VictorJuiz/thesis huggingface dataset:
The population dynamics of plasmid-mediated antibiotic resistance in salmonella typhimurium in chickens

A model of growth and plasmid transfer between strains of Escherichia coli and Salmonella typhimurium was developed with reference to the literature. This was the organising principle for the collection of a complete set of in vitro life history parameters of one S. typhimurium and one E. coli strain. In the course of estimating these parameters two results of note were obtained. Fits of the Lotka-Volterra competition model were obtained for data on S. typhimuiurm growing in competition with E. coli. The first noteworthy discovery was the failure of this model to account for several characteristics of growth of these strains under competition. The growth rates of plasmid-bearing and plasmid-free strains were obtained. The second main result came from examination of the results of the growth rate data, which revealed that the cost to S. typhimuiurm 576 of bearing the resistance plasmid was low (4%). The model was also used to simulate the effect of antibiotic dose on the density of the donor, recipient and transconjugant populations over time. These simulations predicted that there would be a convex relationship between antibiotic dose and transconjugant density (i.e. that the density would first rise, then fall, with increasing dose). Following from this result, laboratory experiments and in vivo experiments in chickens were directed towards obtaining information on the relationship between these two variables. This convex relationship was not demonstrated within a single experiment, although some experimental environments produced an increase in transconjugant density with dose, and others, a decrease. Few transconjugants were formed in vivo. In order to investigate the low cost of resistance and low rate of in vivo transconjugant production, cost of resistance and plasmid transfer rate of this plasmid in several strain combinations of E. coli and S. typhimuiurm was evaluated.

Advisor: McLean, A
Gupta, S
Barrow, P
Communists constructing capitalism: socio-economic uncertainty, Communist party rule, and China's financial development, 1990-2008

To what extent does China's experience of economic reform since 1989 compel a reconsideration of the ontological foundations of contemporary capitalist development? China's political economy remains characterized by a unique and resilient political structure (the Chinese Communist Party) that penetrates both 'private' (market) and 'public' (state) organizations. The conceptual rootedness of contemporary theories of comparative and international political economy in a distinctly Western historical experience of capitalist development hinders their ability to understand Chinese capitalism on its own terms—as historically, culturally, and globally embedded. To generate greater analytic traction in understanding China's otherwise paradoxical constellation of actors and dynamics, I argue that contemporary capitalism should be studied as a set of mechanisms for managing and exploiting socio-economic uncertainty, rather than according to the binary logics of state regulation and market competition. These mechanisms can be conceptualized as an overarching risk environment. On this basis, I trace how the cognitive frames, social institutions, and relational networks that emerged within the 'socialist market economy' in China's post-Tiananmen financial system have placed the Chinese Communist Party at the nexus of the state and the market. I argue that specific ideas emerged about how to manage the flow of capital, playing a significant role in underpinning expectations of financial growth and stability. During this period the financial system underpinned the CCP's capacity to both manage and exploit socio-economic uncertainty through the path of reform, forming a central explanatory factor in a developmental trajectory marked by a trifecta of rapid economic growth, macroeconomic stability, and deepening socio-economic imbalances. Rather than viewing the path of financial reform in China solely in terms of 'partial' or 'failed' free- market reform, it thus becomes possible to cast China's development in a new light as the product of a more concerted vision of how the financial system would enable a mode of economic development that combined the drive for capital accumulation with the distinctive socio-political circumstances of post-1989 China.

Keywords: China
Chinese Communist Party
economic sociology
capitalism
financial governance
Advisor: Hurrell, A
Applications of focal-series data in scanning-transmission electron microscopy

