Accelerated cell line development and improved characterisation of lentiviral vector production through application of MALDI-ToF mass spectrometry and multivariate data analysis.

Ph. D. Thesis.Several cell and gene therapies will be commercially launched within the next few years using lentiviral vectors as the gene delivery vehicle. Oxford BioMedica’s Lentivector® platform is an advanced lentiviral-based gene delivery system designed for improved safety and efficacy. The growing interest in these vectors has created a strong demand for large scale production of lentiviral vectors as well as for development of packaging and producer cell lines. This EngD project used a combination of matrix assisted laser desorption ionisation time of flight mass spectrometry (MALDI-ToF MS) and multivariate data analysis (MVDA) to analyse cell and lentiviral vector samples. A comparison between mass spectra of samples produced across small and large scale in adherent and suspension culture was used to identify what aspects of the manufacturing process had the biggest impact on cell and vector variation. Principal component analysis was applied to compare different lentiviral vector production methods, assess data structure of the process parameters and examine whole cell and vector mass spectrometry data. This approach led to improved characterisation of lentiviral vectors and HEK293T cells. It demonstrated the capability to differentiate between adherent and suspension cells as well as cell lines of different levels of performance as defined by lentiviral vector infectious titre. Partial least squares discriminant analysis (PLS-DA) was used to calibrate and validate a predictive model of cell line performance based on mass spectrometry and viral vector titre data obtained from multiple HEK293T cell lines. PLS-DA model validation resulted in 87.5% accuracy in classification of cell lines as high or low producers based on a discrimination threshold determined by viral vector titre. The results of PLS-DA modelling indicated that this method can be used for accurate cell line performance prediction, accelerating cell line development by several weeks, improving cell selection and reducing campaign timelines.EPSR

NPM, e-government and the modernization of public services in the Sultanate of Oman

PhD ThesisThis thesis critically examines the development and implementation of e-government projects in the Sultanate of Oman after 2003 when the government published its intention, in the spirit of new public management (NPM), to raise the quality and performance of key public services. At the core of the research is a comparative analysis of five in-depth case studies of representative service modernization projects driven by the introduction of new information systems. The goal of the research is to evaluate the performance of NPM inspired projects in Oman to learn lessons that might lead to beneficial changes in future policy and practice. The study considers inter alia the goals and strategy of the Omani government, the selections and design of modernization projects, problems of execution and obstacles to change, and the reasons for differing degrees of success achieved in meeting project objectives. The five case studies of Omani e-government modernization projects were developed mainly from interviews conducted with officials in government departments at different levels of management and managers directly responsible for project design and implementation. Further interviews with experts and policymakers focused on government strategy, policymaking and project monitoring. These interviews were especially important in locating the five case studies in a wider strategic, cultural and historical context. Documentary evidence was gathered whenever possible on individual projects and on government’s strategic plans and policies. Taken together, the researcher accumulated a large and rich collection of data sources, which were analyzed taking a bottom up, inductive, grounded theoretical approach, enabling the researcher to develop fresh theoretical perspectives, interpretations and practical recommendations. The study is the first to document, analyse and evaluate the modernization of public services in Oman, and one of few to examine in-depth the adoption of NPM methods in developing countries. Lack of financial resources, failure to define appropriate measures of individual and organizational performance and lack of interest in training were found to be the main reasons limiting the success of projects. From a comparative perspective, however, degrees of success varied considerably, highlighting that proper planning, project management and training invariably paid dividends, explaining differences in outcomes. Finally, the research extends our theoretical understanding of NPM projects in developing countries, highlighting the importance of feasibility studies and stakeholder participation in formulating public sector improvement policies

The Intersection of Entrepreneurial Identity and Ethnic Identity: An Interpretative Phenomenological Analysis of Black African Migrant Entrepreneurs in the UK

