VictorJuiz/thesis huggingface dataset:
Prime boost vaccination with viral vectors targeting apical membrane antigen1

Apical membrane antigen 1 (AMA1) is a leading candidate vaccine antigen against blood stage malaria and several clinical trials using mostly protein-in-adjuvant vaccines have shown limited success. This thesis describes the development of recombinant adenoviral (AdHu5) and poxviral (MVA) vectors encoding AMA1 from Plasmodium chabaudi murine parasites. In this murine malaria model, AdHu5 and MVA encoding AMA1 when used in a heterologous prime boost regime showed excellent immunogenicity, both humoral and cellular. The vaccination regime was protective against blood stage challenge and both antibodies and CD4+ T cells found to be important for vaccine induced blood stage protection. In parallel to this novel P. falciparum vaccines encoding AMA1 were also developed and administered in a similar prime boost regime to mice and rabbits. The vaccination regime induced cellular immune response and high titre antibodies against AMA1 and these antibodies showed growth inhibitory activity against the homologous parasite strain. In an effort to overcome the issue of antigenic polymorphism and to circumvent pre-existing immunity to human adenovirus, biallelic simian and human adenoviral vectors and MVA encoding AMA1 vaccines were also developed and administered to mice and macaques. These vectors also induced high titre antibodies and the serum from macaques was found to have growth inhibitory activity. These vaccine candidates are now being taken forward to Phase I/II clinical trials in Oxford. This work also described the attempt to improve MVA as a antibody inducing vector to allow better antibody mediated immunity to blood stage malaria.

Keywords: immunology
infectious disease
malaria vaccines
Advisor: Hill, A
Draper, S
Classicism, Christianity and Ciceronian academic scepticism from Locke to Hume, c.1660-c.1760 

This study explores the rediscovery and development of a tradition of Ciceronian academic scepticism in British philosophy between c.1660-c.1760. It considers this tradition alongside two others, recently recovered by scholars, which were recognised by contemporaries to offer opposing visions of man, God and the origins of society: the Augustinian-Epicurean, and the neo-Stoic. It presents John Locke, Conyers Middleton and David Hume as the leading figures in the revival of the tradition of academic scepticism. It considers their works in relation to those of Anthony Ashley Cooper, third earl of Shaftesbury, and Bernard Mandeville, whose writings refashioned respectively the neo-Stoic and Augustinian-Epicurean traditions in influential ways. These five individuals explicitly identified themselves with these late Hellenistic philosophical traditions, and sought to contest and redefine conventional estimations of their meaning and significance. This thesis recovers this debate, which illuminates our understanding of the development of the ‘science of man’ in Britain.
Cicero was a central figure in Locke’s attempt to explain, against Hobbes, the origins of society and moral consensus independent of political authority. Locke was a theorist of societies, religious and civil. He provided a naturalistic explanation of moral motivation and sociability which, drawing heavily from Cicero, emphasised the importance of men’s concern for the opinions of others. Locke set this within a Christian divine teleology. It was Locke’s theologically-grounded treatment of moral obligation, and his attack on Stoic moral philosophy, that led to Shaftesbury’s attempt to vindicate Stoicism. This was met by Mandeville’s profoundly Epicurean response. The consequences of the neo-Epicurean and neo-Stoic traditions for Christianity were explored by Middleton, who argued that only academic scepticism was consistent with Christian belief. Hume explored the relationship between morality and religion with continual reference to Cicero. He did so, in contrast to Locke or Middleton, to banish entirely moral theology from philosophy.

Keywords: Locke
history
seventeenth century
secular ethics
Mandeville
classical reception
Christian ethics
eighteenth century
intellectual life
Cicero
Hume
Religious thought
Shaftesbury
political science
philosophy
Middleton
Advisor: Robertson, J
Harris, B
On shared systems

Most computing systems are shared between users of various kinds. This thesis treats such systems as mathematical objects, and investigates two of their properties: refinement and security. The first is the analysis of the conditions under which one shared system can be replaced by another, the second the determination of a measure of the information flow through a shared system.
Under the heading of refinement we show what it means for one shared system to be a suitable replacement for another, both in an environment of co-operating users and in an environment of independent users. Both refine- ment relations are investigated, and a large example is given to demonstrate the relation for cooperating users.
We show how to represent the security of a shared system as an 'inference function', and define several security properties in terms of such functions. A partial order is defined on systems, with the meaning 'at least as secure as'. We generalise inference functions to produce 'security specifications' which can be used to capture the desired degree of security in any shared system. We define what it means for a shared system to meet a security specification and indicate how implementations may be derived from their specifications in some cases.
A summary of related work is given.

