VictorJuiz/thesis huggingface dataset:
Beyond corsairs: the British-Barbary relationship during the French revolutionary and Napoleonic wars

The North African Barbary States are usually dismissed as an unimportant, though bothersome, pirate base of little consequence in the late eighteenth and early nineteenth centuries. This thesis challenges that idea by providing qualitative and quantitative evidence of Barbary's role in trade and diplomacy during the French Revolutionary and Napoleonic Wars, especially as it affected Britain and how the British were able to carry out their military and political goals in the Mediterranean. The study is based on the correspondence between the British government and its military leaders in the region, the correspondence and reports generated by British consuls working in Barbary, import/export records, and a database tracking British shipping to and from North Africa during the conflict.
To the British, Barbary was not an irritation but an asset. Britain was able to manage Barbary's trade and foreign policy over the course of the twenty-three-year conflict. This was accomplished in two key ways: as a source of supplies for British forces and through the diplomatic role provided by Britain's extensive consul network. Though the North African states were neutral for the majority of both wars, Britain worked strenuously to maintain and increase its trade and diplomacy with Barbary for the benefit of the British armed forces. British trade with Barbary, supported by the British-Barbary diplomatic relationship, directly contributed to British successes in the Mediterranean and Iberian Peninsula.

Keywords: Piracy
French Revolutionary War
Barbary States
Barbary
Barbary Pirates
Logistics
Royal Navy
Napoleonic War
Corsairs
North Africa
Pirates
supply
Advisor: Rodger, N
Tudor noble commemoration and identity: the Howard family in context, 1485-1572

This thesis examines the relationship between the commemorative strategies of English noblemen in the period 1485-1572 and their identity both as individuals and as a social group. In particular, it will look at the Howard dukes of Norfolk in the context of their peers. The five chapters each address a different aspect of noble identity. The first two chapters deal with the importance of kinship and of status. The importance of kinship is evident across commemorative strategies from burial locations to the heraldry displayed at funerals to the references to ancestry in elegies. Having achieved a particular status, noblemen were defensive of their rank and the dues accorded to it. Funerals were designed to reflect social status and the choice of burial location could also indicate a concern with status. However, there was not always a correlation between the scale of commemoration and status. The third chapter examines the role that service to the Crown played in noble identity. Late medieval ideals of military service and a chivalric culture survived well in to the sixteenth century and traditional commemorative forms remained popular, even amongst noblemen newly ennobled from the ranks of the Tudor administration. Chapter four addresses the importance of local power to the nobility of the period. Burial and commemoration acted as a visible reminder of the social order and were of benefit in maintaining local stability. Noblemen could also use their death as a means of demonstrating good lordship through charity and hospitality. The final chapter examines the importance of religion to a nobleman's identity during a century of turbulent religious change. Studying commemorative strategies allows us to trace noble responses to religious change, the constraints on their public show of belief, and the ways in which they could express individuality.

Advisor: Gunn, S
Imaging ionic flux through individual pores in droplet interface bilayers

Optical measurements of ion flux are a powerful technique when studying the functional properties of ion channels and the dynamics of pore formation in biological membranes. The simultaneous read-out of optical single channel recordings (oSCR) provides an alternative way of measuring electrical activity and is more feasible than parallelising electrical measurements. Channel activity is monitored with ion specific indicator dyes whose response is proportional to the magnitude of the current. Here, two novel applications of oSCR in a droplet interface bilayer model membrane system are presented.
Firstly, a technique for potassium-flux imaging through individual electropores is developed. Three indicator dyes are characterised with fluorescence spectroscopy and oSCR of potassium-flux are shown for the first time. Dynamic fluorescence response when applying a voltage protocol can be observed while monitoring currents through several pores in parallel. The response time is between 2.5-10 s and the minimum resolvable current is estimated to be -2 nA.
Secondly, pore formation in the presence of four antimicrobial peptides (melittin, magainin 2, alamethicin, indolicidin) is visualised by calcium-flux imaging combined with single-molecule imaging of labelled peptides in the same membrane region. Calculations of radial distribution functions show a uniform distribution of peptides on the membrane surface. Punctate poration events observed with calcium-flux most likely originate from barrel-stave (alamethicin) or toroidal pores (melittin and magainin 2), whereas indolicidin does not promote pore formation.
The techniques developed in this thesis are an important contribution to the field of oSCR.