Ph. D. ThesisRecently, entrepreneurship research is beginning to identify how identity shapes the practice and discourse of entrepreneurship. This burgeoning stream of research explores how multiple dimensions of identity intersect, to create and reproduce inequality in entrepreneurship. This study builds on such area of research to explore the role of identity in entrepreneurship. In particular, it explores the intersection of entrepreneurial identity and ethnic identity among black African migrants practising entrepreneurship in Britain. The research focuses on the question: ‘how do black African migrant entrepreneurs balance, negotiate and experience their (potentially disparate) identities as ‘entrepreneurs’ and ‘ethnic minorities’ within their lives?’ Qualitative data was elicited by phenomenologically exploring the narratives of the lived experiences of participants. The analysis is based on the different ways black migrant entrepreneurs perceive, interpret and make sense of their identity in entrepreneurship. Research findings show the pervasiveness of whiteness in entrepreneurship. The entrepreneurial space in Britain structurally excludes black ethnic identity. Structural forces that create and sustain inequality in the labour market are also at play in entrepreneurship. Entrepreneurship is a site of identity negotiation. To navigate this entrepreneurial space, they employed different dramaturgical performances and enacted certain identity work such as hard work and different masking strategies, in their attempt to be seen as legitimate entrepreneurial actors. Ethnicity plays different roles in entrepreneurship. It is perceived as a source of advantage for exploring ethnic and co-ethnic markets and as a source of disadvantage for accessing mainstream markets in the host country. Findings show the gendered nature of identity work, as black female migrant entrepreneurs tend to compensate more for their identity in entrepreneurship. This research contributes to the study of migrant entrepreneurship by showing how intersectional identities influence entrepreneurial venturing and activities.Newcastle University Overseas Research Scholarshi

Bilingual Code Switching Patterns in Libyan Arabic-English School-Aged Children: A Study of Linguistic and Communicative Competence

Ph. D. Thesis.The aim of this study was to investigate language use in school-aged Arabic-English bilingual children growing up in the UK. Specifically, the main focus was to examine how bilingual children’s linguistic and communicative competence is reflected through their use of code switching in their interactions with other bilingual speakers. 30 children of Libyan families living aged between 8 and 11 were recruited for this study and were audio recorded while interacting with their friends in a Libyan Arabic school context, and with members of their families at home. Standardized language tests in both languages and sociolinguistic questionnaires were used to measure language competence, language use and the social context underpinning the children’s language development. All the children had been living in the UK since their early childhood and were fluent in both languages but were English-dominant. All of the parents had good command of English and positive attitudes towards their children’s bilingualism but preferred their children to use Arabic at home. Analyses of the children’s code switches revealed advanced levels of linguistic and communicative competence. This was exhibited through the children’s ability to alternate between the two codes without violating their syntactic or morphological constraints; it also showed in the way the children capitalized on their combined repertoire to index particular social and/or pragmatic motivations during their interactions with their interlocutors, enhancing their communicative strategies. The study makes an original contribution to the grammatical study of code switching, presenting results from two languages rarely looked at in combination; it also adds to existing research demonstrating the positive contribution of CS to bilingual discourse strategies.Libyan Ministry of Higher Educatio

The balance between predators and prey in a mixed seabird colony: managing biodiversity and the conservation of rare species

