VictorJuiz/thesis huggingface dataset:
Performance limitations in practical transparent conducting oxide thin films

Zinc oxide (ZnO) has long been advanced as a low cost, earth-abundant transparent conducting oxide (TCO) with potential as a replacement for high-performance, but costly, indium oxide (In2O3) based materials in a wide range of technological applications. However, despite decades of research and development efforts, ZnO-based materials have still failed to displace the incumbents in any large-scale applications.
Given the compelling materials cost advantages of ZnO, it is almost certain that its poor adoption is due to deficits in its technical performance. This thesis aims to fulfill the need for systematic, fundamental work to identify and examine the factors that limit TCO performance, and in particular, those that limit ZnO relative to In2O3.
Using spray pyrolysis as the primary deposition method, many different series of ZnO and In2O3 films have been prepared and examined using a range of chemical, structural, and optoelectronic characterization techniques. After essential background information on the basic physics and chemistry of TCOs, as well as a detailed discussion of the chosen deposition and characterization methods, three main classes of performance limitations will be covered: 1) those related to the intrinsic properties of electronic transport in crystalline TCO domains, 2) those arising in the course of impurity doping, and 3) those occurring due to grain boundary effects and the polycrystalline nature of thin film TCO samples.
Taken together, these results will show that preparing ZnO-based TCOs with performance approaching that of the best In2O3-based materials, while very likely to be technically possible, will almost certainly involve overcoming significant engineering and process development challenges that, importantly, are not required to make high quality In2O3. Ultimately, whether ZnO will ever find significant, real-world use as a TCO will depend on whether the deep differences between ZnO and In2O3 performance limits that will be highlighted and examined in this thesis can be bridged in a practical and cost-effective manner.

Keywords: Grain Boundaries
Materials
Thin Films
Semiconductor Doping
Chemistry
Transparent Conductive Oxides
Pyrolysis
Advisor: Edwards, P
Biochemical studies on the role of the  XPF-ERCC1 endonuclease  in repairing damaged DNA replication forks

The human XPF (ERCC4) and ERCC1 proteins form a heterodimeric endonuclease that plays a critical role in maintaining genome stability. Mutations in the XPF gene cause several heritable disorders including Fanconi anemia (FA). This highlights the importance of DNA repair processes controlled by XPF-ERCC1, including the repair at replication forks stalled by DNA interstrand crosslinks (ICLs), for human health. Unrepaired ICLs, formed by by-products of cellular metabolism, are believed to be responsible for the genomic instability, cellular attrition and cancer predisposition seen in FA patients. Additionally, ICL-inducing agents are extensively utilised in anti-cancer therapy.
Previous reports suggest that ICL processing is triggered when the leading strand of a replication fork collides with an ICL, where XPF-ERCC1 catalyses fork incisions to initiate a process termed 'ICL unhooking'. However, the mechanism(s) of fork processing by XPF-ERCC1 remain poorly explored. Using biochemical reconstitution, I show that ICL unhooking, the initiating steps of replication-coupled ICL repair, is driven by the collaborative efforts of XPF-ERCC1; the replicative single-stranded DNA binding protein RPA; and the 5' to 3' exonuclease SNM1A.
XPF-ERCC1 incises ICL-containing fork structures within the duplex DNA region. However, the presence of a model nascent leading strand, mimicking the effects of replication arrest by ICL, eliminates this activity. Strikingly, addition of RPA restores XPF-ERCC1 activity on such structures. SNM1A is able to load onto XPF-ERCC1-RPA induced incisions and digest past the ICL to unhook the ICL from duplex DNA.
I postulate that during replication-coupled ICL repair, the arrest of nascent leading strands by ICLs produces a substrate that is inhibitory to XPF-ERCC1. This inhibition can be overcome through the marked stimulation of XPF-ERCC1 by RPA. XPF-ERCC1-RPA induced-incision enables SNM1A to digest past the ICL, which unhooks the ICL from the duplex DNA, enabling subsequent repair process to occur.

