VictorJuiz/thesis huggingface dataset:
Electrochemical and infrared spectroelectrochemical methods applied to the NiFe hydrogenases of Ralstonia eutropha
Keywords: protein film electrochemistry
hydrogenase
infrared spectroelectrochemistry

Hydrogenases are a class of metalloenzymes which catalyse H₂ oxidation and its reverse reaction, H⁺ reduction. There is interest in investigating how H₂ as an energy carrier is cycled in biology. Hydrogenases have also been studied extensively because there are potential applications for them as catalysts for H₂ oxidation in fuel cells or H₂ production via light-driven water splitting. For these applications, the ability for the hydrogenase to work in the presence of O₂ is an important issue. The microorganism Ralstonia eutropha is a well-studied model aerobic H₂ oxidiser: it can adopt H₂ as the sole energy source to grow cells in the presence of O₂. It produces at least three distinct O₂-tolerant NiFe hydrogenases: the membrane-bound hydrogenase (MBH), the NAD⁺-reducing soluble hydrogenase (SH) and the regulatory hydrogenase (RH). This Thesis employs protein film electrochemistry (PFE) to study the SH and RH. It is found that the SH is able to work in both direction (H₂ oxidation and H⁺ reduction) with minimum overpotential, which is critical in coupling 2H⁺/H₂ cycling with the closely spaced NAD⁺/NADH potential. Reactions of the SH with O₂ have been investigated, revealing at least two distinct O₂-inactivated states, but consistent with the requirement for the SH to function in air, it can be reactivated in the presence of O₂ at low potentials which could be provided by the NAD⁺/NADH pool in vivo. The affinity of the RH for H₂ was determined by PFE and found to be slightly higher than that of the SH and MBH. This may provide a way for the microbe to regulate hydrogenase expression in response to the H₂ availability. Carbon monoxide and O₂-inactivated states of the RH have been identified for the first time, confirming that a constricted gas channel is not sufficient to explain its O₂ tolerance. Observation of potential dependent reactions in hydrogenases means that it is important to have spectroscopic methods for characterising states triggered by inhibitors and potential. An Infrared spectroelectrochemical approach suitable for studying metalloenzymes has been developed and preliminary spectra on RH recorded. This method should provide many opportunities for future studies of redox states of hydrogenases.
Variability of the polar stratosphere and its influence on surface weather and climate
Keywords: Atmospheric Dyanmics
Annular Mode
Seasonal Prediction
Polar Vortex
Stratosphere

Research during the last two decades has established that variability of the winter polar stratospheric vortex can significantly influence the troposphere, affecting the likelihood of extreme weather events and the skill of long-range weather forecasts. This influence is particularly strong following the rapid breakdown of the vortex in events known as sudden stratospheric warmings (SSWs). This thesis addresses some outstanding issues in our understanding of the dynamics of this stratospheric variability and its influence on the troposphere.
First, a geometrical method is developed to characterise two-dimensional polar vortex variability. This method is also able to identify types of SSW in which the vortex is displaced from the pole and those in which it is split in two; known as displaced and split vortex events. It shown to capture vortex variability at least as well as previous methods, but has the advantage of being easily applicable to climate model simulations.
This method is subsequently applied to 13 stratosphere-resolving climate models. Almost all models show split vortex events as barotropic and displaced vortex events as baroclinic; a difference also seen in observational reanalysis data. This supports the idea that split vortex events are caused by a resonant excitation of the barotropic mode. Models show consistent differences in the surface response to split and displaced vortex events which do not project stongly onto the annular mode. However, these differences are approximately co-located with lower stratospheric anomalies, suggesting that a local adjustment to stratospheric potential vorticity anomalies is the mechanism behind the different surface responses.
Finally, the predictability of the polar stratosphere and its influence on the troposphere is assessed in a stratosphere-resolving seasonal forecast system. Little skill is found in the prediction of the strength of the Northern Hemisphere vortex at lead times beyond one month. However, much greater skill is found for the Southern Hemisphere vortex during austral spring. This allows for forecasts of interannual changes in ozone depletion to be inferred at lead times much beyond previous forecasts. It is further demonstrated that this stratospheric skill descends with time and leads to an enhanced surface skill at lead times of more than three months.
Computational studies of talin-mediated integrin activation
Keywords: Integrin
membrane
NMR
protein
talin
FERM
lipid
molecular dynamics simulations

