VictorJuiz/thesis huggingface dataset:
Understanding neighbourhood income poverty dynamics in England

This thesis advances the study of neighbourhood income poverty dynamics in England: neighbourhood change in low income areas; the dynamics of low income people within neighbourhoods; and the individual-level dynamics that drive aggregate neighbourhood change. The research questions ask whether income poor individuals are becoming more evenly spread across neighbourhoods in England, and what processes are associated with this change; what characterises poverty dynamics in disadvantaged neighbourhoods and what the implications are for area-based policy; and what demographic processes are associated with recent neighbourhood gentrification.
The research is conducted in an empirical quantitative framework using analysis of administrative, census and panel survey data. Poverty is operationalised as a relative poverty measure and Lower Layer Super Output Areas are used as proxies for neighbourhoods. The thesis makes several methodological contributions including using administrative data to study income poverty dynamics in neighbourhoods and using propensity score matching for researching neighbourhood change processes.
The findings show that the stability in the neighbourhood geography of poverty can mask some important dynamics. First, children and working age people living in low income households are becoming less concentrated in the highest poverty neighbourhoods; this is associated with the increasing propensity for low income households to be living in private rented housing. Second, the low income population living in deprived areas is shown to be highly dynamic. Deprived areas are characterised by a heightened risk of becoming poor and a higher risk of staying poor; but arguably the risk of becoming poor is more important in explaining high poverty rates. Third, in those neighbourhoods that have changed significantly there is stronger evidence that this proceeds via changes in the composition of inward migrants rather than an outward displacement of existing low income residents. A dynamic view of neighbourhood income poverty has the potential to improve the targeting and design of area-based initiatives, and provide a more nuanced picture of the nature of income poverty in disadvantaged areas.

Keywords: social policy
poverty dynamics
neighbourhood
poverty
gentrification
Advisor: Dorling, D
Loopstra, R
High performance pixels for CMOS image sensors

Complementary Metal-Oxide Semiconductor (CMOS) image sensors are the principal technology employed in commercial image sensing applications. The research interest in these devices is driven by the high demand of cameras. High-quality imagers are relevant in the mobile devices business and are even more important in the automotive market segment where the image quality is crucial for safety. However, CMOS image sensors performance can still be improved. In particular, a leakage current, intrinsic to the process of manufacturing CMOS technology, reduces the sensitivity in low light and should be minimised. In addition, the capability of the sensor to collect electrons, known as full well capacity, should be maximised.
The methods proposed in the literature to reduce the leakage current and to increase the full well capacity are either insufficient or costly as they may require process modifications. To overcome these limitations, a different approach based on simple layout modifications is proposed. The principal source of leakage current is due to the photodiode isolation. By designing pixels adjacently, the isolation can be removed thereby reducing the leakage current contribution. In order to maximise the full well capacity, a novel technique is proposed here which consist in minimising the area reserved to the transistors in the pixel array by sharing the maximum number of diffusions. The result is a pixel with a 50% increase in fill factor compared to a traditional pixel.
The proposed optimisation strategy results in a staggered pixel arrangement. This may introduce artefacts in the image when displayed. Hardware-efficient image reconstruction algorithms able to correct the artefacts are presented. Test chips were manufactured to prove the performance improvement and experimental data showed that the proposed layouts effectively reduces the leakage current and improved the full well capacity of the presented pixels. In addition, the proposed algorithms are shown to correctly reconstruct and represent the staggered acquired image on a standard display.