Advisor: McHugh, P
Creating warm dense matter and studying structural properties

Warm dense matter is an area of the phase diagram between solids and classical plasmas, but poorly described by theoretical descriptions of both. Collective oscillations and quantum effects all play significant roles in its structural behaviour and equations of state. Aside from its complexity, work on this state is significant as a stepping stone towards achieving energetically viable nuclear fusion, as well as representing a laboratory analogue for planetary cores and other astrophysical phenomena.
X-ray scattering, using beams from X-ray free electron lasers, is used to probe the structure of samples in this state, and is shown to compare well to theoretical descriptions. Angle-resolved scattering showed sharper than expected peaks, suggesting stronger interparticle correlation than expected. Using the beam in self-seeded mode, scattering from ion acoustic waves in warm dense matter was observed for the first time, confirming theoretical descriptions of the phenomena but raising further questions due to an elastic peak in the spectra. Similar experiments in the future will allow models of ionic behaviour to be tested directly, and potentially determine the source of this feature.
X-ray diffraction was used to study the evolution of samples heated by proton, electron or photon irradiation, with the aim of resolving the temperature evolution of the species within the sample. The results suggest that, although the behaviour in metallic samples is well described by lowtemperature approximations, that of graphite is more complex and does not agree with the models available.

Advisor: Gregori, G
Climate-carbon feedback of the high latitude ocean

The warming induced by anthropogenic carbon emissions affects the climate system through a multitude of physical mechanisms. Changes in the dynamics, thermodynamics and biogeochemistry of the ocean alter the different ocean carbon reservoirs, potentially resulting in further carbon emissions and a climate- carbon feedback. Surface wind stress and surface warming are two of the most influential forcings acting on the ocean carbon system in past, present and future climates due to their influence on the mixed layer dynamics and the large scale ocean circulation.
This thesis quantifies the climate-carbon feedback of wind stress and surface warming, with a particular focus on the mechanisms driving the feedbacks and the role of the Southern Ocean and the North Atlantic. To study the feedbacks, a set of theoretical scalings and a hierarchy of numerical simulations are used. Of the climate feedbacks examined, increased surface warming is likely to result in large atmospheric CO2 anomalies while the effects of North Atlantic wind stress are likely to be negligible. The atmospheric feedback of surface warming is constrained by compensating changes in separate ocean carbon reservoirs as a result of warming-induced circulation changes. Southern Ocean winds affect atmospheric CO2 through both local upwelling of carbon as well as the remote modification of Equatorial and North Atlantic chemistry. As a result, the net Southern Ocean wind stress feedback could be significant and even comparable to the temperature feedback. This thesis provides a quantification of regional and global climate-carbon feedbacks due to ocean dynamics. The estimates of carbon-climate feedbacks are useful tools for understanding past, present and future climates.

Advisor: Zanna, L
Lowe, J
Integrated characterisation of carotid atherosclerosis - from magnetic resonance imaging to plaque macrophage profiling

Cardiovascular morbidity and mortality remain the most serious global public health challenge. With the evolution in global socio-economic activities and the associated lifestyle changes, there is an impending epidemic of obesity, insulin resistance, metabolic syndrome, and diabetes mellitus, all of which fuel premature coronary artery disease and stroke. In the post-statin era, despite considerable efforts in anti-atherosclerotic drug development, a significant number of these potential compounds with initial success in early phase clinical studies failed to translate to clinical outcome benefits. This shows a disparity of various biomarkers and molecular disease mechanisms, and highlighted the inadequacy of current methods of risk stratification and atherosclerosis characterisation.
Atherosclerosis imaging such as by MRI does not only serve as 'gate keepers' in the contemporary drug development process; but in combination with modern "omics", would allow precise disease stratification with resolution never achieved before. This integrated characterisation of atherosclerosis will generate novel insights about plaque biology, bridge the gap between molecular insights and clinical outcomes, and help achieve the goal of stratified, personalized, medicine.
This thesis hypothesized that plaque compositional heterogeneity such as lipid content is associated with specific gene expression profiles or signatures in human carotid plaque macrophages in a spatially distinct pattern; and that this macrophage functional heterogeneity may in turn play a role in altering response to anti-atherosclerotic treatment. To test these hypotheses, human subjects with carotid atherosclerosis were recruited before carotid surgery and scanned using novel MRI T2 mapping technique. Explanted carotid plaques were then examined by immunohistochemistry-guided laser capture microdissection and microarray analysis.
T2 mapping was shown to be able to accurately and reproducibly discriminate all major plaque components, and in particular, quantify plaque lipid content with excellent histological validation. Symptomatic plaques were shown to contain larger lipid-core by T2 mapping compared to asymptomatic plaques, despite similar degree of luminal stenosis. Macrophages from the same cohorts of plaques were procured by immunohistochemistry-guided laser capture microdissection and they were shown to display distinct gene expression profiles based on their micro-anatomical locations and clinical presentations; importantly, macrophages from plaques with high lipid content detected by T2 mapping were found to activate specific interferon / STAT1 pathways. Finally, using nicotinic acid as an example, the functional significance of plaque macrophage heterogeneity was shown in vitro to affect response to pharmacological intervention.