Since its development, the scanning transmission electron microscope has rapidly found uses right across the material sciences. Its use of a finely focussed electron probe rastered across samples offers the microscopist a variety of imaging and spectroscopy signals in parallel. These signals are individually intuitive to interpret, and collectively immensely powerful as a research tool. Unsurprisingly then, much attention is concentrated on the optical quality of the electron probes used. The introduction of multi-pole hardware to correct optical distortions has yielded a step-change in imaging performance; now with spherical and other remnant aberrations greatly reduced, larger probe forming apertures are suddenly available. Probes formed by such apertures exhibit a much improved and routinely sub-Angstrom diffraction-limited resolution, as well as a greatly increased probe current for spectroscopic work.
The superb fineness of the electron beams and enormous magnifications now achievable make the STEM instrument one of the most sensitive scientific instruments developed by man, and this thesis will deal with two core issues that suddenly become important in this new aberration-corrected era. With this new found sensitivity comes the risk of imaging-distortion from outside influences such as acoustic or mechanical vibrations. These can corrupt the data in an unsatisfactory manner and counter the natural interpretability of the technique. Methods to identify and diagnose this distortion will be discussed, and a new technique developed to restore the corrupted data presented. Secondly, the subtleties of probe-shape in the multi-pole corrected STEM are extensively evaluated via simulation, with the contrast-transfer capabilities across defocus explored in detail. From this investigation a new technique of STEM focal-series reconstruction (FSR) is developed to compensate for the small remnant aberrations that still persist – recovering the sample object function free from any optical distortion.
In both cases the methodologies were developed into automated computer codes and example restorations from the two techniques are shown (separately, although in principal the scan-corrected output is compatible with FSR). The performance of these results has been quantified with respect to several factors including; image resolution, signal-noise ratio, sample-drift, low frequency instability, and quantitative image intensity. The techniques developed are offered as practical tools for the microscopist wishing to push the performance of their instrument just that little bit further.

Keywords: Scan-noise
Focal-series
Advisor: Nellist, PD
Kirkland, A
Quantitative study of Clostridium difficile transmission using extensive epidemiological data and whole genome sequencing

Clostridium difficile is a leading healthcare-associated infection, which causes diarrhoea, and is almost exclusively precipitated by antibiotic exposure. Traditionally C. difficile infection (CDI) has been considered predominantly transmitted within hospitals. However, endemic spread hampers identification of the source of infections, and therefore control and prevention of disease.
A cohort of consecutive hospital and community CDI cases in Oxfordshire from September 2007 to March 2011 was investigated. For each case hospital admission, ward movement and demographic data were available allowing contact events between cases to be reconstructed. Initially 944 cases to March 2010 underwent multilocus sequence typing (MLST), subdividing the endemic cases into 69 distinct lineages and demonstrating unexpectedly that ward-based contact with known symptomatic CDI cases only accounts for <25% of disease.
To better determine the extent of transmission arising from symptomatic patients, irrespective of the route transmission, isolates from 1223 cases to March 2011 underwent whole genome sequencing. Serially sampled patients with recurrent or on-going disease were used to estimate rates of C. difficile evolution and within-host diversity and to show 0-2 single nucleotide variants (SNVs) are expected between transmitted isolates obtained <124 days apart (95% prediction interval). Mixed infection with more than one strain was investigated, but probably plays only a minor role in onward transmission.
In the Oxfordshire CDI cohort, 333/957 (35%) CDI from April 2008 – March 2011 were within 2 SNVs of ≥1 previous case since September 2007 (consistent with transmission). 428/957 (45%) were >10SNVs from all previous cases: these distinct subtypes continued to be identified consistently throughout the study, suggesting cases arise from a considerable reservoir of C. difficile. Surprisingly, declines in the incidence of genetically-related CDI were similar to those in genetically distinct CDI suggesting interventions not just targeting symptomatic individuals, e.g. antimicrobial stewardship, have played a significant role in recent CDI declines.
Finally, the feasibility of studying asymptomatic inpatients as potential source of the unexplained transmission was investigated.
This thesis provides convincing evidence, in a setting with typical CDI incidence and infection control practice, that only the minority of CDI arises from other symptomatic cases. It demonstrates that much CDI arises from genetically diverse reservoirs, with each exposure resulting in relatively few secondary cases. Future control strategies therefore need to focus on identifying these reservoirs, one of which is plausibly asymptomatic inpatients, and also on interventions that prevent the transition from exposure and colonisation to disease, such as antimicrobial stewardship.

