VictorJuiz/thesis huggingface dataset:
Identifying and comparing meteorological and geographical influences on high resolution climate signals in the oxygen isotope values of different environmental archives

This thesis explores how δ18O values in horse hair relate to local meteorological observations; how Greenland ice core records relate to European terrestrial climate records; and how atmospheric changes are reflected in terrestrial and biological records. Bringing together analysis of increasingly complex palaeoenvironmental proxies, δ18O measurements within atmospheric, terrestrial and biological systems are critically assessed across geographical transitions, ultimately leading to greater understanding of the utilisation of oxygen isotope data for seasonal climate analysis. Horse hair sampling and δ18O analysis were conducted on horse hair from: the Icelandic Food and Veterinary Authority (MAST) in Selfoss, Iceland; the Thordale Stud in the Shetland Islands, United Kingdom; the Exmoor Pony Centre (EPC) in Somerset, UK; and the Pigeon House Equestrian centre in Oxfordshire, UK. The North Greenland Ice Core (NGRIP2) was sampled and analysed for δ18O, and compared to a master tree ring dataset of compiled δ18O values in the UK. The results confirm that rainfall quantity and continental effects dominate both the horse hair and ice core δ18O records. The growth rates of the hair were seen to decrease with an increase in latitude; and comparison between horse hair δ18O and meteorological variables clearly indicates a rainfall influence. Comparison between the ice core δ18O and historical coastal temperature reconstruction shows a similar gradient to what is seen in modern temperature records. The comparison between tree ring isotopes can be interpreted as showing a similar amplitude to the historic temperatures, but with a slight dampening in regards to lower peaks values. Comparison of the tree ring and ice core values indicated a significant negative correlation, with smaller amplitude changes within the tree ring δ18O results. Wavelet analysis suggested a common influence from teleconnections at several timescales in both the tree ring and ice core datasets, including the El Niño Southern Oscillation and the North Atlantic Oscillation. This study demonstrates that geographical and meteorological influences are similarly reflected within palaeoenvironmental proxies of increasing complexities. It also identifies periods of common influence from climate drivers and provides detail of the greatest effects on isotopic variation in the UK, Iceland and Greenland.

Keywords: palaeoclimate
oxygen
Greenland
oscillation
proxy
Exmoor
isotope
tree ring
climate variability
horse hair
ice core
Iceland
United Kingdom
Advisor: Ramsey, C
McConnell, J
Biologic therapies and the need for hip and knee replacement amongst patients with rheumatoid arthritis: A population-based epidemiology study using electronic medical records and registry data

Registry reports indicate over 200,000 hip or knee replacements are performed annually in England, Wales and Northern Ireland, with approximately 1-2% carried out for inflammatory conditions such as rheumatoid arthritis (RA). The aim of this DPhil was to estimate the impact of biologic therapies on the need for major joint replacement amongst RA patients using observational health data.
An interrupted time-series analysis was used to estimate the impact of NICE approval of biologics on population-level temporal trends of total hip replacement (THR) and total knee replacement (TKR) amongst RA patients in England and Wales. Similar analyses were repeated for Denmark and Ontario. Overall, these studies indicated a decrease in TKR but not THR for RA patients following the introduction of biologics. When the rates in non-RA patients were taken into account (in Denmark and Ontario only), there was an inferred reduction in both THR and TKR for RA patients within the biologic era. There was a lack of guidance on sample size planning for such analyses, so a simulation study was also conducted to estimate power in various time-series scenarios.
A patient-level analysis was then conducted using UK registry data, applying various novel methodologies to account for the inherent problem of confounding by indication. The results suggested no significant impact of biologics on rates of joint replacement, although in age-stratified analyses biologics was associated with a 40% reduction in THR rates amongst patients ≥60 years old.
To conclude, a reduction is observed in population-level rates of THR and TKR amongst RA patients (compared to non-RA patients) following the introduction of biologics. Patient-level analyses confirmed a favourable impact on THR rates amongst older patients, but otherwise no significant associations. More patient-level analyses are required to confirm and/or further elucidate the impact of biologic therapies on the need for joint replacement in RA.

