VictorJuiz/thesis huggingface dataset:
Dynamic nuclear polarisation as a probe of metabolism in pathophysiology

Spin-half nuclei in a magnetic field possessing a population difference in excess of that expected at thermal equilibrium are said to be hyperpolarised. Dynamic Nuclear Polarisation (DNP) is a method to generate hyperpolarised systems, pumping nuclear spins into a given state at low temperature. Hyperpolarised samples can be rapidly dissolved in a hot solvent, and maintain a highly polarised spin population that relaxes to the new thermal equilibrium over several minutes. It is possible to inject hyperpolarised molecules into an organism, sample the population difference through NMR spectroscopy, and obtain spectra with a large (&GT; 104) increase in their signal-to-noise ratio compared to thermal equilibrium. The use of hyperpolarised [1-13C]pyruvate allows for the quantification of the rate of [1-13C]lactate production, increases of which are a defining characteristic of cancer; or the rate of 13C-bicarbonate production, which is altered in heart disease.
This thesis describes the development of magnetisation-efficient sequences of spectrally-and-spatially selective radiofrequency pulses and rapid imaging readouts that are able to image the metabolism of hyperpolarised [1-13C]pyruvate in three dimensional space, with a reconstructed resolution of 1 × 1 × 2 mm3. The technique’s sensitivity to metabolism is demonstrated, and attempts are made to image cancer that has metastasised to the brain prior to the point of conventional detection through its metabolic phenotype. It is also used to image metabolism in the post ischæmic myocardium, where it reports on regions of non-viable tissue.
Additionally, hyperpolarised 13C-urea is used as a 'metabolically inert' probe of perfusion in the myocardium. Flow-sensitisation gradients and a spiral readout allow 13C-urea to be resolved in the myocardium. The ability to 'co-polarise' [1-13C]pyruvate and 13C-urea is demonstrated. This technique could simultaneously resolve perfusion deficits and metabolic changes in the acutely damaged heart, with several potential advantages over current clinical methods.
Finally, several methods for analysing data generated by hyperpolarised experiments are proposed: weighted averaging for combining spectroscopic data of varying quality; novel Bayesian approaches to quantifying metabolic rate constants of interest following the injection of hyperpolarised [1-13C]pyruvate; and the Fast Padé Transformation as an improved method for the reconstruction of truncated hyperpolarised spectral data.
DNP is a technique that, following its development for particle physics experiments in the 1970s, is transitioning to clinical practice as a safe, novel molecular imaging modality. It is hoped that the techniques proposed in this text ultimately find wide utility in the assessment of cancer and heart disease, which combined are responsible for approximately 50% of deaths occurring in the developed world.

Keywords: MRI
Metabolic imaging
Hyperpolarized 13C
DNP
Metabolic data analysis
Hyperpolarized Carbon
Pulse-sequences
Dynamic Nuclear Polarisation
MRS
Advisor: Tyler, D
Sibson, N
Jones, H
Tucker, S
Tethered flurophore motion studies of DNA segregation machinery

Tethered fluorophore motion (TFM) is a single-molecule fluorescence technique, used to monitor an effective length along a biopolymer, such as DNA. In this work, I start by characterising TFM, focussing on the theoretical basis and potential applications, and then use TFM to study the bacterial site specific recombination system, XerCD-dif. I present a description of the sources of noise in TFM and derive an analytical expression for the resolution, which is compared to simulations and experiments. The work demonstrates that length changes as low as 100 bp of double-stranded DNA are distinguishable using TFM. The optimum pixel size for TFM is derived and validated experimentally.
XerCD-dif recombination is responsible for chromosome decatenation in most bacteria with circular chromosomes. It is activated by the DNA translocase FtsK. I describe the application of TFM, in combination with Förster resonance energy transfer (FRET) and protein induced fluorescence enhancement, to observe the formation and activation of XerCD-dif synaptic complexes. The work followed the reaction, as Holliday junctions formed by XerD-mediated strand exchange isomerised and were resolved to product by XerC, and measured the lifetimes of all the intermediates observed.
To analyse the role of FtsK in the activation of recombination, and to monitor its assembly, translocation and behaviour when encountering XerCD-dif, TFM was extended with the use of two spectrally distinct fluorophores, allowing simultaneous monitoring of two effective lengths along the same DNA. FtsK was observed to assemble on DNA, stepwise, into a single hexamer, and begin translocation rapidly (&Tilde;0.25 s). Single hexamers approached XerCD-dif, and resided for 0.5s to 1s before dissociating, irrespective of whether XerCD-dif was synapsed or recombination was activated.
The final section of this thesis details the design, construction and evaluation of a three colour microscope. Alternating laser excitation was implemented in the green, red and near-infrared spectral channels with three laser sources, and an inexpensive automatic focus system was implemented using the back reflection of the excitation lasers and a complementary metal oxide semiconductor camera.