Keywords: microarray
lipid
carotid
cholesterol efflux
atherosclerosis
nicotinic acid
MRI
macrophage
laser capture microdissection
GPR109A
transcriptomic
T2 mapping
Advisor: Choudhury, R
On the histochemical labelling and quantitative stereological assessment of synaptic puncta within the dorsal horn: with a focus on synaptic remodelling following a lesion to the peripheral nerve

Peripheral nerve injury often results in neuropathic pain, which is chronic, maladaptive, and hard to treat. Accompanying the injury to the peripheral nerve are a series of changes within the central nervous system. Understanding these changes and how they relate to the neuropathic condition is vital in driving evidence-based treatment strategies. Neuronal connectivity is widely believed to underlie many cognitive processes, and altered connectivity may underlie the development and maintenance of neuropathic pain. Here, a tractable method of analysing connectivity, via the histological marking and fluorescence imaging of synaptic puncta, was developed. This method utilised automated image processing methods, and developed a stereological filter for unbiased object measurement. Using this approach, different synaptic markers were analysed in the superficial dorsal horn of rodents, a key component in the reception and processing of somatosensory information. Analysing PSD95 and SynaptoPhysin fluorescent puncta in naive adult rodents revealed distinct puncta distributions in the dorsal horn, reflecting gross circuit formation throughout this region. Peripheral nerve lesion to aspects of the sciatic nerve of rodents resulted in a selective loss at 21 days post injury of PSD95 puncta from lamina II inner of the superficial dorsal horn, with Synaptophysin puncta remaining unchanged. These experiments were complemented by a transgenic approach, where eGFP was expressed exclusively and permanently in sensory neurons, which also revealed no loss of sensory neuron afferent input to the dorsal horn after nerve lesion up to 21 days post injury. Finally, the hypothesis that microglial cells may be driving this synapse loss was explored by treating animals with minocycline following peripheral nerve lesion, which did not interfere with the PSD95 puncta loss observed at 21 days post injury.

Keywords: connectivity
immunohistochemistry
neuropathic pain
peripheral nerve injury
synapse
microglia
dorsal horn
deconvolution
stereology
Advisor: Bennett, D
The role of A1-MGBv corticothalamic feedback explored with mistuning of harmonic complex tones using ferrets

