual advances in understanding the mechanisms governing the phenomenon known as transcriptional interference.

Advisor: Vasiljeva, L
An urban geography of the Roman world, 100 B.C. To A.D. 300

Although there have been numerous studies of individual cities or groups of cities, there has never been a study of the urbanism of the Roman world as a whole, meaning that we have been poorly informed not only about the number of cities and how they were distributed and changed over time, but also about their sizes and populations, monumentality, and civic status. This thesis provides a new account of the urbanism of the Roman world between 100 B.C. and A.D. 300. To do so, it draws on a combination of textual sources and archaeological material to provide a new catalogue of cities, calculates new estimates of their areas and uses a range of population densities to estimate their populations, and brings together available information about their monumentality and civic status for the first time. This evidence demonstrates that, although there were relatively few cities, many had considerable sizes and populations, substantial amounts of monumentality, and held various kinds of civic status. This indicates that there was significant economic growth in this period, including both extensive and intensive economic growth, which resulted from an influx of wealth through conquest and the intrinsic changes that came with Roman rule (including the expansion of urbanism). This evidence also suggests that there was a system that was characterised by areas of intense urban demand, which were met through an efficient system for the extraction of necessity and luxury goods from immediate hinterlands and an effective system for bringing these items from further afield. The disruption of these links seems to have put this system under considerable strain towards the end of this period and may have been sufficient to cause its ultimate collapse. This appears to have been in marked contrast to the medieval and early modern periods, when urbanism was more able to respond to changes in supply and demand.

Keywords: SETTLEMENT SCALING THEORY
ROMAN
NUMBER
POPULATION DENSITY
SEAS
URBAN POPULATION
RIVERS
GEOGRAPHY
ECONOMIC GROWTH
TOTAL POPULATION
ARCHAEOLOGY
POPULATION
URBAN GEOGRAPHY
CHANGE OVER TIME
ANCIENT HISTORY
CLASSICAL ARCHAEOLOGY
DISTRIBUTION
URBAN HIERARCHY
HINTERLANDS
ECONOMIC INTEGRATION
THE RANK-SIZE RULE
SETTLEMENT HIERARCHY
CONNECTIVITY
RURAL POPULATION
HISTORY
URBANIZATION RATE
TOWNS
URBAN CENTRES
ECONOMICS
CENTRAL PLACE THEORY
MONUMENTALITY
COLONIA
CIVIC STATUS
URBAN
URBANISM
URBAN THEORY
ROADS
URBANIZATION
LONGUE DURÉE
COLONIAE
CLASSICS
GREEK
MUNICIPIAE
MUNICIPIA
CITIES
Advisor: Wilson, A
A study of the square kilometre array low-frequency aperture array

This thesis primarily comprises simulations of SKA1-Low, the low-frequency aperture array of the Square Kilometre Array (SKA) radio telescope. Simulations assess how different design specifications would affect the telescope's performance and ability to undertake one of its key science projects: observing the Epoch of Reionisation (EoR). The simulations are based on the previous baseline design of &Tilde; 260 000 dipole antennas in 1024 stations of 256 antennas each.
It is found that errors in the gain and phase of signals at each antenna can significantly affect observations, with the greatest impact at the lowest frequencies. The EoR signal will be detectable at limited redshifts with gain errors of 10% and phase errors of 6 degrees, however to ensure the systematic noise contribution from these errors is always weaker than the EoR signal between z &Tilde; 10 − 21 and spherical harmonic multipole coefficients l &Tilde; 102 − 104 , the gain and phase errors may need to be less than or equal to approximately 5 × 10−6 and less than or equal to approximately 3 × 10−4 degrees, respectively.
Alternative telescope layouts to the SKA1-Low baseline design of 1024 stations containing 256 antennas each are evaluated. Some telescope models which share antennas between stations, allowing stations to be formed in a flexible manner, are found to provide superior thermal noise sensitivity than the current design, but suffer greater detrimental effects from gain and phase errors when imaging.
The implementation of the digital signal processing of a station beamformer is also discussed. Calculations show that five or nine Field Programmable Gate Arrays (FPGAs) with specifications comparable to the Virtex UltraScale+ XCVU13P could be used to beamform a single 256-antenna SKA1-Low station, depending on the utilisation rate of the FPGAs and the number of channels required.

