VictorJuiz/thesis huggingface dataset:
Parish, people and the English Bible in East Anglia, 1525-1560

This thesis examines the impact of the English Bible upon the people and parishes of Norfolk, Suffolk and Essex between 1525 and 1560. It examines two major themes of this impact: firstly, the level of success of the installation of the Great Bible in the parish churches; secondly, the effects of the publication and open reading of the scriptures in the vernacular upon the laity of East Anglia. The first theme explains the reasons for the order to install English scripture in the churches, and the information on the success of this installation provided by prosecution records and churchwardens' accounts. It then introduces an obscure document set, the church-plate certificates produced during the reign of Edward VI, and using these examines the level of installation of the Bible and of the religious injunctions of 1547. The results of the study of the church-plate certificates and churchwardens' accounts are compared with a number of factors, including parish wealth, proximity to towns and agricultural patterns, to determine which types of parishes were more likely to comply. The second theme examines the various responses of laypersons to the appearance of the English Bible in East Anglia. Although much of this section has been derived from records of prosecution, it also studies the effects of the English Bible on diverse events such as Kett's Rebellion of 1549, popular printing in Ipswich and the production of educational primers. This section also looks at the level of scriptural knowledge of laypersons ranging from that of Robert Reynys, a churchreeve of Acle, of the 1430's, to that of the prosecuted Marian Protestants during the 1550's.

Advisor: Dr Felicity Heal, D
Evildoing: an attack on morality

This thesis presents a comprehensive theory of evildoing as an attack on morality, grounded in objective morality. It introduces evildoing as a distinct category of immorality, arguing that it is the relationship of evil acts to the core of morality that distinguishes them from ordinary wrongdoing. Two projects are undertaken: to provide an account of morality that can ground a theory of evildoing that is both objective and capable of systematically accommodating the diverse phenomena and definitions of evil acts, and to articulate and defend the attack on morality theory of evildoing. The challenge of the first project is met by a minimalist account of morality, structured by what I call the fundamentals of morality. The thesis defends a particular substantive account of these fundamentals, underpinned by the idea of conatus as the end of morality. Ultimately, it is conatus as the striving to persist in existence and prosper inherent in human beings that justifies the objectivity of the fundamentals of morality and with it the objectivity of the theory of evildoing, for it is these fundamentals that are attacked when we speak of an ‘attack on morality.’ Specifying and defending the conditions necessary for such an attack is the task of the second part of the thesis. An act constitutes evildoing, or an attack on morality, when it is wrong, results in serious harm to others, originates in an intention based on the correct belief that the act will cause or risk such harm, and where the perpetrator’s mental states and/or the act’s consequences are antagonistic to the realization of morality via one or more of its fundamentals.

Keywords: conatus
end of morality
fundamentals of morality
evil
evildoing
attack on morality
Advisor: Savulescu, J
Crisp, R
Hierarchy in twentieth-century Sefwi (Ghana)

The dissertation aims to provide an understanding of the relation between political-economic power and the attribution of social value in twentieth-century Sefwi (Ghana). The existing literature on relations of dominance amongst the Akan has flaws: works examine single relations of dominance in isolation; studies focus mostly on discontinuity and change; peripheral areas are neglected. In the dissertation these issues are addressed. Hierarchy is used as an analytical tool which enables one to link diverse expressions of dominance; the persistence of certain hierarchical patterns throughout the twentieth century is analysed alongside transformations; and the focus is on Sefwi, a marginal region of the Akan world.
The dissertation is divided into five sections. The introduction presents the methodological and theoretical approach adopted in the work. Part one is concerned with change in hierarchical patterns: twentieth-century dynamics are analysed to determine the extent of change with reference to chiefly power, capitalist.relations and gender issues. Part two shows that unequal relations inform three hierarchical domains -ancestry, gender and seniority. Part three addresses the issue of the coherence and unity of hierarchy by examining modes of organization of experience that cut across the three domains of inequality: reference is made to the use of kinship terms; concepts of ownership, caretakership and help; recourse to the supernatural; food and drink transactions. In the conclusion, Sefwi hierarchy is examined in a wider comparative and theoretical perspective with reference to the notions of 'encompassing of the contrary' (Dumont) and 'fetishization' (Marx).
Comprehensive assessment of the role of DNA methylation in obesity and type 2 diabetes