The A1-MGBv corticothalamic projection is one of the major descending pathways in the auditory system, projecting from the primary auditory cortex (A1) to the ventral division of medial geniculate body (MGBv). Recent evidence suggests that corticothalamic feedback can sharpen the spectral receptive fields of thalamic neurons and modulate the temporal precision of the responses. The aim of the work presented here was to investigate the role of A1-MGBv corticothalamic feedback using harmonic and mistuned complex tones (HCTs and MCTs) in adult ferrets. The MCTs used comprised a mistuned harmonic shifted to a higher frequency in the otherwise HCTs. The harmonic structure of sounds is an important grouping cue in auditory scene analysis.
We first measured the ability of ferrets to detect mistuned harmonics using a go/no-go behavioural task paradigm. Psychometric functions plotting sensitivity as a function of degree of mistuning were used to evaluate the behavioural performance using signal detection theory. The threshold for mistuning detection was 0.8 ± 0.1 Hz (mean ± sem), with sensitivity indices and reaction times depending on the degree of mistuning. The threshold range for mistuning in ferrets is similar to that previously described in other species.
The responses to MCTs in MGBv neurons were explored using extracellular recordings in anaesthetised animals. The functional organization of the ferret auditory thalamus has not previously been investigated. The ferret MGBv was identified by the short response latency and the sharply tuned frequency response areas of the recorded units and by its tonotopic organization, which was found to be comparable to that of other species. Compared to their responses to HCTs, the firing rates of MGBv neurons were modulated depending on the degree of mistuning and the fundamental frequency of the MCTs. Distinctive temporal response patterns were also observed, phase locked to the periodicities of altered phases of the MCTs.
To investigate whether corticofugal modulation contributes to mistuning detection, A1-MGBv corticothalamic neurons were selectively eliminated bilaterally by chromophore-targeted laser photolysis. Using the behavioural paradigm established above, mistuning detection was tested before and after these lesions were made. Animals with corticothalamic lesions were impaired in their ability to detect a mistuned harmonic, as indicated by decreased d’ values, increased thresholds, and a shift of the psychometric curves towards higher mistuning values.
Together, these results suggest a possible role for corticothalamic feedback in modulating the firing patterns of MGBv neurons in ways that contribute to accurate recognition of complex auditory stimuli. In other words, this top-down corticothalamic feedback may be important for auditory scene analysis.

Keywords: Auditory scene analysis
Complex sound
Go/no-go task
Ferret
Auditory thalamus
Corticothalamic feedback
Advisor: Bajo, VM
King, AJ
The duty of care: a comparative common law analysis

The general aim of this thesis is to provide a detailed overview of the duty of care enquiry, drawing on both academic analyses and judicial experience in leading common law systems. The thesis starts by exploring the history of the duty concept, including how it first came to be an element of the negligence enquiry, and how it later came to be determined via the use of a general formula. The thesis then explores and analyses the various methods through which the existence of a duty of care has been determined. Having provided an overview of the development of the duty concept, it is then argued that the duty of care is best understood as consisting of two discrete parts: a factual aspect and a notional aspect. It is suggested that the factual aspect of the duty enquiry is superfluous and should be abandoned so that the duty enquiry is a notional issue only. It is then argued that the notional aspect of the duty enquiry is best understood as consisting of two separate types of determinations: those relating to broad situations, and those based on assumptions of responsibility. Both of these types of notional duty determinations are explored in detail. The propriety of basing situational notional duty determinations on considerations of policy, and the necessity of notional duty, are also considered. Finally, the thesis provides an overview of an empirical study of ultimate appellate court duty decisions, investigating, among other things, whether the understanding of duty provided in the thesis is consistent with the practice of the courts.

Keywords: duty of care
negligence
Advisor: Nolan, D
The association between radiographic knee osteoarthritis and pain: an epidemiological analysis of a twenty-year community-based cohort

Background: Knee osteoarthritis (OA) is one of the leading musculoskeletal burdens in the world, causing both structural damage and pain to the joint. Radiographs are the most common imaging method for diagnosing OA, however the relationship between radiographic changes (ROA) and symptoms is not well understood. This thesis will establish the natural history of twenty-year ROA, compare diagnostic methods of ROA assessment, evaluate the cross-sectional relationship between ROA and pain, and will determine the long-term predictive validity of features of ROA with future knee replacements (TKRs).
Methods: Data from the Chingford women's study, a twenty-year prospective UK-based cohort was used for the analysis. Risk factors included atlas-based ROA scoring methods and quantitative joint space width (JSW), which were analysed against pain and TKR outcome measures. A novel method for assessing joint space on low-contrast x-rays was developed which had high reproducibility and validity.
Results: The twenty-year natural history of ROA showed relatively low levels of annual incidence (3.8%), progression (3.6%), and worsening (4.5%), and emphasised the involvement of both medial and lateral osteophytes. Severe joint space narrowing (JSN) had the best construct validity with pain, while any size of lateral tibial osteophyte had good construct validity. Medial quantitative JSW had good construct validity, but no predictive validity with future TKRs. Lateral JSN and osteophytes had the best predictive validity for future TKR.
Conclusion: This research demonstrates that radiographic scoring methods have strong construct and predictive validity with symptomatic knee OA. These results support the use of x-rays to identify early disease changes which indicate future joint failure.