Integrins are large heterodimeric (αβ) cell surface receptors that play a key role in the formation of focal adhesion complexes and are involved in various signal transduction pathways. They are ‘activated’ to a high affinity state by the formation of an intracellular complex between the membrane, the integrin β-subunit tail and talin, a process known as ‘inside-out activation’. The head domain of talin, a FERM domain homologue, plays a vital role in the formation of this complex. Recent studies also suggest that kindlins act in synergy with talin to induce integrin activation. Despite much available structural and functional data, details of how talin activates integrins remain elusive.
In this thesis a multiscale simulation approach (using a combination of coarse-grained and atomistic molecular dynamics simulations) together with NMR experiments were employed to study talin-mediated integrin inside-out activation. A number of novel insights emerged from these studies including: (i) the crucial role of negatively charged lipids in talin/membrane association; (ii) a novel V-shape conformation of the talin head domain which optimizes its interactions with negatively charged lipids; (iii) that interactions of talin with negatively charged moieties in the membrane orient talin to optimize interactions with the β cytoplasmic tail; (iv) that binding of talin to the β cytoplasmic tail promotes rearrangement of the integrin TM helices and weakens the integrin α/β association; and (v) that an increase in the tilt angle of the β integrin TM helix initiates a scissoring movement of the two integrin TM helices. These results, combined with experimental data, provide new insights into the mechanism of integrin inside-out activation.
The same multiscale approach was used to demonstrate the crucial role of the Gx3G motif in the packing of the integrin transmembrane helices. Using recent structural data the integrin/talin complex was modelled and inserted in bilayers which resemble the biological plasma membrane. The results demonstrate the dynamic nature of the integrin receptor and suggest that the integrin/talin complex alters the lipid organization and motion in the outer and inner bilayer leaflets in an asymmetric way and that diffusion of lipids in the vicinity of the protein is slowed down.
The work in this thesis demonstrates that multiscale simulations have considerable strengths when applied to investigations of structure/function relationships in membrane proteins.
Study of shape effect of Pd promoted Ga2O3 nanocatalysts for methanol synthesis and utilization
Keywords: photodecomposition
CO2 hydrogenation
shape effect
methanol
heterogeneous catalysis

The area of methanol synthesis and utilization has been attracting research interests due to its positive impact on the environment and also from energy perspectives. Methanol synthesis from CO2 hydrogenation not only produces methanol which is a key platform chemical and a clean fuel, but can also recycle CO2 which is one of the major greenhouse gases causing global warming. As a mobile energy carrier (particularly as a hydrogen carrier), methanol is a versatile molecule which is able to generate H2 via its decomposition. Catalysis plays a decisive role in the success of both methanol synthesis from CO2 hydrogenation and its reverse decomposition reaction. Pd/Ga2O3 binary catalyst has recently been identified as an active catalyst for the methanol synthesis reaction. In this thesis, it is reported the shape effect of Pd promoted Ga2O3 for this reaction. The catalytic H2 evolution from methanol photodecomposition has also been studied over these catalysts. Three shapes of Ga2O
3 nanomaterials (i.e. rod and plate β-Ga2O3, and particle γ-Ga2O3) have been synthesized, followed by doping with Pd metal to form corresponding Pd/Ga2O3 nanocatalysts.
It was found that a (002) polar Ga2O3 surface which was dominantly presented on the plate form was unstable, giving a higher degree of oxygen defects and mobile electrons in the conduction band than the other non-polar (111) and (110) surfaces of the rod form. It was shown that a significantly stronger metal support interaction was found between the (002) polar Ga2O3 on the plate form and Pd, which gave higher methanol yield and selectivity.
For methanol photodecomposition, it was found that, for pure Ga2O3 catalysts of different shapes, the plate form with a highest degree of defects (unstable polar surface) could encourage a non-radiative catalytic recombination of electron and hole pairs upon irradiation, hence giving a highest photocatalytic activity for H2 production. Once Pd was introduced onto these oxide surfaces, it was noted that there was a fast and readily electron transfer from the conduction band of Ga2O3 to Pd due to the formation of a Schottky junction between the two materials. This produces metal sites for hydrogen production and further enhances the rate of the photocatalytic reaction over the radiative recombination of excitons. However, it was also found that at higher Pd content (>1%), the significantly shortened exciton lifetimes reduce the catalytic rate hence giving an overall volcanic response of activity to increasing Pd content for each shape of Ga2O3. At the higher Pd content, the plate form appeared to sustain a longer lifetime for photocatalysis compared to the other forms at the equivalent Pd loading.
Constructing and solving variational image registration problems
Keywords: image registration
variational methods

