VictorJuiz/thesis huggingface dataset:
Scaling up the generation of metallofullerenes for QIP

Endohedral fullerenes are remarkable molecules with unique electronic, magnetic, photovoltaic and quantum properties. They have found a number of applications in various fields. Among all the potential applications, one particularly interesting application is to employ them as building blocks for a quantum computer. However, the scientific and commercial exploitation of these materials is held back by their low productivity. In this project, the arc discharge synthesis of endoedral fullerenes which remains the most promising candidate for producing bulk quantities of Endohedral Metallofullerenes (EMFs) was divided into 4 steps, and in this thesis, I discuss the attempts that had been made to optimise each of them. In this project, I focus on Y&commat;C82, which is a spin active endohedral fullerene with attractive quantum properties. I obtained sights into the dynamics of the Soxhlet extraction of fullerenes, and developed an optimised Soxhlet scheme which is able to extract 95% of Y&commat;C82 from the soot within 60 hours (Chapter 4). Further progress on the optimization of Soxhlet extraction was made when a two-stage Soxhlet extraction/purification was independently developed (chapter 9). This method employs two solvents (toluene and DMF) to extract fullerenes with different dipolar moment. It was not only able to extract fullerenes effectively from the soot, but also to purify EMFs/Trimetallic nitride template(TNT) into high purity (97%).
Efforts were made to search for the best conditions for generating Y&commat;C82 with a patented pilot arc discharge system. After analysing the data of the yield of fullerenes in various conditions with a "22 factorial design of experiment", I believe the yields of Y&commat;C82 can be increased by using high He pressure (Chapter 5).
The scaling up the production of EMFs was also tackled from a more fundamental and theoretical aspect. Although fullerenes have been efficiently synthesized by several methods to date, the formation mechanism of these materials remains a mystery. The study of the fullerene formation mechanism in arc discharge is particularly rare due to intrinsic technical difficulties. In chapter 6, I propose a new "bottom up" formation scenario in the arc discharge synthesis of fullerenes that adopts the so called "closed network growth".
Attempts that were made to improve the efficiency and safety of the current system were introduced in Chapter 7. Concepts to develop a more efficient safe arc discharge system were suggested and discussed in the same chapter. The Lewis acid separation method was reported to be an efficient approach to remove the empty cages from the EMFs1, however, this method is only suitable for a lab equipped with specialized facilities and cannot be characterized as generic (Chapter 8).
Finally, I have applied a functionalization scheme to C60 which may be a promising scheme to functionalize spin-active metallofullerenes to produce a two-qubit quantum information system (Chapter 10).

Advisor: Porfyrakis, K
Generation of short pulse THz radiation from accelerator based light sources

High power and short pulse THz radiation has become increasingly important in the investigation of dynamics of organic and chemical molecules. Such radiation can be effectively generated with accelerator-based light sources. This thesis reports a series of studies on the generation of short pulse THz radiation from storage rings and from compact accelerators that can be based in University sized laboratories. The first part of this thesis reviews THz radiation, synchrotron radiation and free electron laser (FEL). The second part presents the studies of short pulse THz radiation generated from the Diamond storage ring in a new operating mode known as ultra-low alpha mode to extend spectrum of coherent radiation to higher THz frequency. The numerical simulations of a single bunch dynamics show qualitative agreements with the measurements taken at the Diamond storage ring. The third part is dedicated to the design of a compact RF linac-based THz radiation source for producing short pulse THz self-amplified spontaneous emission (SASE) FEL with an undulator and THz coherent synchrotron radiation (CSR) with a bending magnet. Start-to-end simulations of SASE FEL and CSR were performed to analyse the beam dynamics and the generation of THz radiation. The SASE FEL reaches saturation within the undulator length of 5 m, whereas the CSR spectrum covers frequency below 16 THz. In the fourth part, we investigated a THz/IR radiation source driven by a Laser Plasma Wakefield Accelerator (LPWA). Extensive 2D particle-in-cell (PIC) simulations were done to generate an ultra-short electron bunch from self-injection in a nonlinear bubble regime. The 60-MeV electron bunch was obtained with 6% energy spread and 18 mrad beam divergence. The self-injected electron beam was used to drive the SASE FEL using a normal undulator and a transverse gradient undulator (TGU) to exploit the electron bunch with large energy spread. The results show that the energy spread of 6% is too large even for the TGU. Although the energy spread is reduced to 1%, the FEL saturation cannot be reached because the bunch length of the LPWA driven beam is shorter than the FEL cooperation length. The last part of this thesis discusses the Accelerator Science Laboratory (ASL) project at the University of Oxford. The designs of THz radiation sources driven by the RF linac and the LPWA previously presented were considered as potential options for the ASL. The radiation shielding for the ASL was investigated with Monte Carlo simulations to design a proper beam dump and shielding covering the beam dump.

