VictorJuiz/thesis huggingface dataset:
Cohabitation and convivencia:  comparing conviviality in Casamance and Catalonia

This thesis explores conviviality, a set of processes surrounding everyday living with difference. Based on 18 months of fieldwork (2007-2010) equally split between Casamance, Senegal, and Catalonia, Spain, the comparison takes the transnational lives of Casamançais and their embeddedness in both local fields into account. Locally, Casamançais often spoke of cohabitation (French) and convivencia (Castilian). Exploring discourses as well as practices related to encounters with difference and everyday socialising, this thesis addresses three questions: (1) How do migrants who come from a context of religious and ethnic diversity manage to make their way within new social contexts of cultural diversity? (2) How do their pre-migration experiences of diversity affect the ways in which they deal with the changing configurations of diversity that they encounter in Europe? (3) How do ways of living together with difference change over time in both sending and receiving contexts due to migration and other concurrent societal transformations?
In four ethnographic chapters, I firstly explore everyday neighbourhood encounters and the centrality of multilingual greeting and temporary gatherings in open spaces for conviviality. A second chapter focuses on cultural and religious festivities and argues that, apart from the political recognition of diversity, the local residents’ sensuous experiences of difference are a crucial dimension of conviviality. Addressing challenges to conviviality, the third chapter engages with the processes of social closure, isolation and homogenisation which reveal alternative ways of living with difference. The fourth ethnographic chapter puts migration-related inequalities centre-stage, showing how conviviality also involves subtle forms of inequality.
Analytically, this thesis suggests that conviviality is not a static conception of sociality, but one that is in-process. I find that socio-cultural differences are permanently negotiated, that ways of dealing with difference are translated between the old and new contexts of diversity, and that discourses and practices of living with difference are continuously (re)produced in everyday interactions. Casamançais perspectives reveal ways of maintaining minimal sociality among local residents who remain different.

Keywords: difference
everyday life
ethnic diversity
migration
Southern Europe
West Africa
transnationalism
Casamance
conviviality
multilingualism
cosmopolitanism
Spain
religious diversity
Senegal
Catalonia
Advisor: Vertovec, S
Neveu-Kringelbach, H
Structural studies on foot-and-mouth disease virus

Foot-and-mouth disease viruses (FMDVs) constitute the aphthovirus genus of the Picornaviridae. The structures of Oi subtype viruses OiK and G67 have been solved and comparisons reveal the structural basis of monoclonal antibody escape mutations in G67. Escape mutations are seen to occur at surface-exposed residues and to provoke structural changes limited to the altered side chains. Comparisons of the structures of O1 and O1BFS (Acharya et al., Nature 337, 709-716 (1989)) suggest that changes occurring 'in-the-field' in response to polyclonal antibody pressure may be subtly different from mutations produced by monoclonal antibody pressure in vitro. Field mutations are seen to alter less exposed residues and to have more far-reaching structural effects than the in vitro, monoclonal provoked mutations.
Crystals of G67 are seen to be 'intimately twinned', the data possessing extra symmetry due to a mis-packing of the crystals. A protocol, based on current real-space averaging procedures with a novel constraint imposed, has been used successfully to deconvolute these data. This method might be more generally applied to deconvolute the wavelength overlaps that occur when using the Laue method.
The structures of C-S8cl and mutant SD6-6 have been solved at a resolution of 3.5Å. These structures enable comparisons between members of different FMDV serotypes to be made for the first time, namely: serotype 0 (O1BFS) and serotype C (C-S8cl). Flexibility of the Arg-Gly-Asp containing G-H loop of VP1 is seen to be amongst the most conserved structural features. This loop is implicated in receptor binding and possible roles for the observed flexibility are discussed. The CS8cl structure also reveals more detail in previously disordered regions of the capsid, namely: the N-terminal residues of VP2 and potential myristate density under the 5-fold axis of the virion.
Analysis of structures from the Protein Data Bank reveals different patterns of amino acid use in proteins involved in the two halves of the immune recognition event i.e. immunoglobulins and viruses. These patterns seem to be based not only on the characteristics of the most used amino acids but also on characteristics of the nucleotide codons used to code for them.