Advisor: Wallace, M
Tucker, S
Preaching and Christianization: reading the sermons of John Chrysostom

The rise of Late Antiquity as a separate discipline, with its focus on social history, has meant that the vast homiletic corpus of John Chrysostom has received renewed attention as a source for the wider cultural and historical context within which his sermons were preached. Recent studies have demonstrated the exciting potential his sermons have to shed light on aspects of daily life, popular attitudes and practices of lay piety. In short, Chrysostom's sermons have been recognised as a valuable source for the study of 'popular Christianity' and the extent of Christianization at the end of the fourth century.
This thesis, however, will question the validity of some recent conclusions drawn from Chrysostom's sermons regarding the state of popular Christianity. A narrative has been developed in which Chrysostom is often seen as at odds with the congregations to whom he preached. On this view, the Christianity of élites such as Chrysostom had made little inroads into popular thought beyond the fairly superficial, and congregations were still living with older, more culturally traditional views about religious beliefs which preachers were doing their utmost to overcome. It is the argument of this thesis that such a portrayal is based on a misreading of Chrysostom’s sermons, and which fails to explain satisfactorily the apparent popularity that Chrysostom enjoyed as a preacher.
What this thesis sets out to do, therefore, is to reassess how we read Chrysostom's sermons, with a particular focus on the harsh condemnatory language which permeated his preaching, and on which the image of the contrary congregation is largely based. To do this, this thesis sets out to recover a neglected portrayal of Chrysostom as a pastor and preaching as a pastoral and liturgical activity, through an exploration of four different but overlapping aspects of the socio-historical context within which his preaching was set. A consideration of the scholastic, therapeutic, prophetic and liturgical nature of his preaching will shed light on the pastoral relationship between the preacher and his congregation and will, significantly, provide a backdrop against which his condemnatory language can be explained and understood. It will become clear that his use of condemnatory language says more about how he understood his role as preacher than about the extent of Christianization in late-antique society. Through focussing on the issues of the social composition of the congregation and the level of commitment to (Chrysostom's) Christianity, it will be argued that sermon texts are in their nature resistant to being used as sources for this kind of social history. Despite this, however, glimpses will also emerge of a very different picture of late-antique Christianity, in which Chrysostom's congregation are rather more willing to listen and learn from their preacher than is often assumed.

Advisor: Morgan, T
Ligand hydration and bridging waters molecules

Water is the most abundant molecule in biological systems and is ubiquitous in nature. Despite this prevalence, water has long been considered a backdrop for bio-processes. However, with increasing sophistication in experimental and computational methods, water has now been recognized to interact and influence the behaviour of biomolecules in complex, subtle, and essential ways. The structure of water is unique in that it is small yet able to form multiple hydrogen bonded interactions. Water molecules are thus ideally suited to bridge interactions on biomolecular surfaces. Specifically, they have been identified to play an important role in mediating protein-ligand interactions. A methodology for the inclusion of these mediating waters has often been stated to be a major challenge facing the field of rational drug design. While notable successes exist in the design of better binders using water molecules, no single method has been able completely predict the locations of water molecules and its propensity to interact with the binding ligand.
This thesis is intended to explore the possibilities of using the hydration of ligands as a pathway to study bridging water molecules in holo structures. To this end, a method of discretizing and scoring water-sites around ligands from their Molecular Dynamics (MD) simulation is first developed. This was then used to correlate the hydration shells of ligands with the locations of the bridging water molecules. Further, the hydration shell of ligands is used to improve WaterDock - a protocol to predict the locations of water molecules within binding sites. Finally, a comparison of MD is made with Empirical Potential Structure Refinement - a combined experimental and computational method that is often used to resolve the solvation structure of small molecules.

Keywords: Water
Drug Molecules
Hydration
Advisor: Biggin, P
McLain, S
Epigenetic silencing of RASSF1A promotes tumourigenesis via alternative transcript expression, SFK activation and exosome secretion