Keywords: SKA
Beamformer
Square Kilometer Array
Beam former
Beamforming
Square Kilometre Array
Phased array
Aperture array
Interferometry
Beam forming
Pain characterization in knee osteoarthritis

Osteoarthritis (OA) is the most common form of arthritis in the world, and it has been estimated that about one tenth of the world’s population, aged over 60, have symptoms that can be attributed to OA. Despite the size of the global impact of OA, there is a significant unmet need for effective treatments. Knee replacement surgery is commonly used in patients with moderate to severe knee OA, in order to reduce pain. However, 10-34% of patients report an unfavourable long-term outcome with persistent pain after surgery.
The neural mechanisms for the generation of pain in knee OA are not fully understood. Previous work has shown that around 20% of patients have features of neuropathic pain, and that the underlying mechanism for this may be through central sensitisation. This mechanism-based understanding of pain is important in order to aid targeted intervention, and it may be that this patient group is more likely to have an adverse outcome following surgery.
This thesis uses a combination of methods to investigate the neural mechanisms underlying pain experienced by patients with knee OA, across the full spectrum of disease severity. Quantitative sensory testing (QST) was initially used in a community-based cohort to show that pain sensitisation can be detected in early disease, and also contributes to the observed discordance between radiographic structural and symptomatic disease.
The clinical relevance of neuropathic pain was then investigated in patients with knee OA, who were awaiting knee replacement surgery. Prior to surgery patients with neuropathic pain had increased sensitivity to experimental pain, as well as higher symptom severity and psychological distress. Functional magnetic resonance imaging (fMRI) was then used to confirm that these features were also associated with central sensitisation in the form of increased descending facilitation as well as reduced descending inhibition prior to surgery. The presence of neuropathic pain prior to surgery was associated with statistically and clinically significantly worse outcome following surgery, compared to those with purely nociceptive pain in the absence of any significant structural differences between the two groups.
Taken together, this mechanism-based understanding of the pain provides an opportunity for targeted therapy prior to surgery, which may enhance outcome following surgery.

Advisor: Tracey, I
Price, A
Javaid, K
Mortality prediction and acuity assessment in critical care

Accurate mortality prediction in intensive care units (ICUs) allows for the risk adjustment of study populations, aids in patient care and provides a method for benchmarking overall hospital and ICU performance. ICU risk-adjustment models are primarily comprised of an integer severity of illness score which increases with increasing patient risk of mortality. First published in the 1980s, the improvements to these scores primarily consisted of increasing the dimensionality of the model, and hence also increasing their complexity. This thesis aims to improve upon these models. First, the field is surveyed and the major models for risk-adjusting critically ill patient cohorts are identified including the acute physiology score (APS) and the simplified acute physiology score (SAPS).
A key component of model performance is data preprocessing. The effect of preprocessing ICU data is quantified on a dataset of 8,000 ICU patients, and it is shown that after preprocessing to remove extreme values a logistic regression (LR) model performed competitively (AUROC of 0.8633) with the more complex machine learning model; a support vector machine (SVM) which had an AUROC of 0.8653. For validation, model development was repeated in a larger database containing over 80,000 patients admitted to 89 ICUs in the United States. Results were similar (AUROC of 0.8895 for the LR vs 0.8917 for the SVM) but showed the performance gain when using automated outlier rejection is less pronounced in well quality controlled datasets (0.8883 for LR without rejection). It is hypothesised from this that simpler models can perform competitively with more complicated models, while having a greatly reduced burden of data collection. A severity score is developed on the large multi-center database using a Genetic Algorithm and Particle Swarm Optimisation. The severity score, named the Oxford Acute Severity of Illness Score (OASIS), is shown to outperform the APS III (AUROC 0.837 vs 0.822) and perform competitively with APACHE IV when used as a covariate in a regression model (AUROC 0.868 vs 0.881). The severity score requires only 10 variables (58% as many as APS III), reducing the burden of quality control and data collection. These variables are routinely collected in critical care by continuous monitors and do not include comorbidities, diagnosis or laboratory measurements. The severity score is then externally evaluated in an American hospital and shown to discriminate well (AUROC 0.790 vs. 0.782 for the APS III) with excellent calibration. Finally, the severity score was evaluated in an English hospital and compared to other severity scores. OASIS again had excellent calibration and discrimination (AUROC 0.776 vs 0.750 for APS III) whilst requiring a much smaller number of variables. OASIS has many applications, including both simplifying data collection for studies and improving the risk assessment therein.