Ph. D. ThesisIncreases in seabird population sizes on islands, resulting from reduced mortality and/or increased reproductivity, has resulted from the control of avian predators when predation was confirmed to be the main driver of seabird decline. A substantial conflict in conservation management arises when the control operation targets a protected predator. Tensions and divisions between regulators and conservation managers can be exacerbated when the prey species is of high conservation concern. This latter situation underpins this research study based on Coquet Island, UK, where the core of conservation management is targeted at mitigating predation on Roseate Tern (RT) by breeding Large Gulls (LG), represented by Lesser Blackbacked Gull Larus fuscus (LBBGU) and Herring Gull L. argentatus (HGU). In recent years, the conservation status of HGU has changed to red and LBBGU to Amber categories in the light of increasing concern of notable decline for unknown reasons in the UK. Hence, it is important to have evidence on which to base management strategies for conserving Roseate Terns which minimises the conservation conflicts between prey and predators, all of which are of conservation concern. A complete understanding of predator-prey relationships relies on determining the dynamic stability of prey and predator populations, and how the food web containing predator-prey pairs responds to environmental influences and other indirect effects. This research investigates the main drivers of LG predation activity over the RT colony during the breeding season. A particular dilemma in estimating the impact of predation by breeding LG on the Coquet Island RT colony resulted from the presence of loafing LG, either non-breeding subadult birds or birds from other colonies, using the intertidal area around the island. Therefore, to test the hypothesis that LG breeding on the island also used the island’s seabird colonies as a foraging resource, indirect (Camera traps and dietary analysis of LG pellets) and direct (Observation of predation activity, foraging range estimation from tracking technologies) methods were used. The results of this study suggest that the frequency of LG events over the RT colony increased towards the end of the breeding season in relation to the number of loafing LG in the intertidal area, and was influenced by tidal state and decreased during the period of RT chick biomass availability. This study provided evidence that LG breeding on the island also used the reserve as part of their foraging territory. The outputs of the tracking data were compatible with the outputs of the pellet analyses which showed a high utilization of available prey from the reserve. LG on Coquet Island utilizing all types of prey sources with no difference between of breeding or roosting LG with respect to the range of prey types. Indirect evidence that LG predation would be a threat to the small colony of RT was based on the finding that other tern species nesting on Coquet Island were identified using combined molecular and morphological techniques as prey in LG pellets collected from the breeding and roosting LG on Coquet Island. In addition, a study of laser hazing carried out as part of the thesis work shows that this is an efficient non-lethal deterrent for LG management on Coquet Island. Overall, the results of this study provide evidence showing how small numbers of LG may be allowed to breed on Coquet Island by managing the timing of their breeding in relation to the arrival and breeding of RT, and by efficient deterrence of loafing, non-breeding birds. Such an approach will facilitate a wider understanding of how to resolve conservation conflicts between protected predator and protected prey species.LIFE programm

Revitalising intra-party democracy through digital democratic innovations : the case of Danish political party Alternative

PhD ThesisIn light of increasing concern about the democratic recession spreading across established representative democracies this PhD explores how digital democratic innovations are used in emerging political parties, to involve members and supporters directly in intra-party policy formation and decision-making. This is explored through a case study of Danish political party Alternativet, which constitutes a recent example of an emerging political party that claims to promote and practice new and inclusive ways of doing politics, experimenting with digital technologies for this purpose. In this respect the case of Alternativet illustrates a larger trend of what has been labelled connective parties (Bennett et al., 2017) or movement parties (Porta et al., 2017) by other authors. As with many of these parties, Alternativet experienced electoral success relatively quickly and has been represented in parliament since 2015, and in several local councils since 2017. Thus, Alternativet, like similar emerging parties, is an attempt to combine democratic innovations with party politics and traditional political institutions in liberal representative democracies. This is interesting considering how democratic innovations are often conceptualised in contrast to classic representative political institutions. Both democratic innovations and Internet technologies have promised, but struggled to deliver, an increase and deepening of citizen participation in democratic decision making. While they have demonstrated that they can engage citizens in political questions, it has been a particular challenge to turn engagement into impact on final political decisions. These decisions are usually taken in decision-making fora dominated by political parties, such as governments, parliaments and local councils. So connective parties, such as Alternativet, posses a potential ability to provide consequentiality to citizen participation by combining democratic innovations with party politics. However, so far insufficient attention has been given to the kind of (re-invigorated) democracy these parties promote, and what kind of participation the digital platforms they use facilitate. This thesis address exactly those questions. The study employs a mixed methods approach, combining semi-structured interviews and participant observation with a party member survey. Interviews with key stakeholders in the party and participant observations during a two months visit at the party’s national secretariat are used to explore how and why the party uses digital tools to engage party members and supporters in policy formation and decision-making. This includes the motivation to engage members actively in policy formation in the first place. Based on this, the thesis identifies four dimensions of intra-party democracy promoted by the party elite: An aggregative crowd sourcing dimension, a deliberative dimension, a developmental dimension, and a more traditional delegation dimension. Each of the (many) digital platforms used in the party have affordances that speak to each of these dimensions. A survey distributed among party members and supporters is then used to explore the support for each of these four dimensions of intra-party democracy. This data indicates that support for intra-party democracy among the party supporters can reasonably be considered along the same four dimensions. These findings are significant for our understanding of the role both democratic innovations and political parties can play in revitalising democracy

