VictorJuiz/thesis huggingface dataset:
Public priorities and public goods: the drivers and responses to transitions in flood risk management

This thesis examines the role of the public in Flood Risk Management (FRM) service provision at a time when the perceptions of the distribution of beneﬁts provided by FRM interventions are in ﬂux, and the role the public should play in FRM highly contested among stakeholders. Two schemes have marked the revised role of the public in FRM – Partnership Funding and Flood Re – both of which challenge existing judgments of the excludability and rivalry of beneﬁts delivered by FRM interventions. The Partnership Funding scheme allocates capital for FRM projects proportionately to the public beneﬁts they provide, allowing communities to top-up grants through local contributions. In comparison, by increasing accessibility to affordable insurance through cross-subsidies and pricing signals, Flood Re highlights a growing recognition that the distribution of gains as a result of widespread insurance uptake is greater than the beneﬁts received by the policyholder alone. Following the identiﬁcation of these schemes, we tested their social feasibility, examining both the scale and distribution of beneﬁts. Due to the different stages of implementation of each scheme at the time of writing this thesis, two distinct methods were developed. The Partnership Funding Chapter used ﬁeld data to examine how public-private funding of ﬂood defences has changed service provision and the public acceptance of this transition. Whereas the Flood Re chapter used computer-based experiments to hypothesize how Flood Re may make the purchase of insurance a more or less attractive investment for different types of consumer. We found that Partnership Funding enabled more FRM projects to go ahead, raised public awareness of ﬂood risk, and improved collaboration between stakeholders, but encouraged lower-cost projects, which, in the longer term, could transfer the expense of managing residual risk to the householder. In comparison, Flood Re provided peace of mind to householders struggling to afford rises in insurance premiums, but disproportionately beneﬁted those who annually purchased insurance. Combining this proposed inequity in Flood Re with increasing residual risks, we identify a gap in service provision for the public who cannot afford household mitigation measures. We propose that loss mitigation and ﬂood defence should become increasingly collaborative in line with the complexities of ﬂooding within a community. We seek a move away from the information asymmetry which currently exists between insurance providers and policyholders, and yet simultaneously call for local authorities to recognise the capacity of the public to participate in FRM, and sustain resilience in the face of rising ﬂood risk.

Keywords: insurance
agent based models
Partnership Funding
agent-based modelling
flood risk management
decision making
social feasibility
Prospect Theory
social contract theory
multiagent systems
Flood Re
Advisor: Hall, J
Market design, borders, and gravity in the virtual world

This thesis consists of three separate papers which examine different aspects of the economics of online commerce.
The first paper studies a natural experiment in the release of a new ad targeting feature onto an online advertising platform. The experiment affects the specificity of advertising assets in certain geographic ad markets. The paper finds evidence that the additional specificity negatively affects auction participation in the treated areas, an effect that has not been anticipated by the incumbent theoretical literature. The paper also finds evidence that despite negatively affecting auction participation, the additional specificity leads to higher revenue growth for the online platform in the treated areas. The paper’s results highlight the importance of considering entry and exit decisions in theoretical models of specificity choices by market designers.
The second paper uses a proprietary data set from Google to find that online trade between two US states or two Canadian provinces is 6.7 times higher than trade between a US state and a Canadian province. This finding is surprising given that in the online environment, information costs and business-to-business transactions involving intermediate inputs are largely absent. When disaggregating the data by sectors of economic activity, the study finds that the largest US-Canada border effects occur for services whose consumption is tied to a particular location and goods that face large regulatory hurdles at the border.
The third paper analyzes geographical patterns of cross-country Internet transactions using proprietary data from Google. The paper finds the effect of distance on online trade to be around -0.53. The study also finds that cultural characteristics, such as shared languages or religions, have a large impact on e-commerce, while economic ties, such as a common currency, have an insignificant effect. The paper underlines the importance of accounting for selection into trade in worldwide gravity estimations and identifies two exclusion restrictions that can be used when examining online trade flows.