Nonrigid image registration has received much attention in the medical imaging and computer vision research communities, because it enables a wide variety of applications. Feature tracking, segmentation, classification, temporal image differencing, tumour growth estimation, and pharmacokinetic modeling are examples of the many tasks that are enhanced by the use of aligned imagery. Over the years, the medical imaging and computer vision communties have developed and refined image registration techniques in parallel, often based on similar assumptions or underlying paradigms. This thesis focuses on variational registration, which comprises a subset of nonrigid image registration. It is divided into chapters that are based on fundamental aspects of the variational registration problem: image dissimilarity measures, changing overlap regions, regularizers, and computational solution strategies. Key contributions include the development of local versions of standard dissimilarity measures, the handling of changing overlap regions in a manner that is insensitive to the amount of non-interesting background information, the combination of two standard taxonomies of regularizers, and the generalization of solution techniques based on Fourier methods and the Demons algorithm for use with many regularizers. To illustrate and validate the various contributions, two sets of example imagery are used: 3D CT, MR, and PET images of the brain as well as 3D CT images of lung cancer patients.
Rewriting the Egyptian river: the Nile in Hellenistic and imperial Greek literature
Keywords: rivers
Diodorus Siculus
Strabo
Nile
Ancient Egyptian literature
Herodotus
Aristides
Ancient Greek literature

This thesis explores Hellenistic and imperial Greek texts that represent or discuss the river Nile. The thesis makes an original contribution to scholarship by examining such texts in he light of the history of Greek discourse about the Nile and in the context of social, political and cultural changes, and takes account of relevant ancient Egyptian texts. I begin with an introduction that provides a survey of earlier scholarship about the Nile in Greek literature, before identifying three themes central to the thesis: the relationship between Greek and Egyptian texts, the tension between rationalism and divinity, and the interplay between power and literature. I then highlight both the cultural significance of rivers in classical Greek culture, and the polyvalence of the river Nile and its inundation in ancient Egyptian religion and literature.
Chapter 1 examines the significance of Diodorus Siculus' representation of the Nile at the beginning of his universal history; it argues that the river's prominence constructs Egypt as a primeval landscape that allows the historian access to the distant past. The Nile is also seen to be useful to the historian as a conceptual parallel for his historiographical project. Whereas Diodorus begins his universal history with the Nile, Strabo closes his universal geography with Egypt; the second chapter demonstrates how Strabo incorporates the Nile into his vision of the new Roman world.
Chapter 3 presents a diachronic study of Greek discourse concerning the two major Nilotic problems, the cause of the annual inundation and the location of the sources. It examines first the construction of the debates, and second the transformation of that tradition in Aelius Aristides' Egyptian Oration. The functions of the Nile in Greek praise-poetry are the subject of chapter 4; it is shown that the Nile and its benefactions are used by poets to lay claim to political, religious or cultural authority, and to situate Egypt within an expanding oikoumene. The fifth and final chapter turns to Greek narrative fictions from the imperial period. The chapter demonstrates that the Nile is more familiar than exotic in these texts. It is shown that Xenophon of Ephesus and Achilles Tatius play with the trope of 'novelty' in this very familiar literary landscape, while Heliodorus articulates a more profound disruption of the expected Egyptian tropes, and ultimately replaces Egypt with Ethiopia as a new Nilotic environment.
Contemporary just war doctrine:  a critical comparison of theological and philosophical proposals
Keywords: ethics of war
philosophy
contemporary
mediation
theology
political theology

