VictorJuiz/thesis huggingface dataset:
The assessment of a number of different meso-porous silica nanoparticles for delivery of chemotherapeutics and siRNAs

Mesoporous silica nanoparticles (MSNPs) are of interest as effective drug carriers because of their controllable physical properties and biomedical compatibilities. A number of different MSNPs have been assessed for their suitability as intracellular nano-scale carriers of chemotherapeutics and siRNAs.
Four morphologically different MSNPs were synthesised after optimisation of existing protocols. The MSNPs were characterised with regards to size, porosity, surface area, surface charge, cytotoxicity and biodegradability. Their suitability as drug carrier in vivo was examined in terms of cargo loading, ability to be endocytosed by cells and take ad-vantage of the Enhanced Permeability and Retention effect.
The loading and unloading profiles of two model compounds and a potential chemotherapeutic agent LY294002 were investigated. The release behaviours of the cargoes were altered by modifying the particle surface with polymeric capping agents. In addition, the particles were capped with pH-sensitive molecules, and the release behaviour in low pH was assessed since tumours are known to have an acidic microenvironment.
The physiological function of LY294002 on selected cancer cell lines was also studied. LY294002 was shown to affect the proliferation, survival, and metabolism of selected cells under different oxidative conditions. The effect differed when cells were under oxi-dative stress and/or glucose stress. Cell viability was also compromised after treatment with LY294002 loaded MSNPs. The sensitivity to each LY294002 loaded MSNP differed between cell lines.
Engulfment and cell motility 1 (ELMO1) - targeted siRNA was also delivered using MSNPs to two distinct rhabdomyosarcoma lines. Significant knock-down of the ELMO1 gene was shown, illustrating that MSNPs could be efficient transfection agents for siRNA. In particular, the two MSNP candidates were shown to be significantly better than a current commercial product.
A co-delivery system for LY294002 and ELMO1-targeted siRNA was established. Cell viability and ELMO1 expression were both suppressed after treatment with the co-delivery system.

Keywords: Chemotherapeutics delivery
Nanomaterials
siRNA delivery
Mesoporous silica nanoparticles
Advisor: Townley, H
Thompson, I
Small molecule inhibitors and substrate analyses of protein arginine methyltransferases

Chapter 1 introduces the Protein Arginine Methyltransferases (PRMTs) as epigenetic regulators that decorate peptidic arginine with methyl groups. Evidence for PRMT involvement in cancer pathogenesis is reviewed and their plausibility as therapeutic targets is introduced. The methylation patterns conferred by the PRMTs is described, and the existence of novel patterns is considered. Techniques for assaying PRMT activity are compared and contrasted and a discussion of current PRMT inhibitors is presented. The chapter concludes by outlining the aims of the thesis.
Chapter 2 describes synthesis towards novel methylated arginine molecules that are fully protected for inclusion in peptides via solid phase peptide synthesis.
Chapter 3 outlines the total synthesis of protected δ-monomethylated arginine for peptide synthesis. This methylation pattern is known in yeast but has not yet been identified in humans.
Chapter 4 details a new mass spectrometry-based assay that can be applied for inhibitor and substrate analyses. Synthesis of a novel histone peptide containing the δ-monomethylated arginine, produced in Chapter 3, is also described and this is tested for relevance as a human epigenetic marker. Novel polymethylation patterns are also explored in a total of five histone peptides. This chapter concludes with discussion of possible methylation pattern rearrangements.
Chapter 5 describes the synthesis and testing of two series of putative PRMT inhibitors based on previously identified scaffolds within this research group. Data obtained from three different assays, including that outlined in Chapter 4, are analysed and suggestions as to the direction of PRMT assay design are offered.
Chapter 6 provides the experimental data to support Chapters 2-5, including all organic synthesis procedures, protein & peptide syntheses and assay methodology.

Keywords: Mono-methyl Arginine
Epigenetics
Protein Arginine Methyltransferases
Advisor: Russell, A
Schofield, C
Brennan, P
Continuity of care and clinical outcomes in the community care of patients with psychosis

Continuity of care in mental health care is considered both an important objective of NHS policy and vital to clinical practice. However, it remains poorly defined and there is little research into its association with outcomes. Mental health services are unique in their ability to legally compel patients to adhere to treatment in the community and there has been no research into how this may affect continuity. My thesis aims to critically appraise the definition of continuity of care and systematically review the literature on its association with outcomes. It also measures its association with readmission by conducting a longitudinal study, and measures the association between community compulsion and continuity of care.
The literature review confirmed that continuity of care is best understood as the process of care of an individual patient over time. This is perceived by both the patient and providers of care as comprehensive, consistent, and connected. The systematic review found little evidence for an association between continuity of care and outcomes but that this may be due to persisting variation in both measures and outcomes.
Results from the longitudinal study suggested that better continuity was associated with both better and worse hospital outcomes. Community compulsion had no association with continuity of care.
My findings suggest that patient follow-up has improved considerably in the last three decades and, because of this, some traditional measures of continuity may be redundant. Measures of frequency of contact do not accurately measure the flexible, assertive practice that is a feature of current services. Continuity of care is useful as an indicator of the process of care but for it to be an effective research tool there needs to be a radical change in the way it is measured. Current mental health services are characterised by separation and specialisation into different components of care. Therefore, the most useful measures of continuity of care may be ones which successfully measure how it can be maintained between these services.