Keywords: Health Services Research
Rheumatoid Arthritis
Joint Replacement
Interrupted Time Series
Musculoskeletal
TNFi therapy
Hip
Biologics
Knee
Epidemiology
Advisor: Prieto-Alhambra, D
Judge, A
Ali, M
Augmentation strategies in rotator cuff repair

Rotator cuff repair surgery is commonly performed for symptomatic tears failing to resolve with conservative measures. This thesis investigated the healing rate following rotator cuff repair, and the influence of age and tear size. Patient tissue responses to 2 commercially available biological patches used in cuff repair were subsequently investigated. Finally, safety and efficacy of 2 novel biodegradable polymeric scaffolds to repair an ovine tendon defect, was investigated.
The overall rate of healing following rotator cuff repair was 58% at 1 year. Healing was influenced by age and tear size, however age was the predominant prognostic factor. A predictive model for healing was generated, demonstrating likelihood of healing as low as 17%. Patient supraspinatus tendon biopsies demonstrated an adverse response to dermal allograft and xenograft patches currently used in cuff repair augmentation, whereby significant extracellular matrix disruption was observed. One patient receiving the xenograft experienced a significant adverse immune response, characterised by extensive infiltration of pro-inflammatory cells. A novel biodegradable polydioxanone / polycaprolactone patch was investigated in an ovine tendon injury model. At 3 months, this patch induced tendon healing, without adverse systemic or tissue responses. Significant fibroblast infiltration and neovascularisation was observed within the scaffold. A biodegradable polydioxanone multifilament suture was also developed. This novel suture demonstrated bioactivity, inducing tendon healing without adverse systemic or tissue responses. Fibroblast infiltration and neovascularisation was observed when compared to monofilament polydioxanone control suture.
Healing following cuff repair remains a challenge. Current biological patches used to augment repair are not supported by clinical efficacy trials, and demonstrated a deleterious effect on the native tendon. Novel synthetic implants tailored for tendon repair successfully induced tendon healing in an ovine model. Future work will explore the safety and clinical efficacy of these implants for rotator cuff repair augmentation in humans.

Keywords: Scaffold
Supraspinatus
Electrospun
Tendon
Rotator cuff
Advisor: Carr, A
Dakin, S
Snelling, S
Integrating logarithmic wide dynamic range CMOS image sensors

Complementary Metal Oxide Semiconductor (CMOS) image sensors are widely used in many applications such as consumer electronics, automotive and security. One of the key requirements in today’s imaging applications is the ability to capture natural scenes faithfully; a feature known as wide dynamic range (WDR). Current digital image sensors have a linear response that results in saturation and loss of details. Conventional CMOS image sensors with a logarithmic response attempt to address the limited dynamic range of the linear digital image sensors by exploiting the subthreshold operation of a transistor in a pixel. This results in CMOS pixels that are able to capture light intensities of more than six decades (120 dB). However, the approach comes at the expense of high fixed pattern noise (FPN) and slow response.
The work presented in this thesis describes a five all nMOS transistor (5T) pixel architecture that aims to achieve wide dynamic range. This feature is obtained using a time-varying reference voltage that is applied to one of the transistors of the pixel. The reference voltage varies in a logarithmic fashion in order to modulate the effective integration time of the pixel. This allows the pixel to avoid saturation; hence extending the dynamic range. In addition, the slope of the reference voltage that can be adjusted means the pixel response is adaptive and can be more robust towards temporal noise. To have a well-controlled pixel response, the pixel non-ideal effects such as source follower gain, body effect and subthreshold effect are characterised and included as an improved model to the reference voltage.
Measurement results from fabricated chips using UMC 180 nm technology are presented and analysed. A dynamic range of 80 dB with a logarithmic response of 600 mV/decade has been achieved. This is a significant improvement in comparison to that of conventional logarithmic pixel response (60 mV/decade). An analysis of the effect of chip variations that causes FPN has been conducted and correction methods that can reduce the illumination error to less than 2% have been proposed. In addition, the first experimental study comparing different dynamic range extension methods has been performed. In the study, a method to control the response of a WDR approach using a stepped voltage that has achieved a dynamic range of up to 120 dB is also presented. The result of the study leads to a modification to the reference voltage that allows an implementation of an analogue circuit to generate the reference voltage.

Keywords: wide dynamic range
CIS
ADAS
WDR
CMOS
image sensors
Advisor: Collins, S
Choubey, B
Distributed computing of large-scale singular value decompositions