Advisor: Hoare, C
He, J
Hoare, T
Disturbance, recovery and resilience in tropical forests: a focus on the coastal peat swamp forests of Malaysian Borneo

Tropical forests have existed for up to one hundred million years, and today provide many ecosystem services vital for human well-being. They also harbour great biodiversity, which, in addition to its intrinsic value, plays a key role in the functioning of these ecosystems. Despite their local to global significance, there are still many knowledge gaps concerning the dynamic processes that govern the functioning of tropical forests. Rapid rates of deforestation and landscape conversion, predominantly for logging and industrial agriculture, are limiting the time and opportunity available to collect the information needed to fill these gaps. This research aims to shed light on the long-term ecological functioning of tropical forests, specifically investigating the history of disturbance in these ecosystems and the response of forest vegetation to past perturbations. The carbon-rich tropical peat swamp forests found along the coast of Sarawak, Malaysian Borneo, are a central focus of this study. For these forests in particular, a large deficit of knowledge surrounding their history and unique ecological functioning is coupled with some of the highest conversion rates of all tropical forest ecosystems across the world. In this thesis, palaeoecological data has been used to reconstruct temporal variability in forest vegetation coincident with external perturbations in order to identify changes in the resilience of these ecosystems through time, via indicators such as slowing rates of recovery and reduced regeneration of forest vegetation. Results suggest that tropical forest ecosystems have, for the most part, shown resilience to natural disturbances in the past, ranging from instantaneous localised tree-fall to longer-term regional climatic change; but that recent anthropogenic disturbances, of novel forms and greater intensities, are jeopardizing the potential for forest recovery and thus compromising ecosystem resilience. These findings enhance our understanding of the ecology of tropical peat swamp forests, and tropical forests more broadly. They also provide a context for contemporary tropical forest management, allowing for predictions on future responses to disturbance and enabling more ecologically sustainable landscape planning.

Keywords: climate change
Southeast Asia
fire
Sarawak
peat swamp forest
fossil pollen
biodiversity conservation
Malaysia
peatland
disturbance dynamics
vegetation change
long-term ecology
resilience
sustainable management
tropical forest
Advisor: Willis, K
Bhagwat, S
After constructivism

This thesis examines the legacy and consequences of Constructivism in art, from the early days of the Russian avant-garde to recent times and today. The Introduction explains how the concept of faktura, first theorised around 1912 by David Burliuk and others, came to designate the material qualities rather than the subject-matter of art. Chapter 1: Towards A Constructive Ideal, traces the progress of faktura in the reliefs of V.Tatlin from 1913. The ancestry of faktura in the Eastern icon tradition is emphasised, where a close relation between sight and touch already suggested a new type of encounter between the viewer and the object of art. The chapter further examines the importance of faktura to Suprematism, and examines A.Rodchenko’s appeal to line as a rational element of construction and as a weapon against ‘composition’ in art. Chapter 2: Time and the Viewer presents evidence of the importance to artists in the period 1940-70 of the real-time encounter between viewer and the art-object, first in American and British ‘Constructionism’, and then in the Minimal art of Judd, Morris and others. The chapter ends with a discussion of temporality in relation to abstract paintings of Rothko and de Kooning. Chapter 3: Irregular Curves: Science and ‘The Organic’ reprises the minority Constructivism of Mikhail Matyushin and Pyotr Miturich that claimed organic structures were superior to technicist ones. Evidence is presented that the rectilinear grid was always subject to challenge, initially in the art of Emma Kunz, Jean Arp and other pre-war modernists but latterly among those for whom ‘field’ and ‘curvature’ became relevant formats after 1945. Particularly with the development of computing from the 1970s, new geometries based on iteration and scale-invariancy assumed major relevance to constructed art. Chapter 4: Constructivism Now presents evidence of the application of Constructivist principles in recent art, initially in Dan Flavin’s ‘monuments’ to Tatlin and others and subsequently in so-called Neo-Geo and Op art of the 1970s and 1980s. From that period on, albeit often in a register of irony and ‘serious play’, faktura in a Constructivist sense continued, and continues today, to define the relation between viewer and object of art.