Advisor: Javorcik, B
Moving towards an evidence-base of democratic police training: the development and evaluation of a complex social intervention in the Israeli border police

The centrality of the police in everyday life means police officers are in position of power to actively support or threaten democratic activities (Sklansky, 2008) for example during protests. In democracies, policing duties should be performed in ways that sustain democratic values, rather than undermine them (Loader, 2006), yet that is not always the reality. Police training is one of the tools for aligning officers' behaviour with societal norms; it is considered a protection against the possibility that police officers abuse the wide-ranging powers they hold (Manning, 2010). Training programs are therefore a basic feature of all police forces' organizational approach. Despite its centrality, training has not received extensive academic attention; there is a pressing need to understand the impact of training on police behaviour and the mechanisms thorough which it operates (Skogan & Frydl, 2004).
This thesis attempts to advance the evidence-base of democratic police training following the Medical Research Council's framework for the development and evaluation of complex social interventions (Craig et al., 2008). The Israeli Border Police was chosen as the context to examine the potential of training to advance democratic norms. The three stages of the research project included: theoretical modelling of the existing complex training intervention to assess its alignment with existing evidence; participatory development and piloting of a training curriculum on policing of protests in a democracy that used an Adult Education approach and introduced Procedural Justice-related components; and a pilot quasi-randomised study to evaluate this training. Analysis and reporting are carried out in a way that allows assessment of prospective scale-up and generalisability.
Flowing from the empirical work, four strands of theoretical contributions are put forward. First, a theoretical model of police training is proposed, drawing on social psychology constructs. Second, contact theory, which originates in peace education, is proposed as a possible platform for designing both police training and their evaluation studies. Third, four factors limiting the efficacy of Procedural Justice & Legitimacy based training interventions in deeply divided societies are outlined. Fourth, the Border Police case study is used to substantiate the value of participatory research methods for advancing knowledge translation and evidence-based policing.

Keywords: protests
democratic policing
evidence-based practice
police training
Advisor: Montgomery, P
Fruits of the forest: human stable isotope ecology and rainforest adaptations in Late Pleistocene and Holocene Sri Lanka

Despite ecological, anthropological, and archaeological debate surrounding their desirability as habitats for human occupation, tropical rainforests have received relatively little attention in discussions of Homo sapiens' Pleistocene dispersal. Sri Lanka has yielded some of the earliest dated fossil and material culture evidence (c. 38-35,000 cal. years BP) for our species in a modern rainforest context beyond Africa. Nevertheless, assertions in Sri Lanka, and elsewhere, regarding early human rainforest reliance have been largely based on coarse or 'off-site' palaeoenvironmental records, and the overall role of these environments in human subsistence strategies has remained uncertain.
This study applies stable carbon and oxygen isotope analysis to Sri Lankan human fossil, and associated faunal, tooth enamel dated to between 36-29,000 and 3,000 cal. years BP, in order to directly test human rainforest resource reliance, reconstruct a stable isotope ecology, and develop 'on-site' palaeoenvironmental records for Late Pleistocene-Holocene Sri Lankan rainforest foragers. Stable carbon and oxygen isotope analysis of modern Sri Lankan primates, and stable carbon, oxygen, and nitrogen isotope analysis of modern plant samples from the Polonnaruwa Nature Sanctuary, are also performed to investigate the ecology of Sri Lankan primates on which Late Pleistocene-Holocene forager subsistence strategies were focused.
The results demonstrate that Homo sapiens relied on rainforest resources in Sri Lanka from c. 36-29,000 cal. years BP until the Iron Age c. 3 cal. years BP, even when open environments, and their corresponding resources, were available. This remains the case through periods of evident environmental change at the Last Glacial Maximum and even upon the arrival of agriculture in the island's tropical forests. The primate stable isotope data prove difficult to interpret as ecological niche separation in the absence of observation data. Nonetheless, humans were evidently able to not only use but also rapidly specialise in the exploitation of South Asia's rainforests.

Advisor: Lee-Thorp, J
Petraglia, M
Paleovirology and the evolution of virus-host gene exchange