Keywords: Psychosis
Community Mental Health
Psychiatry
Continutiy of Care
Advisor: Burns, T
Rugkåsa, J
Life is in the manuscript: Virginia Woolf, historiography, and the "mythical method"

Virginia Woolf's writing is aesthetically complex, politically engaged, and remains relevant today—an astonishing achievement. This thesis begins by asking how and why this is the case, and thinks through Woolf's relationship to history as a means of suggesting some answers. References to the past abound in Woolf's fiction in the form of meaningful names, stories, myths, and national histories. I am especially interested in allusions that are not immediately obvious, but still work to convey something about human nature. These were sometimes inspired by artifacts in museums, or by articles in magazines or newspapers, or literature she owned, or borrowed, or was being written by her contemporaries—sources that a careful researcher can track down. Other references are more difficult to prove; for example, they may have come from travel experiences related by friends, or personal experiences not recorded in her diary. In this case we need to balance circumstantial evidence, common sense, and an understanding of the spirit and concerns of the age.
In the first chapter I highlight Woolf's early interest in the tension between fact and fiction as it is expressed in her 1906 short story, "The Journal of Mistress Joan Martyn". The chapter serves as way of demonstrating my process. I point out the interplay between form, content, and autobiography that is in her other work. In short, a good deal of what is imagined may have been inspired by personal experience and real historical material. The next three chapters reveal new character types and source material for Jacob's Room, To the Lighthouse, and The Waves—the novels in which Woolf worked out what I have called her "mythical method". I end by inviting scholars to reconsider tensions in her work such as fact and fiction, self and other, art and politics from a new angle: not only as thematic preoccupations but also as crucial to thinking of—to borrow from Gertrude Stein—composition as a form of explanation. Woolf's project in fiction was to figure out what modernism can and should do.
Although it is not necessary for all readers to do the kind of research demonstrated here in order to understand the novels, having an awareness of this work is important. This new way of looking at how and why Woolf wrote both in and outside of time as part of the process of composition makes us think again about the reasons that we should care so much about "Mrs. Brown". It helps us appreciate that the project of conveying both the ephemeral and temporal qualities of human experience is what makes the study of literary modernism (and its current global, transnational forms) a dynamic, political, and expanding phenomenon today.

Keywords: Historiography
"Mythical Method"
Modernism
Creative Nonfiction
Virginia Woolf
Advisor: Whitworth, M
Bradshaw, D
The role of autophagy in intestinal T cell homeostasis

A polymorphism in the essential autophagy gene ATG16L1 is associated with susceptibility to inflammatory bowel disease. However, the role of autophagy in maintenance of intestinal immune homeostasis remains unclear. Using targeted deletion of Atg16l1 in T cells, we demonstrate critical requirement for autophagy in generation of appropriate adaptive immune cell responses within the mucosa. Selective deletion of Atg16l1 in T cells resulted in spontaneous intestinal inflammation, characterized by accumulation of Th2 cells and aberrant antibody responses towards dietary and microbiota antigens. Foxp3+ Treg cells were dependent on autophagy for their survival and function within the intestinal lamina propria, where they acted to limit Th2 cell accumulation. In addition, we demonstrate a novel role for autophagy in limiting Th2 cell survival in a cell-intrinsic manner. The distinct requirements for autophagy in the survival of different intestinal CD4+ T cell subsets reveals a novel role for autophagy in mucosal T cell homeostasis, with potential implications for understanding and treatment of chronic inflammatory disorders.

Keywords: Autophagy
T cells
IBD
Mucosal immunology
Advisor: Maloy, K
Pyrrhic progress - antibiotics and western food production (1949-2013)

