VictorJuiz/thesis huggingface dataset:
Design of a non-scaling fixed field alternating gradient accelerator for charged particle therapy
Keywords: particle therapy
particle accelerator design
Accelerator physics

This thesis describes the design a novel type of particle accelerator for charged particle therapy. The accelerator is called a non-scaling, Fixed Field Alternating Gradient (ns-FFAG) accelerator, and will accelerate both protons and carbon ions to energies required for clinical use. The work is undertaken as part of the PAMELA project. An existing design for a ns-FFAG is taken as a starting point and analysed in terms of its ability to suit the charged particle therapy application. It is found that this design is particularly sensitive to alignment errors and would be unable to accelerate protons and carbon ions at the proposed acceleration rate due to betatron resonance crossing phenomena. To overcome this issue, a new type of non-linear ns-FFAG is developed which avoids resonance crossing and meets the requirements provided by clinical considerations. Two accelerating rings are required, one for protons up to 250 MeV and fully stripped carbon ions to 68 MeV/u, the other to accelerate the carbon ions up to 400-430 MeV/u. Detailed studies are undertaken to show that this new type of accelerator is suitable for the application. An alignment accuracy of 50 micrometers will not have a detrimental effect on the beam and the dynamic aperture for most lattice configurations is found to be greater than 50 pi.mm.mrad normalised in both the horizontal and vertical plane. Verification of the simulation code used in the PAMELA lattice design is carried out using experimental results from EMMA, the world's first ns-FFAG for 10-20 MeV electrons built at Daresbury Laboratory, UK. Finally, it is shown that the described lattice can translate into realistic designs for the individual components of the accelerator. The integration of these components into the PAMELA facility is discussed.
The role of non-coding regions of the alpha-synuclein gene in protein expression and the determination of alternatively spliced alpha-synuclein isoforms in oxidatively stressed cells
Keywords: Parkinson's disease
5' untranslated regions
alpha synuclein

Parkinson’s disease (PD) is a neurodegenerative disorder caused by substantial loss of dopaminergic neurons and has been extensively linked to alpha synuclein (α-synuclein). This thesis has investigated the non-coding regions and alternatively spliced isoforms of α-synuclein and an improved cell model of PD in which this might be studied. The results indicate that there are several different 5’ untranslated region isoforms of α-synuclein expressed and that these stimulate significantly different levels of protein expression when analysed using a luciferase assay. Real-time PCR data indicates that these isoforms are differentially expressed; particularly isoform 202 which was up-regulated in both oxidatively stressed cells and a sample of cingulate gyrus from a dementia with Lewy body (DLB) patient. Interestingly this α-synuclein 202 isoform stimulated the lowest levels of protein expression in the luciferase assay. Three of the four previously reported splice isoforms of α-synuclein were detected; 112, 126 and 140 and the expression levels determined by real-time PCR. Results indicate that isoform 112 expression is up-regulated in oxidatively stressed cells and a sample of cingulate gyrus from a DLB patient but this is not seen when levels of total α-synuclein are normalised. The three spliced isoforms were also cloned and used to determine that a novel antibody was able to detect specifically the 126 α-synuclein isoform by western blotting. Finally, progress was made in developing a new protocol for the differentiation of induced pluripotent stem cells (iPSCs) into dopaminergic neurons using modified messenger RNAs encoding dopamine-specific transcription factors (TFs). Five of required TFs were cloned and ligated to the UTRs needed to produce RNA. Additionally we discovered that iPSCs could not only survive plating onto neuronal substrate in neuronal medium with two daily transfections, but they start to express neuronal markers after four days of culture.
Identifying causative elements within structural variants associated with developmental disorders
Keywords: genomics
genetics
CNVs

