Induction of plasticity in subcortical structures and its application in spinal cord injury

Ph. D. ThesisMost current non-invasive plasticity protocols target the motor cortex and its corticospinal projections. Approaches for inducing plasticity in sub-cortical circuits and alternative descending pathways such as the reticulospinal tract (RST) are less well developed. The overall aim of this thesis was to gain a better understanding of the extent to which corticospinal transmissions are altered after spinal cord injury (SCI) and to explore the mechanisms of non-invasive stimulation protocols at the cortical and subcortical level. In the first study, transcranial magnetic stimulation was used to elicit motor-evoked potentials (MEPs) in the biceps brachii using different coil orientations, which allows for preferential activation of different neural elements. Analysis of MEP latencies suggests that differences between MEPs elicited by specific coil orientations may not be fully preserved in humans with cervical SCI, both in the biceps and in more distal muscle groups. In a second study, we developed a novel associative stimulation paradigm, which paired loud acoustic stimuli with transcranial magnetic stimulation over the motor cortex in healthy participants and observed enhanced motor output after stimulus pairing ended. Electrophysiological measurements in humans and direct measurements in monkeys undergoing a similar protocol implicate corticoreticular connections as the most likely substrate for the plastic changes. Finally, we used a custom built device to deliver precisely paired auditory clicks with electric stimulation to the muscle. We observed changes in electrophysiological measurements consistent with the induction of sub-cortical plasticity in the biceps muscle. We then used the same protocol to target the triceps muscle in individuals with SCI over the course of 4 weeks. Notably, we did not observe the same changes as in the biceps muscle, suggesting that elbow flexors and extensors have a different potential for plasticity, perhaps due to a differential control of flexor and extensor motoneurons by corticospinal and reticulospinal pathways.International Spinal Research Trus

Quantification of the demands of elite rugby union players and understanding the subsequent physiological and epigenetic responses : b an applied approach towards prescription and individualisation

Phd ThesisThe development of effective training load monitoring tools has enabled key insights into elite rugby union players' training and game demands and significantly improved the physical management of players. Whilst the use of training load quantification methods is common practice in elite sport, in the scientific literature, little information is known about the training and periodisation strategies of professional rugby union clubs, and how this may change throughout a competitive season. Throughout a season, coaches and practitioners face frequent decisions on daily training sessions, team selection, and competition scheduling. Understanding the load imposed on players from training and competition informs and aids this decision making. These decisions are integral to the optimisation of repeated player performance throughout a season. Diagnostic tools provide another piece of the puzzle to support player management decisions. The integration of both diagnostic measures and workload quantification aids the understanding of the dose-response relationship between fatigue and physiological adaptation. Building an effective individualised training load monitoring system is key within an elite rugby union club. Currently, practitioners are exposed to vast amounts of information that can be collected on individual athletes, slowing and limiting the ability to make effective choices on players’ health and performance. There is a need to synthesise this process and optimise athlete monitoring without creating additional staff and player burden. This thesis aimed to explore the multitude of factors that may influence the optimisation of elite rugby union players and explored the reasons for variation between individual players. The first part of this thesis quantified the external training load demands throughout a competitive season and evaluated the stress-induced effects of acute and chronic rugby training and match-play. Data from Chapter 4 demonstrated a strategical variation in training load prescription throughout a competitive season and showed key differences in external load metrics between position and the match status of players. Chapter 5 assessed changes in performance measures, biomarkers and subjective wellness throughout a full professional season. Certain periods of the season reported significant deviations from baseline measures and associations were observed between GPS variables and measures of performance and biomarkers. iv The second part of the thesis explored novel circulating miRNA (ci-miRNA) biomarkers and their role in the observed variation between players in response to training. Chapter 6 revealed associations between specific ci-miRNAs and anthropometric and performance variables that are consistent with the current understanding of plausible biological mechanisms. Lastly, Chapter 7 revealed the variability in training-induced responses to preseason training and, reported associations between certain baseline ci-miRNA levels with the observed anthropometric and strength changes. In summary, this thesis emphasises that even within a team sport, managing individual players is crucial to optimising performance; a one size fits all approach is not appropriate. A consistent and effective monitoring system needs to observe both external load and measures of fatigue, in order to inform and support the decision making of practitioners. Additionally, there is a great potential for the use of epigenetic information to inform practitioners of player management processes. However, this research in an elite sport setting is very much in its infancy and caution should be taken trying to implement this strategy