Keywords: Pixels
Image Sensors
Layout
CMOS sensors
IC design
Advisor: Choubey, B
Addressing cognitive biases in the treatment of irritable bowel syndrome with mindfulness based therapy

Irritable Bowel Syndrome (IBS) is a chronic disorder of brain-gut interaction. Using the translational model of treatment development, the aim of this thesis was twofold: 1) to identify cognitive factors involved in maintaining IBS, and 2) to subsequently adapt and test a treatment addressing these factors. Previous research has highlighted the role of illness-specific cognitions (e.g., gastrointestinal symptom-specific anxiety, paincatastrophizing) for maintaining IBS, predominantly using self-report measures. Employing a cross-sectional design, I compared IBS patients and healthy participants on implicit reaction-time based measures of attentional control (i.e., executive attentional regulation) and identification with illness and health. IBS patients showed a deficit in attentional control and biased self-referential processing of information relating to health. The findings corroborated my theoretical premise that Mindfulness-Based Cognitive Therapy (MBCT) adapted for patients with IBS would address the identified maintenance factors. In order to determine the best time point to measure changes in implicit cognitive functions in mindfulness-based interventions, I designed a quasi-experimental proof-ofconcept study. It found that an increase in attentional control in healthy students can be measured after two weeks of the ‘Finding Peace in a Frantic World’ programme. Subsequently, a treatment protocol of MBCT for IBS was developed, which aimed to reduce IBS symptoms and increase quality of life. It was hypothesised that this treatment would alleviate symptoms by attenuating illness-specific cognitions, supported by improvements in attentional control, and by changing how cognitive, emotional, illness and health related information is processed. A randomised wait-list controlled clinical trial assessed the efficacy of MBCT for IBS at four time points. MBCT for IBS reduced IBS symptom severity by reducing maladaptive illness-specific cognitions paired with a shift towards self-referential processing of health related information and more accepting, non-judgemental processing of emotions and thoughts. These results suggest that MBCT for IBS is a promising treatment for IBS patients. The treatment protocol awaits further testing in bigger samples and with active control groups.

Advisor: Martin, M
Gjelsvik, B
Cold state-selected radicals for the study of low temperature chemistry

Generating a controllable and pure source of molecular free-radicals or open-shell atoms has been one of the primary barriers hindering the detailed study of radical processes in the laboratory. In this thesis, a novel source of state-selected radicals -- composed of a Zeeman decelerator interfaced with a newly-designed magnetic guide -- is introduced. This tuneable source generates a pure beam of velocity-selected hydrogen atoms that will enable the study of radical interactions with exceptional control over the properties of the radical species.
In Zeeman deceleration, time-varying spatially inhomogeneous magnetic fields are used to create packets of translationally cold, quantum-state-selected paramagnetic particles with a tuneable forward velocity, which are ideal for cold reaction dynamics studies. In a proof-of-principle experiment, the Zeeman deceleration of nitrogen atoms in the metastable 2D5/2 state from 460 to 410 m/s is demonstrated for the first time. The covariance matrix adaptation evolutionary strategy (CMA-ES) is adopted in order to optimise deceleration switching sequences for the operation of a 12-stage Zeeman decelerator. Using the optimised sequences, a 40% increase in the number of decelerated H(2S1/2) atoms is observed compared to standard sequences for the same final velocity, imposing the same experimental boundary conditions. Furthermore, up to 98% of the initial kinetic energy of particles in the incoming beam is removed by the optimised sequences, compared to the removal of a maximum of 83% of kinetic energy with standard sequences. Three-dimensional particle-trajectory simulations show that the optimal solution uncovered by the evolutionary algorithm is not merely a local optimisation of the experimental parameters -- it is a new mode of operation that goes beyond the standard periodic phase stability approach typically adopted.
A novel magnetic guide is designed and constructed to purify the post-deceleration beam. Only radicals with a selected velocity are transmitted through the guide; all other components of the incoming beam (radical species travelling at other velocities, precursor molecules and seed gases) are removed. The guide is composed of four Halbach arrays -- hexapolar focusing elements -- and two skimming blades. The relative positions of these components can be adjusted to tune the properties of the resulting beam and to optimise transmission for a given velocity. Experimental measurements of Zeeman-decelerated H atoms transmitted through the guide, combined with extensive simulations, show that the magnetic guide successfully removes 99% of H atoms travelling outside the narrow target velocity range.