Keywords: whole genome sequencing
Clostridium difficile
transmission
Advisor: Peto, T
Walker, A
Harding, R
Towards understanding Internet loyalty through customer preference structures

This research is an exploration of how the capabilities of the Internet may have influenced customer preference structures and how these influences may, in turn, have affected loyalty behaviours. These relationships are explored from both customers’ and companies’ perspectives.
A theoretical model is developed which comprises four main components. These are (1) pre-purchase preference structures; (2) post-purchase preference structures (3) the Internet channel and (4) loyalty behaviours. The Internet channel is shown as having a modifying effect on pre- and post-purchase preference structures, which in turn relate to influences in loyalty behaviours.
From the customer’s perspective the theoretical model was quantitatively tested by developing pre- and post-purchase preference structures from a choice-based conjoint experiment on a sample of online and offline grocery shoppers. The results showed that these preference structures differed significantly on a number of attributes. The theoretical model was further tested by linking the utility values from the choice-based conjoint experiment to loyalty variables in a structural equation model. The results showed that the theoretical model needed adjustment to fit the underlying data. The offline shoppers’ group model had a better fit to the data than did the online group.
The company perspective was developed through a longitudinal study of four U.K. companies in different industries. The qualitative data collected in these studies was compared and contrasted with the theoretical model. The emergent pattern within this analysis showed that companies with a strong understanding of customer preference structures in a traditional marketing channel, was no guarantee that the capabilities of the Internet would be used to strengthen performance on those preferences. One common theme that emerged from interviews with companies was that those who rapidly developed new levels of performance on customer preferences using the capabilities of the Internet had made the Internet a major component of their business model. The qualitative data showed companies as either adopting a transactional or an informational approach to their Internet channel strategy with radically different implications for their business models.

Keywords: on-line business
e-commerce
e-business
loyalty
Internet
consumer behaviour
retailing
structural equation modeling
choice based conjoint
marketing
on-line retailing
preference structures
Advisor: Reynolds, J
Macroeconomic policy in resource-rich economies

This thesis considers how fiscal and monetary policy should be conducted in resourcerich economies. It consists of three papers addressing: whether governments should spend, save or invest volatile oil income; the assets they should save in; and how monetary policy should respond.
The first, “Eight principles for managing resource wealth”, shows that capital-scarce countries should save relatively less against oil price volatility, and invest more in domestic capital. They also should prepare for volatility in advance, and treat savings as a source of income rather than a temporary buffer. To show this the paper develops a framework that nests a variety of existing results, which are presented in eight principles.
The second, “The Elephant in the Ground: Oil extraction and asset allocation in sovereign wealth funds”, shows that governments should use sovereign wealth funds to offset oil price risk, extract oil faster if its price is pro-cyclical, and use precautionary savings to manage any residual volatility. To do this it combines three strands of literature for the first time: on continuous-time portfolio theory, oil extraction and precautionary savings.
The third, “Optimal monetary responses to oil discoveries”, addresses the anticipation effects around an oil discovery. It shows that the terms of trade will need to appreciate twice: once when oil is discovered and consumers anticipate future revenues; and again when the government begins spending the revenues. Oil wealth will give the monetary authority an incentive to appreciate the terms of trade, in addition to stabilising domestic inflation and the output gap. Optimal policy is well-approximated by a standard monetary rule that also responds to expected changes in the natural level of output.

Keywords: oil
news shock
monetary policy
sovereign wealth funds
Natural resources
fiscal policy
Advisor: van der Ploeg, R
Southern Iberia in the early Iron Age

During the first half of the 8th century, people from the Phoenician Levant came to southern Iberia and founded a chain of settlements along the Spanish Mediterranean coast, as well as the city of Gadir (modern Cadiz) on the Atlantic seaboard. It is generally agreed that these colonisers came to the region to exploit the rich deposits of precious metals. Oriental style objects, which indicate the exchange between the Phoenician settlers and indigenous communities, can be found in almost all indigenous early Iron Age sites in the region.
Initially, the purpose of this study had been to detect the elements of Greek and Phoenician influence in the material culture of the early Iron Age (the 8th century until around 600 BC), but as work progressed it became increasingly clear that this undertaking was far more complex than it had been assumed. The Phoenicians turned out to be only one factor in a complex process of transformation from the late Bronze Age way of life to the development of the early Iberian states after 600 BC.
While the examination of the interaction between the indigenous communities and the eastern Mediterranean colonisers remained an important part of the study, my investigation now attempts to generate a more general picture of the early Iron Age in modern Andalusia, including the analysis of the social and economic processes which transformed society throughout the period.
The investigation is organised on the basis of three major parts:
An introduction: including the geography and climate of the region, as well as the history and archaeology of the Pheonician colonisation (with a certain emphasis on Gadir, and the excellently excavated site of Castillo Doña Blanca); as well as the indigenous Bronze Age background, and a number of theoretical considerations.
The central part introduces the archaeological evidence, organised in two sections: a topographical section, describing the settlement and cemetery evidence; and a second section, discussing a selection of artefacts which, in my opinion, are particularly useful for a reconstruction of the social processes.
Finally, the synthesis attempts to reconstruct various aspects of the early Iron Age culture in the region: such as the economic organisation, social development, ritual practice, and significance of the Phoenician presence for the development of the local cultures, as well as to introduce a regional division of the area under discussion.
English Romantic theatre during the Peninsular War