Paleovirology is the study of viruses at large evolutionary timescales through the investigation of endogenous viral elements (EVEs) that are found in host genomes. EVEs are the result of a heritable, genomic integration of a viral genome in a host germline cell. The presence of retroviral sequences in animal genomes has been recognized since the 1970’s, but discoveries made in the last five years have revealed that viruses of all genome types can endogenise. Moreover, although most EVEs are non-functional relics, there are a number of examples of functional EVEs that are co-opted to benefit the host. There remain some methodological challenges in the identification and analysis of EVEs, and we have yet to fully understand the evolutionary processes involved in the rare instances of co-option. In this thesis, I develop novel techniques to identify and characterize large herpesviruses, which lead to the discovery of the first endogenous herpesvirus in the genome of the Philippine tarsier. The same methods were redeployed to identify a new family of dsDNA virus in the genome data of their hosts. Among the 15 different new species of virus, at least four viruses in four different host fish exhibit characteristic features of EVEs such as non-sense mutations and the accumulation of transposable elements. Moreover, more than half of the predicted genes in a full-length salmon virus have no detectable similarity to known genes. The second investigative theme of this thesis explored the idea that EVEs can sometimes be the result of adaptive gene transfer, and that this is the conceptual equivalent of viral genes that are host-derived. Considering a subset of rare, functional EVEs that act as antiviral genes, I developed an evolutionary framework to understand such gene transfers as a biological strategy within the evolutionary arms race between viruses and hosts. In viruses, I conducted a systematic genome-wide evolutionary analysis of host-derived genes, which revealed a consistent shift towards higher purifying selection when switching from host to virus genome. Finally, this thesis also considered the evolution of gene transfer between viruses, by investigating the intriguing history of a retroviral superantigen gene with similarity to genes in unrelated herpesviruses. Through the evolutionary reconstruction of a large group of mammalian EVEs, I was able to prove the independent horizontal gene transfer of superantigens from retroviruses to herpesviruses from two different donor lineages. This shows that viral gene capture can occur in an evolutionary manner, and demonstrates the utility of paleovirological methods in understanding the evolution of pathogenicity. Altogether, this thesis highlights the results of synthesizing methods from paleovirology with metagenomic techniques, demonstrating that genomic databases are themselves rich with novel viral biodiversity that hold key insights for virology, genomics and evolution.

Keywords: Paleovirology
Horizontal gene transfer
Advisor: katzourakis, A
Probing tandem epigenetic reader domains

Epigenetic signals include chemical modifications on DNA and post-translational modifications to amino acids in histone proteins. One of the most common sites of modification are lysine residues: addition of acetyl or methyl groups are recognised by "reader" domains including bromodomains and plant homeodomains (PHDs). These domains mediate protein-protein interactions, affecting downstream events including gene transcription. PHDs and bromodomains are found in close proximity within some proteins, raising the possibility of combinatorial signalling eliciting a range of responses. Tripartite motif-containing proteins 24 and 33 (TRIM24 and TRIM33) contain an adjacent PHD and bromodomain which recognise methylation and acetylation states of lysine residues, respectively (Figure 1). These interact with histone-mimicking peptides that display a specific combination of unmodified, trimethylated and acetylated lysine residues. Work has been carried out towards inhibition of these epigenetic readers, through target analysis, assay development, and screening of putative binding partners. Refinement of expression systems for TRIM24 and TRIM33 enabled structural investigations, and development of biophysical assays to provide screening capacity. These assays were used to further characterise interactions through profiling varyingly modified histone-like peptides. Based on structural information and computational modelling, an in silico screen was performed to identify putative binding partners, and generate a chemical pharmacophore. In vitro screening of a bespoke collection of compounds based on these results, was supplemented with a broad screen targeting protein-protein interactions. Subsequent rounds of validation identified four compounds which bind to either TRIM24 or TRIM33 (Figure 2). Prompted by the reliance of competition based assays on knowledge of a high affinity interaction with a ligand or peptide, a dimethylisoxazole unit was used as an acetyl lysine mimicking residue. Incorporation in a histone-like peptide, via selective alkylation, resulted in increased affinity of the peptide to the BRD4 bromodomain. Application to epigenetic reader systems with unknown cognate binding partners would improve assay capacity for ligand identification. This approach will facilitate synthesis and screening of novel probe molecules, to elucidate the function of tandem recognition domains in interpreting the "epigenetic code".

Advisor: Conway, S
Grimley, R
Storer, I
Dynamic functional imaging of the response of lung tumours to a potential hypoxia modifier

In this thesis, the kinetics of fluoromisonidazole (FMISO) uptake by lung tumours in patients with advanced stage non-small cell lung cancer (NSCLC) is analysed. The uptake data was extracted from dynamic positron emission tomography (PET) images collected in the course of a clinical trial designed to investigate the impact of Buparlisib, a potentially hypoxia-modifying drug, on perfusion and hypoxia in NSCLC patients. The trial design is a 3+3 dose escalation study exploring the effect of daily doses of 50 mg (Cohort 1), 80 mg (Cohort 2), and 100 mg (Cohort 3) Buparlisib.
Many trials combining drug and RT fail in the clinical setting despite yielding promising pre-clinical data: the work described here uses and develops kinetics analysis techniques that can be applied to proof-of-principle dynamic PET imaging studies. For whole tumour FMISO kinetics analysis it has been shown that an irreversible three-compartment model is optimal, whereas for voxel-by-voxel analysis an irreversible two-compartment model is optimal. A clustering method is also presented to distil the information from the noisy voxel-by-voxel kinetics data into the minimum number of clusters that adequately describe the data.
Analysis of both PET kinetics and perfusion CT has shown significant decreases in the rate of tracer flow from blood into the tumour post-Buparlisib (in Cohorts 2 and 3). Voxel-by-voxel analysis found that this occurred throughout the tumour volume. The volume of blood within the tumour was shown to increase significantly after Buparlisib according to the PET kinetics analysis, whereas analysis of perfusion CT data showed a decrease post-Buparlisib. For Cohorts 2 and 3, significant decreases were seen in tumour volumes hypothesised to be hypoxic (tumour-to-blood ratio greater than 1.4) after administration of Buparlisib. The estimated FMISO intracellular binding rate-constant (associated with cellular oxygen concentration) according to the voxel-by-voxel kinetics analysis was found to significantly decrease at the tumour edge and significantly increase in the tumour centre, with an overall decrease for Cohort 3.