Keywords: Zeeman deceleration
Deceleration
Radicals
Cold chemistry
Evolutionary algorithms
Velocity selection
Molecular beams
Purification
Optimisation
Hydrogen
Nitrogen
Magnetic guiding
Advisor: Heazlewood, B
Softley, T
Face-to-face and internet-based cognitive therapy for social anxiety disorder: Mechanisms of change and treatment dissemination

While effective psychological interventions for common mental health difficulties exist, our understanding of how they work, and our ability to disseminate them at scale, is limited. This thesis aimed to 1) examine the mechanisms underlying clinical improvement in one such intervention, Cognitive Therapy for Social Anxiety Disorder (CT-SAD), and 2) disseminate and evaluate an internet-based version (iCT-SAD) in a new culture (Hong Kong).
Following an introduction and literature review (Chapters 1 and 2), eight studies are presented. Studies 1, 2a, and 2b (Chapters 3 and 4) investigated three candidate mediators (negative social cognitions, self-focused attention, and depressed mood) of the relationship between time in therapy and social anxiety symptoms. Results indicated that cognitions consistently mediated subsequent clinical improvement, with weaker and less consistent effects for self-focused attention and depressed mood.
Studies 3a, 3b, and 3c (Chapter 5) examined ‘sudden gains’: large and stable symptom reductions between consecutive therapy sessions, in CT-SAD and iCT- SAD. Sudden gains were common in both treatments, occurring with similar frequency and magnitude. They were associated with better overall therapy outcome. There was some evidence of reductions in negative cognitions and self- focused attention prior to, and concurrently with, gains. Clients in CT made more statements indicating ‘generalised’ learning in ‘pre-gain’, relative to control, sessions.
Study 4 (Chapter 6) implemented a new iCT-SAD therapist training programme with three therapists from Hong Kong, who delivered the treatment in a pilot case series. Study 5 (Chapter 7) then evaluated the efficacy of iCT-SAD in Hong Kong compared to waitlist controls in a randomized controlled trial. Results indicated the training was effective at developing iCT skills and competence, and that iCT-SAD was superior to waitlist, showing large effect sizes comparable to UK studies. Implications for theory, research, and practice are discussed (Chapter 8).
Overall, the findings indicate that negative social cognitions play an important role in determining clinical improvement in CT-SAD and iCT-SAD, that the therapy mechanisms of change investigated appear to be similar between these treatment formats, and that iCT-SAD was successfully disseminated to another culture without losing efficacy.

Keywords: social anxiety disorder
cognitive therapy
internet interventions
Advisor: Clark, D
Ehlers, A
Three-dimensional recapitulation of neuroblastoma: from model to drug screening platform

Neuroblastoma is one of the most common yet fatal paediatric cancer. Nevertheless, few drug treatments are available in the market. One of the difficulties is the drug responses reported in 2-D in vitro tests does not always accurately reflect those observed in 3-D in vivo models. As the process consumes time, money and animal lives, a 3-D in vitro drug testing bioreactor recapitulating neuroblastoma tumours are needed to screen out any unsuccessful drug candidates before they enter in vivo tests.
In this thesis, a 3-D in vitro model comprised neural stem cells (NSCs) or neurob- lastoma cells (SH-SY5Ys) and human umbilical vein endothelial cells (HUVECs) were initially optimised and developed in the laminin-rich hydrogel matrix to recapitulate neuroblastoma tumours. Next, a modified polydimethylsiloxane bioreactor (TissueFlex®) was developed to extend the viability of the 3-D in vitro model by enhancing the mass transport of nutrients and oxygen. The bioreactor was continuously perfused with a supplemented endothelial basal medium (EGM-2) co-treated with cisplatin, retinoic acid (RA), both cisplatin and RA, or EGM-2 as a control for three weeks. Cell morphology, cell viability and expressions of markers (TuJ1, Nestin and CD31) were measured weekly. Results were compared to parallel cultures of 2-D monolayer and 3DFlo® automatic cell culture systems.
Our results show that hydrogel fragmentation allowed the formation of concentrated laminin and cellular networks along the gel granule boundaries with neurite extensions observed. Besides, cell surface marker expressions suggested an optimal NSC-HUVEC seeding density ratio of 3:1, cultured in 100% EGM-2 medium. The incorporation of perfusion culture to the model gave rise to significant increases in the number of cells and the expression of Nestin compared to static culture. After 3 weeks, only 2-D cultures showed a significant decrease in marker expressions upon treatment with cisplatin or cisplatin and RA in combination. Also, drug treatments were significantly less effective in 3-D bioreactors than in 2-D cultures. This suggests that the 3-D interactions between cells and hydrogel have created a microenvironment that recapitulates phenomena present in neuroblastoma and provides resistance to cancer therapeutics.
Our 3-D in vitro model and perfusion bioreactor have implications for a more efficient drug discovery process by closing the gap between cell culture and physiological tissue investigations. These can be applied towards personalised medicine, where a patient’s biopsy specimen can be tested in the system against a series of drugs to identify ones giving rise to optimal therapeutic outcomes.

