VictorJuiz/thesis huggingface dataset:
Pushing the boundaries: molecular dynamics simulations of complex biological membranes
Keywords: Influenza virus
antimicrobial peptides
biological membrane
molecular dynamics
membrane proteins
coarse-grained

A range of simulations have been conducted to investigate the behaviour of a diverse set of complex biological membrane systems. The processes of interest have required simulations over extended time and length scales, but without sacrifice of molecular detail. For this reason, the primary technique used has been coarse-grained molecular dynamics (CG MD) simulations, in which small groups of atoms are combined into lower-resolution CG particles. The increased computational efficiency of this technique has allowed simulations with time scales of microseconds, and length scales of hundreds of nm.
The membrane-permeabilizing action of the antimicrobial peptide maculatin 1.1 was investigated. This short α-helical peptide is thought to kill bacteria by permeabilizing the plasma membrane, but the exact mechanism has not been confirmed. Multiscale (CG and atomistic) simulations show that maculatin can insert into membranes to form disordered, water-permeable aggregates, while CG simulations of large numbers of peptides resulted in substantial deformation of lipid vesicles. The simulations imply that both pore-forming and lytic mechanisms are available to maculatin 1.1, and that the predominance of either depends on conditions such as peptide concentration and membrane composition.
A generalized study of membrane protein aggregation was conducted via CG simulations of lipid bilayers containing multiple copies of model transmembrane proteins: either α-helical bundles or β-barrels. By varying the lipid tail length and the membrane type (planar bilayer or spherical vesicle), the simulations display protein aggregation ranging from negligible to extensive; they show how this biologically important process is modulated by hydrophobic mismatch, membrane curvature, and the structural class or orientation of the protein.
The association of influenza hemagglutinin (HA) with putative lipid rafts was investigated by simulating aggregates of HA in a domain-forming membrane. The CG MD study addressed an important limitation of model membrane experiments by investigating the influence of high local protein concentration on membrane phase behaviour. The simulations showed attenuated diffusion of unsaturated lipids within HA aggregates, leading to spontaneous accumulation of raft-type lipids (saturated lipids and cholesterol).
A CG model of the entire influenza viral envelope was constructed in realistic dimensions, comprising the three types of viral envelope protein (HA, neuraminidase and M2) inserted into a large lipid vesicle. The study represents one of the largest near-atomistic simulations of a biological membrane to date. It shows how the high concentration of proteins found in the viral envelope can attenuate formation of lipid domains, which may help to explain why lipid rafts do not form on large scales in vivo.
The effects of a novel substrate on exercise energetics in elite athletes
Keywords: ketones
exercise
nutrition
metabolism

The physiological ketosis of starvation makes sound evolutionary sense, as ketone bodies have several thermodynamic advantages over other nutritional substrates, in addition to their actions to conserve protein and glucose stores. Utilising the body’s metabolic responses to ketosis by delivering a novel nutritional source of ketone bodies, the work in this thesis explored the metabolic effects of ketosis on physical performance in humans. First, the pharmacokinetics and dosing requirements for ketone containing drink preparations were characterised in a population of athletes and healthy controls (n = 45). Using endurance exercise as a model of physiologic stress, the functional impact of ketosis during sustained high intensity effort was investigated in high performance athletes (n = 22). It was shown that nutritional ketosis improved performance in 18/22 athletes, who set 14 new best performances during 30 min of rowing. Furthermore, when ketones and glucose were delivered together, cycling performance was improved by 2% (n = 8) following 1.5 hours of fatiguing effort, compared with optimal carbohydrate intake. Blood D-β-hydroxybutyrate reached 3-5 mM following ketone drinks, equivalent to several days of total fasting, but rapidly decreased during exercise. It was found that higher physical workloads correlated with larger decreases in plasma ketone concentration (n = 8), consistent with their oxidation as respiratory fuels. Nutritional ketosis significantly altered fuel metabolism during exercise in elite athletes (n = 10), decreasing peripheral lipolysis, skeletal muscle glycolytic intermediates, blood lactate, and branched chain amino acid release. In conclusion this work suggests a new hierarchy of substrate preference during physical stress, whereby mimicking the physiology of starvation, the energetic consequences of oxidising ketones may significantly enhance athletic performance. The extrapolation of these findings may have therapeutic implications for patient populations where energetic demands are high, and deleterious switches in substrate selection occur.
Aberration free extended depth of field microscopy
Keywords: focusing
two photon microscopy
aberrations
microscopy
confocal microscopy