This dissertation addresses the history of antibiotic use in British and US food production between 1950 and 2013. Introduced to agriculture in the 1950s, antibiotics underpinned the 20th-century revolution in Western food production. However, from the late 1950s onwards, controversies over antibiotic resistance, residues and animal welfare began to tarnish antibiotics' image.
By mapping both the enthusiasm and the controversies surrounding antibiotic use, this dissertation shows how distinct civic epistemologies of risk influenced consumers', producers' and officials' attitudes towards antibiotics. These differing risk perceptions did not emerge by chance: in Britain, popular animal welfare concerns fused with new scenarios of antibiotic resistance and drove reform. Following 1969, Britain pioneered antibiotic resistance regulation by banning certain feed antibiotics. However, subsequent reforms were only partially implemented, and total antibiotic consumption failed to sink. Meanwhile, scandals and public pressure forced the American FDA to install the first comprehensive monitoring program for antibiotic residues. However, differing public priorities and industrial opposition meant that the FDA failed to convince Congress of resistance-inspired bans. The transatlantic regulatory gap has since widened: following the BSE crisis, the EU phased out growth-promoting antibiotic feeds in 2006. The US proclaimed only a voluntary and partial ban of antibiotic feeds in December 2013.
In the face of contemporary warnings about failing antibiotics, the dissertation shows how one group of substances acquired different meanings for different communities. It also reveals that the dilemma of antibiotic regulation is hardly new. Despite knowing about antibiotic allergies and resistance since the 1940s, no country has managed to solve the dilemma of preserving antibiotics' economic benefits whilst containing their medical risks. Historically, effective antibiotic regulation emerged only when differing perceptions of antibiotics were broken down either by sustained regulatory reform or large crises.

Keywords: Agricultural intensification
Antibiotic regulation
Bacterial resistance
Non-human antibiotic use
Agricultural antibiotic use
Risk Management
Advisor: Harrison, M
The dynamics and demography of socially structured carnivores

Sociality in carnivores is theoretically expected to produce quantitatively different dynamics compared to solitary species, exhibiting Allee effects, increasing extinction risk and limiting population growth. There is also evidence in social species that demographic stochasticity can impact the population when densities are high. Empirical support for these processes is lacking and the effects of socio-spatial structure on population dynamics is now widely debated. The roles of social structure, reproductive suppression, communal predator vigilance, communal hunting and babysitting on population responses to perturbations away from carrying capacity have important implications for species management. Social systems also possess inherent spatial structure. Such structure is known to influence dynamics in solitary species. This thesis investigates the relative contributions of spatial and social structure on population dynamics in three contrasting carnivores, from three different families; badgers (Meles meles), lions (Panthera leo) and grey wolves (Canis lupus), that each demonstrate comparable and different life history strategies with one another. Simple and complex structured population models are used to demonstrate how intra-group processes interact within inter-group process and habitat features to produce population wide dynamics. The models are used to investigate whether general rules governing the dynamics of social species can be drawn across species.

Advisor: Coulson, T
Ameliorating β-thalassaemia by manipulating expression of the α-globin gene

β-Thalassaemia is a disorder of haemoglobin production characterised by severe anaemia requiring life-long blood transfusions. The common genetic defects are predominantly based in and around the β-globin gene resulting in reduced or absent β-globin chain synthesis. The resultant excess of free α-globin chains, which precipitates in red blood cells and their precursors and causes ineffective erythropoiesis, is the main pathophysiological mechanism of anaemia in these patients. Clinical and genetic data accumulated over the last 30 years have indicated that reduction of α-globin expression is clinically beneficial to patients with β-thalassaemia, and in the subset of patients with HbE β-thalassaemia it could be transformational. Attention has been centred on pathways that increase γ-globin expression and hence the production of foetal haemoglobin, but I have explored avenues that down regulate the α-globin gene expression without affecting the β-like globin expression, to equalise globin chain imbalance and could have potential clinical applications.
Initially, an in vitro erythroid differentiation system in serum-free medium was optimised and characterised. This generates a large number of erythroid cells from human CD34+ cells with minimal non-erythroid contamination. This system appears to be a faithful recapitulation of normal erythropoiesis and was validated with newly developed assays. A library of epigenetically active small molecules and licenced drugs was then screened and this identified a number of interesting compounds including IOX1, a histone demethylase inhibitor. Secondary assays confirmed IOX1 as a selective down regulator of α-globin expression, with no significant adverse effects on β-like globin expression, erythroid cell viability, erythroid differentiation or global erythroid transcriptome.
Next, CRISPR/Cas9 genome editing technique was used to introduce targeted deletions of multispecies conserved sequences (MCS) R2 region, the most critical distant cis-acting regulatory element enhancing α-globin expression in humans. High transfection and mutation efficiencies were achieved in human CD34+ cells and single cell assays confirmed high frequency of homozygous and heterozygous deletion events. More importantly, and analogous to patients with an identical mutation, the deletion of MCS-R2 element resulted in selective knockdown of α-globin expression without altering β-globin expression or erythroid differentiation. In conclusion, I have demonstrated that selective down regulation of α-globin expression is plausible through pharmacological and genome engineering approaches and these findings unveil new pathways of therapy for β-thalassaemia.