Advisor: Fenwick, J
Higgins, G
Gleeson, F
The lived experience of inequality in post-apartheid South Africa: measuring exposure to socio-economic inequality at small area level.

South Africa has undergone a remarkable political transformation since the birth of democracy in 1994, yet it remains plagued by extremely high levels of socio-economic inequality, violent crime and social unrest. Although inequality is often regarded as a major driver of many social problems, the evidence base concerning inequality in South Africa is relatively limited, consisting primarily of national level Gini coefficients or General Entropy measures based upon household income, expenditure or consumption data. In this thesis I argue that these broad national level measures say little about people's actual day-to-day lived experiences of inequality and how these individual experiences of inequality may be shaped by the local geographical areas in which people live and go about their daily lives. I construct a series of empirical measures of exposure to socio-economic inequality which reflect the socio-spatial environments in which people live. I argue that these new measures can be used as explanatory factors in the study of other social outcomes, both at an individual level (for example, individuals' attitudes) and at an area level (for example, rates of violent crime). Exposure to inequality is measured both from the perspective of the 'poor' population and the perspective of the 'non-poor' population and the measures are constructed and presented at small area level using the Datazone statistical geography. I analyse the spatial distribution of exposure to inequality and find that exposure to inequality is typically highest in urban neighbourhoods, particularly in the major metropolitan areas. I develop a measure of intensity of exposure in order to highlight areas with both high exposure and high levels of deprivation. I also present one example of how my new measures can be used to explore associations with other outcomes, specifically looking at the relationship between people’s lived experience of inequality and their attitudes towards inequality and redress.

Keywords: Residential segregation
Neighbourhood
South Africa
Inequality
Poverty
Lived experience of inequality
Advisor: Noble, M
Wright, G
Enhancing communication privacy using trustworthy remote entities

Communication privacy is the property of a communication system that enables two or more distrusting participants to exchange information without compromising their privacy, with respect to internal and external adversaries. It encompasses aspects of anonymous communication as well as data privacy. A real-world example of the need for communication privacy is the smart energy grid, in which networked smart meters frequently measure energy consumption and communicate with grid operators. Privacy concerns arise from the possible inference of sensitive information from these measurements.
Using smart grid communication privacy as a case study, this thesis introduces the concept of the Trustworthy Remote Entity (TRE). The TRE is an intermediary between distrusting participants that performs privacy-enhancing computations on the exchanged information. Unlike cryptographic secure multiparty computation protocols, this approach does not increase participants' computational or communication complexity. In contrast to a trusted third party, this trustworthy entity uses trusted computing and remote attestation to establish attestation-based trust relationships. As a single-function system, the TRE requires only a minimal software Trusted Computing Base, thus minimizing its attack surface and making it an ideal candidate for security audits. Two research hypotheses are investigated: firstly that the TRE can be realized and used to enhance consumers' privacy in the smart grid, and secondly that the TRE concept can be formalized and used in other application domains.
This thesis confirms both hypotheses and, in doing so, presents five main contributions. Firstly, it proposes a new methodology for modelling and analysing communication privacy terms of unlinkability and undetectability, which is implemented in the CSP process algebra and used to enhance the Casper/FDR analysis tool. Secondly, it presents and analyses a new TRE-based smart grid communication architecture. Thirdly, it compares different TRE system architectures and evaluates a fully functional TRE prototype. Fourthly, it defines a new highly-scalable remote attestation protocol for establishing the TRE's trustworthiness. Finally, it formalizes the fundamental characteristics of the TRE concept and demonstrates how the TRE can be used to enhance communication privacy in location-based services and wireless network roaming.

Keywords: Privacy
Trusted Computing
Trusted Third Party
Smart Energy Grid
Advisor: Martin, A
Brown, I