It has been well established that copy number variation contributes substantially to genetic variation within human populations. However, the extent to which de novo and inherited copy number variants (CNVs) underlie human disease is not well known. In this thesis, I investigate the role of de novo and inherited CNVs in a wide range of developmental abnormalities.
First, I compare disease associated and apparently benign CNVs for structural differences, with the aim of identifying distinguishing features of disease causing CNVs. I identified significant enrichments of protein-coding genes, protein-coding genes associated with disease in OMIM and miRNAs amongst disease associated disease. Conversely, inherited CNVs observed in healthy individuals show depletions of these features.
Following this, I employ functional enrichment approaches to identify the copy number variable genes within these de novo CNVs that contribute to the patient’s developmental abnormalities. I predict candidate genes for 143 different developmental abnormalities, with 65% of the candidate genes not having been previously associated with disease in OMIM. Through examining the distribution of these candidate genes within the patient’s CNVs, I found evidence of extensive pleiotropy and epistasis as well as a small number of simple additive effects.
Finally, I extend my analyses to examine the role of inherited CNVs as the underlying cause of human developmental disorders. I implicate inherited CNVs and their overlapping copy number variable genes in the underlying causes of 45 human developmental abnormalities. Additionally, I re-examine the patients possessing both de novo CNVs and inherited CNVs using functional enrichment analyses. I reveal significant enrichments for a greater number of human developmental abnormalities when combining both the de novo and inherited CNVs, suggesting it is de novo mutations in combination with the inherited genomic background that are responsible for many instances of human developmental abnormalities.
Liver specific microRNA control of adenovirus serotype five
Keywords: microRNA
oncolytic
virotherapy
adenovirus

MicroRNAs are small non-coding RNA molecules that regulate mRNA translation by binding to complementary sequences usually within the 3’ un-translated region (UTR). By inserting four perfectly complementary binding sites for the hepatic specific microRNA mir122 into the 3’ UTR of adenovirus wild type 5 (Ad5 WT) E1A mRNA I show that the acute liver toxicity caused by Ad5 WT in mice can be significantly reduced. This virus, termed Ad5-mir122, is a promising virotherapy candidate and causes no obvious liver pathology whilst maintaining Ad5 WT replication in mir122 negative cells.
Data shows that repeat intravenous administration of Ad5-mir122 (2x1010vp) to HepG2 tumour bearing mice mediated significant anti-cancer efficacy. RT-QPCR for E1A mRNA demonstrated a 29-fold reduction when compared to Ad5 WT in murine liver whilst western blot confirmed that all E1A protein variants were knocked down. Viral genomic replication was also reduced in mouse liver by 25-fold compared to Ad5 WT. This control of virus activity reduced alanine and aspartate transaminase release by >15-fold and histological analysis showed little to no pathology in Ad5-mir122 infected livers.
Measurement of mature mir122 levels in Ad5-mir122 infected livers by RT-QPCR showed that the quantity of mir122 remained unaffected at therapeutic doses. Complete genome mRNA array profiling of infected livers showed that the transcript levels of >3900 different mRNAs were changed more than 2-fold following Ad5 WT infection whilst less than 600 were changed by Ad5-mir122. A non-replicating control adenovirus vector altered >550 mRNAs. No known mir122 target mRNAs were affected following infection with Ad5-mir122. Western blot analysis of a known mir122 regulated target (Aldolase A) confirmed these results, demonstrating no change in protein level despite infection with Ad5-mir122. These data combined demonstrate that the exploitation of microRNA mir122 regulation to control adenovirus replication is a safe method of control and does not alter the endogenous level or activity of the microRNA or its endogenous mRNA targets. Ad5-mir122 is a potent anti-cancer agent that replicates to wild-type levels in microRNA mir122 negative cells but is specifically and safely attenuated in hepatocytes.
The Role of the Prefrontal Cortex in Pain Modulation
Keywords: prefrontal cortex
pain
modulation