Keywords: Site-specific recombination
XerCD-dif-FtsK
Single-molecule
Total internal reflection fluorescence microscopy
Advisor: Kapanidis, A
En d'autres mots. L'écriture translingue de soi

For several reasons, translingual writers, defined here as authors who write in a language that is not their native one, have gained increased visibility in recent years. This is particularly true in the context of French literature where, more frequently than before, and with a more explicit recognition of their particular status, translingual writers have received important literary prizes and have been welcomed into the French Academy. Central to this recognition is their rich and diverse mobilisation of life writing, a corpus curiously neglected in the study of the phenomenon of literary translingualism. This thesis focuses on the writers Andreï Makine, Hector Bianciotti, Vassilis Alexakis, Nancy Huston, Agota Kristof and Katalin Molnár. It demonstrates that the translingual experience, in its capacity to question one's sense of self and provide novel tools for the exploration of one's personal history and subjectivity (conceived as an experience in language), appears eminently suited to the genre of life writing and that, in the current configuration of the French literary space, life writing is demanded from translingual authors. It proposes an original cartography of contemporary translingual literature in French, suggesting that more than any similarities in the conditions of their literary adoption of French, what creates family resemblance between translingual writers is the types of relation with their adopted language that are constructed in their autobiographical texts.

Keywords: translingual
Literature
Alexakis
Huston
Molnár
French
Kristof
life writing
Makine
Bianciotti
Advisor: Jefferson, A
Biologically inspired de novo protein structure prediction

Fragment-based approaches are the current standard for de novo protein structure prediction. These approaches rely on accurate and reliable fragment libraries to generate good structural models. We demonstrate that fragments presenting different predominant predicted secondary structures should be treated differently during fragment library generation. Using this information, we developed Flib and shown that it generates fragment libraries with higher precision and coverage than two other methods.
We explored co-evolution to identify pairs of residues that are in contact, which were then used to improve model generation. We performed a comparative analysis of nine methods in terms of their precision and their usefulness to de novo structure prediction. Our results show that metaPSICOV stage 2 produces the most accurate predictions and that metaPSICOV stage 1 generates the best modelling results. In general, contact predictors are good at identifying contacts between β-strands and bad at identifying contacts between α-helices. We also show that the ratio of satisfied predicted contacts can be used to assess whether correct models were generated for a given target.
We also investigated whether the biological process of cotranslational protein folding, the notion that proteins fold as they are being synthesized, can be used to improve de novo protein structure prediction. Our tool for this investigation is SAINT2. SAINT2 differs from conventional fragment-assembly approaches as it is able to perform predictions sequentially from N to C-terminus, starting with a small peptide that is extended as the simulation progresses (SAINT2 Cotranslational). SAINT2 is also able to generate decoys in a standard non-sequential fashion (SAINT2 In Vitro). We compared SAINT2 Cotranslational to SAINT2 In Vitro and shown that SAINT2 Cotranslational generally produces better answers, generating an individual decoy between 1.5 to 2.5 times faster than SAINT2 In Vitro. Our results suggest that biologically inspired structure prediction can improve search heuristics and final model quality.

