VictorJuiz/thesis huggingface dataset:
Dynamics of driven colloidal systems in one-dimensional potential energy landscapes
Keywords: driven
colloidal
potential energy landscape

The dynamics of colloidal particles driven over optical potential energy landscapes is studied. Experiments are conducted using colloids driven by solvent flow or piezo-stage, optical tweezers, magnetic fields, and video-microscopy. Firstly, the properties of optical traps and potential energy landscapes are determined using driven colloidal particles and clusters. The trap stiffness and potential depth of single Gaussian traps are measured directly. It is shown that the nature of optical potential energy landscapes may be fully engineered and predicted using a sum of single Gaussian potentials. Next, the motion of colloidal particles driven by a constant force over a periodic optical potential energy landscape is considered. The average particle velocity is found as a function of the driving velocity, and the wavelength of the optical potential energy landscape, which is found to be sinusoidal at small trap spacings. The critical driving velocity required for a particle to move across the landscape is determined as a function of the wavelength. Brownian motion is found to have a significant effect on the critical driving velocity, but a negligible effect at high driving velocity. Subsequently, the dynamic mode locking caused by adding a modulation to the driving force is studied. This synchronisation manifests as a `Devil's staircase' in the average particle velocity as a function of driving velocity. The amplitude and frequency dependence of the mode locked steps are studied. Furthermore, particle trajectories are examined, and phase portraits show locked (unlocked) states as closed (open) loops in phase space. A state diagram of mode locked steps is constructed. Finally, driven systems of magnetically interacting colloidal particles are examined in potential energy landscapes. The critical driving velocity of a chain of coupled particles driven by a constant force is found to depend strongly on the chain length and the magnetic field. Secondly, a mobile density wave (kink) in an optically pinned chain of coupled particles is exposed to a constant and modulated drive. The kink is found to behave as a quasi-particle, exhibiting analogous dynamic mode locking behaviour to the single particle case. Finally, the mode locking of a finite mobile chain is considered, and found to be affected by the chain flexibility, which is a function of the magnetic field.
The influence of donor body mass index on human pancreatic islet function, structure and islet transplant outcome
Keywords: transplantation
type 1 diabetes
obesity
islet cell
diabetes
BMI

Background: Pancreatic islet transplantation for type-1 diabetes has resulted in considerable success over the past decade. However, the worldwide shortage of pancreatic donors remains a major challenge. In an attempt to expand the donor pool, pancreases from obese organs donors (>30 kg/m²) are now routinely offered to islet transplantation in the UK. In addition, it has been suggested that pancreases from donors with early type-2 diabetes mellitus may also be suitable. However, for both these donor groups, although high islet yields (IEQ) may be obtained, it is unclear whether these islets function optimally. An additional approach to the donor shortage is to minimise the number of donors required per islet recipient. One strategy to achieve this is to use different pharmacological agents to enhance post-transplant islet function.
Aims: The aims of this thesis were fourfold; 1) To determine whether islets isolated from high BMI donors function normally in vitro and in vivo; 2) To establish why islet yields are higher from obese donors; 3) To determine whether islets from donors with type-2 diabetes are suitable for islet transplantation; 4) To investigate whether glucagon-like peptide 1 receptor agonist therapy improves post-transplant islet graft function.
Results: Stimulated insulin and glucagon secretion, and markers of mitochondrial function (intra-islet ATP content and mitochondrial copy number) were compared in islets isolated from obese (BMI>30kg/m²; n= 27) and non-obese (BMI<28kg/m²; n=25) donors. No differences in secretory function or intra-islet ATP were observed between the two groups. Pancreatic lipid and intra-islet triglyceride concentrations were higher in the obese group. In vivo clinical outcomes of patients transplanted in Oxford and a larger cohort (n=35) in Edmonton, Canada with islets from obese or non-obese donors showed no differences in post-transplant outcomes. Improved islet yields were shown to be a result of improved islet recovery of larger islets, in obese donors. Abnormal insulin and glucagon secretory responses were observed in islets from type-2 diabetic subjects (n=6) and islet amyloid content was significantly higher in diabetes. The glucagon-like peptide 1 receptor agonist, exenatide, administered for 20 weeks, significantly improved graft function in patients whom islet function was impaired.
Conclusion: The high lipid environment of islets isolated from donors with high BMI appears not to be deleterious to their function either in vitro or when transplanted, supporting the use of islets from high BMI donors for clinical islet transplantation. However, islet dysfunction and pathological changes indicate that islets from type-2 diabetic donors are unsuitable. Therapeutic options such as exenatide, improve transplanted islet viability and function, and could have a significant role in the future of beta-cell replacement therapy for type-1 diabetes.
Electronic trading in the foreign exchange spot market
Keywords: Electronic trading
foreign exchange market
price formation
market microstructure
quasi-centralized liquidity
limit order book