Big data projects increasingly make use of networks of heterogeneous computational resources for scientific computing purposes. To meet the requirements of big data applications and harness the power of modern computing architectures, novel highly parallel algorithms for numerical linear algebra computations are needed that rely on as little node synchronicity and data communication as possible. Distributed algorithms are particularly important in situations where the data itself is naturally distributed across several or many servers, or where the data collection is decentralised. The singular value decomposition (SVD) is one of the fundamental matrix decompositions and a cornerstone of numerical linear algebra. The computation of leading part SVDs plays an essential role in a variety of models and algorithms and dominates their computational costs.
In this thesis, we analyse a distributed algorithm for leading part SVD computations of large-scale matrices. The algorithm is well adapted to cloud computing or computer networks, as it satisfies the loose coupling requirement (low synchronicity, low communication overhead). The algorithm was first introduced by R. Hauser and D. Goodman and was first published in the latter's DPhil thesis. We will give the geometric intuition behind the algorithm and introduce it formally, but the main part of this thesis will focus on the analysis of the distributed SVD algorithm and its experimental validation.
Two different approaches will be proposed to investigate the convergence of the algorithm. The first approach utilizes classical matrix analysis tools, leading to an error bound. The second approach of analysis provides more geometric insights. The framework based on geometric observations gives bounds on the global aggregation of numerical approximation errors that occur in local computations. Bounds on these local errors are studied probabilistically under the assumption of random input.
Finally, we report numerical experiments, as well as the discussion of the variants of the algorithm. Applications in matrix optimisation problems, including low-rank matrix completion and sparse principal component analysis, will also be presented, and we use these to obtain an experimental validation of the algorithm under non-random input.

Advisor: Hauser, R
Immigration enforcement in the UK: how women experience detention, release and removal

In this dissertation I add nuance to our understanding of the experiences of immigration enforcement by exploring it in terms of the concept of 'dignity.' I draw on interviews with women who were either detained in an Immigration Removal Centre at the point I met them, or had been previously. I used interviews as the main method of data collection and my research spanned three research sites: Yarl’s Wood Removal Centre, The UK community, and Jamaica. I asked the participants about their experiences during and after detention, and for their own interpretations of the concept of dignity. I then used these definitions to make sense of their experiences. Resultingly, two key issues have been addressed in my research: how women subject to immigration control define dignity and the ways that immigration detention undermined it.
The experiences of women in this study were characterised by three key violations to their dignity. The first was vilification, where they were made to feel as though they were a threat to UK citizens, and that they were in some way dangerous and untrustworthy. The second was a lack of autonomy. All aspects of immigration enforcement restricted the women in this study from directing their own lives, from the uncertainty of indefinite detention, to their enforced dependence on the government or friends to survive in the community and finally when ultimately expelled from the country. The third was diminishment. Women felt lessened by the interaction between themselves and the Home Office through an apparent lack of care for their individual circumstances. Together, these factors undermined their sense of self worth, self esteem and self respect.
My work reinforces existing findings around immigration enforcement that are largely negative. I demonstrate throughout this dissertation that the self-worth of women in my study is deeply affected by their time in immigration detention and by what had happened to them after they left, and that these outcomes were linked to the way in which they were treated in relation to their sense of dignity.

Keywords: Women
Immigration Detention
Dignity
Imprisonment
Advisor: Bosworth, M
Farmers and conservation in Post-Brexit Britain; perceptions among the farming community on a changing subsidy regime and implications for on- farm conservation

The UK’s 2016 decision to leave the European Union signals a departure from the Common Agricultural Policy. The current proposals for a post-Brexit agricultural policy describe a shift towards a model that subsidises producers for implementing environmentally beneficial practices, rather than high production levels. Studies on existing forms of this subsidy model demonstrate mixed results in terms of improving biodiversity, and studies on farmer’s uptake of such schemes and their attitudes towards them are similarly mixed. These results have implications for policy design given that farmers are the implementers of such schemes. This study will draw on the existing literature as a context through which to investigate the perceptions of farmers and farm managers regarding the proposed agricultural policy landscape they will potentially inhabit. We conclude that ensuring that future schemes are both evidence- based and are planned and implemented with the help of people with a background in agriculture is paramount to their success.

Keywords: Brexit
Conservation
Farmers
Basic Payment Scheme
Common Agricultural Policy
Biodiversity
Agri-environment schemes
Agriculture
On-farm conservation
Agricultural policy
UK
Sustainability
Subsidy
DEFRA
The relationship between science and religion in Kang Youwei’s Confucianism