Advisor: Bartolini, R
Tsesmelis, E
Development of adjuvanted multi-antigen liver-stage malaria vaccines

Despite promising progress in malaria vaccine development in recent years, an efficacious subunit vaccine against P. falciparum remains to be licensed and deployed. The most advanced candidates in clinical development focus on two pre-erythrocytic antigens (CSP and ME-TRAP), but many more immunogenic antigens have been recently identified. The work described in this thesis aimed to improve on the immunogenicity and efficacy of the leading liver-stage vaccine candidate (ChAd63-MVA ME-TRAP), which is known to confer protection by eliciting high levels of antigen-specific CD8+ T cells. To achieve this, two different strategies were pursued. First, several prime-boost regimens with vectors encoding combinations of two liver-stage antigens were investigated. When mixed, vectors expressing LSA1 and LSAP2 conferred highest levels of protective efficacy in mice and were therefore considered for inclusion in the final second generation viral vectored liver-stage malaria vaccine. Second, the MHC class II invariant chain (Ii) was developed as a molecular adjuvant. Immunogenicity analyses of ChAd63 encoding ME-TRAP fused to several different versions of Ii showed that the transmembrane domain of Ii has the ability to strongly increase antigen-specific CD8+ T-cell responses, even in the absence of the rest of the Ii protein. This finding may lead to the discovery of numerous similar adjuvants (such as the transmembrane domain of the Newcastle disease virus fusion protein). Furthermore, experiments showed that the Ii chain sequence can also be xenogenised without losing adjuvanticity. Both strategies have been combined in numerous novel adjuvanted multi-antigen vaccines, which were ranked for immunogenicity and efficacy in inbred and outbred mice. The viral vectors of the best combination (ChAdOX1-sharkTM/Ii-LSA1-LSAP2 and MVA-tPA-LSA1-LSAP2) are currently being produced to GMP grade and will progress to initial clinical trials in early 2017.

Advisor: Spencer, A
Hill, A
Hypertensive pregnancy and future maternal cardiovascular phenotype

Hypertensive disorders of pregnancy are common and associated with persistent increased risk of maternal cardiovascular disease. However it is unclear which mechanisms are behind this increased risk and whether they are explained by traditional cardiovascular risk factors. I sought to characterise cardiovascular phenotypic patterns after hypertensive pregnancy and explore relevant relationships with risk factors and pregnancy characteristics. Women were identified through the John Radcliffe Hospital maternity records and recruited 5-10 years after hypertensive (cases) or normotensive pregnancy (controls). Detailed phenotyping to characterise cardiac, vascular and cerebral phenotypic differences was carried out using a range of techniques including magnetic resonance imaging, cardiac and vascular ultrasound, intravital video capillaroscopy and ambulatory monitoring. Women after hypertensive pregnancy were more likely to have adverse cardiac structure than women after normotensive pregnancy, with higher left ventricular mass and lower left ventricular volumes compared to women with a history of normotensive pregnancy. They were also more likely to have reduced aortic distensibility. Characterisation of cerebral structure demonstrated that women after preeclampsia had lower grey matter volumes and greater white matter damage compared to a control population. There were also distinct microvascular and blood pressure differences with capillary rarefaction and higher ambulatory blood pressure in women after hypertensive pregnancy compared to women after normotensive pregnancy. There were no significant differences in circulating angiogenic factors or autonomic function. Differences in left ventricular mass, cerebral white matter damage and capillary rarefaction were not explained by conventional risk factors, suggesting novel, disease-specific mechanisms may be responsible. This encompassing characterisation of postpartum maternal cardiovascular phenotype after hypertensive pregnancy highlights widespread adverse differences which are not fully explained by traditional risk factors. Understanding whether targeting these adverse phenotypic features during hypertensive pregnancy or in the early postpartum period affects clinical endpoints will be of future interest.

Advisor: Leeson, P
Structural characterisation of the foot-and-mouth disease virus uncoating pathway