Evaluation of salivary sirtuin 2 as a novel biomarker for periodontitis

PhD ThesisSIRT2 is an NAD-dependent histone deacetylase (HDAC) that is involved in the regulation of gene expression and protein function. This study aimed to evaluate SIRT2 as a salivary biomarker for periodontitis and investigate any association between SIRT2 and the inflammatory processes relevant to periodontitis. Immune responses were investigated in vitro using THP1 monocytes differentiated into macrophages using phorbol 12-myristate 13-acetate (PMA) and stimulated with TLR2 or TLR4 agonists. Analysis using qPCR and western blotting showed there were no significant changes to SIRT2 mRNA or intracellular protein expression respectively after stimulation with TLR agonists. Secreted SIRT2 levels measured by ELISA were significantly elevated after stimulation with TLR2 agonists but not after stimulation with TLR4 agonists. TLR agonists had no effect on SIRT2 deacetylation activity in macrophages. Inhibition experiments in macrophages showed that SIRT2 regulates secretion of TNFα, IL-6, IL-8, and IL-1β as measured by ELISA. Multiple regression analysis (ANCOVA) showed that SIRT2 was significantly elevated in periodontitis when accounting for the influence of age but SIRT2 levels did not correlate with clinical measurements of periodontitis such as bleeding on probing and pocket depth. Receiver operating characteristic (ROC) curve analysis showed that salivary SIRT2 could detect periodontitis with a high degree of sensitivity and specificity (AUC 89%). In summary, SIRT2 levels accurately represent the presence of periodontitis, but do not correlate with clinical measures of periodontitis, which may limit its utility as a diagnostic biomarker. We have demonstrated a novel TLR2-mediated pathway of SIRT2 secretion from THP1-derived macrophages which may explain the elevated levels of SIRT2 present in the saliva of patients with periodontitis but will require further investigation. We have also shown that SIRT2 mediates the secretion of pro-inflammatory cytokines after stimulation with TLR agonists which may be of relevance to the pathogenesis of periodontitis

The discursive mythological construction of the Muslim Brotherhood and their foes: The case of the Arabic and English news articles of Al-Jazeera

IPhD ThesisDrawing on Kelsey’s discourse-mythological approach (2015c) to critical discourse studies, the project at hand aims to examine the extent to which the discursive construction of mythology appears to impact the online portrayals of the Muslim Brotherhood Party and their opponents between the Arabic and English websites of Al-Jazeera. In conducting this research, a corpus of straight news reports and opinion articles covering the period between the ousting of President Muḥammad Mursī (Mohammed Morsi) on 3rd July 2013, until the end of 2014, was collected, downsized, and analysed. The analysis included the usage of two supplementary approaches, one of which is thematic analysis, and the other is a manual analysis technique that was, specifically, improvised for the purpose of the study. Al-Jazeera Arabic (AJA) is argued to have always been broadcasting to the support and sympathy of Islamist parties, including the MB (Sakr, 1999; Cherribi, 2006; Dabbous-Sensenig, 2006; Al-Najjar, 2009, p. 3; Al-Qassemi, 2012; Kessler, 2012; Mellor and Rinnawi, 2016; Seib, 2016; Obaid, 2020). Following the transfer of power in 2013, the majority of AJA journalists are said to have viewed the MB as victims and that it is “the moral duty” of Al-Jazeera to stand up for them (Mellor and Rinnawi, 2016, p. 276). It has been the long argument of critical discourse analysts that different news outlets construct different social realities (Fowler, 1991; Trew, 1991). Putting the MB into the equation, the study seeks to understand whether or not such an argument still holds true between the two sites of the same news provider, Al-Jazeera. More importantly, the study pays specific attention to the practice of mythological storytelling, the extent to which it impacts the narratives on both sites in a similar and different manner. Although the Arabic and English articles across the two sites seem to agree on defending MB and attacking their opponents, each site, however, appears to construct the choice of mythical narratives in line with the social and cultural values of the target audience, resonating more with their collective psyche. Moreover, Al-Jazeera appears to be more inclined towards attacking the anti-MB social actors than defending the MB. Interestingly, such a case appears to be more evident in Arabic data as opposed to the English ones, and even more so with opinion articles than it is the case with straight news stories. Indeed, approaching the study of news through the lens of mythology, storytelling, and narratives has been witnessing a mounting interest by scholars over the past three decades (Bird and Dardenne, 2009; Wahl-Jorgensen and Schmidt, 2020). Nonetheless, its application seems to have been mostly restricted to the analysis of monolingual news discourse. Moreover, Arabic languages, among others, still did not receive enough attention (if anything at all). Therefore, this examination is hoped to provide some insights as to the potential implication of mythological analysis in the context of bilingual news discourse, which includes Arabic, among other languages. Moreover, the application of mythological analysis in news may help in gaining more insights as to the manipulative nature of mythological storytelling and how it is used aesthetically in news discourse, the likes of which Al-Jazeera is known for stirring and mobilising emotions. Keywords: Critical discourse analysis; mythology; archetypes; narratives; storytelling; media discourse; online news; media representation; identity construction; cross-linguistic CDA; religious discourse; aesthetics; journalism; Islamism; politic