Keywords: Bionformatics
Protein Informatics
Protein Structure Prediction
Cotranslational Protein Folding
Using Kolmogorov equations to investigate hedging errors

This thesis presents a study of hedging errors caused by model mis-specification, making use of a Kolmogorov forward equation with δ-function initial conditions. The method is used to calculate the probability distribution of hedging errors at maturity for a number of realistic examples. An analysis of numerical schemes used to solve the Kolmogorov forward equation is presented, making particular use of Fourier transform techniques. Much of the analysis applies to a 'toy' model which captures the main features of the hedging problem. Detailed analysis of a semi-discrete Fourier numerical method for solving the toy model problem leads to a complete description of the accuracy and stability behaviour of the scheme. The thesis also includes a novel time-change method which solves the heat equation with δ-function initial conditions, using the Crank-Nicolson method, and which demonstrates improved convergence of the scheme. The numerical analysis included in the thesis explores further aspects of Fourier transform methods applied to the analysis of Partial Differential Equations with Dirac data and variable coefficients.

Advisor: Reisinger, C
Structure and dynamics of two-dimensional colloidal hard spheres

The structural and dynamic behaviour of quasi-two-dimensional monodisperse and bidisperse colloidal hard spheres are studied by optical microscopy. Firstly, a full characterisation of the equilibrium structure is presented through a consideration of structural correlation functions and number fluctuations. Comparison to fundamental measure theory and Monte Carlo simulations confirms both the behaviour of the system as a model for hard disks and the equation of state. The differing structural behaviour of binary systems at different size ratios is also discussed in relation to the nonadditivity. Next, the short- and long-time self-diffusion of particles is considered. Results for the long-time diffusion coefficient are again compared to Monte Carlo simulations, which demonstrates that at long times the dynamic behaviour is effectively not affected by hydrodynamic interactions. Additionally, simple theoretical expressions for the area fraction dependence of the short- and long-time diffusion coefficients are discussed. The selfdynamic properties of particles are probed further using the self-intermediate scattering function and the self-van Hove correlation function. In particular, the extent to which these quantities may be described by the Gaussian approximation is considered in relation to the relevant hydrodynamic limits for colloidal systems. A scaling relation to describe the crossover between these limits at short and long times is also developed. The consideration of dynamic behaviour is then extended to collective phenomena and, in particular, to the process of interdiffusion. Here, the thermodynamic and kinetic drives for this process are explored for binary systems at two different size ratios. The differing interdiffusive effects seen in the two systems are considered in light of the predictions of the Darken equation. Finally, the melting of quasi-two-dimensional colloidal hard spheres is studied by considering a monolayer of particles in sedimentation-diffusion equilibrium. Density profiles and the equation of state are used to characterise the system. These quantities display a discontinuity, indicating a coexistence gap and hence an interface. This interface is located and analysed using capillary wave theory, from which both the size of the coexistence gap and the anisotropic stiffness of the interface are determined.

Advisor: Dullens, R
Investigating the ligandability of plant homeodomains

Plant homeodomains (PHDs) are protein domains which bind to the N-terminal region of histone 3 (H3) in a manner dependent on the post-transitional modification state of residues near the N-terminus of H3. For example some PHDs will only bind H3 if lysine 4 (K4) is trimethylated, whereas other PHDs will only bind H3 if K4 is unmodified. PHDs play a crucial role in gene regulation in cells and mutations and translocations of PHDs have been linked to disease states.
A search of the human proteome revealed the presence of 173 PHDs. These were aligned using structural information and the alignment used to create a PHD phylogenetic tree, the first time such a tree has been reported for this domain family.
All PHD structures in the Protein Data Bank were computationally analysed using SiteMap in order to assess ligandability. Single PHDs were generally found to be poorly ligandable, but some were predicted to be at the lower threshold of ligandability. The study was expanded and found that PHDs found in tandem with another PHD or other epigenetic reader domain were generally more ligandable due to the formation of ligandable pockets at domain-domain interfaces.
Based on the results from the SiteMap analysis, experimental work was carried out to discover ligands of the tandem PHD-PHD of double PHD finger protein 2 (DPF2) and the PHD-JmjC of PHD finger protein 8 (PHF8). Assays were designed and both virtual and experimental screens conducted. No hits were identified for DPF2, but a single fragment hit for PHF8 was found with an IC50 of 260 μM. Analogues of this fragment were synthesised and tested, but none were more potent than the initial hit.