Advisor: Stuart, D
Numerical solutions of Cauchy integral equations and applications

This thesis investigates the polynomial collocation method for the numerical solution of Cauchy type integral equations and the use of those equations and the related numerical techniques to solve two practical problem in Acoustics and Aerodynamics.
Chapters I and II include the basic background material required for the development of the main body of the thesis.Chapter I discusses a number of practical problems which can be modelled as a singular integral equations. In Chapter II the theory of those equations is given in great detail. In Chapter III the polynomial collocation method for singular integral equations with constant coefficients is presented. A particular set of collocation points, namely the zeros of the first kind Chebyshev polynomials, is shown to give uniform convergence of the numerical approximation for the cases of the index K = 0. 1. The convergence rate for this method is also given. All these results were obtained under slightly stronger assumptions than the minimum required for the existence of an exact solution.
Chapter IV contains a generalization of the results in Chapter III to the case of variable coefficients.
In Chapter V an example of a practical problem which results in a singular integral equation and which is successfully solved by the collocation method is described in substantial detail. This problem consists of the interaction of a sound wave with an elastic plate freely suspended in a fluid. It can be modelled by a system of two coupled boundary value problems - the Helmholtz equation and the beam equation. The collocation method is then compared with asymptotic results and a quadrature method due to Miller.
In Chapter VI an efficient numerical method is developed for solving problems with discontinuous right-hand sides. Numerical comparison with other methods and possible extensions are also discussed.

Advisor: McKee, S
Schrift- und Schreibmystik. Christina von Hane

The subject of my thesis is a little-studied hagiographical work that gives important insights into rewriting processes and their significance in medieval textual culture. The anonymous Life of Christina of Hane, a thirteenth-century Premonstratensian nun from the Palatinate, is an example of bridal mysticism which combines the medieval tradition of the reception of the Song of Songs with hagiographic elements. A codicological and palaeographical analysis of the only manuscript shows it to be a sixteenth-century copy, but the type of mysticism and the theological questions that it discusses suggest that the text was initially composed in the thirteenth century, when Christina is thought to have lived.
The theological and spiritual ideas in the text belong to the wider context of communicating the transcendental within the world. My thesis uses performative language analysis to address the problems of textuality and authorization in the Life of Christina of Hane. It yields new insights into the ways in which this mystical text makes use of hagiographic strategies, how gender and vernacular theology are linked, how liturgical elements support the text’s pragmatic nature, and how somatic spirituality is reflected on an allegorical level in the embodiment of God’s bride. An assessment of three communicative aspects – medial, narrative, and allegorical – highlights the textualization of the mystical experience. The appellative structure of Christina’s text invites the reader to engage with the text.
This study provides the first comprehensive interpretation of the text on Christina of Hane. It compares it to other mystical texts, to a German–Latin prayerbook, and to a fragmentary legend about Mary Magdalene. It challenges existing judgments about Christina’s biography and offers alternative solutions founded in the latest scholarship on female mystical literature.

Keywords: mysticism
Virgin Mary
manuscript culture
Middle Ages
female spirituality
Christina of Hane
bridal mysticism
performativity
Christina von Hane
Premonstratensian Order
Advisor: Suerbaum, A
An assessment of the use of human samples in ancient DNA studies

This thesis addresses gaps that exist in the theory and knowledge of ancient DNA (aDNA). Much of the underlying basis of the field has been neglected in the excitement that followed the first aDNA studies. Therefore the results of many studies have been based on untested assumptions about the nature of post mortem DNA damage, sample preservation, contamination, and the efficacy of sample decontamination techniques. The validity of such results is questionable if the assumptions prove false.
Hydrolytic post mortem DNA damage may modify recovered aDNA sequences. This thesis reports new insights into the biochemical basis of, predisposition of certain sequences and nucleotide positions towards, and subsequent effects of, such damage. Parallels of post mortem damage with in vivo mutation also enable insights into DNA sequence evolution.
The long-term survival of DNA, and contamination of samples with exogenous DNA are two related problems characteristic to aDNA. The survival of endogenous DNA within bone, teeth and hair samples, the susceptibility of such samples to contamination, and the efficacy of decontamination techniques used to remedy such problems are investigated. The results highlight serious flaws in using bone and teeth as a DNA source. In contrast, the results demonstrate that hair may present a valuable DNA source for future studies.
Numerous studies have reported the retrieval of ancient pathogen DNA from human samples. Analyses of the DNA content within teeth extracted from putative victims of the 2nd plague argue that such studies are at great risk from DNA degradation, and contamination arising due to environmental microorganisms. An extrapolation of these results using basic physical and chemical theory is used to evaluate the potential survival of aDNA in ancient Egyptian remains. This suggests that positive results from such samples are unlikely.