Advisor: Ye, H
O'Neill, E
Vital-sign data-fusion methods to identify patient deterioration in the emergency department

In the United Kingdom Emergency Departments (ED), clinical staff requires to diagnose, give treatment and discharge patients, within 4 hours of their arrival. The patients’ vital signs are traditionally managed using paper Track and Trigger (T&T;) charts, prone to human error, and bedside monitors, whose alerts are often ignored. Consequently, patient deterioration might be missed at and between nurses’ observation sets. This thesis has analysed data from a three stage study in the ED of the John Radcliffe Hospital, Oxford, to investigate the use of an electronic T&T; system (VitalPac) and a data-fusion system (Visensia) to help staff identify physiological deterioration in patients attending the majors area.
Data was collected from a total of 10,488 ED attendances receiving standard care in stage 1, followed by two technology interventions in stages 2 and 3, respectively, for a total period of 6 months. It was shown that 9% of the observations sets, conducted on stable ED patients in stage 1, were done on unstable patients when staff was guided by VitalPac in stage 2. One of the causes might have been the increase in the Early Warning Score (EWS) completion from 52% to 100% of the observation sets. In stage 3, 35.7% of the Visensia alerts generated on continuous bedside monitor data, were deemed “technical” alerts due to data artefacts. On the other hand, clinical staff responded within 15 minutes to 85% of the “physiological” alerts.
A two-stage Machine Learning (ML) architecture was proposed to fuse intermittent and continuous vital-sign data and use a sub-population novelty detection model to identify multivariate data deviating from normal physiology. This ML approach out-performed the baseline Visensia model (a population based model, applied over the continuous data), and the National EWS system (applied over the observation sets data) in detecting patients escalated to the Resuscitation area during their ED stay, on a test set of 1,070 ED attendances (AUROCs and 95% confidence intervals were 0.737 (0.623, 0.830), 0.657 (0.521, 0.755), and 0.643 (0.522, 0.749), respectively).

Keywords: EWS
Machine Learning
GP
Biomedical Engineering
Vital-sign monitoring
KDE
SVM
Novelty Detection
Advisor: Tarassenko, L
Clifton, D
Binuclear complexes as quantitative imaging agents