Foot-and-mouth disease virus is a single-stranded RNA virus that belongs to the genus aphthoviruses, in the family Picornaviridae, and causes disease in cloven-hoofed animals. It is one of the biggest hindrances to the international trade of animals and animal products in the world. The virus capsids readily dissociate into pentamers at acidic pH. While there have been several studies on enterovirus uncoating, this process is poorly-understood for aphthoviruses, and there are no published structures elucidating how FMDV undergoes this transformation to infect cells. Furthermore, there are no structures available for a dissociated FMDV pentamer. Thus far, there has been only one paper claiming to show, at low resolution, a disassembly intermediate for another aphthovirus, Equine Rhinitis A Virus (ERAV).
Here, a 5.2Å-structure of an FMDV assembly formed from acid dissociated pentamers, visualised using cryo-electron microscopy (cryo-EM), is presented. This inside-out assembly of the pentamers highlights the extensive conformational changes in the pentamers that may have lead to the disassembly of the native capsid. Also presented here is a lower-resolution structure of the isolated dissociated pentamer (8.2 Å), enabling a comparison of the differences between native FMDV particles, the dissociated- and the re-assembled pentamers. These analyses elucidate why the pentamers may have been unable to re-assemble properly. Together, these data suggest that the ERAV structure mooted to be a disassembly intermediate may have formed from re-assembled dissociated pentamers. Furthermore, it is concluded that there is still no hard structural evidence that aphthoviruses form an intermediate particle during disassembly.
The thesis also includes high-resolution cryo-EM structures of the FMDV serotypes SAT1 and SAT3 (3.8 Å and 3.1 Å respectively), derived from inactivated virus-pellets, thus completing the repository of high-resolution structures for all SAT serotypes. The results provide an insight into the reasons for SAT3 being the most thermally-unstable picornaviruses, and also include predictions and comparative analyses with known antigenic sites of other FMDV serotypes.

Advisor: Stuart, D
Huiskon, J
Organozirconocene nucleophiles in Cu-catalysed asymmetric transformations: methodologies, applications to total synthesis and NMR mechanistic studies

The development of powerful and adaptable methods to form new C-C bond enantioselectively is highly desirable. Many methodologies emerged in recent years using a wide array of nucleophilic organometallics and catalytic metals1,2. In this work, a general introduction on the current development of Cu-catalysed asymmetric additions is primarily described (Chapter 1). We particularly focus on the applications of such methodologies, the study of their mechanisms and the transition from using common organometallics in favour of milder and functional group tolerant nucleophiles such as organozirconocenes. We then present the development of new methods for asymmetric conjugate addition towards its application to the synthesis of prostaglandins (Part I). For example, we describe the use of alkenylzirconocene nucleophiles (Chapter 2) and conjugate additions of alkylzirconocenes to 5-membered rings3 (Chapter 3). We then investigated the application of these methodologies towards the total synthesis of a prostaglandin analogue, Latanoprost (Xalatan®) (Chapter 4). Then we carried out mechanistic studies by NMR (Part II). The mechanism of asymmetric allylic alkylation of alkylzirconocene to allylchlorides4 (Chapter 5) and allylphosphates (Chapter 6) is discussed in detail. We also developed and investigated the heterocyclic asymmetric allylic alkylation of alkylzirconocene5 (Chapter 7). Finally we describe the NMR mechanistic studies of asymmetric conjugate addition of alkylzirconocenes (Chapter 8).

Keywords: Cu-Catalysis
Advisor: Fletcher, S
Graphical model selection for gaussian conditional random fields in the presence of latent variables: theory and application to genetics

The task of performing graphical model selection arises in many applications in science and engineering. The field of application of interest in this thesis relates to the needs of datasets that include genetic and multivariate phenotypic data. There are several factors that make this problem particularly challenging: some of the relevant variables might not be observed, high-dimensionality might cause identifiability issues and, finally, it might be preferable to learn the model over a subset of the collection while conditioning on the rest of the variables, e.g. genetic variants. We suggest addressing these problems by learning a conditional Gaussian graphical model, while accounting for latent variables. Building on recent advances in this field, we decompose the parameters of a conditional Markov random field into the sum of a sparse and a low-rank matrix. We derive convergence bounds for this novel estimator, show that it is well-behaved in the high-dimensional regime and describe algorithms that can be used when the number of variables is in the thousands. Through simulations, we illustrate the conditions required for identifiability and show that this approach is consistent in a wider range of settings. In order to show the practical implications of our work, we apply our method to two real datasets and devise a metric that makes use of an independent source of information to assess the biological relevance of the estimates. In our first application, we use the proposed approach to model the levels of 39 metabolic traits conditional on hundreds of genetic variants, in two independent cohorts. We find our results to be better replicated across cohorts than the ones obtained with other methods. In our second application, we look at a high-dimensional gene expression dataset. We find that our method is capable of retrieving as many biologically relevant gene-gene interactions as other methods while retrieving fewer irrelevant interaction.

