VictorJuiz/thesis huggingface dataset:
The political economy of violence and post-conflict recovery in sub-Saharan Africa

This thesis presents theoretical work on armed group activity and empirical work on post-conflict recovery.
In chapter two, I develop a general equilibrium model of violence to explain observed variation in coercive practices in conflict zones. Armed groups own land in the resource sector and allocate military resources between conflict and coercion, which assign de facto ownership over land and labour respectively. I find that coercion is higher if labour is scare relative to land, production is labour-intensive, or if one group is dominant relative to others. Furthermore, contrary to other studies, I find that coercion could decreases with price if military power is sufficiently decentralised, since conflict draws resources away from coercion.
In chapter three, I evaluate a reconciliation program in post-conflict Sierra Leone. The program provides a forum for villagers to air war-time grievances, and also forges institutions designed to improve conflict resolution and build social capital. I find that respondents who received the intervention are more forgiving and are more charitable in their views of ex-combatants. Furthermore, conflict resolution improved and involvement in village groups and activities increased. However, psychological health---depression, post-traumatic stress disorder and anxiety---deteriorated. This study has direct implications for the design of transitional justice programs, as well as programs that aim to promote institutional change.
In chapter four, I experimentally vary foreigner presence across behavioural games conducted in 60 communities in Sierra Leone, and assess its effect on standard measures of generosity. I find that foreigner presence substantially increases player contributions in dictator games, by an average of 19 per cent. Furthermore, the treatment effect is smaller for players who hold positions of authority; and subjects from villages with greater exposure to development aid give substantially less and are more inclined to believe that the behavioural games were conducted to test them for future aid.
In chapter five, I use a model of repeated bargaining with one-sided asymmetric information to investigate the difficulties of reaching and sustaining power sharing agreements. I show that asymmetric information can explain the persistence of conflict, since learning slows down when there are future opportunities for bargaining.

Keywords: field experiment
reconciliation
conflict
development economics
Advisor: Leaver, C
The effect of obesity upon the lumbar spine

Back pain is a massive global public health problem with multiple contributing factors including obesity. Obesity is thought to be linked to back pain through mechanical factors. However, obesity also causes a systemic low-grade inflammatory milieu. This would suggest a possible biochemical link between obesity, intervertebral disc degeneration, and back pain. Furthermore, the relationship between obesity and the clinical presentation of spine patients is unclear. This thesis aims to examine the effect of and relationship between obesity, the intervertebral discs, and back pain from biochemical, clinical, and epidemiological perspectives
In this thesis, an in vitro study assessed the effect of leptin, a fat-specific cytokine, upon the intervertebral disc. The bovine intervertebral disc was used as a model in a cell culture system. An ex vivo study examined leptin and pro-inflammatory cytokines produced by paraspinal adipose tissue taken during routine surgical procedures from spinal patients. Plasma taken from patients presenting with low back pain was analysed by mass spectrometry and multiplex immunoassay to identify possible protein biomarkers. At an epidemiological level, statistical modelling of the Genodisc patient population was conducted. This was a pan-European study of 2636 patients presenting to tertiary spinal units. Analyses were performed to examine relationships between obesity, quantified by body mass index (BMI), and pain, clinical diagnosis, and spinal degeneration identified on magnetic resonance imaging (MRI).
Leptin was shown to increase the production of and expression of degradative and pain-generating molecules by disc cells. A pro-inflammatory environment, especially IL-6, potentiated this response. Leptin and pro-inflammatory cytokines produced by paraspinal fat were unrelated to clinical symptoms. However, levels of the pro-inflammatory cytokines, TNF-α and IL-6, were raised in the plasma of patients with greater pain or those with spinal stenosis. Furthermore, clusterin and complement were identified, by mass spectrometry, as potential biomarkers for spine patients. Epidemiological analyses revealed that obesity was associated with greater back pain, although the magnitude of this association was small. Similarly, obesity was associated with a diagnosis of spinal stenosis. Finally, increased BMI was found to be an independent predictor of disc degeneration, spinal stenosis, and disc herniation on MRI.
In summary, this thesis has furthered the clinical understanding of lumbar spine pathology and back pain. It will provide clinicians with a better framework to assess spine patients. These results show that obesity is associated with lumbar spine degeneration and pain. Leptin could be a factor mediating this relationship. Further studies should concentrate on clarifying the mechanism of action of leptin upon the intervertebral disc and assessing the longitudinal effect of obesity upon the lumbar spine.