This thesis explores the synthesis of and subsequent use of mono- and binuclear lanthanide complexes in their binding to biologically endogenous dianions.
Chapter 1 outlines the properties of the lanthanides with a focus on their chemical and photophysical behaviour and self-assembly involving lanthanide-containing complexes. Medical applications are also discussed.
Chapter 2 sets the scene for anion binding with lanthanide complexes by establishing the fundamentals and thermodynamics of their interactions with dicarboxylate species. In this chapter, the focus is on the use of luminescence spectroscopy to explore the nature of self-assemblies and establish the role of local and remote structural variations (in concert with solvation effects) in tuning binding affinity for dicarboxylate guests.
Chapter 3 covers the synthesis and characterisation of a set of binuclear lanthanide complexes of ligands in which m-xylyl derivatives bridge two DO3A-derived domains.
Chapter 4 describes the synthesis and characterisation of mononuclear complexes. These exhibit greater structural variation than the m-xylyl systems, containing the DO3A core with pendent benzyl, propargyl and coumarin groups.
Chapter 5 discusses the synthesis and characterisation of two binuclear naphthyl complexes, in which 2,6- and 2,7- substituents are used to form the bridge between the two DO3Ayl domains.
Chapter 6 extends the synthesis of the style of binuclear complex described in Chapter 3 by coupling the amino derivative to the longer wavelength sensitiser acridone.
Chapter 7 provides an overview of the binding studies performed in this thesis with mono- and binuclear host complexes to an array of anionic guests, outlining and comparing methods for using luminescence and NMR to explore guest binding events.
Chapter 8 considers specifically binding to species from the glycolytic pathway and to the similar chain-length carboxylate species tartrate and lactate. These studies reveal that the dianionic species in the pathway can act as bridging ligands, and that differences in structure and photophysics can give rise to selective responses from different guests.
Chapter 9 evaluates binding to endogenous and non-biological phosphate species, both by luminescence measurements and phosphorus NMR.
Chapter 10 focuses on binding to and interactions with catechol species including dopamine. In these systems, the relative instability of catechols in solution combines with inner filter effects to present challenges to method development.
Chapter 11 lays out the conclusions reached over the course of this work and suggests possible opportunities for further work.
Chapter 12 contains experimental procedures and techniques for processing data. 
A series of appendices provide supplementary information to the core thesis, including a reference to the molecular structures of host complexes and guest anions in this thesis, X-ray crystallography data, and published papers.

Keywords: lanthanides
luminescence
supramolecular chemistry
molecular imaging
photophysics
Advisor: Faulkner, S
Nanostructured graphene electrodes for energy applications

Polymer electrolyte (or proton exchange) membrane fuel cells (PEMFCs) are promising for green energy applications, particularly for automobiles. However, the cost and durability issues surrounding the platinum/carbon (Pt/C) electrode materials are barriers to their widespread use. The development of electrodes which have better utilisation of Pt crystals, and which retain their activity for longer periods of time, are of great interest to the fuel cell community. Graphene is a promising candidate for catalyst support applications because of its advantageous properties. For this reason the production of graphene and graphene hybrid catalyst supports, and their interactions with Pt particles, are active areas of research. This project involved the synthesis of 3D graphene and graphene hybrid materials, their integration with Pt nanocrystals, and investigations of their electrochemical stability.
Firstly, 3D multilayer graphene foam was synthesised using a chemical vapour deposition (CVD) method. This was then used as a substrate in order to investigate the role of oxygen-plasma induced defects on the graphene surface on the synthesis of Pt nanocrystals formed through thermal annealing. It was found that the induction of defects could increase the nucleation density, and decrease and narrow the size distribution of Pt nanocrystals. In addition, results suggest that Pt can prevent certain types of defects from healing during heat treatment.
A novel method was then explored to produce 3D graphene and 3D graphene/carbon nanotube (CNT) powders using the thermal annealing of nickel acetate. The synthesis can be varied to produce a variety of materials with different crystallinities, and it was found that rapid heating was a key factor for the formation of the CNTs. These materials were explored as supports for thermally produced Pt nanocrystals and compared to commercially available carbon black, and it was found that good dispersion could not be achieved on the supports with the poorest crystallinity. Some of the materials produced performed similarly to HiSPEC 3000, a commercially available catalyst, in cyclic voltammetry (CV) experiments.
Within the past few years, a popular strategy to increase the durability of Pt/C catalysts has been to cover the Pt crystals with a protective layer. A CVD approach was used to modify a commercially available Pt/C catalyst with graphene layers. These were studied using HRTEM, and their electrochemically active surface areas (ECSAs) and durabilities were examined using CV experiments. Only a detrimental effect of the graphene layers was found in this case, and the reasons for why this might be the case are discussed.

Advisor: Warner, J