In this thesis I analyse the relationship between science and religion in a non-Western and specifically Chinese context through an examination of the writings of Kang Youwei (康有爲1858–1927), a prominent reformer and Confucian thinker of the period of transition from Imperial to Republican China. Described by his followers as the ‘Martin Luther of Confucianism’, Kang envisioned a central social role for Confucianism as a state religion, championing the restoration of a ‘pristine’ religion of Confucius (Kongjiao孔教), by both modelling it after Christian practices and revitalizing the ancient Chinese belief in Shangdi 上帝 (as a universal concept, equated with ‘God’). He upheld the unitary nature of the concept of jiao (教) or ‘religion’, manifested in a variety of religions united by their shared moral aim and in their teachings on reverence for Divinity, the soul’s immortality, and compassion.
My research reveals that, before the rise of radical materialism and scientism, fully one generation before the acceptance by Chinese intellectuals of the ‘Conflict Thesis’, Kang had already sought to conceptualize the relationship between what are now generally categorized as science and religion. Expounding a holistic world-view founded upon a belief in the oneness of knowledge, Kang appropriated Western scientific concepts such as the ‘ether’ in his re-interpretation of the Confucian Classics. He saw no conflict between modern science and Confucian Religion, whose quintessential doctrines, in his view, contained the origins of scientific thought. Acknowledging that conflict with science might occur with other religions like Christianity, he admitted that certain religious doctrines required correction when scientific evidence made it imperative; no matter how far science advanced, however, it could never disprove the existence of God, whose infinite nature he believed lay beyond the grasp of finite—even if brilliant—scientific minds. Closer analysis of Kang’s conception of the complementary relationship between science and religion, I suggest, can contribute to a richer picture of Kang’s thought, a better understanding of the field of science and religion in China, and a more global account of the subject.

Keywords: Confucianism
Kang Youwei
science and religion
Advisor: Iliffe, R
Verification and synthesis of linear systems by abstract acceleration

Embedded systems are constantly growing in number and complexity. A large number of these relate to physical elements that have behaviour that is either linear or can be described using linear dierential equations (e.g., vehicle speed/position, temperature control, oscillators, etc). In this work we explore the application of formal methods for safety checking and controller synthesis in the particular case of Linear Time Invariant (LTI) models where the dynamics may apply to both continuous and discrete variables in both continuous and discrete time. Our work applies to each of these cases independently. To this end, we use abstract acceleration, a method that combines abstract interpretation with acceleration in order to compute precise fix-points for the reach space of the model. Existing techniques have proven to be useful in the verification of discrete time systems, and we extend the method to a wider set of models and improve its performance. Furthermore, by applying control theory and SAT solving techniques, we explore the synthesis of correct by construction digital controllers using abstract acceleration as a model template. Our results show that the technique scales to models with several dozen variables for which sound results can be found in a matter of minutes.

Advisor: Abate, A
Kroening, D
Synthetic two dimensional hexagonal boron nitride and gallium sulfide crystals using chemical vapor deposition growth

Two dimensional (2D) materials have promising potential in the next generation electronics and optoelectronics devices. This requires scalable production methods which can provide high quality material. This DPhil project is about using chemical vapor deposition (CVD) method to grow multilayer hexagonal boron nitride (h-BN) and monolayer gallium sulfide (GaS). A range of characterisation methods is used to examine the morphology of these grown materials, as well as their structural, vibrational, and optical properties. In addition, the growth mechanism of h-BN and GaS are discussed based on the observed results.
Multilayer h-BN films are grown on copper substrates using an atmospheric pressure CVD (APCVD) method and the commonly used precursor, ammonia borane (AB). The h-BN films produced from AB precursor are compared to the films produced from two other precursors, such as dimeric diborazane (DAB) and trimeric triborazane (TAB). SEM results indicate that the DAB leads to fully continuous h-BN film in a shorter period of time. Quantitative surface analysis reveals that DAB and TAB precursors increase the coverage of contaminant nanoparticles on the surface of the grown h-BN films. Finally, the growth mechanism of h-BN on copper substrate is discussed.
Gallium sulfide mixture phase (GaS/Ga2S3) thin film is produced by a one-step thermolysis of single source precursor Ga2S3. It is deposited on both SiO2/Si and glassy carbon substrates via an APCVD method. The as-grown films have flakes and its thickness is between 4.5 nm and 30 nm depending on the growth time. The GaS/Ga2S3 thin films on glassy carbon substrates are explored as hydrogen evolution reaction (HER) catalysts. One of the samples exhibits a 126 mV/dec Tafel slope with 5.50 A/cm2. Its cathodic current behaves almost the same after a 1000-cycle durability test.
At last, the monolayer GaS film with triangular domains is achieved. The diagonal of the monolayer GaS continuous film is about 0.7 cm. The modified APCVD method results the sharp precursor concentration gradient and the change in the kinetic growth dynamics at substrate edge. This project provides important insights of grown 2D GaS material, in term of enlarging the domain size and understanding its growth mechanism.

Advisor: Warner, J