Keywords: Constructivism
modern art
painting
Advisor: Chevska, M
“Lege artis” – Exploring the strategizing craft of consultants through the examination of (analytic) strategy tools in use

Strategy tools are an important part of strategy work. However, there is considerable debate in the management literature about their actual role, deployment, and conceptualization. Scholars claim that there is a lack of fine‐grained analyses to explain strategizers’ activities with regard to their interactions with strategy, their supporting knowledge base, and associated artefacts or tools, despite growing contributions towards the understanding of strategy work dynamics. This study aims to contribute to this gap by discussing research undertaken through ethnographic methods on the day to day work of in-house strategy consultants.
  By interacting with in-house consultants through active participation and observation, this study observes and analyses the enactment of strategy tools in action. The study focuses on the use of strategy tools, the process they are placed in, and the ultimate purposes they serve. A “strategy-as-practice” lens is adopted, theoretically accessing the use of strategy tools through “reflection in action” and sensemaking. By working with and for consultants, this dissertation obtains insights related to both frontstageand backstage aspects of strategy work, obtaining results that contribute to the skewed existing evaluations on the use of strategy tools.
This study proposes a reflexive account on the roles of strategy tools in everyday work by laying out a variety of data items and rhetorical devices. Analysing data, obtained from observations, interviews, written material, and focus groups, takes the findings into the first and second order analysis. Based on hundreds of pages of observations, 47 interviews, two focus groups, numerous data files, and other follow up talks, the continuous engagement with data is conveyed to the reader through data outputs, including narratives, vignettes, and visual representations, which give space to a vivid display of what was encountered in the field through this ethnographic study
The findings show that strategy tools are used more than we think, especially in the backstage work of strategy teams. In addition, the use of strategy tools tends to be sequential (some strategy tools are used more in specific phases of strategy projects). In addition, their presence in strategy projects is not always evident at first sight – tools tend to be disassembled and reassembled by their users to create new tools, which are thereafter addressed explicitly or implicitly by strategizers and their audiences. Hence, the thesis proposes an “invisible presence of strategy tools”, especially as observed in the work of experienced strategy workers.
By embarking on a journey of Cheshire cats and continuous reconfigurations of sensemaking cues, the reader is invited into what makes the adventurous work of strategy practitioners, and the lege artis their work encompasses.

Advisor: Whittington, R
Early life histories: a study of past childhood diet and health using stable isotopes and enamel hypoplasia

The δδ13C and δ15N composition of incremental segments of tooth dentine was used to infer infant and childhood diet in a post-medieval London population, and a hunting and gathering Mesolithic/Neolithic group from Latvia. Health was analysed using defects on the tooth enamel caused by stress, termed enamel hypoplasia. The populations, which differ markedly in their economy, diet and health, were selected because of the difference in childhood experiences between the two groups. The results were used to consider questions about childhood, including how early diet may have been influenced by social factors such as class or status, the effect this could have on population dynamics and how childhood diet and health are related.
The results show that the London individuals were rarely breastfed beyond 6 months and in some instances not at all. A small isotopic difference between males and females was observed which could be caused by dietary or physiological differences. The peak incidence of hypoplasia may be related to developmental patterns, rather than stress caused by weaning. The Zvejnieki individuals had a slightly longer breastfeeding duration. Those buried with pendants consumed a different diet in childhood to those without pendants, suggesting a complex social system, possibly indicating that diet was related to the role a person had within the community. There is a suggestion diet may have shifted between the Middle Mesolithic and Late Neolithic, although not dramatically. Neither population have elevated δ13C often associated with breastfeeding.
The early life histories of the groups are not compared directly, but general observations concerning the children’s lives are considered. It is concluded that economy is not a reliable predictor of infant feeding strategies, as hunter-gatherers provide children with solid foods at a similar time to industrial groups. Intra-population variability was found to be a feature of all socio-economic groups.

Keywords: childhood
stable isotopes
hypoplasia
health
infancy
Victorian
hunter-gatherers
breastfeeding
Advisor: Lee-Thorp, J
Estimating expected first passage times using multilevel Monte Carlo algorithm

In this paper we devise a method of numerically estimating the expected first passage times of stochastic processes. We use Monte Carlo path simulations with Milstein discretisation scheme to approximate the solutions of scalar stochastic differential equations. To further reduce the variance of the estimated expected stopping time and improve computational efficiency, we use the multi-level Monte Carlo algorithm, recently developed by Giles (2008a), and other variance-reduction techniques. Our numerical results show significant improvements over conventional Monte Carlo techniques.
The habitats and feeding stations of birds in Tsavo National Park, Kenya