Probing the dye-semiconductor interface in NiO based p-type dye sensitized solar cells using BODIPY

Ph. D. Thesis.A significant portion of the scientific community is focused on developing new approaches to fulfilling the energy demands of a growing population, whilst also minimising the damage to the environment. Chemistry has played a vital role in developing new molecular systems to turn solar energy into electricity. Dye-sensitized solar cells (DSSC) have gained significant attention by offering a versatile and tuneable molecular system as a promising alternative to traditional silicon devices. Single junction devices usually based around an n-type TiO2 photoanode can be improved by pairing with a p-type photocathode to create a tandem device, which could potentially surpass the Shockley- Queisser limit of solar energy conversion over a single p-n junction. Although most of the research on DSSC focusses on TiO2 based systems, improving the performance of the p-type photocathode is required in order to approach a tandem DSSC which outperforms the TiO2 photoanode. A series of BODIPY sensitizers with small structural modifications to the core of the chromophore were prepared by various synthetic pathways to create a robust and reliable system with different photophysical and electrochemical properties with which to investigate the underlying electron transfer pathways in p-type NiO DSSC. The properties of these dyes were studied using steady state UV-Visible and Fluorescence spectroscopy and coupled with cyclic voltammetry in order to create an energy level map of the system. Although all three dyes appeared to have sufficient driving force for electron injection from the VB on NiO into the HOMO of the dye, the three dyes showed modest performance which appeared to be limited by the efficient regeneration of the dye by the redox electrolyte. BOD2 showed the most promising results when used in a working p-type device (JSC = 0.48 mA cm2) however these results did not agree with the calculated driving force for injection ( Ginj therefore the dye|semiconductor interface was studied using X-ray Photoelectron Spectroscopy (XPS) to create a new map of the energy levels inside the p-DSSC. Inspection of the valence photoelectron spectra at varied X-ray excitation energy allowed for probing of the energy levels in both the bulk semiconductor and at the dye|semiconductor interface. The HOMO energies for all three dyes adsorbed onto NiO were measured experimentally and these results confirm a shift in Fermi level for the NiO upon dye adsorption. These results predict that BOD2 had the highest Ginj and the frontier orbitals of BOD2 were the most well placed to encourage efficient electron transfer between the dye and semiconductor. Femtosecond Transient Absorption Spectroscopy (fs-TAS) was utilized to study the kinetics of the electron transfer processes within the p-type device. Interestingly, the lifetime of the reduced dye appears to be increased in the presence of a redox electrolyte and we postulate this to result from catalytic activity of surface trap states NiO catalysing the conversion of Iodide to triiodide and deactivating a recombination pathway in the p-DSSC. This has implications on future design of dyes for p-type DSSC and outlines new methods on estimating driving forces for electron transfer within a p-DSSC.Newcastle Universit