Advisor: Brennan, P
Schofield, C
Autoimmunity in idiopathic epilepsies and encephalopathies of childhood

Immune mechanisms are thought to be involved in the pathological disease process in a number of childhood epileptic syndromes and encephalitis. Of particular interest is the occurrence of autoantibodies to essential neuronal proteins, for example the N-methyl-D-aspartate receptor (NMDAR), in the blood and spinal fluid in some of these patients. The aims of this study were: to examine the sera of newly diagnosed paediatric epilepsy patients for specific neuronal autoantibodies, correlate to epilepsy phenotype and disease outcomes; to investigate the pathogenicity and epileptogenicity of central nervous system autoantibodies (CNS) in vivo; and to test new therapies in vitro and in vivo based on the potential pathogenic mechanisms.
In 290 paediatric patients with new-onset epilepsy and seizures tested for CNS autoantibodies, 11.4% were positive (33/290 versus 8/112 in controls; p=0.01, Fisher's exact test). Previously unreported contactin-2 antibody positive and contactin-associated-protein 2 (CASPR2) antibody positive epilepsy patients were described. Patients with 'focal epilepsy of unknown cause' were more likely to be antibody positive.
To test the pathogenicity and epileptogenicity of these antibodies, a novel in vivo telemetry system was used to continuously record electroencephalogram (EEG) in mice injected into the cerebral lateral ventricle with NMDAR antibody (NMDAR-Ab) positive immunoglobulin (IgG). Although no spontaneous seizures were seen, mice challenged with the pro-convulsant pentylenetetrazole (PTZ) had increased seizure susceptibility, and more epileptiform "spikes" in the EEG after PTZ compared to healthy control (HC) IgG injected mice. Seizure susceptibility strongly correlated with binding intensity of NMDAR-Ab IgG analysed in post-mortem tissue. Given the hypothesis this epileptogenic effect was mediated by NMDAR-Abs internalising cell surface NMDARs, and to try and rescue this deficit, a neurosteroid, pregnenolone sulphate (PregS) known to increase NMDAR cell surface expression, was therapeutically used. This approach worked in vitro, and although in vivo effects were not yet established, treatment with neurosteroids may be beneficial for autoantibody mediated neurological disease.

Keywords: VGKC-complex
autoimmune encephalitis
epilepsy
NMDAR
antibodies
Advisor: VIncent, A
Upton, L
Application of radiative fluid dynamics scaled from the laboratory to astrophysics

Since its inception, the laser has found numerous applications beyond anything that could have been foreseen at its creation. With scientific and technological advancements, lasers are now capable of delivering a large amount of energy in very short timescales: giving us the ability to form interesting states of matter such as plasmas. As it became possible to create such material on earth, it made sense to consider applications this could be used for.
Astrophysics typically uses a combination of observation, theory and simulation in order to further our understanding of the cosmos. The ability of the laser to create matter in similar states to those found in many astrophysical phenomena opened up a complimentary research area: laboratory astrophysics.
The thesis begins by describing the basic physics underlying plasmas and fluid theory, before extending this to a non-dimensional form in the ideal hydrodynamic case: the so-called Euler equations. A novel way of including non-ideal terms, such as radiative, magnetic and quantum effects, is shown. Restrictions, and guidelines, to creating suitable lab experiments are drawn from this, and an experimental analogue of a polar star system is described. The design, simulation, execution and analysis of the experiment, led by the author, is given. Good agreement is found between experimental results, simulations and astrophysical theory. An experimentally measurable quantity, the structure factor, is then derived from hydrodynamics, and extended to include radiative effects, using the framework introduced in the first section. The impact of including such effects is discussed and determined to be non-negligible. Finally, we conclude by drawing together all these areas.