Obesity and type 2 diabetes (T2D) are major risk factors for cardiovascular and other diseases and are currently undergoing an increase in global prevalence. The work presented in my thesis addresses the role epigenetics, specifically DNA methylation, plays in the susceptibility to obesity and T2D and deals with methodological issues in the analysis of DNA methylation data.
I first combined epigenome-wide DNA methylation data across 38 adipose tissue samples with corresponding SNP and mRNA data for the same subjects. At 5% false discovery rate (FDR), methylation of 149 regions associated with at least one cis-SNP. When 19 of the 149 regions were tested for association in an additional 181 independent samples, five regions replicated. These results indicate a genetic influence on DNA methylation in adipose tissue.
I then analysed 90 epigenome-wide methylation samples taken from 15 South Asian controls and 30 T2D cases participating in the LOLIPOP study at two time points ∼7 years apart. I found global differences at both follow-up and baseline between the normal glucose tolerant and T2D groups, as well as strong differences with aging. I further used the main EpiMigrant data from 2,687 individuals, with 36 samples measured in duplicate to assess approaches to quality control, data normalisation and batch correction through control probe adjustment. A null hypothesis for epigenome-wide association studies (EWAS) by permutation testing and I investigated the effects of correlation between individual methylation markers.
Using the developed methods, I carried out an EWAS of body mass index (BMI) with subsequent meta-analysis amongst 10,261 individuals of European and South Asian ancestry. DNA methylation markers at 187 genetic loci were associated with BMI. Mendelian randomisation experiments suggested that association of DNA methylation with BMI is the consequence of BMI.
Lastly, I tested haplotypes of 85 SNPs currently known to be associated with T2D and 118 SNPs associated with obesity traits for an enrichment of CpG creating or abrogating SNPs and found that 9 T2D and 23 obesity SNPs showed a significant difference in CpG count between the SNP alleles as established by permutation testing. Amongst these is FTO, a locus which has been previously been shown to have a haplotype-specific methylation effect.
My work provides novel insights into the role of DNA methylation in metabolic diseases. The methods that I developed to robustly detect association are flexible and scalable and will further be useful for larger, future EWAS.

Keywords: Epigenetics
Genomics
DNA Methylation
Obesity
T2D
Epigenomics
EWAS
Advisor: Lindgren, C
McCarthy, M
Software architecture for capturing clinical information in hadron therapy and the design of an ion beam for radiobiology

Hadron Therapy (HT) exploits properties of ion radiation to gain therapeutic advantages over existing photon-based forms of external radiation therapy. However, its relative superiority and cost-effectiveness have not been proven for all clinical situations. Establishing a robust evidence base for the development of best treatment practices is one of the major challenges for the field. This thesis investigates two research infrastructures for building this essential evidence.
First, the thesis develops main components of a metadata-driven software architecture for the collection of clinical information and its analysis. This architecture acknowledges the diversity in the domain and supports data interoperability by sharing information models. Their compliance to common metamodels guarantees that primary data and analysis results can be interpreted outside of the immediate production context. This is a fundamental necessity for all aspects of the evidence creation process. A metamodel of data capture forms is developed with unique properties to support data collection and documentation in this architecture. The architecture's potential to support complex analysis processes is demonstrated with the help of a novel metamodel for Markov model based simulations, as used for the synthesis of evidence in health-economic assessments. The application of both metamodels is illustrated on the example of HT.
Since the biological effect of particle radiation is a major source of uncertainty in HT, in its second part, this thesis undertakes first investigations towards a new research facility for bio-medical experiments with ion beams. It examines the feasibility of upgrading LEIR, an existing accelerator at the European Organisation for Nuclear Research (CERN), with a new slow extraction and investigates transport of the extracted beam to future experiments. Possible configurations for the slow-resonant extraction process are identified, and designs for horizontal and vertical beam transport lines developed. The results of these studies indicate future research directions towards a new ion beam facility for biomedical research.

Keywords: slow extraction
model-driven engineering
health informatics
evidence based medicine
data capture
case report form
ion beam
beam transport
radiobiology
synchrotron
charged particle therapy
software architectures
domain-specific model
markov model
metamodel
system description languages
Advisor: Peach, K
Davies, J
Coevolutionary adaptation in mutualisms