In recent years, the confocal and two photon microscopes have become ubiquitous tools in life science laboratories. The reason for this is that both these systems can acquire three dimensional image data from biological specimens. Specifically, this is done by acquiring a series of two-dimensional images from a set of equally spaced planes within the specimen. The resulting image stack can be manipulated and displayed on a computer to reveal a wealth of information. These systems can also be used in time lapse studies to monitor the dynamical behaviour of specimens by recording a number of image stacks at a sequence of time points. The time resolution in this situation is, however, limited by the maximum speed at which each constituent image stack can be acquired. Various techniques have emerged to speed up image acquisition and in most practical implementations a single, in-focus, image can be acquired very quickly. However, the real bottleneck in three dimensional imaging is the process of refocusing the system to image different planes. This is commonly done by physically changing the distance between the specimen and imaging lens, which is a relatively slow process. It is clear with the ever-increasing need to image biologically relevant specimens quickly that the speed limitation imposed by the refocusing process must be overcome.
This thesis concerns the acquisition of data from a range of specimen depths without requiring the specimen to be moved. A new technique is demonstrated for two photon microscopy that enables data from a whole range of specimen depths to be acquired simultaneously so that a single two dimensional scan records extended depth of field image data directly. This circumvents the need to acquire a full three dimensional image stack and hence leads to a significant improvement in the temporal resolution for acquiring such data by more than an order of magnitude.
In the remainder of this thesis, a new microscope architecture is presented that enables scanning to be carried out in three dimensions at high speed without moving the objective lens or specimen. Aberrations introduced by the objective lens are compensated by the introduction of an equal and opposite aberration with a second lens within the system enabling diffraction limited performance over a large range of specimen depths. Focusing is achieved by moving a very small mirror, allowing axial scan rates of several kHz; an improvement of some two orders of magnitude. This approach is extremely general and can be applied to any form of optical microscope with the very great advantage that the specimen is not disturbed. This technique is developed theoretically and experimental results are shown that demonstrate its potential application to a broad range of sectioning methods in microscopy.
Heterogeneity in Ewing sarcoma
Keywords: Resistance
Ewing sarcoma
next generation sequencing

Ewing sarcoma, an aggressive primary bone and soft tissue tumour is characterised by the expression of the chimeric transcription factor EWS-FLI1 in 90% of patients. This alters expression of many genes including activation of the Insulin Growth Factor (IGF) pathway via IGFBP3 supression. Phase I/II trials with an IGF-1 inhibitor have demonstrated tumour regression in a modest number of Ewing sarcoma patients.
The aim of this thesis was to identify mechanisms contributing to the heterogeneity of resistance in Ewing sarcoma following inhibition with OSI-906, a dual kinase inhibitor of IGF-1 (IGF-1R) and Insulin (IR) receptors. The hypothesis was that mechanisms of resistance relate to heterogeneity of responses to signalling pathway activation and inhibition. Through selection, disruption of the pathway would identify subpopulations of cells both sensitive and resistant in their response allowing for interrogation of resistance mechanisms.
A genome wide approach was taken to model the resistance profile of cell lines. Through developing a method of unbiased quantification, a panel of validated Ewing sarcoma cell lines (EuroBoNet) were imaged and segmented to assess the responses of biomarkers on signalling pathway activation. Heterogeneity was confirmed between cell lines. The application to diagnostic biopsies led to the identification of prognostic classifiers and cellular subpopulations with clinical prognostic significance. The distribution of Ki67 was found to be predictive of survival and cells with lower levels of CD99 in the cytoplasm were most discriminative. Parallel sequencing strategies (RNA-seq, whole exome sequencing, and aCGH/ SNP array) for genome-wide screening was carried out for point mutations, copy number changes and rearrangements. Systematic detection was used to characterise genomic rearrangements and functional validation performed. Resistant clones, formed via ENU mutagenesis of cell lines, were sequenced in order to demonstrate the resistance profile of OSI-906.
In summary heterogeneity of Ewing sarcoma at the genomic and proteomic level can influence the signalling dependency of tumours and response to inhibitors. Genomic and proteomic profiling of tumour cells may be relevant to future developments of novel therapies.
Melancholy and the doctrine of reprobation in English puritan culture, 1550-1640
Keywords: predestination
sickness
puritan
suicide
melancholy