Keywords: obesity
epidemiology
intervertebral disc
spine surgery
orthopaedic surgery
IVDD
back pain
Advisor: Urban, J
Fairbank, J
Judge, A
Mathematical modelling of compaction and diagenesis in sedimentary basins

We begin by analysing the simplest case of poroelastic compaction which in a 1-D case results in a nonlinear diffusion equation, controlled principally by a dimensionless parameter λ
, which is the ratio of the hydraulic conductivity to the sedimentation rate. We provide analytic and numerical results for both large and small λ
in Chapter 3 and Chapter 4. We then put a more realistic rheological relation with hysteresis into the model and investigate its effects during loading and unloading in Chapter 5. A discontinuous porosity profile may occur if the unloaded system is reloaded. We pursue the model further by considering diagenesis as a dehydration model in Chapter 6, then we extend it to a more realistic dissolution-precipitation reaction-transport model in Chapter 7 by including most of the known physics and chemistry derived from experimental studies. We eventually derive a viscous compaction model for pressure solution in sedimentary basins in Chapter 8, and show how the model suggests radically different behaviours in the distinct limits of slow and fast compaction. When λ≪1
, compaction is limited to a basal boundary layer. When λ≫1
, compaction occurs throughout the basin, and the basic equilibrium solution near the surface is a near parabolic profile of porosity. But it is only valid to a finite depth where the permeability has decreased sufficiently, and a transition occurs, marking a switch from a normally pressured environment to one with high pore pressures.
In vitro studies on cytochrome c biogenesis

C-type cytochromes are essential for almost all organisms and are mainly involved in electron transport; they are characterised by the covalent attachment of heme to protein through two thioether bonds to a CXXCH peptide motif.
This thesis describes the development of in vitro systems to establish chemical aspects of the process of cytochrome c maturation. Initially, the uncatalysed reaction of heme and apocytochrome c from Hydrogenobacter thermophilus cytochrome c552 was studied in vitro, yielding the desired thioether bonds under mild conditions and in the absence of any biosynthesis apparatus. The reaction proceeded via a b-type cytochrome intermediate, showing the ability of the apoprotein to bind heme noncovalently prior to thioether bond formation. It was also determined that the two cysteine residues of the CXXCH motif can form a disulfide. Optimal reaction conditions for thioether bond formation required both the heme and the cysteine residues to be reduced. Mechanistic insights were gained by showing that the thioether bonds can form independently from one another. Furthermore, it was shown that, in the case of H. thermophilus apocytochrome, thioether bonds can form stereoselectively with respect to the α, 𝛾 mesoaxis of heme.
These findings were extended to a broader range of apocytochromes. It was discovered that mitochondrial apocytochromes c from horse heart and yeast also formed thioether bonds with heme, as well as the bacterial Paracoccus denitrificans apocytochrome c550. It was established that apocytochromes show a trend to bind hydrophobic ligands or heme to yield b-type cytochromes. Thioether bonds can form in vitro in these heme-protein complexes.
In the second part of this thesis the heme chaperone CcmE, which is part of the cytochrome c biogenesis apparatus in many Gram-negative bacteria, was studied as an extension to the establishment of in vitro systems. It was discovered that CcmE can bind heme initially non-covalently and then covalently upon reduction of the heme. However, CcmE seems to have a preference for ferric rather than ferrous heme. The involvement of the vinyl groups of heme is suggested. Mutation of the heme-binding histidine residue of CcmE established the involvement of this residue in the covalent binding of heme for the in vitro reaction; mechanistic insights were gained from the observation that a histidine to cysteine mutant could still bind heme covalently in vivo and in vitro. Effects of the presence of a His tag on CcmE were shown and are discussed. Furthermore, in vitro heme transfer from CcmE to certain apocytochromes c was achieved.
All these in vitro results mimic, and thus have implications for, the molecular pathway of heme transfer during the complex process of c-type cytochrome maturation in vivo.

Advisor: Ferguson, S
Geogrid reinforcement of granular layers on soft clay

The mechanisms by which a geogrid acts to reinforce a granular layer over a soft clay were investigated with reference to trafficking of unpaved roads. The research involved a programme of physical testing at both model and full scale.
Model tests were carried out for monotonic and cyclic loading of a dual footing on to a layer of granular material that was compacted over a consolidated kaolin sample. The tests were made in conditions of plane strain at a quarter scale, and included a scaled geogrid at the base of the granular layer. Measurements of footing load, displacements and photographic observations through a perspex front face to the test box were used to identify the reinforcing actions of the geogrid.
A virtual work procedure was adopted in analysis of the results for both unreinforced and reinforced layers. The procedure accounts for lateral restraint of the subgrade and a membrane action in the reinforced tests, and allows a comparison of the cyclic test results with an equivalent monotonic bearing capacity.
Load tests were also made on footing plates at full scale, involving a similar arrangement of compacted granular layers over a prepared London clay and including a high strength polymer geogrid. Examination of the test results allowed a qualitative assessment of the model performance and the reinforcing mechanisms attributed to the geogrid.