Natural selection favours those individuals that respond best to novel features of their selective environment. For many, a critical challenge is responding to evolutionary change in mutualistic species. These responses create complex feedbacks, so only coevolutionary approaches are able to fully answer key questions about the maintenance or disruption of mutualistic behaviour, and explain the range of mechanisms that allow individuals to benefit from these associations. I first consider the hypothesis that economic models studying multiple classes of traders, where each trader seeks to optimise its own payoffs will yield insights into mutualistic systems. I show that individuals can be favoured to discriminate amongst potential partners based on the price for which they provide resources. Then, I show that market mechanisms can maintain cooperation and drive specialisation in mutualistic systems. I extend this market model to allow individuals to restrict a mutualistic partner's access to resources, and show that this strategy can stabilise cooperation and increase the fitness of both partners. I also explicitly incorporate relatedness in my market model. I show that high relatedness sometimes increases cooperativeness in members of a mutualistic species, but sometimes decreases cooperativeness as it narrow the scope for partner choice to maintain cooperation. Having studied market mechanisms, I consider indiscriminate costly help to members of another species. I discover that this trait can be favoured by natural selection and can be classified as either altruism between or altruism within species. Finally, I consider a framework for analysing coevolved phenotypic responses to a partner's cooperativeness, a challenging process to model. I demonstrate that this framework can yield firm predictions about behaviour whenever partners hold private information about their costs and benefits.

Keywords: adaptation
mutualism
social evolution
cooperation
coevolution
Advisor: West, S
Gardner, A
Stable moduli spaces of manifolds

In this thesis we make several contributions to the theory of moduli spaces of smooth manifolds, especially in dimension two.
In Chapter 2 (joint with Soren Galatius) we give a new geometric proof of a generalisation of the Madsen-Weiss theorem, which does not rely on the tangential structure under investigation having homological stability. This allows us to compute the stable homology of moduli spaces of surfaces equipped with many different tangential structures.
In Chapter 3 we give a general approach to homological stability problems, especially focused on stability for moduli spaces of surfaces with tangential structure. We give a sufficient condition for a structure to exhibit homological stability, and thus obtain stability ranges for many tangential structures of current interest (orientations, maps to a simply-connected background space, etc.), which match or improve the previously known ranges in all cases.
In Chapter 4 we define and study the cobordism category of submanifolds of a fixed background manifold, and extend the work of Galatius-Madsen-Tillmann-Weiss to identify the homotopy type of these categories. We describe several applications of this theory.
In Chapter 5 we compute the stable (co)homology of the non-orientable mapping class group, and find a family of geometrically-defined torsion cohomology classes. This is in contrast to the oriented mapping class group, where few are known.
In Chapter 6 (joint with Johannes Ebert) we study the divisibility of certain characteristic classes of bundles of unoriented surfaces introduced by Wahl, analogues of the Miller-Morita-Mumford classes for unoriented surfaces. We show them to be indivisible in the free quotient of cohomology.

Keywords: 57R50
57R15
55P47
57M07
MSC Classification: 57R90
55R40
57R56
Advisor: Tillmann, U
Investigation of the potential of Pb/Pb radiometric dating for the direct age determination of carbonates

Recent studies have demonstrated the potentially robust nature of U-Pb and Pb/Pb systematics within certain sedimentary and metamorphic carbonates (e.g. Moorbath et al., 1987; Jahn, 1988; Jahn et al., 1990; DeWolf and Halliday, 1991). During the course of this work, the Pb/Pb dating technique has been applied successfully to the direct dating of Proterozoic stromatolitic carbonates from Western Australia and India, Silurian stromatoporoidal carbonates from Sweden and Archaean marbles from India, permitting the direct age determination of depositional/early diagenetic, late diagenetic and metamorphic events. Results indicate that large variations in μ value (238U/204Pb) and virtually homogeneous initial Pb isotopic compositions are a recurrent feature of sedimentary and metamorphic carbonates.
Authigenic marine carbonates may incorporate U and Pb through a variety of geochemical mechanisms;
organic complexing;
crystal lattice substitution;
adsorption onto particulate oxyhydroxides and
early diagenetic reduction.
Since modern and ancient carbonates have U and Pb concentrations of the order of ppm, whereas dissolved U and Pb in the oceans occur at 3.2 ppb and 0.003 ppb, preconcentration within the water column must be an important factor in the establishment of appropriate geochemical conditions. The rapid scavenging of Pb, compared to rates of U fixation under suboxic conditions, means that depositional μ values seldom approach the sea water figure of c.80,000.
Owing to the largely independent geochemical behaviour of U and Pb, early diagenetic, late diagenetic and metamorphic recrystallisation may either partially disturb Pb/Pb and U-Pb systematics or effect complete resetting of radiometric ages. Consequently, results from geochronological studies should be interpreted only after due consideration of all available geological information.
The extensive distribution of metamorphic and sedimentary carbonates throughout the geological record, coupled with the apparent robustness of Pb/Pb systematics, means that this technique can offer an effective means of event dating, stratigraphic correlation and time scale calibration, particularly in the Precambrian where independent age constraints are limited. In addition, the identification of late diagenetic recrystallisation ages offers exciting potential for constraining the diagenetic histories of sedimentary basins.