This thesis for the first time critically and comparatively examines contemporary Christian and philosophical ethics of war. Thus it contributes to an investigation of current possibilities of moral-political action. Exploring various combinations of political ethics and the tenets of faith, it compares three Christian with two secular thinkers. Each chapter first shows how Just War ethics are constructed between ‘realism’ and ‘idealism’. The former prioritizes individual or national self-defence and power; the latter the universal value of each individual. Each analytical section reconstructs the author’s moral understanding of political authority, violent force and political reality. These foci are investigated in terms of how they understand, envision or reject the mediation between politics and Christian morality. As the inner logic of each Just War proposal is thus brought out, continuities and differences between authors can be explained.
Part I looks at Christian authors. Jean Bethke Elshtain’s realistic, ‘naturalistic’ Just War ethic of the sovereign state rejects humanist idealism. For Paul Ramsey Christian agape provides a transformative ethic between idealism and realism. Developing this, Oliver O’Donovan’s evangelical approach practically fuses idealism and realism. Dogmatically, this is conditioned by moving from Elshtain’s modern theological dualism to Ramsey’s Christ-transforming the world, though still indebted to philosophical idealism. O’Donovan, however, suggests that after the singular mediation of the Christ event, moral-political categories disclose the divine order.
Part II investigates the idealism-realism divide amongst philosophers. Both David Rodin’s idealist demand for a global state and Uwe Steinhoff’s individualist Machiavellianism seek to protect human rights. After Kant, they presuppose an unbridgeable division between politics and ‘religious’ morality. Theology, having become anthropology, replaces the mediation of Christ with immanent mediators: legal, statist or individualist moral agents. But this echoes and intensifies the Christian tradition. Whereas Rodin introduces a renewed, violent papacy, Steinhoff seeks to renew the liberal-democratic status quo through a secular ‘radical reformation’.
It is concluded that both modern Christian and philosophical ethics of war can oscillate between impractical triumphant justice and the failure of tragic antagonism. If the singular mediation between Is and Ought in Christ is recognized as a universal paradox, doing justice effectively becomes possible.
The birth pangs of the Messiah
Keywords: Transnational History
Millenarianism
Petrus Serrarius
Islam
Christianity
World History
Atlantic World
Sabbatai Sevi
James Nayler
Apocalypticism
Mediterranean World
religion
Early Modern History
Judaism
networks

Between 1648 CE and 1666 CE, news, rumours, and theories about the messiah and the Lost Tribes of Israel were disseminated amongst diverse populations of Jews, Christians, and Muslims. Employing a world history methodology, this thesis follows three sets of such narratives that were spread through the American colonies, England, the Dutch Republic, the Italian peninsula and the Ottoman Empire, connecting people separated by linguistic, religious, national, and continental divides. This dissertation starts by situating this transmission within a broader context that dates back to 1492 CE and then traces the three-stage process in which eschatological constructs originating in the Americas in the 1640s were transmitted across Europe to the Levant in the 1650s, preparing the minds of Jews and Christians for the return of these ideas from the Ottoman Empire in the 1660s. In this manner, this study seeks to make three contributions to the existing literature. It brings together often isolated historiographies, it unearths fresh archival sources, and it provides a new conceptual framework. Overall, it argues that one cannot understand the growth of apocalyptic tension that reached its peak in 1666 without examining the major historical events and processes that began in 1492 and affected Jews, Christians, and Muslims across the Atlantic and Mediterranean worlds.
Evaluation of strain circulation and the epidemiology of enteric fever caused
Keywords: Enteric fever
Typhi
Kathmandu
Paratyphi
strain circulation