Advisor: Milligan, G
Computer-aided detection and classification of microcalcifications in digital breast tomosynthesis

Currently, mammography is the most common imaging technology used in breast screening. Low dose X-rays are passed through the breast to generate images called mammograms. One type of breast abnormality is a cluster of microcalcifications. Usually, in benign cases, microcalcifications result from the death of fat cells or are due to secretion by the lobules. However, in some cases, clusters of microcalcifications are indicative of early breast cancer, partly because of the secretions by cancer cells or the death of such cells. Due to the different attenuation characteristics of normal breast tissue and microcalcifications, the latter ideally appear as bright white spots and this allows detection and analysis for breast cancer classification. Microcalcification detection is one of the primary foci of screening and has led to the development of computer-aided detection (CAD) systems.
However, a fundamental limitation of mammography is that it gives a 2D view of the tightly compressed 3D breast. The depths of entities within the breast are lost after this imaging process, even though the breast tissue is spread out as a result of the compression force applied to the breast. The superimposition of tissues can occlude cancers and this has led to the development of digital breast tomosynthesis (DBT). DBT is a three-dimensional imaging involving an X-ray tube moving in an arc around the breast, over a limited angular range, producing multiple images, which further undergo a reconstruction step to form a three-dimensional volume of breast. However, reconstruction remains the subject of research and small microcalcifications are "smeared" in depth by current algorithms, preventing detailed analysis of the geometry of a cluster. By using the geometry of the DBT acquisition system, we derive the "epipolar" trajectory of a microcalcification. As a first application of the epipolars, we develop a clustering algorithm after using the Hough transform to find corresponding points generated from a microcalcification. Noise points can also be isolated. In addition, we show how microcalcification projections can be detected adaptively.
Epipolar analysis has also led to a novel detection algorithm for DBT using a Bayesian method, which estimates a maximum a posterior (MAP) labelling in each individual image and subsequently for all projections iteratively. Not only does this algorithm output the binary decision of whether a pixel is a microcalcification, it can predict the approximate depth of the microcalcification in the breast if it is.
Based on the epipolar analysis, reconstruction of just a region of interest (ROI) e.g. microcalcification clusters is possible and it is more straightforward than any existing method using reconstruction slices. This potentially enables future classification of breast cancer when more clinical data becomes available.

Keywords: CAD
Breast Cancer
Tomosynthesis
DBT
Classification
Computer-Aided Detection
Digital Breast Tomosynthesis
Mammography
Microcalcifications
Advisor: Brady, M
Schnabel, J
For Christ and Germany: German Catholicism and the Second World War

This dissertation examines the roles played by Catholicism on the German Home Front during the Second World War. It analyses to what extent German Catholics supported their nation’s war effort, and how they sought to reconcile their religious convictions with Nazism and its conduct of the conflict. The thesis examines the oscillations of morale within the Catholic ‘milieu’ during the war years, and analyses its responses to German defeats from 1943 onwards. In addition to these overtly political themes, this dissertation analyses the social history of religion during this period. In order to focus its analysis on a manageable scale, this thesis focuses on the experiences and activities of Catholics from the Rhineland and Westphalia. Its concluding chapter uses its findings concerning Catholicism during the war years to revise current understandings of the formation of a conservative ‘restoration’ in West Germany after May 1945.
Many existing works concerning German Catholicism during this period provide a monolithic portrayal of the confession’s internal coherence, and domination of its adherents’ political beliefs. This thesis, by contrast, argues that profound divides existed amongst German Catholics during the Second World War. Younger clergymen were frequently more sympathetic to völkisch nationalism than their older colleagues, and desired a more pro-Nazi stance from the German episcopate. The Catholic laity, moreover, was similarly often frustrated by the conservatism of episcopal Neo-Scholastic theology, and wanted sermons and pastoral letters that would endorse the German war effort in more unambiguous terms. The war years witnessed a complex negotiation of religious, political and national loyalties amongst Catholic communities, ensuring the thesis provides a nuanced picture of the confession’s place in German society during this period.

Keywords: History of the Third Reich
Advisor: Stargardt, N
Social mobilisation and national consciousness in 20th century Ukraine