Loss of the tumour-suppressor gene RASSF1A upon promoter methylation is one of the most frequent events in sporadic human malignancies. Loss of RASSF1A is associated with progression and pathogenesis of solid tumours; and more aggressive clinical phenotype, leading to poor prognosis in breast, lung and colon cancers, amongst others. RASSF1A functions in a number of cellular processes, inducing apoptosis in response to DNA damage, cell cycle arrest and growth control. In tumours with RASSF1 promoter methylation, an alternative isoform, RASSF1C, is expressed and we find is able to bind and activate SRC. We also identify a novel tumour-suppressor role for RASSF1A, associating with the kinase inactivation of SRC. RASSF1C expression promotes SRC-dependent phosphorylation and internalisation of adherens junctions, leading to loss of cell-cell contacts and subsequent increase in cell motility, growth and invasiveness, both in vitro and in vivo. RASSF1C, via active SRC, mediates the phosphorylation of β-catenin and YAP1, promoting their nuclear localisation and association with the transcription factors TEAD1 and TBX3, resulting in the upregulation of anti-apoptotic and pro-survival genes. We show that RASSF1C expression leads to differential packaging and secretion of exosomes, modulating the communication between cancer cells and increasing their tumourigenicity. Finally, we find that cells expressing RASSF1C undergo phenotypic and transcriptional changes associated with the generation of cancer stem cells. We conclude that RASSF1C is an oncogene that plays a variety of roles in cell adhesion, invasion, survival and extracellular communication, resulting in increased tumourigenesis. These functions are inhibited by the tumour suppressor RASSF1A. This work highlights the association of the epigenetic inactivation of the RASSF1A gene with the more aggressive, metastatic tumours, and its relation to increased cancer outcome and risk.

Keywords: RASSF1
Cancer
YAP
Epigenetics
SRC
Exosomes
Advisor: O'Neill, E
Semiclassical transition state theory for chemical reactions

First-principles calculations of chemical reaction rate constants have useful applications in a variety of areas. Quantum reactive scattering approaches are the most accurate, but their computational costs scale significantly with system size. Semiclassical Transition State Theory (SCTST) constitutes a more efficient approach. In SCTST, rate constants are calculated from frequencies and anharmonic constants, which depend on the second, third, and fourth derivatives of the reaction's potential energy surface (PES) at the transition state. Further gains in efficiency can be achieved by calculating anharmonic constants for only a subset of degrees of freedom. SCTST can be improved by imposing more realistic behaviour of the reactant and product asymptotes of the potential barrier used in calculations.
This thesis investigates the accuracy of one- and two-dimensional SCTST in relation to accurate quantum scatteirng calculations performed on the same PESs. Calculations are performed for four H atom abstraction and exchange reactions: H + CH4, H + C2H6, H + cyc-C3H6, and CH3 + CH4. Two methods are presented for calculating frequencies and anharmonic constants from PESs developed previously for these reactions, which are defined in Jacobi coordinates. 2-D SCTST rate constants exhibit acceptable agreement with results from previous quantum scattering calculations. 1-D SCTST rate constants agree very well with 2-D results, although barrier corrections must be applied in the case of the CH3 + CH4 reaction. These corrections did not significantly improve the accuracy of other calculations. Agreement between 2-D and 1-D results suggests the validity of reducing the number of degrees of freedom considered in an SCTST calculation.
A practical ab initio approach is presented to facilitate evaluation of the accuracy of 1-D SCTST in relation to FD SCTST. Richardson extrapolation is discussed as an approach to improving the accuracy of purely numerical calculations of third and fourth derivatives. FD calculations for the H + CH4 and H + C2H6 reactions exhibit good agreement with previous results and with results from two different 1-D methods. The second of these methods requires only 4 single-point energy calculations in addition to those required for TST. The agreement of 1-D and FD results suggests the potential applicability of 1-D SCTST to larger systems.

Keywords: semiclassical transition state theory
Advisor: Clary, D
Hotbeds of unrest and extremism: how social context influences political participation in the 21st century: Britain, from rioting to far right party membership

British politics at the start of the 21st century provide a good setting for examining factors associated with mobilisation for extremist politics. This thesis is concerned with the relationship between individuals' preferences, their local setting and political behaviour. With focus on two outcomes – participation in urban rioting and support for a far right party – this thesis is divided into two parts and consists of five research papers addressing different aspects of mobilisation.
In the first part we focus on urban disorder and examine police arrest records from the London riot of 2011. Much of the sociological literature has focused on variation in rioting across cities; here we examine variation within London by mapping the residential addresses of 1,620 rioters onto over 25,000 neighbourhoods. Our findings challenge the orthodoxy that rioting is not explained by deprivation or by disorganisation. Furthermore, we present evidence suggesting the importance of political grievances, in particular relations with the police, and examine the process of mobilisation to show that it was aided by spatial proximity and social similarity.
In the second part we look at factors associated with engagement with far right politics. We use individual attitudinal data from the British Election Study to examine whether concerns over immigration are associated with the actual experience of immigration in one's place of residence. The results suggest that local setting does play some role, although individual factors seem to be more important. Secondly, we use leaked British National Party membership list to map 12,536 far right supporters onto over 200,000 neighbourhoods in Britain. Our findings underline the importance of a larger geographic context, where some spatial configurations present particularly fertile grounds for the far right; we also report the relative unimportance of cultural threat and significance of the social distance. Lastly, we question the recently advocated 'legacy effect' and suggest that white flight mechanism may possibly be an alternative way of thinking about organisational continuity.