During the past 30 years, the proliferation of electronic trading has catalysed profound structural change in the global foreign exchange (FX) spot market. Today, more than 60% of the market's volume occurs via electronic trading platforms, which provide traders with round-the-clock market access from anywhere in the world. Such platforms offer several practical benefits that have encouraged market participation from a broad new class of financial institutions and have thereby spurred market growth.
The most widely used electronic trading platforms in the FX spot market incorporate several features that differentiate them from those used in other financial markets. These features raise many important questions about order flow, market state, price formation, trader behaviour, and volatility. Despite the enormous trade volumes that such platforms facilitate, these questions have received almost no attention to date.
In this thesis, we study a recent, high-quality data set from a large electronic trading platform in the FX spot market in order to investigate several aspects of trading via this mechanism. We calculate a wide range of statistics regarding order flow and market state, and we highlight how our findings contrast to those reported by empirical studies of electronic trading platforms in other markets. We study the autocorrelation properties of returns, absolute returns, and order flow, and we investigate the extent to which the market's organization impacts price formation. We also introduce a model designed to reproduce the most important properties of trading via such a platform. We derive several results regarding the model's temporal evolution, and we simulate the model to investigate how the interactions between individual traders influence volatility. We conclude that electronic trading platforms in the FX spot market retain many desirable features of centralized markets while providing traders with explicit control over their personal trading partnerships.
A theological response to the "illegal alien" in federal United States law
Keywords: aliens
Book of Psalms
Christian ethics
territory
illegal immigration
Gospel of Luke
Edward Coke
corrective justice
Hugo Grotius
Emer de Vattel
Martin Luther
attributive justice
international relations
1880's Chinese immigration
deuteronomy
Aristotle
Book of Genesis
Mexico-US migration
moral theology
common law
migrants
Thomas Hobbes
nationhood
legal history
1 Corinthians
political theology
political theory
Karl Barth
sovereignty
William Blackstone
distributive justice

Today, some twelve million immigrants are unlawfully present in the United States. What response to this situation does Christian theology suggest for these immigrants and those who receive them? To this question about the status of immigrants before the law, the theological literature lacks an understanding of how federal U.S. immigration law developed, and it lacks a robust theological account of the governance of immigration. To fill this gap, the thesis presents three stages in the formation of the laws that designate some immigrants as aliens unlawfully present or illegal aliens, drawing out the moral argumentation in each phase and responding with moral theology. In the first stage, non-citizens were called aliens in U.S. law. In response to the argument that aliens exist as a consequence of natural law, Christian teaching indicates that immigrants are not alien either in creation or for the church. In the second stage, the authority of the federal government to exclude and expel aliens was established, leaving those who do not comply to be designated illegal aliens. To the claim that the federal government has unlimited sovereignty over immigration, interpretations of the Christian Scriptures respond that divine sovereignty limits and directs civil authority over immigration. In the third stage, legal reforms that were intended to end discrimination between countries allowed millions from countries neighboring the U.S. to become illegal aliens. These reforms turn out to be unjust on philosophical grounds and unneighborly on theological grounds. While federal law classes many as aliens unlawfully present in the United States, Christian political theology indicates that immigrants are not alien, the government of immigration is limited by divine judgment, and nationals of neighboring countries deserve special regard.
Mechanism of SigR inhibition by the anti-sigma factor RsrA from Streptomyces coelicolor
Keywords: Biochemistry
Biophysics
microbiology
protein interactions