The thesis examines the relationship between reprobation fears and melancholic illness in puritan culture over a period of approximately ninety years. Reprobation formed part of the Calvinist doctrine of double predestination, by which God had chosen a few for salvation (the elect), and many for destruction (the reprobate). When a person came to believe that they were reprobate, this could give rise to symptoms of fear and despair similar to those associated with melancholy (an imbalance of black bile believed to affect the brain). The thesis shows how puritans used explanations based on melancholy in order to explain how otherwise godly people came to doubt their election.
The first chapter shows how the Calvinist physician, Timothy Bright, incorporated ideas from medieval scholastic and medical texts into his Treatise of melancholie (1586), in order to explain how physiological causes could be at the root of reprobation fears. The second and third chapters examine the religious context in which Bright was writing. The second chapter shows puritan ambivalence about pronouncing a person to be reprobate through an examination of responses to the death of the apostate, Francesco Spiera. The third chapter shows how the Elizabethan puritan clergy developed a form of consolation for those suffering from despair of salvation based on the medieval idea that melancholy was the ‘devil’s bath’. The fourth and fifth chapters show the importance of physiological explanations for despair in defending the reputations of the dying. When a godly person despaired on their death-bed, or committed suicide, this was blamed on a combination of forces external to themselves – melancholy and the devil. The final chapter shows how Robert Burton’s Anatomy of Melancholy adapted puritan ideas about despair, to be more acceptable in the context of growing resistance to the preaching of double predestination in the 1620s and 30s.
Atmospheric Sounding using IASI
Keywords: retrievals
radiative transfer models
channel selection
remote sensing
atmospheric physics
IASI

The Infrared Atmospheric Sounding Interferometer (IASI) provides atmospheric observations with high spectral resolution and its data have been shown to have a significant positive impact on global Numerical Weather Prediction (NWP) and trace gas retrievals.
A fundamental component of the retrieval of atmospheric composition is the radiative transfer model used to simulate the observations. An accurate representation of the expected emission spectrum measured by the satellite is essential given that differences in the reproduced atmospheric spectra propagate through a retrieval procedure and produce an altered estimate of the atmospheric state.
The importance of the assumptions within the forward model are discussed and it is established that in the simulation of spectra from satellite-borne instruments the choice of the model parameters can have a large impact upon the resulting output. These assumptions are explored in the context of the Reference Forward Model (RFM), which is further configured to optimise its output for simulating the IASI spectrum in the troposphere.
In order to ascertain the consistency of different radiative transfer models, comparisons are carried out between the RFM and the Radiative Transfer model for TOVS (RTTOV) in order to quantify any discrepancies in the reproduction of IASI measurements. Good agreement is shown across the majority of the spectrum, with exceptions caused by CO2 line mixing effects and the H2O continuum. Alongside model comparisons, the RFM is validated against real IASI measurements.
Being a Fourier Transform Spectrometer, there are a large number of channels available from the IASI instrument, which leads to a very large quantity of data. However, this can lead to problems within retrievals and data assimilation. Choosing an optimal subset of the channels is an established method to reduce the amount of data; maintaining the information contained within it whilst eliminating spectral regions with large uncertainties. The method currently used at the UK Met Office to select their spectral channels is re-assessed and a modified method is presented that improves upon the modelling of spectrally correlated errors.
Living with environmental change in the endorheic oasis systems of the Northern Sahara
Keywords: oasis
Sahara

The oases of the northern Sahara illustrate the possibility that people and nature can work together to enhance life in a harsh and variable environment. This research investigates fifty years of experiences of living with environmental change in oasis systems, bringing together new data, archived environmental records and cultivators` observations. These are combined to gain insight into the environmental change processes, and the experiences gained by people through living with them in this regional context. Two detailed case studies deepen understanding of the socioeconomic dimensions and significance of these changes over the past two decades.
The findings show how environmental changes constrained smallholders` traditional ecosystem management practices. Collective associations were weakened or disintegrated. National systems for environmental management and monitoring were overwhelmed. International recommendations for economic approaches to resource management and innovation to address water scarcity did not prove effective. On the other hand, instances where the international market transition appeared to be creating new opportunities for the restoration of common pool resource management were also identified.
This investigation enabled a new perspective on the global dryland management debate to be generated in a context where research has most commonly been concentrated on national sectoral objectives for productivity and desert reclamation. Theoretical insights regarding the application of interdisciplinary research to understand environmental change, further research needs, and potential solutions are directly transferable to other regions where desiccation, salinization and groundwater degradation are accelerating due to climatic and global market-driven changes in land and water use.
Modulation of innate immune responses by hepatitis C virus
Keywords: hepatitis c virus
interferon
natural killer cells
liver transplantation
toll-like receptors
dendritic cells
lymphotropism