Keywords: political extremism
British politics
British National Party
London Riots 2011
far right
Advisor: Biggs, M
Towards an understanding the perceptual foundations of prejudice

In-group identification is a central aspect of human social behaviour. There is evidence of the effects of in-group identification on different aspects of cognition but it is still unclear how in-group identification might affect basic perceptual mechanisms. Relying on an interdisciplinary perspective, this work investigates the extent to which in-group identification affects perception. This thesis explores the issue under three main themes.
The first theme deals with the effect of in-group identification on perception using behavioural paradigms and relies on the measures of accuracy and reaction time as well as questionnaire measures of the strength of in-group identification. In this case, individuals show enhanced perceptual matching performance for stimuli associated with an in-group as opposed to the stimuli associated to rival and neutral groups. Moreover, the enhanced performance for in-group associated stimuli correlated with the satisfaction subcomponent of an in-group identification measure.
The second theme aimed to gain a better understanding of the effects of in-group identification on both automatic (prosaccade) and inhibitory (antisaccade) aspects of explicit attentional orienting. In this case, the results provide evidence on the effect of in-group identification on the inhibitory control of overt attention, as well as on pupillary responses.
The third theme examined the neural underpinnings of in-group identification effects on perception. Neural correlates of in-group biases were found in brain networks previously associated with social saliency, emotion and attention, notably the posterior superior temporal sulcus, the dorsolateral prefrontal cortex and anterior insula. Moreover, carrying out a perceptual matching task changed the functional connectivity between the anterior insula and the inferior frontal gyrus, and this change in connectivity was related to the magnitude of behavioural biases to the in-group. This suggests that such rapid changes in functional connectivity may provide a neural basis for the development of in-group favouritism.
The overall findings across the different chapters confirm that in-group biases affect perceptual matching in a variety of ways and through a specific neural network. In general, the results are in line with the hypothesis that our perception favours stimuli linked to our in-group. The limitations and future possible lines of study are discussed.

Advisor: Humphreys, G
Hewstone, M
Blood pressure, atrial fibrillation and diabetes: evidence from observational and randomized analyses

The subgroup-specific relationships between blood pressure (BP), risk of atrial fibrillation (AF) and risk of diabetes are unclear. These two chronic diseases have key epidemiologic and clinical similarities, are difficult to examine through traditional cohort studies, and are of high clinical and public health importance. Using observational analyses of electronic health records and meta-analyses of randomized trials, the relationships between blood pressure, atrial fibrillation and diabetes are investigated in this thesis. First, I show that blood pressure is modestly associated with risk of atrial fibrillation in a population free of cardiovascular disease [HR 1.21 95% confidence interval 1.19, 1.22 per 20 mm Hg higher systolic blood pressure (SBP)]. While a non-significant effect of BP lowering on AF in non-heart failure populations is observed in a meta-analysis of randomized trials, this randomized estimate is similar in magnitude to the observational association, suggesting that BP lowering may modestly lower the risk of AF. Second, I show that elevated BP is associated with a higher risk of incident diabetes (HR 1.76 CI 1.56, 198 per 20 mm Hg higher SBP), although the causality of this finding is unclear. Third, I demonstrate in both observational and randomized analyses that the relationship between blood pressure and cardiovascular events appears to be modified by achieved BP in type 2 diabetes, with attenuated proportional reductions at achieved SBP less than 130 mm Hg. However, I also show that BP lowering to levels lower than those recommended in current guidelines (&LT;130 mm Hg SBP) may lower the risk of stroke, renal disease and retinopathy. These findings are of clinical and public health importance, as they suggest that BP lowering therapy can be used to reduce the risk of AF, that elevated BP may be a risk factor for incident diabetes, and that BP lowering in type 2 diabetes to lower levels than currently recommended in guidelines may further reduce the burden of cardiovascular disease in diabetic populations.

Keywords: Epidemiology
Blood pressure
Advisor: Rahimi, K
Woodward, M