Keywords: Laboratory Astrophysics
Binary Star System
MagnetoHydroDynamics
Scaling Laws
MHD
Radiative Hydrodynamics
Radiation
Advisor: Gregori, G
Ultrasound-enhanced delivery of therapeutic agents to tumours using submicron cavitation nuclei

Cancer therapy is severely hampered by the poor delivery of agents out of the blood vessels and into tumours. This is due to the irregular vasculature, high interstitial pressure and dense extracellular matrix associated with tumour tissue. As a consequence, high doses of agents must be administered intravenously for effective accumulation in the tumour. This leads to a low therapeutic index, necessitates multiple administrations of the same drug, and for many cancer drugs, also leads to toxic side-effects. Increasingly complex therapeutics, such as antibodies and viruses, only exacerbate this delivery problem as their greater size leads to lower coefficients of diffusion and, consequently, even greater portions of the tumour remain untreated.
There have been studies aimed at improving therapeutic outcomes using microbubble-nucleated, ultrasound-induced cavitation, which provides a mechanical impetus to drive drugs out of the vasculature and into tumours. However, microbubbles are limited by their large size, their instability in the blood and their destruction upon cavitation. This thesis details the formulation of two alternative cavitation nuclei to overcome the limitations of microbubbles: mesoporous carbon particles and polymer cups. These are solid, submicron particles that contain crevices into which nanobubbles can be stabilised. Initial studies of their biocompatibilty have indicated that these formulations may be safe for intravenous administration.
A tumour mimicking phantom was first used to quantify drug delivery caused by cavitation. Both polymer cups and mesoporous carbon particles were found to significantly enhance delivery of a model therapeutic agent by this method.
In vivo the polymer cups were used to enhance the delivery of an oncolytic vaccinia virus: intravenous administration of 1x105 pfu vaccinia virus, polymer cups and ultrasound treatment was shown to cause a 780-fold increase in genome copies in the tumours of a SKOV-3 tumour model, and 5,700-fold, in the tumours of a HEPG2 tumour model 20 days after the treatment. In mice treated with 1x106 pfu of virus cavitation caused by cups and ultrasound was shown to cause regression in 7 of the 8 tumours in comparison to just 1 of the 8 tumours that were treated with virus alone.

Keywords: Ultrasound
Cancer
Virology
Drug delivery
Nanotechnology
Cavitation
Advisor: Coussios, C
Carlisle, R
Elasticised ecclesiology : the concept of community after Ernst Troeltsch

Churches are always already in crisis. In this study, I take the current crisis of churches as a point of departure in order to offer a critical and constructive account of church as open(ed) community. In conversation with Ernst Troeltsch (1865-1923) – a conversation which concentrates on a hermeneutical-constructive rather than a historical-critical retrieval of his interdisciplinary thinking – I argue that the communities which constitute church need to be elasticised in order to engage the ‘finite other’ (the creature) and the ‘infinite other’ (the creator).
My study counters common characterisations of the current crisis of churches in which diversification is interpreted as the reason and de-diversification is interpreted as the response to crisis. In these characterisations, churches are closed off against the ‘other’. In three parts which examine the controversial but connected concepts of ‘religiosity’, ‘community’, and ‘identity’, I suggest that the sociological closure against the finite other and the theological closure against the infinite other are connected. Taking trust as a central category, I argue that both the finite other and the infinite other are constitutive of church. Trust opens identity to alterity. Thus, I advocate a turn in the interpretation of the identity of Christianity – from identity as a ‘propositional possession’ to identity as a ‘performative project’. The identity of Christianity is ‘done’ rather than ‘described’ in the practices of church. Church, then, is a ‘work in movement’, continually constituted through the encounter with the finite and the infinite other in Jesus Christ.
My study contributes to ecclesial practices and to reflections on ecclesial practices in the current crisis of churches through the elasticisation of ecclesiology. It retrieves Troeltsch’s interdisciplinary thinking for the controversies which revolve around the construction of community today, opening up innovative and instructive approaches to the investigation of the practices of Christianity past and present.

Advisor: Jeanrond, W