The extracytoplasmic function (ECF) sigma factor SigR (σR) is a bacterial transcription factor involved in the regulation of cytosolic redox homeostasis in Streptomyces coelicolor. SigR activity is regulated by its cognate anti-sigma factor RsrA. RsrA is a member of the zinc-anti-sigma (ZAS) family, which in its reduced state binds a single Zn2+ ion coordinated by 3 cysteine residues and a histidine. RsrA senses oxidative stress within the cytosol and responds by the formation of intramolecular disulphide bonds between its Zn-ligating cysteine residues. This results in the loss of the metal ion, a conformational rearrangement, and dissociation of SigR by an unknown mechanism. This releases SigR to bind RNA polymerase and direct the expression of a large regulon including that of the thioredoxin pathway, thereby re-establishing redox homeostasis. No structural information is available for the SigR-RsrA complex in Streptomyces coelicolor. Moreover, little is known of the mechanism by which RsrA associates with SigR and regulates gene transcription, or the role of zinc in SigR binding. In this work, a stopped-flow fluorescence-based assay was developed for investigating the kinetics of SigR-RsrA complex formation to aid our understanding of the role of the metal ion. Ultimately, trying to understand how oxidative stress causes dissociation of the Streptomyces coelicolor complex. Through tryptophan fluorescence emission quenching experiments, the SigR region 2 tryptophan (W88) and region 4 tryptophan (W159) were found to be sensitive to RsrA binding, likely denoting the binding sites for the anti-sigma factor. Pre-steady state experiments demonstrated that the metal ion has little effect on the rate of association (Kon 8.9 and 17.3x106 M-1s-1 at 35°C in the presence and absence of zinc, respectively) but a large effect on the dissociation rate constant (>500-fold faster in the absence of zinc at 35°C). Moreover, the kinetically derived Kds (0.27 nM and 62.4 nM with and without zinc respectively) agreed with the equilibrium constant for the complex derived through isothermal titration calorimetry (0.78 nM and 101.7 nM), validating the kinetic model for binding experiments. Zinc therefore has an important role in the structure of RsrA, affecting SigR-RsrA complex affinity, the off-rate for the complex and inhibition of SigR activity. Future work will exploit these assays to determine the role of zinc in redox sensing by RsrA.
Tuning ultrafast chemical reaction dynamics in photoactive proteins
Keywords: Retinal protonated Schiff-base
Ultrafast
Green Fluorescent Protein

This dissertation investigates the origins of tunable and efficient photochemistry in three different photoactive proteins, bacteriorhodopsin (BR), rhodopsin (RHO) and green fluorescent protein (GFP). In all cases, significant differences exist between the photoreactivity of model chromophores in solution and in the protein environment, in terms of excited state lifetime and efficiency of the primary photochemical process (opsin proteins) or the type of reaction (excited state proton transfer versus C=C double bond photoisomerisation for GFP).
The work presented here investigates for each case to what extent the protein environment is necessary to alter the photochemistry of model chromophores in solution. For GFP and BR steric and electrostatic interactions between the protein pocket and the chromophore are shown to be likely responsible for shaping the excited state surface along which the photoreactions take place. For RHO it is suggested, contrary to current belief, that selection of a reactive ground state conformer might be the main effect generating the observed differences between solution and protein environment.
The solution photochemistry of structurally modified retinal protonated Schiff bases, taken as model chromophores for the opsin proteins, is studied with continuous wave irradiation experiments and ultrafast transient spectroscopies. Surprisingly large differences are observed for the isomerisation reaction depending on the starting configuration (trans or cis) of the photoactive double bond. The current model for BR based on the tuning of the excited state barrier encountered along the isomerisation coordinate is expanded to include the changes in selectivity, speed and efficiency observed for a series of all-trans derivatives.
For 11-cis, the photoisomerisation in solution is proposed to take place along a barrierless isomerisation coordinate, in contrast with the models currently available in literature. It is suggested that the protein might be discriminating between ground state conformers rather than significantly changing the topography of the reaction coordinate.
For GFP, excited state Raman spectra are recorded for the wild-type protein, two mutants and a model chromophore in solution. It is suggested that the high frequency vibrational modes observed in the excited state spectra of the proteins but not of the model chromophore in DMSO are a sign of a tighter chromophore environment that inhibits the photoisomerisation reaction occurring in solution.
Agricultural development in Mid Saxon England
Keywords: Anglo-Saxon
archaeology
archaeobotany
zooarchaeology
agriculture

Over the past decade, historians and archaeologists have become increasingly aware that the Mid Saxon period in England (7th-9th centuries AD) witnessed a transformation in agricultural practices. According to the emergent consensus, in contrast to the heavily pastoral, broadly subsistence-based mode of agriculture characteristic of the Early Saxon period (5th-7th centuries), Mid Saxon agriculture was geared towards higher levels of surplus production and placed a greater emphasis upon arable farming. The increased cultivation of bread wheat and the specialist production of sheep’s wool have been identified as particularly important innovations of this period.
This thesis represents the first attempt to explore agricultural development in Mid Saxon England on a systematic archaeological basis. It considers settlement, zooarchaeological, and archaeobotanical evidence in detail, with a special emphasis on charred plant remains. The analyses utilize data gathered from excavation reports, published and unpublished, covering two case study regions: (i) the Upper/Middle Thames valley and environs, and (ii) East Anglia and Essex. In addition, a sub-assemblage of charred plant remains from a Mid Saxon monastic site at Lyminge (Kent) is studied at first hand.
In this way, a series of agricultural innovations is identified in the archaeological record, including in particular: specialized pastoralism, an increased emphasis on sheep in some regions, an expansion of arable production, growth in fibre production, growth in cereal surpluses, a consequent investment in specialist storage and processing facilities, and a general diversification of crop spectra. These innovations were contingent upon, and adapted to, local environmental factors. The process of agricultural development is thought to have begun in the 7th century and continued through the 8th and 9th centuries, facilitated and stimulated by newly consolidated élite landholdings and, probably, a growing population.
Writing (hi)story : Gascony in Jean Froissart’s chroniques
Keywords: Gascony
historiography
France
medieval chronicles
narratology
polyphony
late medieval ideology
Jean Froissart
fourteenth century
Aquitaine

