VictorJuiz/thesis huggingface dataset:
Peeping in, peering out: monocularity and early modern vision

One of the central theoretical tenets of linear perspective is that it is based upon the idea of a monocular observer. Our lived perception, also referred to in the Renaissance as perspectiva naturalis, is always rooted in binocular vision, however, the guidelines for perspectiva artificialis often imply a single peeping eye as a starting point. In the early modern period, a number of rare art forms and instruments follow the prescriptive character of linear perspective to ludic ends. By focusing on this special class of what I would call 'monocular art forms', I will analyse the extent to which the perspectival method has been successfully applied in material form beyond the classic two-dimensional paintings. This special class of objects include: anamorphosis, peep-boxes, catoptrics, dioptric perspective tubes, and perspective instruments. It is my intention to draw attention to the different ways traditional perspectival paintings, exceptional cases such as perspective boxes and anamorphoses, and optical devices were encountered in the early modern period. In this thesis I will be examining the specific sites of each case study in depth so as to describe the various contexts—aristocratic, intellectual, religious—in which these items circulated. In Chapter 1 I illustrate a special class of perspective and anamorphic designs that confined their illusions to a peepshow. Chapter 2 examines one of the most consummate applications of the monocular principle of perspective: seventeenth-century Dutch perspective boxes. In Chapter 3, monocular catoptric designs are studied in light of the vogue for mirror cabinets in the seventeenth century. Chapter 4 examines the innovative techniques of drawing machines and their collection in early modern courts through close study of the 'perspectograph.'

Keywords: anamorphosis
optical illusion
monocular vision
linear perspective
Advisor: Grootenboer, H
Cortical reorganisation and tinnitus following restricted peripheral deafferentation in the ferret: targeting neural plasticity by optogenetic silencing

Subjective tinnitus is the perception of a sound in the absence of an environmental source, and is thought to derive from maladaptive neuroplasticity that occurs following hearing impairment. However, the underlying structural and functional mechanisms remain unresolved. Our aims were thus to develop a model of trauma-induced tinnitus, and to investigate whether primary auditory cortex played a causal role.
We tested ferrets on a gap-in-noise detection task to assess auditory temporal processing, which is impaired in tinnitus and hearing loss. Ferrets displayed robust gap-detection performance, with sensitivity that varied with the frequency content and bandwidth of the acoustic carrier noise, as we also found in human subjects tested on a comparable task. This confirmed the ferret as a relevant model of auditory temporal processing.
To investigate hearing-loss-related neuroplasticity, ferrets underwent a partial, unilateral lesion of the spiral ganglion (SG), replicating aspects of otopathology described in tinnitus. Behaviourally, this lesion induced heterogeneous outcomes, with some ferrets displaying temporal processing impairments, and others showing post-lesion adaptation. These behavioural outcomes correlated with features of the auditory brainstem response, indicating a possible predisposition towards adaptation/maladaptation. Anatomical and physiological analysis of auditory cortical cells showed evidence for lesion-related central neuroplasticity that correlated with each animal’s behavioural phenotype.
We finally sought to determine whether these cortical changes underpinned the behavioural changes described. The optogenetic protein Archaerhodopsin-T was expressed bilaterally in auditory cortical neurons of SG-lesioned ferrets, allowing suppression of neural spiking during behaviour. Only contralesional suppression mediated any substantive behavioural effects, improving the performance of animals with temporal processing impairments, and impairing performance in animals with post-lesion improvements. The mechanistic basis for these effects was shown, through physiological recordings, to derive from optogenetic enhancements in cortical temporal processing.
Together, these results suggest that primary auditory cortex plays an important role in mediating deafferentation-related neuroplasticity, suggesting possible strategies for remediation of the maladaptive processing potentially underpinning tinnitus in humans.

Advisor: King, A
Lorenzana, V
Studies of carbon monoxide activation and poison on metallic and enzymatic sites: The new ATR-IR spectroelectrochemical approach