Existing knowledge identifies the prefrontal cortex (PFC) as the modulatory area for pain. Previous neuroimaging studies suggest the existence of the cortico-cortical pathway, an alternative pain modulatory pathway distinct from the descending modulatory pathway of pain. However, little is known of the extent, mechanism and underlying substrate of the modulation. The objective of this study is therefore to explore the role of the PFC in pain modulation. To examine the extent of PFC involvement in pain, meta-analyses of imaging studies in healthy volunteers and patients with chronic pain were performed. Using Gaussian-process regression (GPR) analysis, brain maps were produced from foci of activation as reported in the studies. Since structure dictates function, our next study was to performprobabilistic tractography on diffusion-weighted brain images to ascertain the connection probability of lateral PFC subdivisions and pain-related brain regions as well as intrinsic PFC connections. Two behavioural studies were conducted to investigate cognitive modulation of pain. The first was a study to assess the subjective and physiological correlates of cognitive stress, as previously used in stress-induced analgesia studies. The second was to investigate the involvement of the endogenous opioid system inthe cognitive modulation of pain through effortful reappraisal and contextual modulation.
Meta-analyses in healthy volunteers and chronic pain patients revealed activation mainly in the lateral aspect of the PFC due to pain. Distinct pattern of activation was demonstrated in patients with significant ventrolateral PFC (VLPFC) activation across subtypes of chronic pain. Probabilistic tractography further illustrate the functional significance of lateral PFC subdivisions by demonstrating differential connection probability to pain-related brain regions; dorsolateral PFC (DLPFC) regions displayed higher connection probability with brain regions serving more sensory-discriminative function while VLPFC showed high connection probability with both sensory-discriminative and affective regions. Behavioural study of stress showed that cognitive stress failed to induce significant increases in biomarkers of stress, and was not affected by increased level of difficulty. Lastly, behavioural study on contextual modulation and reappraisal confirmed opioid mediation for contextual modulation while negating its involvement in effortful reappraisal.
Findings from this studyillustrate the extent of PFC involvement in pain modulation especially in chronic pain patients and provide further evidence of an alternative pathway distinct from the opioid-mediated descending inhibitory pathway.
Voltammetric sensing
Keywords: Electroanalysis

Electrochemical analysis using mercury electrodes has been a prominent methodology since the beginning of voltammetry, however, due to its toxic nature their use is being slowly phased out in favour of environmentally friendlier alternatives. In this thesis, carbon electrodes feature heavily as a means to provide a cheaper and non-toxic approach to voltammmetric sensing. Pulse techniques have been used for the sensitive detection of commonly studied analytes, including antimony and iron.
A simple fabrication of a vibrating electrode is presented by modifying a commercially available vibrating toothbrush with platinum foil as a means to enhance mass transport for electroanalytical work.
Finally, pH determination at carbon electrodes is investigated. Carbon electrodes have been proposed as a simple sensor for pH determination by exploiting the pH sensitive nature of surface quinone groups intrinsic within carbon edge-plane like sites. Using this approach, both EPPG and GC electrodes are suggested as new materials for pH determination and can be used in aqueous solutions over the pH range 1.0 to 13.0, as a cheap and simple alternative to the classic glass electrode.
The innate immune effector cell response against HIV-1
Keywords: AIDS
antibody-dependent cellular cytotoxicity
monocytes
neutrophils
HIV
NK cells
Stem Cells
Immunology
neutralising antibody
antibody