Advisor: Jostins, L
McVean, G
Substrate metabolism and cardiomyogenic differentiation of cardiac progenitor cells

Despite being resident in the heart, which derives most its energy needs from the oxidation of fatty acids, cardiac stem/progenitor cells are assumed to be glycolytic. Therefore, the transition of these non-contractile progenitor cells into beating cardiomyocytes necessitates an obligatory transformation of the metabolic infrastructure with mitochondrial network expansion and a distinctive switch from glycolysis to oxidative phosphorylation. However, expansion of progenitor cells in culture may impair their ability to upregulate fatty acid metabolism and increase mitochondrial function. Therefore, the main objective of this project was to determine, for the first time, substrate and energy metabolism in cardiac stem/progenitor cells before, during and after cardiomyogenic differentiation. Control passage two cardiosphere-derived cells (P2-CDCs), created through culture on fibronectin/poly-D-lysine (FN/PDL) or collagen IV/hanging drops (ColIV/HD), have been shown to derive most of their energy needs from glycolysis with elevated lactate efflux. However, after 3-weeks of treatment with 5-Azacytidine (5-Aza) and ascorbic acid (AA), differentiated cells started to upregulate fatty acid oxidation and significantly reduced glycolytic flux and lactate production. Therefore, different metabolic mediators were used to stimulate fatty acid oxidation in differentiated cells. Various media with or without synthetic small molecule(s) were tested to optimize differentiation capacity and to stimulate aerobic oxidative phosphorylation in P2-CDCs. WY-14643+TGFβ supplemented medium was able to induce cardiomyogenic differentiation of P2-CDCs into mature, differentiated myocytes. The differentiated cells showed a significant increase in expression of both cardiac-specific genes and proteins, calcium handling genes as well as transforming glycolytic metabolism into more efficiently producing higher energy system, fatty acid, and carbohydrate oxidation in addition to glycolysis, suggesting they may be forming ventricular myocytes.

Keywords: Metabolism of cardiac stem/progenitor cells
Advisor: Carr, C
Clarke, K
Russell, A
Geographic and socio-economic inequalities and access to higher education: is the proximity of higher education institutions associated with the probability of university attendance for young people in England?

The relationship between geography and university choice is well documented and suggests that a student’s location substantially limits their selection of university. However, there are relatively few studies investigating the interplay between geography and university participation. These few studies reach varied and conflicting conclusions. The most recent study of geography and participation in England used a dataset over ten years old, and, since which, tuition fees have risen over ninefold (Gibbons & Vignoles, 2011). This study aims to establish if distance to university is associated with the probability of participating in higher education in England and if this relationship is evenly spread across regions. It also explores how distance may impact student’s university decisions. The project uses a mixed methods research design that combines a quantitative analysis of secondary datasets with an analysis of interviews. The study employs a partially mixed sequential dominant status design with a regression analysis of HEFCE participation data forming the core of the study. Controlling for deprivation, the regression analysis uses average direct measures of distance between each ward and university campus in England to determine the relationship between distance and university participation. The findings suggest that geographical distance to university has a significant negative association with university participation indicated by an average 1% drop for every 6km the distance measure increases. A regional analysis suggested that the association was greatest in the East of England region and an interaction analysis indicated that students in deprived and distant wards suffered a double disadvantage. Interview responses from experts on Key Stage 5 student progression complemented the regression analysis and uncovered that participation in rural areas is subject to greater financial and social costs. It is hoped that the findings of the research may help to raise awareness of geographical inequalities and inform policy on university access.
Investigations on anti-IGF-1R therapy response in a colorectal cancer cell line panel

Therapies targeting the type 1 insulin like growth factor receptor (IGF-1R) have so far failed to show significant benefit for colorectal cancer (CRC) patients in large clinical trials, emphasising the importance of identifying biomarkers for therapy response and developing rational combination therapies.
In this thesis, a large panel of 82 colorectal cancer cell lines was used to discover and validate associations between anti-IGF-1R therapy response, gene mutations and gene expression.
Mutations in PIK3CA exon 9 and 20 were found to be associated with resistance to inhibition with the tyrosine kinase inhibitor OSI-906 and the monoclonal antibody figitumumab. In a number of PIK3CA wild type cell lines, combination therapy with OSI-906 and the pan-Akt inhibitor GSK690693 yielded synergistic effects. PIK3CA wild type cell lines resistant to this combination therapy are characterised by KRAS mutations, a low expression of the cell surface protein CD24, and Akt-independent GSK-3β phosphorylation.
In summary, the findings of this thesis indicate an important role of the PI3K/Akt signalling pathway in anti-IGF-1R response in CRC. We have identified PIK3CA mutations as a biomarker for anti-IGF-1R therapy resistance in CRC. Furthermore, our study demonstrates a synergistic effect of the combination of OSI-906 with a pan-Akt inhibitor in a molecularly defined subgroup of CRC cell lines.

Keywords: Targeted therapy
IGF-1R
Cell line panel
Colorectal cancer
Advisor: Bodmer, W
Niedzwiedz, W