Essays in option market liquidity

Ph. D. Thesis.This study investigates equity option market liquidity with different aspects of the bid-ask spread, open interest, and trading volume in the US. We find a newly discovered determinant of option liquidity: excess cash (that is, the level of cash reserve in excess of what can be captured by firm characteristics) after accounting for underlying stock liquidity. We display evidence that an increase of 1% in excess cash holding leads to a 0.58% reduction in option bid-ask spread, 0.28% increase in open interest, and 0.26% increase in trading volume. We also demonstrate that there is a significantly positive linkage between stock and equity option market liquidity. The results show that funding liquidity is a liquidity supplier of their market liquidity linkages. Stocks with a higher probability of informed trading or facing greater short-selling pressures register a significant reduction in the stock-equity option market liquidity interactions. What is more, we analyse the effects of option market liquidity on stock price crash risk. We find that the magnitude of crash risk will increase when the companies with a higher trading volume and open interests of the options, while the option bid-ask spread will decrease market crashes

Constraining Models of Collective Motion in Biological Systems

PhD ThesisAnimals moving together as one is a commonly seen spectacle in both the sky, with flocks of birds, and in the oceans, with school of fish. Mathematical models have been developed over the last 50 years to gain a deeper understanding into how such coordination occurs or to recreate the behaviour digitally. There has been extensive numerical simulation and analysis done for these models but little comparison to actual data. This is due to the complexity of obtaining high quality data suitable for analysis. We were able take advantage of lightweight high definition cameras and drone technology to collect footage of collective behaviours. In this thesis we describe a computer vision algorithm we devised to detect and track individual sheep in the drone footage we collected. The algorithm emphasises the differences in the colours of the sheep and the grass background in order to locate the sheep. It then tracks the individuals throughout the video. In total the trajectories of 45 or more sheep were extracted from 14 videos ranging from 150 frames to 593 frames. In some of these videos the quadbike and farmers herding the sheep were also tracked. From these trajectories we were able to extract quantities such as average speed and global alignment which can then be used to compare to simulated data. We describe a number of models from the literature which aim to reproduce the types of behaviours we observed in our sheep flocks and some of these we expand on to make them include new features such as allowing agents speeds to change or allow agents to interact with a predator whist in an enclosed area. We go on to compare our observational data to two different types of these models. The first of these was a family of models which were able to replicate the emergent flocking behaviour seen in some of the observations. The second was a model able to simulate data to compare to our observations of “steady-state” flocking as well as being able to include the movement of the quadbike or farmer herding the animals. We will compare our observational data to simulated data using an approximate Bayesian computation rejection scheme to calculate an approximate joint posterior distribution for the parameters in each of the models. The parameters of these models were sampled from a Latin hypercube meaning we are able to cover the full parameter space efficiently

Longitudinal changes following acute brain injuries

PhD ThesisAlthough it is known the human brain can recover after a brain lesion, the response mechanisms of recovery are not yet fully understood. Using longitudinal data, our aim was first to characterise the ways in which brain networks change after an acute brain lesion either as a result of trauma/insult or following brain surgery. Secondly, we investigated if those changes are associated with recovery or disease progression. In this thesis, we analyse longitudinal structural changes in mild TBI, and epilepsy patients following temporal lobe resection using graph theory and connectometry. Alterations in brain structure were later related with cognitive recovery or seizure freedom using regression models. In addition, we analysed longitudinal, functional changes following moderate to severe TBI using clustering algorithms. We investigated the network flexibility over functional connectivity patterns/states by calculating the entropy of time spent in these states. Shifts in entropy were compared with longitudinal white matter integrity and blood biomarkers using linear models. In patients who underwent temporal lobe resection, we found alterations in structural connectivity and in the density of anisotropic diffusing water over time. Some of the observed changes were related with seizure freedom. Similarly, we found that a set of alterations in structural connectivity following mild TBI were related with changes in cognitive trajectory. When investigating longitudinal functional changes in moderate to severe TBI patients, we found a set of cognitive functional connectivity patterns. Changes in entropy after TBI were related to alterations in the concentration of plasma tau. Our studies suggest that early alterations in brain structure and function occur following acute brain lesions such as TBI or those as result of temporal lobe resection. While some of these alterations are the result of the injury itself in the network, other alterations may be a result of brain reorganisation and promote patient recovery