Since being identified as the cause of AIDS in 1983, HIV-1 infection has reached pandemic proportions. Despite public awareness about prevention, the growing incidence of HIV-1 infection and the limitations of current antiretroviral therapy underscore the imperative need for a vaccine. Understanding the basis of an immune response that controls infection or provides sterilizing immunity remains a major goal in the search for effective vaccines or immunotherapies. Research into correlates of immunity to HIV-1 have largely focused on CD8+ T cells or neutralising antibodies (NAbs) but to date these responses have not proved effective in containing viral replication in vaccinees who become infected.
Natural killer cells (NKs), monocytes (MCs), and neutrophils (PMNs) are cells of the innate immune system with intrinsic cytotoxic function that can be enhanced by antibodies (Abs) in what is termed antibody-dependent cellular cytotoxicity (ADCC). In my studies I investigated the production of PMNs from human stem cells, the elimination of HIV-1 infected cells by these effector cells, the modulation of cellular cytotoxicity by Ab, and characterized how Abs facilitate a potent ADCC response. I developed a novel flow cytometry assay to measure cytotoxic activity against HIV-1 infected CD4+ T cells. Using this, effector cells were shown to have different cytotoxic capacities which were enhanced by Ab. Comparing ADCC mediated by patient serum revealed that higher levels correlated with IgG binding to infected cells. I observed no correlation between serum-mediated ADCC and markers of disease progression including patient status, viral RNA load, CD4+ T cell count, or NAb titers. The data presented here have implications for acquisition and control of early HIV-1 infection by NKs, MCs, and PMNs prior to activation of an adaptive immune response, at later stages in the presence of HIV-1-specific Abs, and are relevant to vaccine-induced anti- HIV-1 Ab-based effector mechanisms.
Ultra-small open access microcavities for enhancement of the light-matter interaction
Keywords: cavity quantum electrodynamics
microcavities
microcavity
quantum dot
nanocrystal
diamond
nanodiamond

The design, construction and characterisation of a novel, arrayed, open-access optical microcavity is described. Included in this thesis are the precise fabrication details, making use of the focused ion beam. A technique for analysing and optimising the microcavities constructed, making use of an atomic force microscope is also included. Results from the optical characterisation of the fabricated microcavities are presented, including quality factors of around 104, and fitnesses of around 400. The optical analysis then progressed onto coupling colloidal semiconductor nanocrystals to the microcavity modes. This yielded room temperature Purcell enhancements, single particle sensing, and also allowed for the characterisation of a second iteration of cavities. This improved set was shown to achieve fitnesses in excess of 1800 and quality factors with a lower limit of 15000. The optical identification of single NV centres in nanodiamond is discussed, along with the development of an optical apparatus to couple them to microcavities at cryogenic temperatures. Finally several results from finite difference time domain simulations will be presented, showing ultimate mode volumes of less than 0.5 cubic wavelengths are possible for this approach.
The recruitment and selection of young managers by British business 1930-2000
Keywords: graduates
executives
recruitment
selection

A pervasive critique argues that the educational and social background of senior managers, determined largely by recruitment policies and practices, was an important contributor to the relative economic decline of Britain. The current thesis argues that this critique, even in nuanced form, suffers from serious flaws. For example, long term results of recruitment are confused with information on recruitment processes. In fact, corporate performance can only be judged by understanding the challenges that faced companies, and the limits of the options available to them. The objective of the work, then, is to outline the steps sensible recruiters should have taken to secure their needs for bright young entrants, and to describe and measure what in fact happened. Key findings are that: the criteria used by companies to define high-flier entrants – intelligence, certain personal skills, and signs of character - have remained fundamentally unchanged even if emphasis has moved. Business pursued these attributes through proxies, the most important of which was that of educational qualifications. Business was rightly slow, until the 1950s, to recruit graduate entrants because most bright young people did not attend university. Although British peculiarity in terms of non-vocationalism has been exaggerated, a lesser focus on ‘relevant’ qualifications for non-technical positions was not an economic disadvantage. Proxies for personal qualities were less robust but, over time, were replaced by better direct measurement of individual qualities. The solution found in Britain to bring educated young people together with employers through regional and national recruitment institutions, including the graduate milkround, has proven highly successful. The selection of entrants has been approached at least as well as abroad, and notably unreliable tools were avoided. Business obtained an ever growing proportion of young talent, and did so by integrating educated young people from new social strata to an extent unmatched abroad.
Writing for freedom: body, identity and power in Goliarda Sapienza's narrative
Keywords: Goliarda Sapienza
Italian Studies
Literary Criticism
Women Writers