Keywords: Yersinia
DNA
pestis
ancient
contamination
humans
Advisor: Cooper, A
Holmes, E
Energy transfer processes in supramolecular light-harvesting systems

This dissertation attempts to understand how energy transfer in a molecular wire and a spherical organic assembly are affected by molecular structure. The molecular wire is a DNA-hybrid structure composed of a strand of thymine bases appended by a cyanine dye. Hydrogen bonded to each base is a naphthalene-derivative molecule. Using time-integrated photoluminescence and time-correlated single photon counting measurements, energy transfer from the naphthalene donors to the cyanine acceptors was confirmed, and its dependence on temperature and DNA-template length investigated. Donor-thymine bonding was disrupted at temperatures above about 25 degrees Celcius resulting in poor donor template decoration and low rates of energy transfer. Increasing numbers of donors attach to the scaffold, forming an orderly array, as the template length increases due to the stabilising effects of the donor-donor pi-stacking interactions. Conversely, modelled energy transfer rates fall as the scaffold length increases because of the longer donor-acceptor distances involved. Therefore, the energy transfer rate was greatest for a template built from 30 thymines.
The spherical organic assemblies (nanoparticles) are formed by fast injection of a small volume of molecularly dissolved fluorene-derivative amphiphilic molecules into a polar solvent. The amphiphilic molecules contained either a naphthalene (donor) or a benzothiadiazole (acceptor) core. The donor-acceptor mixed nanoparticles resemble an amorphous polymer film and were modelled as such using the Foerster resonance energy transfer theory. The Foerster radii extracted from the measurements depends intricately on the donor-acceptor spectral overlap and distance. The latter effect was controlled by the stacking interactions between the molecules.
Altering the morphology of the structural units is the key to optimising energy transfer in molecular structures. To achieve efficient organic molecule-based devices, the importance of this property needs to be fully appreciated and effectively exploited.

Keywords: molecular structure
time-correlated single photon counting
resonance energy transfer
condensed matter physics
spherical organic asssembly
DNA-hybrid structure
morphology
molecular wire
time-integrated photoluminescence
Advisor: Laura, H
Mathematical modelling of flow and transport phenomena in tissue engineering

Tissue engineering has great potential as a method for replacing or repairing lost or damaged tissue. However, progress in the field to date has been limited, with only a few clinical successes despite active research covering a wide range of cell types and experimental approaches. Mathematical modelling can complement experiments and help improve understanding of the inherently complex tissue engineering systems, providing an alternative perspective in a more cost- and time-efficient manner.
This thesis focusses on one particular experimental setup, a hollow fibre membrane bioreactor (HFMB). We develop a suite of mathematical models which consider the fluid flow, solute transport, and cell yield and distribution within a HFMB, each relevant to a different setup which could be implemented experimentally. In each case, the governing equations are obtained by taking the appropriate limit of a generalised multiphase model, based on porous flow mixture theory. These equations are then reduced as far as possible, through exploitation of the small aspect ratio of the bioreactor and by considering suitable parameter limits in the subsequent asymptotic analysis. The reduced systems are then either solved numerically or, if possible, analytically. In this way we not only aim to illustrate typical behaviours of each system in turn, but also highlight the dependence of results on key experimentally controllable parameter values in an analytically tractable and transparent manner. Due to the flexibility of the modelling approach, the models we present can readily be adapted to specific experimental conditions given appropriate data and, once validated, be used to inform and direct future experiments.

Keywords: asymptotic reduction
multiphase flow
tissue engineering
Advisor: Waters, S
Oliver, J
Shipley, R
Biochemical characterization of a novel deubiquitinating enzyme otubain 1 and investigation into its role in Yersinia infection

Deubiquitinating enzymes (DUBs) constitute a diverse protein family. The specificities and functions of the majority of DUBs are unknown, although their impact on many biological and pathological processes is widely appreciated. This dissertation entails a detailed characterization of otubain 1 (OTUB1), an ovarian tumor domain-containing DUB. The presented work describes OTUB1’s specificity, localization, protein interactions, importance in infection with Yersinia, and proposes a novel model of regulation of its enzymatic activity.
I first discuss the structural and biochemical properties of OTUB1, demonstrating its selectivity towards ubiquitin and NEDD8. Moreover, I show that OTUB1 cleaves lys48- but not lys63-linked polyubiquitin, emphasizing its role in ubiquitin-mediated proteasomal degradation. Mass spectrometric identification of interaction partners and localization studies suggest possible involvement of OTUB1 in RNA processing and cell morphology.
Furthermore, I demonstrate that invasion of the host cells by the enterobacteria Yersinia can be altered by changing OTUB1 expression. This effect is dependent on the catalytic activity of OTUB1 and its ability to stabilize RhoA-GTP prior to infection. YpkA and OTUB1 modulate RhoA-GTP stability in opposing ways, leading to cytoskeletal rearrangements that may be involved in bacterial invasion. Moreover, OTUB1 is post-translationally modified by phosphorylation that modulates its ability to stabilize RhoA-GTP and counteracts its effect on bacterial invasion. These findings provide a novel entry point for the manipulation of the host—pathogen interactions.
Lastly, a kinase screen revealed that FER, an oncogenic kinase with a role in cell morphology, phosphorylates OTUB1, as demonstrated by overexpression, siRNA and in vitro studies. The phosphorylated site was mapped to tyr26 and the activity-based labeling revealed that this modification interferes with the deubiquitinating activity of OTUB1.
In summary, the results presented in this thesis confirm that OTUB1 exerts properties of a “classical DUB” and uncover some of its physiological functions.