Direct liquid fuel cells (DLFCs) offer a great opportunity to replace traditional fuel combustion with cleaner localised energy production. One of the biggest challenges for developing a commercial DLFC device is the production of CO during fuel oxidation. CO is not only one of the most common intermediates of hydrocarbon fuels oxidation but also a poison of most metal catalysts. In situ infrared (IR) spectroelectrochemical (SEC) techniques have been intensively used to understand the reaction mechanisms for oxidation of different fuels and to study the presence and activation of CO on different bulk metal electrodes. However, there have been few studies of supported nanocatalysts during electrocatalytic turnover relevant to realistic fuel cell devices. In this Thesis, a new attenuated total reflectance IR (ATR-IR) SEC approach is used to study the electrocatalytic oxidation of formic acid and methanol on a commercial carbon supported Pd nanocatalyst (Premetek, USA, 60% Pd / XC-72).
The results from ATR-IR SEC studies of formic acid oxidation on the Pd nanoparticles show CO poisoning, and reveal that this is derived from trace organic impurities present in reagent grade formic acid, rather than from the dehydration of formic acid itself.
The supported Pd catalyst shows very different activities for methanol oxidation in different pH conditions. In acidic conditions, the catalyst is strongly poisoned by adsorbed CO and shows very low activity towards methanol oxidation. On the other hand, in alkaline conditions, only very weak IR signal from adsorbed CO can be detected and the activity of methanol oxidation is much higher compared to the acidic conditions. The detection of strong IR signals from formate suggests that formate acts as a significant reactive intermediate.
In the final part of this Thesis, the possibility of developing a more efficient electrocatalytic system to reduce greenhouse gas CO2 to hydrocarbon feedstocks is demonstrated by using a composite catalyst which comprises an enzyme to reduce CO2 to CO, and copper nanoparticles for further reduction of CO.
Overall this Thesis provides insight into the activation of CO at metal sites during electrocatalytic reactions which are relevant to energy technologies.

Advisor: Vincent, K
Intestinal tissue engineering

Tissue engineering (TE) principles have been successfully clinically applied to treat disease affecting specific organs (e.g. trachea) but developments in some organs has lagged behind. The inability to repair or replace significantly damaged intestinal tissue remains a barrier to improving patient outcomes and the promise of Tissue Engineered Intestine (TEI) that was first made more than 20 years ago, is yet to be realised.
This work explored the potential of TEI and literature review formed a basis for developing a clinically transferrable experimental model. It was hypothesised that, porcine large intestine could be retrieved from pigs and decellularized to create a biological scaffold that demonstrated favourable properties for TE, including potential for vascular perfusion and cell engraftment. Novel experiments were performed in intestinal retrieval and decellularization, resulting in scaffolds characterised by a number of methods (e.g. histology, immunohistochemistry). Assessment of the scaffold’s ability to support cell engraftment required development of protocols for isolation and culture of appropriate progenitors, including adipose/ bone marrow derived mesenchymal stromal cells and intestinal organoid units. Finally, in-vitro cultures combining scaffolds and cells were used to assess the ability of scaffolds to promote tissue regeneration.
Perfusion decellularization methods proved effective in creating biological scaffolds that retained radiologically demonstrated vascular perfusion networks, permitting a future route for recellularization and/or transplantation. Scaffolds demonstrated retention of essential extracellular matrix components (e.g. glycosaminoglycans, collagen) and an absence of cell nuclei. Mesenchymal stem cells were isolated, cultured and combined in-vitro with scaffolds in an attempted scaled-down seeding model. Control of culture conditions was challenging and results inconclusive with respect to the scaffold’s regenerative potential. The work demonstrates an exciting prospect for biological scaffold development for a clinically transferrable, semi-xenogeneic transplant or drug delivery model but further experiments in scaffold seeding are required to assess the full potential.

Keywords: Tissue Engineering
Transplantation
Intestine
Advisor: Friend, P
Ansari, T
Clinical translation of a simple cognitive task to reduce the occurrence of intrusive memories after a psychological trauma

Preventive interventions after psychological trauma are lacking. Intrusive memories in the first few weeks after a traumatic event can be highly distressing, and also predict later post-traumatic stress disorder (PTSD). Laboratory studies with healthy volunteers have found that engaging in a visuospatial cognitive task soon after an experimental trauma film can reduce the frequency of intrusive memories over the following week. The aims of this research were to a) develop the a simple cognitive task intervention (a memory reactivation cue followed by playing the computer game "Tetris") for use in a hospital emergency department (ED) with patients who had experienced a road traffic accident, and b) provide a preliminary test of the efficacy of the intervention using a randomised controlled trial design.
First, the current evidence base for preventive interventions after trauma was reviewed, and theory was drawn from experimental psychology and clinical psychology to propose that delivering a simple cognitive task involving playing Tetris in the immediate aftermath of trauma may offer a novel preventive intervention for PTSD symptoms (Chapter 1). Next, the laboratory procedure was adapted for use in a hospital ED, based on direct observation in the ED, and existing literature (Chapter 2).
An initial pilot study (n = 10) tested key procedures in the ED, namely recruitment of road traffic accident patients, practical delivery of the intervention and completion of an intrusion diary over the first week (Chapter 3). A second pilot study (n = 23) was conducted to improve the study procedures, test both the intervention and control conditions, and assess participant experience (Chapter 4). The recruitment rate, eligibility criteria, drop-out rate and completion rate of the intrusion diary were all improved. Participant feedback was used to refine the intervention and control procedures.
Finally, a main randomised controlled study (n = 71) was conducted, comparing the simple cognitive task intervention with usual care in the emergency department (with a simple activity diary). As predicted, participants in the intervention group had fewer intrusive memories in the first week, and less severe clinical intrusion symptom scores, than those in the control group. Further, participant feedback highlighted the value of being offered an intervention in the emergency department. This research was the first to successfully translate laboratory findings to a clinical emergency department setting. Findings provide a first step towards developing an accessible, low intensity preventive intervention to target intrusive memories after trauma. Further trials and mechanism studies are warranted.