Advisor: Moorbath, S
Whitehouse, M
Taylor, P
Numerical modelling of real-time sub-structure testing

Current dynamic testing methods can prove unrealistic due to the scale at which test components are modelled, the rate at which they are loaded or the boundary conditions to which they are subjected. A new test method, termed "Real-Time Sub-Structure Testing" seeks to provide a more realistic testing environment for energy dissipative components. The method tests structural components at full or large scale and in real-time. The physical test interacts with a computer model of the structure surrounding the test component. In this way, the in-situ behaviour of the test component is evaluated in relation to the overall structural response. The testing method requires fast and realistic modelling of the surrounding structure and a rapid interaction with the physical test specimen. For these reasons, a new non-linear finite element method has been proposed in order to model the surrounding structure behaviour efficiently. The method uses the Central Difference Method time stepping integration scheme together with a newly devised basis. The proposed basis consists of the structure’s elastic modes and additional Ritz vectors, which are calculated from the inelastic static displacement shapes of the structure. The displacement shapes correspond to the same static spatial distribution of loading as the intended dynamic excitation, and are intended to characterise the inelastic behaviour of the structure. The method has been validated against a Newmark event to event algorithm as well as Drain2DX. The non-linear dynamic response of a propped cantilever beam and portal frame structure was investigated. The response evaluated by the algorithm agrees closely with both validation analyses. The new algorithm was also shown to be faster than the Newmark procedure in simple benchmark tests. In addition, a numerical model of the testing apparatus has been developed in order to simulate complete tests for the purposes of testing procedure development and validation. The model is developed using Matlab Simulink. Parameters for the model are deduced from published data, experimental component tests and open loop step response calibrations. The model behaviour was found to be very sensitive to the parameters used. However, after calibration against open loop tests the model reproduces the observed laboratory behaviour to a good degree of accuracy. In an attempt to predict the behaviour of an actual test, the laboratory model has been coupled with the new structural solution algorithm to simulate a virtual test. The simulated results compare well with experimentally observed data demonstrating the usefulness of the overall simulation as a test modelling tool.

Keywords: dynamic testing
real-time sub-structure testing
Advisor: Williams, M
Blakeborough, A
Reading revolution

This thesis explores the involvement of Russian emigres in disseminating and informing the reception of Russian literature in England. It examines their use of translations and literary commentary as vehicles for propaganda, and considers the impact of their unique approach to literature on both Anglo-Russian relations and English letters.
Part One describes the arrival of Russian émigrés in England and their mixed reception: as victims of a brutal regime, mysterious sages, exotic outcasts, Slavic barbarians, or at worst, as dangerous 'incendiarists' to be feared and reviled. It reflects on the welcome and assistance offered them by socialists, feminists, literati and Nonconformists, as well as the dangers they faced from Russian government agents and their English confreres. It then introduces, in turn, each of the five Russian exiles featured in this thesis, providing biographical details, outlining their work in Britain as propagandists and political agitators, and mapping out their political and literary affiliations.
Part Two opens with an analysis of the motives - financial, political, cultural, and personal - which compelled Russian exiles to promulgate Russian literature in England. A chapter is then devoted to each of the five émigrés, chronicling their work disseminating the Russian canon, and outlining the circumstances surrounding their translations, lectures, books, journal articles, and publishing activities. Interspersed within these five narratives are discourses on each propagandist's aesthetic vision.
Part Three is a case study of the émigré impact on Turgenev's English reputation. It starts by tracing the author's early reception, showing how he was initially regarded in England as a European novelist whose artistry took precedence over his politics, and whose exquisite writing revealed universal truths through its careful selection and presentation of minute details. It then shows how émigré commentary altered perceptions of the author, transforming him from a disinterested artist dealing only in universal themes into a radical critic of various epochs of Russian national life, whose novels revealed important inner truths about the state of Russian society and politics.
The conclusion examines what may be termed the 'collateral' effects of émigré commentary on Russian literature and their involvement in translation projects in England. Firstly, it looks at the political impact of their criticism: how the émigré presentation of Russian literature affected Anglo-Russian relations and attitudes towards the first Russian revolution in 1905. It then considers how émigrés helped or hindered reputations of writers according to their own politically and aesthetically motivated preferences. Finally, it looks at the possible ramifications of émigré literary theory on English approaches to literature and criticism, and suggests further avenues of inquiry.

Advisor: Sloan, J