The thesis analyses social and political change in twentieth-century Ukraine and its impact on the development of the national consciousness of Ukrainians. In the pre-revolutionary era Ukrainians had a weak sense of national identity because the strategic sectors of society were dominated by non-Ukrainian minority and because the infrastructures of national life were poorly developed. The 1917 revolution saw the rise of a Ukrainian national movement which, while unable to achieve independence, proved strong enough to force major concessions, such as the creation of a Ukrainian Soviet Socialist Republic and acceptance of the principle of Ukrainization policies, from the Bolsheviks. The transformation of socio-economic relations in the course of the revolution facilitated the entry Ukrainians into the socially-mobilised sectors of society, which, together with the development of the infrastructures of national life, brought Ukrainians to the threshold of nationhood by the end of the 1920s. During the first five-year plan Stalin's policies generated much opposition in Ukraine. The purges, the abandonment of Ukrainization, the great famine and the imposition of a totalitarian socio-political order in the 1930s, destroyed much of the fabric of Ukrainian national life. However, the rapid urbanization and industrialization saw Ukraine emerge as a majority of the socially-mobilised population. Also, the fact that many republican institutions survived, at least in form, facilitated the resurgence of Ukrainian national assertiveness in the post-Second World War period. Ukraine lagging economic development, large-scale Russian immigration and the Russification of Ukraine's educational system created a highly competitive environment in the republic which served as the social backdrop for a recrudescence of Ukrainian nationalism in the post-Stalin era. While the Ukrainian intelligentsia were the most vocal exponents of national claims, they were often backed by the new generation of Ukrainian political leaders who, having been trained for responsible positions, were anxious to assume them free from excessive interference from the centre. The Russian leadership's response to this new autonomism was to accelerate Russification and central control of the republic. These policies generated new national conflicts rather than resolve old ones.
Conceptual investigation and the ontology of law

An important question for general jurisprudence concerns method: what is the right way to form a philosophical understanding of law? Exploration of this question has, in one form or another, featured as a constant part of the work of those within the discipline, and many different answers have been given. The aim of this thesis is to argue that a controversial conception of philosophical method – as an investigation into our rule-bound conceptual practices and uses of language – is the appropriate means of understanding the nature of law. The first three chapters establish the initial connection between conceptual or linguistic analysis and the ability to gain insight into the social reality of law. I argue, in chapter one, that institutional concepts have a linguistic basis and, in chapters two and three, that legal systems are borne out of the shared use of certain basic concepts on the part of those who make up their law applying institutions, i.e. the courts. To understand the rules according to which such concepts are deployed, I suggest, is to understand the essential structure of legal practice. An assumption of that argument is tested in chapter four by considering Ronald Dworkin’s famous claim that certain forms of disagreement between lawyers and judges are incompatible with a picture of law dependent upon their agreement in the use of basic legal concepts. Chapter five takes up the question of whether the account of social ontology contained in the thesis is compatible with the fact of philosophical disagreement about the nature of law. Finally, chapters six and seven discuss alternate models of theoretical success in general jurisprudence, the first inspired by externalist views of linguistic and mental contents, and the second dependent upon a naturalistic conception of philosophy.

Keywords: philosophy of law
law
jurisprudence
Advisor: Green, L
The social drama of a learning experience: how is drama appropriated as a pedagogical toolkit in secondary classrooms?

The thesis presents a qualitative study which examines teachers’ and pupils’ experiences of drama tasks in secondary school subject lessons other than Drama, where the tasks are incorporated in pursuit of curriculum-defined teaching and learning goals. I take a cultural-historical perspective in my analysis, interrogating the possibilities for meaningful appropriations of drama as a pedagogical toolkit by examining social interaction and communication within the cultural context of the classroom and how these practices may have developed over time.
Set in four secondary school classrooms in the UK, the study focused on the experiences of teachers, (who are not trained drama specialists), and their pupils as they undertook drama tasks as part of curriculum lessons. I carried out a series of lesson observations, supplemented by interviews with participants. Using Cultural Historical Activity Theory (Cole 1996, Engeström 1987, Engeström 1999) as a heuristic tool, I created an analytical framework that explored the tensions between communicative tools, rules of the classroom space, and teacher-pupil and peer relations. This theoretical stance appreciates both the dynamic nature of classrooms and the possibilities for pedagogies of choice. The emphasis on tool-mediated action offers a fresh perspective in that it creates a structured and detailed framework for exploring the subtle and complex process of empathetic thought.
This study reveals some of the ways in which tensions occur and existing and historically-embedded cultural practices are brought to the surface, and reinforced or challenged. I provide extracts from the data to illustrate a concern for an assessment-driven acquisition of curriculum content is a particular constraint, along with varying opportunities for both teacher and pupils to construct a framework for spontaneous in-role action within the dramatic form. The appropriation of communicative tools, although influential in achieving goals, does not always preclude emotional investment in the tasks. Although there are shifts from teacher authority to increased pupil decision-making, the way in which the teacher and pupils operate in these drama tasks reveals as much about the established and reinforced learning and social practices of the classroom, as the way these practices are changed.
The research considers how drama as a pedagogical toolkit has developed historically, and it reveals implications for future study and practice relating to the understanding of drama-as-toolkit within formal educational settings.

Keywords: pedagogy
drama
social
learning
secondary
Advisor: Ellis, V