Keywords: Trauma
Behavioural intervention
Computerized treatment
Cognitive intervention
Intrusive memories
Preventive intervention
Post-traumatic stress disorder
Advisor: Holmes, E
Geddes, J
Nobre, K
A GIS-based analysis of hillfort location and morphology

Moving away from the highly regionalised and constrained purely humanistic and empirical studies of hillfort location and morphology, this study is a multi-regional GIS-based analysis of the form and siting of several groups of hillforts across Britain.
Hillforts in Dartmoor, Aberdeenshire, The Gower and Warminster are assessed, four regions that are topographically diverse. The highly varied topography of these regions also tests the GIS-basis of this study, another important intrinsic aspect of this novel research. GIS-based analysis has never before been applied to a study of hillfort location and morphology to this degree and, as with any innovative methodology its worth has to be tested and assessed.
The thesis demonstrates that GIS-based analysis, when combined with field visits, provides a fundamental insight into the possible influences of hillfort location and morphology, which fieldwork alone will never be able to do. The GIS-based analysis developed here focuses largely upon examining degrees of movement and visibility. Unlike other GIS-based analyses of movement and visibility this integrates the two to examine visual pathways across landscapes to further investigate the visual qualities of hillforts within the various test areas.
The study demonstrates that GIS-based analysis when combined with fieldwork can be affectively applied to qualitative based questions surrounding hillfort location and morphology. The overall results of this analysis had some relatively predictable results whilst there were some very surprising cases. A large number of entrances were placed within the most accessible area, however in the case of Battlesbury there was evidence for the complete disregard to accessibility within the orientation of its northwestern entrance. There were also numerous examples of the placement of a site's most prominent morphological components in correlation with the blind pathways. In these cases sites were orientated to encourage an element of surprise upon the approaching travellers.

Advisor: Lock, G
Ralston, I
Assume-guarantee strategy synthesis for stochastic games

This thesis presents a framework for the automatic strategy synthesis from quantitative specifications, in order to control autonomous systems. We model systems as turn-based two-player zero-sum stochastic games, which are able to express both stochastic and nondeterministic environmental uncertainty. Given a system model and a specification, we define the strategy synthesis problem as that of finding a strategy for the system that is winning against every environment. Since large, complex systems are typically built from multiple components, we consider synthesis of strategies for the individual components separately, which can then be composed to a winning strategy for the full system. Modelling interaction between components is facilitated using assume-guarantee rules, which can express contracts such as "maintain the room temperature of at least 20°C, as long as the windows are closed at least 30% of the time." For the synthesis of strategies for the individual components, we develop synthesis algorithms for Boolean combinations of long-run objectives, specifically, maintaining above a threshold (i) a mean-payoff, almost surely; (ii) an expected mean-payoff; (iii) a ratio of rewards, almost surely; or (iv) a ratio of expected rewards. We implement our algorithms in the PRISM-games 2.0 tool and demonstrate their viability on four case studies.

Advisor: Kwiatkowska, M
Bias and discrimination in intra-household food allocation: case study of a rural labour population in northeast Brazil