Enteric fever caused by Salmonella enterica serovars Typhi and Paratyphi A are a major public health concern in Kathmandu. The aim of this thesis was to identify and assess the population most at risk by investigating epidemiologic trends of enteric fever within a subset population of Kathmandu. Therefore,the burden and incidence of enteric fever within the study population and the seasonal and gender distribution of enteric fever was assessed. Considerable burden of enteric fever, unrelated to population density, correlating with the seasonal fluctuations in rainfall was observed. This thesis also aimed to improve the understanding of enteric fever transmission by identifying probable transmission routes,hence various water and food samples were analysed and the extent of faecal contamination in them was determined. S. Typhi isolates were sequenced and genotyped and combined with GPS data to longitudinally study the local distribution and infer transmission of this human restricted bacterial pathogen. Extensive clustering of typhoid independent of population size and density and existence of an extensive range of genotypes within typhoid clusters including individual households with multiple cases was observed. These observations predict that indirect transmission had an overwhelming contribution for disease persistence, potentially through contaminated water. Consistent with this hypothesis, S. Typhi and S. Paratyphi A were detected in water supplies and it was observed that typhoid was spatially associated with public water sources and low elevation. A concurrent case-control study was also conducted which allowed for the determination of risk factors in the population at risk. These studies imply that resources should be allocated toward controlling the most important vectors of enteric fever, including food sold by vendors, chlorination of drinking water, construction of proper water distribution and sewage networks,vaccination campaigns and hygiene education.
Interactions of nanoparticles with cells for nanomedical applications
Keywords: Escherichia coli
nanotoxicology
nanomaterials
silver
nanomedicine
red blood cells
nanotechnology
bacteria
toxicology
E. coli
methodology
AFM
nanoparticles
atomic force microsocopy

Nanotechnology is a rapidly growing field focused on the manipulation and control of materials with dimensions under 100 nm. The novel electronic, optical and mechanical properties observed at the nanoscale have resulted in a number of applications in catalysis, light emitting devices, solar power, self-cleaning surfaces and medicine. Medical applications of nanotechnology (“nanomedicine”) are particularly promising for rapid clinical diagnosis and targeted treatments.
Understanding the interactions of nanoparticles with living matter is of fundamental importance for all application areas: manufacture, use and disposal of the growing number of nanoproducts will result in increased environmental exposure in addition to direct exposure through nanomedical applications. However, there is a lack of standard methodologies for assessing these interactions.
In this work the stability of silver-based nanoparticles was established by UV- Visible (UV-Vis) spectroscopy, atomic force microscopy (AFM) and transmission electron microscopy (TEM). The presence of a higher valence metal or polymer on the nanoparticle surface was demonstrated to improve stability.
A standard methodology was developed to study nanoparticle-cell interactions: an “atlas” of the effects of known drugs on a cell is created, and compared with the effects of a nanoparticle. Escherichia coli was selected as a model organism and the effects of a range of antibiotics were characterised through a combination of microbiological assays and AFM. Susceptibility, population cell growth and individual heights, widths, lengths and volumes of bacteria were obtained on a 2% agarose substrate in air.
The methodology was applied and adjusted for silver nanoparticles due to the interactions of silver with the bacterial growth medium. 10 and 30 nm silver nanoparticles and ions were found to kill E. coli through an internal mechanism of action, with a size-specific effect on the height of bacteria.
Finally, a novel AFM characterisation method is described to examine the mechanical properties of live bacterial and human cells in liquid.