Keywords: host-pathogen interactions
phosphorylation
Yersinia
proteomics
ubiquitin
deubiquitinating enzymes
Advisor: Kessler, B
Investigations of the potential schizophrenia susceptibility gene Kinase Interacting with Stathmin (KIS)

Single nucleotide polymorphisms (SNPs) within the gene encoding the serine threonine kinase KIS (Kinase Interacting with Stathmin, also known as UHMK1) have recently been associated with schizophrenia. However, little is known about the neurobiology of KIS or the mechanisms through which disease-associated SNPs may increase susceptibility to schizophrenia. The studies presented in this thesis focus on the distribution of KIS and its mRNA, address the mechanisms through which KIS may confer susceptibility to schizophrenia, and investigate the physiological role(s) of KIS in the brain using two lines of knockout mice.
The regional and cellular distribution of KIS was characterised in the brains of adult humans and mice, and through mouse neurodevelopment. The results of these experiments demonstrated that KIS is widely expressed in neurons in the brain regions examined in both species, its encoded protein is localised to the nucleus and cytoplasm, and KIS expression in mouse brain peaked around seven days after birth.
KIS protein and mRNA was quantified in two large human post-mortem brain series to determine if KIS expression is altered in schizophrenia or bipolar disorder, or in relation to the leading schizophrenia-associated SNP (rs7513662). Using tissue from the superior temporal gyrus, dorsolateral prefrontal cortex, anterior cingulate cortex, and cerebellum, no difference in KIS expression (either mRNA or protein) was found between diagnostic or genotype groups in any brain region examined. Furthermore, KIS expression in lymphoblast cell lines also did not differ between diagnostic or genotype groups.
Lastly, KIS expression (mRNA and protein) was characterised in two separate lines of KIS knockout mice. The results were complex, and left uncertainty as to whether either line was a true knockout or, conversely, whether any of the available KIS antibodies were specific. Nevertheless, the absence of KIS mRNA was robustly confirmed in one knockout mouse line, and brains from this line were subsequently used in three experiments. First, investigation of the quantity and phosphorylation state of the KIS targets stathmin and p27kip1; no differences were found compared to wildtype mice. Second, quantification of mRNA expression of several other genes of interest with regard to schizophrenia; altered expression of GAP43, VGlut1, MAP2, spinophilin, and stathmin was found. Finally, stereological measurements were performed, and while no differences in whole or regional brain volumes in KIS knockout mice were found, there was a relative reduction in hippocampal volume.
The results of these studies do not support the hypothesis that altered expression is the mechanism by which genetic variation of KIS may increase susceptibility to schizophrenia, nor that KIS expression is altered in the disease. However, the knockout mice data suggest that KIS may play a role in synaptic plasticity and function, providing novel information on the potential neurobiological roles of KIS.

Keywords: schizophrenia
UHMK1
KIS
Advisor: Harrison, P
Eastwood, S
Deference in international human rights law

Deference in international human rights law has provoked animated discussion, particularly the margin of appreciation doctrine of the European Court of Human Rights. Many commentators describe the practice of deference but do not explain how it affects judicial reasoning. Some approve characteristics of deference but do not provide a justification to defend the practice against criticism. Others regard deference as a danger to human rights because it betrays the universality of human rights or involves tribunals either failing to consider a case properly or missing an opportunity to set human rights standards. This thesis employs a different approach by focussing on deference as the practice of assigning weight to reasons for a decision on the basis of external factors. This approach draws on theories of second-order reasoning from the philosophy of practical reasoning. The thesis offers a conceptual account of deference that accords with the practice not only of the European Court of Human Rights, but also the Inter-American Court of Human Rights and the UN Human Rights Committee. Additionally the thesis presents a normative account of deference, that the role of these tribunals entails permitting a measure of diversity as states implement international human rights standards. Deference in international human rights law then is the judicial practice of assigning weight to the respondent states’ reasoning in a case on the basis of three factors: democratic legitimacy, the common practice of states and expertise. This affects judicial reasoning by impacting the balance of reasons in the proportionality assessment. The account defended in this thesis dispels concerns that deference is a danger to human rights, whilst providing a theory that justifies the practice of the tribunals. The thesis thus provides the contours of a doctrine of deference in each of the three international human rights systems.

Keywords: deference
margin of appreciation
proportionality
Advisor: Finnis, J
Sarooshi, D