Jean Froissart’s Chroniques, composed of four Books, relate the first stages of the Anglo-French conflict later known as the Hundred Years’ War (1337–1453).
This thesis explores Froissart’s textual journey(s) to Gascon lands (south-west of modern-day France) and history/stories. Relying on Gérard Genette’s and Mikhail Bakhtin’s narrative theories, it uses literary and narratological tools to analyse three passages from Book I and III concerned with Gascony: the Earl of Derby’s Gascon campaigns (Chapter 1); the Black Prince’s Gascon campaigns and the principality of Aquitaine (Chapter 2); Froissart’s personal journey to and stay at the court of Gaston Fébus, count of Foix-Béarn (Chapter 3).
One aim of the study is to investigate the representation of the region but it also argues that the Gascon passages have wider implications for the Chroniques, Froissart’s work as a whole, and the writing of history in the fourteenth century. At the turn of the twentieth century, Froissart’s ‘history’ was often disparagingly discussed by scholars due to factual inaccuracy and literary embellishments: such a ‘historical narrative’, it was felt, fell short of history and was nothing more than an entertaining story presenting outdated chivalric ideals. Although this approach has been partly revised, some critics still view the Chroniques’ earlier Books as being a narratively straightforward reflection of such a chivalric ideology, lacking critical hindsight on fourteenth-century events and society, and thus presenting paradoxical and irreconcilable tensions with later Books to the extent that they are occasionally deemed to be an entirely different kind of work than their later counterparts.
The narrative thread of Froissart’s Gascon (hi)story explored here allows the revision of such views and shows that Froissart’s narrative is far from narratively and ideologically straightforward. This complexity is present as early as the first versions of the Book I, which should be envisaged in parallel, not in opposition, with the ‘later’ Chroniques. Similarly, the various tensions (e.g. fiction/history; ideal/real) underpinning the whole work, manifested in the portrayal of Gascony/the Gascons, are best approached in terms of co-existence, not antagonism. Such a multi-faceted work (a mirror and/or product of the fourteenth century?), à mi-chemin between history and fiction, between conflicting yet co-existing perspectives, is precisely what makes Froissart’s Chroniques valuable to literary critics, philologists, and historians alike.
The social biography of ethnomusicological field recordings: eliciting responses to Hugh Tracey's 'the sound of Africa' series
Keywords: sound archiving
Ethnomusicology
Xhosa music
Hugh Tracey
field recording

This thesis is an ethnographic analysis of a collection of field recordings of music from sub-Saharan Africa: The Sound of Africa series made and published by Hugh Tracey between 1933 and 1973. I analyse the aims, methods, value and potential use of this collection, now held at the International Library of African Music (ILAM), in order to address a gap in the ethnomusicological literature and to begin to develop a critical framework for an evaluation of field recording and aural ethnography.
An archival analysis of the collection enables me to trace the scope and intended uses of Tracey’s recordings. Identifying a primary intended audience that has not to date been engaged, I argue for the need to develop a new way to circulate recordings among a source community that has never before been reached through institutional archival practice.
I use a small sample of Tracey’s archival Xhosa recordings and develop a method of sound elicitation designed to take the recordings back to urban Xhosa communities in the townships located near ILAM. By circulating archival recordings using local mechanisms in township communities, rather than institutional archival methods, I assess the potential relevance of historical recordings to an urban source community more than fifty years after the recordings were made.
Having collected and analysed contemporary Xhosa responses, I consider the limitations and the potential for the recordings to connect with indigenous audiences and generate value. I argue that non-analytical responses to historical recordings may contribute to ethnographic understanding, to people’s own sense of Xhosa identity, and to archiving practice in future. Such responses may help increase our understanding of the relationships between music collectors in the field and the people recorded, whether fifty years ago, today or in future.