Keywords: medical informatics
mortality prediction
severity of illness
critical care
intensive care unit
machine learning
Advisor: Clifford, G
Kramer, A
Between being and nothingness : sin in Jean-Paul Sartre

This thesis argues that Jean-Paul Sartre’s early philosophy retained a recognizable inheritance from the Christian doctrine of original sin. On the standard reading, Sartre’s most fundamental and attractive idea —the idea that brought him his reputation as ‘the philosopher of his generation’ —is freedom. But, as Sarah Richmond notes, Sartre’s interest in phenomenology ‘co-existed with and was an instrument for his wish to demonstrate the existence of human freedom, and his sense that the way to do this was by establishing an essential connection of consciousness with nothingness.’ Taking Being and Nothingness as its primary exegetical focus, this thesis argues that the early, anti-humanist Sartre retained a recognizable descendant of the Christian doctrine of original sin in his concept of le néant.
Previous scholars have noted the resemblance between Sartre’s and Augustine’s ontology: to name but one shared theme, both thinkers describe the human as the being through which nothingness enters the world. But no in-depth examination of this ‘resemblance’ has been made. Using historical, exegetical, and conceptual methods, my research demonstrates that Sartre’s intellectual formation prior to his discovery of phenomenology included theological elements which are often overlooked by Sartre scholars – especially in the English-speaking philosophical community, where his phenomenological influences receive greater attention.
The thesis therefore (i) outlines the French Augustinianisms by which, I argue, Sartre’s account of the human as ‘between being and nothingness’ was informed; in order to (ii) undertake a close reading of Being and Nothingness, which shows (a) that the psychological, epistemological, and ethical consequences of Sartre’s le néant closely resemble the consequences of its theological predecessor and (b) that his account of freedom can be read as an anti-theodicy; and finally (iii) to argue constructively that Sartre is a useful resource for contemporary hamartiology. In doing so it contributes to both Sartre scholarship and the theological sub-discipline of modern doctrine.

Keywords: nothingness
sin
existentialism
phenomenology of religion
Sartre
Advisor: Anderson, PS
Pattison, G
Subgroups of quantum groups

In this thesis we investigate the notion of a subgroup of a quantum group. We suggest a general definition, which takes into account the work that has been done for quantum homogeneous spaces. We further restrict our attention to reductive subgroups, where some faithful flatness conditions apply. We give examples of quantum subgroups, some known and some new, which are all part of the family of spherical subgroups. The ultimate goal would be to quantize all spherical subgroups. Furthermore, we proceed with a categorical approach to the problem of finding quantum subgroups. We translate all existing results into the language of module and monoidal categories and give another characterization of the notion of a quantum subgroup.

Advisor: Kremnizer, K
Preoperative symptom burden in the knee replacement population - the role of the Oxford knee score

The Oxford Knee Score (OKS) represents a validated Patient Reported Outcome Score (PROM), routinely utilised following knee replacement (TKR). Healthcare commissioners have proposed its application as a threshold criterion to define eligibility for TKR, despite an absence of supporting evidence. This thesis explores the role of preoperative OKS, using local and national PROMs data, as a measure of symptom burden and highlights potential issues as a threshold criterion tool.
Examination of the preoperative OKS profile in three orthopaedic centres showed a normal distribution profile, and wide-ranging preoperative symptom burden. Some patients appeared to proceed to TKR with a seemingly minimal symptom burden, raising question about TKR selection criteria. Further analysis of national PROMs data confirmed wide variability in preoperative symptom burden prior to TKR to be common practice. Some variation existed between centres and individual surgeons, but patient level factors were a greater contributor, suggesting poor selection criteria may not be to blame. Case note analysis of a TKR cohort from a single centre identified that those with a high preoperative OKS still exhibited a significant symptom burden, remaining clinically justified for TKR. An appropriate consultation process was evident, rejecting inappropriate selection criteria as an explanation. Analysis of linked national pre- and postoperative OKS data showed that patients with highest preoperative OKS had best overall outcomes following TKR, despite minimal change in OKS. Preoperative OKS&LT;16 was associated with worse outcomes and minimal further benefit as OKS decreased.
Preoperative OKS alone may not encapsulate the true clinical indications for TKR. Utilisation of OKS-based thresholds, may exclude equally eligible patients, risking greater inequity and variation in TKR practice. Restricting TKR to those with the worst preoperative OKS may compromise subsequent outcomes. Its role as an indicator of preoperative symptom burden and potential eligibility for TKR should be used with extreme caution.