This thesis explores the theme of freedom in Goliarda Sapienza's narrative, focusing in particular on three works: Lettera aperta (1967), L'arte della gioia (1998, posthumous) and Io, Jean Gabin (2010, posthumous). The analysis concentrates on the interplay between body and power in processes of identity formation; the main aspects taken into consideration are gender, sexuality and political ideology, with specific attention to the power involved in human relationships.
This thesis comprises four chapters. The first three develop a close textual analysis of individual works, each one progressing from the exploration of the internal composition of the self to the analysis of identity in its interpersonal and socio-political dimension. The fourth chapter engages with a comparative analysis of the same works’ narrative structures, accounting for the role of writing in the evolution of Sapienza’s narrative.
I identify the pivotal tension of Sapienza's works in the ideal of freedom, and propose to define her narrative as Epicurean and anarchic, characteristics that place it at the intersection of post-structuralist and Marxist-feminist discourses. Overall, I argue in favour of Sapienza's originality and significance within the context of 20th-century Italian literature. I suggest an affinity between Sapienza's works and the literary legacy of Pirandello and Svevo, as well as certain tenets of postmodern fiction, but also a significant difference, concerning the presence of a tension towards agency and subjectivity, extraneous to the trajectory of the modern and postmodern subject.
From a position of marginality and ex-centricity, Sapienza gives voice to a radical aspiration to individual and social transformation, in which writing and literary communication are granted a central role. Her works trace the parable of a strenuous deconstruction of oppressive norms and structures, aimed at retrieving a space of powerful bodily desire, which constitutes the foundation of the process of becoming a subject.
Development of sindbis virus as an oncolytic agent
Keywords: MicroRNA
Virology
Oncolytic
Pharmacokinetics
Virotherapy

The poor stability of most therapeutic viruses in the human bloodstream is a major obstacle in the field of cancer virotherapy, preventing systemic intravenous delivery to treat tumour metastases. Delivery is typically limited by inactivation of virus particles by blood components and rapid scavenging by hepatic phagocytes. Members of the Alphavirus family are exposed to blood during natural infections; as such, we hypothesised that evolutionary pressure may have led to blood stability and clearance kinetics superior to those of other viruses currently in development for use as oncolytic agents.
Sindbis virus is a member of the Alphavirus family that has shown promising anti-cancer activity in pre-clinical models. A concern for the clinical use of Sindbis virus as an anticancer agent is its pathology in humans, known as Pogosta disease. The symptoms of Pogosta disease may be a result of Sindbis virus replication in neuronal, muscle or haematopoietic tissues. Inhibiting virus replication in these tissues could, therefore, alleviate such potential side effects of virotherapy treatment. Introduction of microRNA response elements, perfectly complementary to microRNAs specifically expressed in liver (miR122), neuronal (miR124), muscle (miR133 and miR206) and haematopoietic (miR142-3p) cells, successfully attenuated SV replication in these tissues.
In contrast to all other viruses studied, data presented in this thesis show that Sindbis virus infectivity in vitro is not significantly inhibited by incubation with neat, whole naïve human blood. Despite full infectivity in naïve mouse blood, virus particles were rapidly cleared from the circulation of mice in vivo by the liver. An attempt to decrease the clearance rate by depletion of Kupffer cells through pre-treatment of mice with clodronate liposomes was ineffective. We also explored the use of Sindbis virus packaged in mosquito cells to more closely mimic virus particles exposed to blood in the wild during mosquito mediated transmission, but this also failed to improve virus circulation kinetics in mice. Despite rapid clearance from the circulation, intravenous administration of Sindbis virus had significant anti-cancer efficacy in C57BL/6 mice bearing syngeneic B16F10 metastatic melanomas.
Overall, data presented support our proposed use of Sindbis virus as a systemically delivered oncolytic agent and suggest decreasing the rate of clearance by the liver could dramatically enhance therapeutic outcomes. In addition it is shown that microRNA targeting of Sindbis virus provides a means of alleviating potential side effects of the administration of large virus doses.