My thesis examines food allocation and nutritional outcomes in a sample of 152 individuals in thirty-two households of sugarcane workers in the municipality of Gameleira, Northeast Brazil. Anthropometric data show that undernutrition and overnutrition coexist in the study population, and often within households – a consequence of the changes in diet and physical activity linked to the nutrition transition. Food allocation was examined using an indicator of the frequency of consumption of high status foods - non-staple foods which are considered more desirable than staples because they add variety and taste to an otherwise monotonous diet. I created an intra-household index of food allocation in order to observe each individual's consumption in relation to the average in his or her household at two seasonal points of the year. The sample was split into two groups, a group of more affluent households in which high status foods were eaten on the harvest and non-harvest dietary recalls, and a group of less affluent households in which no-one ate high status foods on the non-harvest recall.
I found gender biases in the allocation of food in favour of men relative to women, and girls relative to boys, in the higher income group, but no gender biases in the group of less affluent households. In relation to age, I found biases in favour of children relative to adults in less affluent households, but not during seasonal shortage in the higher income households. The biases were greater in households with higher incomes, but lower in households in which women controlled some household income relative to households in which men controlled all income. I considered whether discriminatory behaviour underpins these biases, based largely on periods of observation in a sub-sample of six households, and concluded that food distribution operates as a powerful medium for the expression of differential status among men and women, but not among boys and girls, who have equal status in this population.

Keywords: nutrition transition
mixed methods
Brazil
food systems
seasonality
gender
food security
discrimination
intra-household food allocation
Advisor: Harriss-White, B
Improvements to ensemble methods for data assimilation in the geosciences

Data assimilation considers the problem of using a variety of data to calibrate model-based estimates of dynamic variables and static parameters. Geoscientific examples include (i) satellite observations and atmospheric models for weather forecasting, and (ii) well-log data and reservoir flow simulators for oil production optimization. Approximate solutions are provided by the set of techniques deriving from the ensemble Kalman filter (EnKF), which combines a Monte Carlo approach with assumptions of linearity and Gaussianity. This thesis proposes some improvements to the accuracy and understanding of such ensemble methods.
Firstly, a new scheme is developed to account for model noise in the forecast step of the EnKF. The main aim is to eliminate the sampling errors of additive, simulated noise. The scheme is based on the previously developed "square root" schemes for the analysis step, but requires further consideration due to the limited subspace spanned by the ensemble. The properties of the square root scheme in general are surveyed.
Secondly, the "finite size" ensemble Kalman filter (EnKF-N) is reviewed. The EnKF-N explicitly considers the uncertainty in the forecast moments (mean and covariance), thereby not requiring the multiplicative inflation commonly used to compensate for an intrinsic bias of the analysis step of the standard EnKF. Thus, in the perfect model setting, it avoids the process of tuning the inflation factor. This presentation consolidates the earlier literature on the EnKF-N, substantiates the scalar inflation perspective, and rectifies a deficiency.
Thirdly, two ensemble "smoothers" expressed by different recursions, used in different applications, and hitherto thought to yield different results, are shown to be equivalent. The theory is revisited under practical considerations, where equivalence is broken due to inflation and localization, but the methods remain equally capable.
In each case, the theory is tested and the accuracy performance is benchmarked against standard methods using numerical twin experiments.

Keywords: Ensemble Kalman filtering
State estimation
Data assimilation
Advisor: Farmer, C
Moroz, I
Bertino, L
Strong state, weak system: social health insurance in rural China 1956-2007

A question of great interest to China watchers is whether or not central mandates are successfully implemented, and how. The issues surrounding this question are at the heart of the analysis in this thesis about China's attempts to institute social health insurance schemes in rural areas from 1949 to 2007.
The thesis looks at central government attempts to institute social health insurance schemes between 1949 and 2007 and tries to explain the significant variation in enrolment in social health insurance across this experience.
The study shows that implementation of social health insurance schemes in rural China, measured in terms of their widespread uptake, succeeded on two occasions. There also have been a number of failures and collapses of social health insurance schemes in rural China.
To explain the variation, the thesis first constructs a framework of how rank and authority of decrees work in the Chinese Communist Party. This framework allows an evaluation of how implementation decrees are transmitted down from the centre to local areas (who implement policy).
The thesis argues that the issuing of a central decree holding the local Party secretary to account for high enrolment is the necessary and sufficient condition for the central government to ensure high enrolment in social health insurance schemes. The issuing of a central decree is shown only to be a necessary condition, but not a sufficient condition. And the holding of the local Party secretary to account must occur through the Party governance system rather than through the health governance system.
The thesis shows that the rise, fall, failure to rise, and then unexpected rise of social health insurance can be explained by the systems of coordination and control used to hold the local Party secretary responsible for ensuring high levels of enrolment in health insurance. It shows that only the local Party secretary can mobilise the local state sufficiently to meet central decree. And only certain central decrees can motivate the local Party secretary sufficiently to mobilise the local state.
The thesis concludes by applying this framework to broader questions of health system reform in modern-day China. It draws tentative conclusions as to how wider health system reform can be understood through the thesis' analytical framework and suggests testing this framework in other policy contexts.

Advisor: Yip, W
Drysdale, P