Hepatitis C virus (HCV) establishes a chronic infection in about 70% of infected individuals that is associated with the development of liver cirrhosis and hepatocellular carcinoma. The mechanisms by which HCV avoids clearance by the host immune response are not fully understood.
The first aim of this project was to determine whether immune cell subsets could become infected by HCV in vitro. None of the haematopoietic subsets analysed expressed all of the required entry factors, CD81, SR-BI, claudin-1 and occludin. Also, PBMCs were not susceptible to infection with HCVpp and HCVcc expressing glycoproteins of hepatotropic strains. Infection by a supposedly lymphotropic strain (SB) was found to be inefficient.
The second aim was to identify in vitro immunomodulatory effects of HCV on innate immune cells that may impact on the immune response activated in acute infection. Crosslinking of CD81 on NK cells by antibody was found to have a minor inhibitory effect on their activation via CD16, but CD81 crosslinking by viral particles had no detectable effect. In contrast to other viruses, HCVcc elicited very little interferon-α production by pDC. HCVcc also did not affect pDC or mDC responses to TLR ligation.
Systemic cytokine and chemokine responses were analysed in subjects with primary acute HCV infection and in HCV-infected patients undergoing liver transplantation (LT). Interestingly, induction of systemic type I and type III interferon was not observed in either group. Marked perturbations in systemic cytokine and chemokine levels were detected in uninfected LT patients, precluding use of HCV-infected LT patients to study the innate immune response activated in response to acute viral replication.
Together, these results suggest that HCV may principally evade innate immune cell responses by avoidance rather than impairment strategies.
Bayesian analysis of stochastic point processes for financial applications
Keywords: point processes
Bayesian statistics

A recent application of point processes has emerged from the electronic trading of financial assets. Many securities are now traded on purely electronic exchanges where demand and supply are aggregated in limit order books. Buy and sell trades in the asset as well as quote additions and cancellations can then be interpreted as events that not only determine the shape of the order book, but also define point processes that exhibit a rich internal structure.
A large class of such point processes are those driven by a diffusive intensity process. A flexible choice with favourable analytic properties is a Cox-Ingersoll-Ross (CIR) diffusion. We adopt a Bayesian perspective on the statistical inference for these doubly stochastic processes, and focus on filtering the latent intensity process. We derive analytic results for the moment generating function of its posterior distribution. This is achieved by solving a partial differential equation for a linearised version of the filtering equation. We also establish an efficient and simple numerical evaluation of the posterior mean and variance of the intensity process. This relies on extending an equivalence result between a point process with CIR-intensity and a partially observed population process.
We apply these results to empirical datasets from foreign exchange trading. One objective is to assess whether a CIR-driven point process is a satisfactory model for the variations in trading activity. This is answered in the negative, as sudden bursts of activity impair the fit of any diffusive intensity model. Controlling for such spikes, we conclude with a discussion of the stochastic control of a market making strategy when the only information available are the times of buy and sell trades.
The USA and Southern Rhodesia, 1953-1969
Keywords: USA
Wilson
Rhodesia
Johnson
Smith
UDI

Existing studies of this topic have not made enough use of the British archives. Nor have they analysed the American domestic response to UDI in sufficient depth. The policies of successive American administrations as regards the Rhodesian problem can only be fully understood as part of Washington’s attitude to Britain, to Africa in general, and to southern Africa in particular. And, because the issue of white minority rule in Africa raised powerful emotions both in the African American community and among white opponents of civil rights, the Rhodesian crisis became a part of the politics of racial equality within the USA, playing a key role in the developing ideologies of these two communities.
This thesis is based on research in both American and British archives and aims to show that the prevailing interpretation, especially of the policies of the Johnson Administration once Rhodesia had made its illegal declaration of independence in November 1965, is mistaken. Scholars have tended to take at face value the oft-repeated claim of US policy-makers that Rhodesia was a British problem, that they wished to be no more than helpful bystanders, supporting British efforts to see the downfall of the illegal regime and the creation of a government based on majority rule, and that when they did intervene, it was merely to urge the British to be firmer in their resolve to end the rebellion. The central contention of this thesis is that the officials shaping African policy in the Johnson Administration were intimately involved in the management of the crisis and that, far from resisting a solution that legitimised the white minority regime, they actively encouraged the British to settle with the illegal government.