Keywords: preoperative
patient reported outcome measures
knee replacement
symptoms
Advisor: Beard, D
Price, A
A metamaterial waveguide incorporating electric coupling for contactless data and power transfer

The background to this study is an effort to exploit a magneto-inductive waveguide (MIW) for near-field contactless data and power transfer applications. MIWs are almost purely magnetically coupled metamaterial waveguides whose coupling strengths can never exceed the limit of conservation of magnetic flux.
This study raises the hypothesis that the coupling strength limit of MIWs can be overcome by incorporating additional electric coupling into the structures; therefore, more strongly coupled metamaterial waveguides can be built and serve as contactless near-field communication channels with wider passbands and lower attenuations. The hypothesis was tested in this study by investigating a new variant of the metamaterial waveguide: the Capacitor-Connected Grid (CCG), in which additional electric coupling is introduced by connecting coupling capacitors over inter-element gaps between conventional MIW metallic loop resonators.
The study investigates the dispersion and attenuation characteristics of both one- (1-D) and two-dimensional (2-D) CCG devices, leading to a discussion on their potential uses in ultra- wideband (UWB) contactless near-field data transfer applications. A mixed coupling model calculating inter-element mixed coupling coefficients for arbitrarily configured CCG waveguides is derived based on the state-of-the-art, taking into account the shift of resonant frequency caused by electric coupling. The study also looks at terminal optimizations for 1-D CCG with a view to maximizing power transfer efficiency.
A highlight of this study is that a 1-D CCG demonstration device in theory should be able to achieve 192.4% fractional bandwidth, which exceeds the 20% requirement of a UWB channel by a factor of 9.6, and is only 1/10 of the minimum attenuation of an equivalent-sized MIW device. Similar communication characteristics have also been found at selected transmission paths on a 2-D CCG demonstration structure.
The results of this study on CCG waveguides verify the hypothesis that incorporating additional electric coupling into an almost purely magnetically coupled waveguide can improve its coupling strength and thereby achieve a communication channel with larger bandwidths and lower losses.

Keywords: electro-inductive wave
Capacitor-connected grids
electric coupling
data and power transfer channels
magneto-inductive wave
magnetic coupling
Advisor: Stevens, C
Edwards, D
Spatio-temporal image analysis with application to cancer

Cancer is one of the main causes of premature death worldwide, leading to almost one in three deaths in the UK. Medical imaging plays a fundamental role in the diagnosis and treatment of cancer patients. This thesis focuses on the assessment of early stage clinical trials of novel cancer treatment, which is performed based on dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and perfusion computed tomography (pCT). From a clinical viewpoint, the objectives are tumour microenvironment characterisation, which involves the assessment of tumour perfusion and vascularity, and early prediction of response to treatment. From a methodological viewpoint, this thesis is at the interface between pharmacokinetic (PK) modelling and image registration for dynamic images. Major challenges addressed in this work are PK model selection and arterial input function derivation, as well as intrasequence motion correction for dynamic imaging data. Registration of dynamic imaging data is a particularly challenging problem due to the variety of motion types that appear in these data: bulk patient motion, periodic motion due to breathing, and random motion of small features due to peristalsis. Moreover, contrast-enhanced modalities such as DCE-MRI and pCT pose additional challenges as image intensities change due to contrast inflow. The key contributions of this thesis are the derivation of patient-specific arterial input functions from pCT data, which are employed for performing PK modelling of contemporaneous DCE-MRI scans of the same patients, and the development of an MRF-based discrete optimisation framework for the nonrigid registration of dynamic sequences. While the former was applied on DCE-MRI and pCT images from an early stage trial of new treatment for colorectal cancer, the latter was employed for the motion correction of DCE-MRI images from the same trial. Additionally, this new registration framework was applied to dynamic CT images of the lung to demonstrate the advantage of temporal regularisation in an application where there is periodic motion (i.e. breathing). Experimental validation shows that the proposed registration framework improves over state-of-the-art methods based on continuous optimisation in terms of registration accuracy and computational complexity.

Advisor: Schnabel, J
Chappell, M