The land-bird community of Tsavo East National Park was studied for two years. There are two wet seasons each year: November-December and April- May, but the latter were very poor in both study years. Six habitat types were designated on the basis of canopy cover of woody vegetation. Riverine vegetation was also studied. Most ofthe open habitats extant are derived from woodland by destruction of trees, a process largely caused by elephants.
Food supplies are seasonally variable. Insects and grass seeds are most abundant in December and January. In the open habitats the few fruits also peak then, but Commiphora spp., which is only in woodland and is the most abundant fruit in Tsavo, peaks July to September.
The ecology of each species of land-bird is described and most are found to be ecologically separate from each other.
The annual cycle of numbers of birds in each habitat is closely correlated with the food supplies. In the open habitats birds are almost all insectivorous, granivorous or both, and peak numbers (about five times the dry season density) occur in December and January. In woodland, numbers remain fairly constant through the year and frugivores are more prominent, especially around August. The wet season peaks in all habitats are caused by immigrations of different species, both from elsewhere in Africa most of which come in to breed, and species which breed in the Palaearctic. The August peak in Woodland consists mainly of species which have resident populations.
The results are particularly related to the recent habitat changes in the Park. They are compared with other bird studies in African savannas and other components of the Tsavo ecosystem. Finally, the means by which birds are able to survive in the harsh and unpredictable conditions of Tsavo are discussed.

Advisor: Coe, M
Perrins, C
Coe, D
When I touch my hand it touches me back: an investigation of the illusion of self-touch

Following stroke, a patient may fail to report touch administered by another person but claim that s/he feels touch when it is self-administered. In Part One, the self-touch rubber hand paradigm was used to investigate different explanations for this phenomenon, termed self-touch enhancement. The most important finding was that patients reported touch based on feeling rather than by using proprioceptive information. Some patients have residual sensation that could be targeted in sensory rehabilitation.
Part Two is a systematic investigation of the illusion of self-touch conducted with neurologically healthy participants. Participants used the right hand to administer touch to a prosthetic hand while the left (receptive) hand, positioned 15 cm from the prosthetic hand, received Examiner-administered touch. Proprioceptively perceived position of the administering and receptive hand was measured. Most participants experienced the single event of self-touch at the location of the receptive hand. Previous investigations have relied on measurement of only one hand and have concluded that participants experience self-touch at the location of the prosthetic hand. Our findings have implications for the role of ownership in this illusion.
There is also a series of experiments in Part Two which test four potential constraints on the illusion of self-touch – violated expectations about the object that is administering touch, increased distance between the hands, alignment mismatch, and anatomical implausibility. For example, one study uses a novel paradigm to demonstrate that, although the subjective intensity of the illusion of self-touch is diminished by anatomical implausibility, most participants report the impossible experience of touching their left elbow with their own left index finger. Taken together, these experiments highlight the malleability of body representation, and provide a comprehensive framework for understanding the illusion of self-touch.

Keywords: sensation
illusion
body representation
Advisor: Aimola Daves, A
Davies, M
Improving instruments for infrared remote sensing

Remote sensing of the Earth's atmosphere, typically performed in the infrared region of the spectrum, plays an important role in scientific research. In the past the instruments used to perform these observations have been large, massive devices and correspondingly have only been able to be placed on large satellites. There is currently a trend toward smaller Earth observing platforms, so-called micro-satellites, and there is therefore a need for smaller, less massive instruments. Typically these instruments utilise a semiconductor device that responds to incoming infrared radiation in a known way. Such devices are subject to a number of noise sources that reduce their performance. By cooling them to temperatures around 80K it is possible to significantly reduce the amplitude of this noise compared to the incoming radiation of interest, thus increasing the signal-to-noise ratio (SNR). Typically this cooling is performed by a mechanical cooler, but currently many of them are too massive and require too much power to be suitable for use on a small remote sensing satellite.
By considering a typical application, a performance target for a miniature cooler was determined to be a heat lift of 200mW at a cold tip temperature of 80K. Hardware has been created to investigate the feasibility of achieving this aim with a hybrid cooler/radiator. The cooler is a miniature integral Stirling machine and uses flat spiral flexures with a newly designed linear motor to drive the compressor piston; the displacer is driven pneumatically.
The prototype initially underwent characterisation without first being pre-cooled by the radiator. Although significant cooling was observed (to below 170K), initial characterisation highlighted a low thermal resistance between the warm end of the cooler and the cold tip. With pre-cooling the cold tip was able to reach a minimum no-load cold tip temperature of 92K, and with 200mW applied to the cold tip a temperature of 122.4 K was sustainable. Attempts were made to increase the thermal resistance between the warm end and cold tip by introducing thermal breaks into the regenerator, and whilst these did increase the thermal resistance, the overall performance of the cooler decreased.
The concept of a hybrid miniature cooler/radiator has been shown to be feasible. To achieve the target performance of a heat lift of 200mW at 80K further work needs to be performed to characterise loss processes within the cooler and increase the thermal resistance between the warm end and cold tip.

Advisor: Taylor, F
Peskett, G