Keywords: Radiography
Pain
Knee Osteoarthritis
Epidemiology
The effect of Schedule 21 on sentencing for manslaughter

This thesis examines the origins of Schedule 21 and the intention behind it by making detailed recourse to Parliamentary debate on the passage of that statutory provision and other related ones. Based on that scrutiny, it contends the harm of death is to be treated as more serious than before. It asks by virtue of that principle whether the statutory sentencing guidelines for murder have implications for other crimes in a sentencing regime where the gravity of the crime is the sole desiderata for determining the length of adult custodial punishment. Finding they do, it fleshes out what those ramifications are, viz. that other crimes where the actus reus is death are subject to that increased valuation on the loss of life as a harm, translating into longer terms of imprisonment. Manslaughter is noted as anomalous in being a major homicide offence not subject to recent express legislative reform on this ground. The thesis then proceeds to investigate whether the aforementioned necessity has been adverted to and implemented in sentencing practice for manslaughter. It does so by analysing a substantial canon of case law, comparing sentencing levels and their justifications before and after the remit of Schedule 21. It finds that only recently has Sch.21’s true influence been appreciated by the Court of Appeal, and maps the journey to that point, asking why it was such a long one. It concludes that much is owed to the leadership of the Court of Appeal (Criminal Division) in the form of the Lord Chief Justice, Lord Judge for effecting overdue alterations to the sentencing levels for manslaughter. However it also points to the infancy of this epiphany, and identifies challenges and changes that still need to be made to deliver ordinal proportionality within this genus of harm, and questions ordinal proportionality between harm genuses, intending to explore this in subsequent research.

Advisor: Ashworth, A
Evaluation of the effects of a pre-school intervention on literacy development in children

This short-term longitudinal study investigates the effects of the 'Peers Early Education Partnership' (PEEP), a pre-school intervention in Oxfordshire, which aims to increase the educational achievement (especially literacy skills) of disadvantaged children from infancy to 5 years. PEEP strives to form partnerships with parents and carers by recognising and supporting their contribution to children’s learning during their formative pre-school years.
The study evaluated the effects of the PEEP Project over the year following children's entry at age 3. The study aimed to observe closely, at a micro level, what effects the PEEP programme had upon children's development. Based on a comparison with children without PEEP experience, the study looked particularly, first, at how the PEEP parent education programme affected the literacy and numeracy development of children and, second, whether there was a difference one year later in children's self-esteem and social-emotional development.
The method was a quasi-experimental design, which included pre- and post-testing measures. In order to assess the outcomes of the PEEP intervention on children's cognitive, language and social-emotional development, standardised tests and educational tasks were administered to the children at the start of the intervention and after one year. The same assessments were applied to the 'intervention' and 'comparison' children.
The sample consisted of 160 children and their families. Seventy-three of these children attended the intervention in the PEEP catchment area in Oxfordshire while their parents attended weekly group sessions. A comparison group of 87 children were recruited from five playgroups in a nearby town also in Oxfordshire, matched for age and social characteristics with their Oxford counterparts. Neither the children in the comparison group, nor their parents, attended any PEEP group sessions.
Children in the PEEP group had significant gains in the following areas of development: Language and Literacy (Verbal Comprehension, Vocabulary, Phonological Awareness, Concepts about Print, Writing), Numeracy (Early Number Concepts) and Self-esteem (Maternal Acceptance)

Advisor: Sylva, K