Between 1808 and 1814 England was committed to an expensive and bloody campaign against the French invasion of the Iberian Peninsula. The Peninsular War, as it came to be known, was initially celebrated as a war of national independence that attracted widespread support. Soon after, it was characterised by political scandal and public controversy.
Literary scholars have devoted much attention to the political, social and cultural effects of the French Revolution, but have written surprisingly little about the later years of the campaign against Napoleonic France. The principle objective of this thesis is to offer the first in-depth study of English theatre during the Peninsular War. It considers the most popular plays in performance, and asks what their staging, publication, and reception history reveal about a nation’s literary tastes and its political self-awareness.
Sheridan’s Pizarro, a play about the Spanish conquest of Peru, was one of the most successful plays on the Romantic stage. A close analysis of this play considers its popularity between 1799 and 1815, and what it suggests about the flexibility of the contemporary repertoire system. Audiences’ ability to ascribe topical inflections to old plays helps explain the demand for Shakespeare and the bard’s political import to wartime audiences. This thesis explores the London patent stages and popular minor theatres, where programmes were restricted to song, dance, and spectacle. It also offers a case study of provincial theatre in Bristol, underscoring the significant limitations in assumptions that the metropolitan stage was representative of national trends.
Archival research on the London and Bristol stages has been crucial to this study, which is based on an examination of playbills, memoranda, letters, playtexts, and prints. The newsprint and cartoons discussed offer an important political and historical framework, suggestive of the cultural expectations likely to have influenced contemporary playgoers.

Keywords: political prints
theatre
national identity
Peninsular War
nineteenth century
Iberian Peninsula
Advisor: Stafford, F
Taste, ethics and the market in Guatemalan coffee. An ethnographic study

For more than two decades there has been a growing niche for ethically sourced coffees, at the same time as a revitalisation and development of sourcing models focused on indicators of coffee quality and measures of taste. Small independent and multinational buyers and roasters have become progressively interested in sourcing coffee in a way that privileges sustainable and/or high quality indicators, and are increasingly engaged in debates about solidarity versus mainstreaming, quantity versus quality, and provider of caffeine versus taste. Research on one coffee producing country, Guatemala, suggests how these debates have affected the historical evolution of the coffee market. This ethnographic study traces the qualifications of Guatemalan coffee and argues that responses to both the enactment of the technologies, as well as the perceived limitations of sourcing models have produced new articulations of ethics and taste. Producers and small entrepreneurs located in Guatemala reconfigure the practices of cultivation, processing, and selling/buying in relation to circulating market indicators. They create locally situated attachments to the coffee through skill transfer and knowledge exchange and in this way they imitate and also transform international valuations of taste, ethics and quality. This thesis works to make visible the range and diversity of processes and agencies involved in the production of markets for ethical coffee and considers coffee as vital and mobile; an active producer of public effects rather than a passive object moved through a commodity network. This view enables a more open, relational and mobile account of both coffee and of ethics, one which is capable of making clear the important and emerging role of taste. This thesis extends the qualifications of coffee to the daily enactments of cultivation and the skills and techniques that work to reveal taste. On this view, taste mediates the agency of the materials in both high quality and sustainable coffees and this expands and extends ethics to interpersonal, material and bodily relations that link producers and consumers in multiple ways.

Keywords: affect
STS
ethnography
quality
coffee
Guatemala
fair trade
ethical coffee
taste
Advisor: Barry, A
Bell, V