Keywords: genome editing
alpha-globin
epigenetic drug targetting
thalassaemia
Advisor: Higgs, D
Gibbons, R
Essays on health care operations management

The aim of operations management in health care is to enhance the provision of services to patients and to decrease costs. Overall worldwide health care expenditures represent around 10.5% of the global GDP and are projected to increase at an annual rate of 5.3% from 2015 to 2017 [74]. In order to investigate how to curb health care costs, I study the English NHS, a health care system that provided universal care to around 54 million people in 2014 [243]. The NHS has launched many initiatives to improve the performance of hospital operations such as the "QIPP" program, which has the objective to save £20 billion of costs by 2015 [98]. Given this framework, this research aims to contribute to the theory that is guiding these operational changes, using data on all admissions to hospitals and focussing on the inguinal hernia, one of the most common surgical procedures [86]. In the next chapters, this research describes inguinal hernia care delivery in the English NHS, examines the impact of spillovers and complementarities on costs, and investigates the effects of length of stay reduction on risk of re-admission and risk of death. The findings of this thesis indicate that one of the possible problems in the delivery of inguinal hernia care in the NHS is the decrease in the number of elective operations performed and the increase in readmission rates. They also clarify how decisions on allocation of resources can affect hospital expenditures by showing that loss in focus can increase health care costs and by pointing out that there is little evidence to support the theory of spillovers and complementarities in the surgical context. Finally, the results of this research can be used to suggest the logic of a policy to decrease length of stay that can inform hospital decisions and can decrease hospital costs.

Advisor: Tufano, P
Dopson, S
MacMahon, S
Post-translational modifications of BRAF and MITF

Malignant melanoma is the deadliest and most aggressive form of skin cancer. Despite the development of targeted molecular therapies which specifically target oncogenic pathways in melanoma, melanoma remains highly refractory to treatment and prone to relapse. In order to develop more effective therapies, there is a need to investigate additional ways of manipulating aberrant molecular pathways in melanoma. To this end, we have identified novel sites of post-translational modifications in two oncogenic proteins that are known to play pivotal roles in driving melanoma tumorigenesis. We showed that BRAF, the most commonly mutated oncoprotein in melanoma, can be acetylated at K473 and K475 by the p300/CBP acetyltransferases. Importantly, acetylation of BRAF reduced its activity regardless of its mutational status at the commonly mutated V600 residue. We also identified a novel phosphorylation site targeted by GSK3 in microphthalmia-associated transcription factor (MITF), the melanocyte master regulator. GSK3 phosphorylation of S69, together with ERK-mediated phosphorylation of the nearby S73 residue, was found to promote MITF nuclear export via a previously undescribed nuclear export signal comprising of the S69, S73, M75, L78 and L80 residues. Importantly, phosphorylation-induced nuclear export was associated with reduced MITF activity, which may have important functional implications for melanocyte development and melanoma oncogenesis. In addition, we showed that the cyclin-dependent kinases CDK1 and CDK2 can also phosphorylate MITF at S73.

Keywords: drug screening
BRAF
MITF
nuclear export signal
Advisor: Goding, C
High-resolution characterisation of stress corrosion cracking

The degradation of reactor grade stainless steels and their susceptibility to stress corrosion cracking (SCC) when exposed to the pressurised water reactor (PWR) primary water environment has been a topic of intense research for many decades. Nevertheless, our understanding of the underlying mechanisms of SCC remains incomplete to date. It has been generally accepted that only high-resolution (electron) microscopy techniques are capable of revealing the yet unidentified processes involved in SCC crack propagation. For this reason, one of the main objectives of this project was to make new techniques with improved spatial resolution accessible to SCC research. While low-keV energy dispersive X-ray spectroscopy (EDX) was used for the preliminary analysis of SCC cracks, transmission Kikuchi diffraction (TKD) and atom probe tomography (APT) were used for high-resolution studies of the microstructure and chemistry near the crack tip. In particular, TKD proved very beneficial for revealing the extent of the strain concentration around the crack tip. For the application of APT to SCC research, a novel method for preparing APT needles containing entire SCC crack tips was developed. The method was then used for acquiring very localised compositional measurements of the crack tip and GB oxide chemistry with extraordinary accuracy.
The second objective of this thesis was to understand the impact of the SCC test temperature on the crack growth rate (CGR) in SUS316 stainless steel. It was found that after steady growth with increasing temperature, a peak in the CGR occurred at &Tilde; 320°C, followed by a substantial drop towards higher temperatures. The inhibition of the CGR with increasing temperature between 320° and 360°C and its impact on the microstructure were studied via analytical transmission electron microscopy (TEM) and TKD. Furthermore, the potential impact of thermally activated diffusion and mechanical response-based mechanisms was investigated. It appears that higher dislocation density and strain concentrations around the crack tips at lower temperature (i.e. 320°C) lead to possibly enhanced brittle-like fracture at the crack tip. An enhanced model for the ongoing processes involved in SCC crack propagation based on the experimental results is presented at the end of this work.

Advisor: Lozano-Perez, S
Moody, M