Regulation of ribosome biogenesis in health and disease

PhD ThesisRibosome biogenesis is one of the most energy consuming and regulated cellular processes. Due to the fundamental importance of ribosomes in cellular biology, it is unsurprising that defects in their biogenesis are linked to a range of human disorders, termed ribosomopathies. This project aimed to investigate different mechanisms through which ribosome production is regulated in relation to health and disease. When ribosome biogenesis is defective, the 5S RNP, a large subunit (LSU) assembly intermediate, accumulates, activating the tumour suppressor p53 through inhibition of its regulator. Unexpectedly, small subunit (SSU) production defects also activate p53 through the 5S RNP. In this study, SSU production defects were found to activate p53 early and in the absence of changes in mature SSU levels, contrary to previous research. SSU production defects result in impaired export of the pre-LSU and reduced levels of the late, cytoplasmic pre-5.8S ribosomal RNA. This implies that defective SSU production activates p53 through stalling the late stages of LSU maturation. Ribosomal proteins are produced in excess and are protected from aggregation by chaperones. RPL3 and its dedicated chaperone GRWD1 were both shown to be required to produce the LSU and SSU and were both shown to bind a novel inhibitor of ribosome biogenesis, C8ORF33. The GRWD1 binding site of RPL3 is required for this interaction and is required for ribosome production. These proteins had different but diverging roles during ribosome production and may be involved in regulatory mechanisms. The chaperone binding site of RPL3 is highly conserved between humans and yeast except for serine residues in humans that have been reported as phosphorylation sites. Phosphorylation offers a mechanism through which protein functions can be modified to diversify cellular responses. However, such modifications do not impact GRWD1 binding but are linked to minor changes in pre-ribosomal RNA processing.MR

The application and impact of a public health intervention supported by a speech and language therapist in the early years foundation stage

PhD ThesisIntroduction Prevalence estimates indicate up to 50% of children in areas of social deprivation have speech, language and communication needs (SLCN). Three-tiered service delivery models are widely recommended to support early communication, however there are few studies examining the effectiveness of entire multi-tiered systems of support (MTSS). This thesis presents a longitudinal evaluation of a locally developed MTSS, with two overarching aims: 1) evaluating the impact of inclusion in this MTSS on vocabulary growth, and 2) exploring how children with differing SLCN move through the MTSS. Method Data about SLC skills, EYFS attainment and social deprivation were collected for 409 participants attending a cluster of school-based nurseries over two years. Participants were within the control cohort (n=165), the experimental cohort (n=128), or the controlexperimental cohort (n=116). Staff received training and support to implement the MTSS. Data were analysed to explore distinct patterns through the MTSS. Longitudinal multi-level modelling was used to explore vocabulary growth and the impact of the MTSS. Results Participants followed three distinct pathways: universal tier only, specialist tier only, or multiple tiers over time. At nursery entry, 100% of participants were below age related expectations for communication (EYFS) and the mean standard score for receptive vocabulary (BPVS) was M = 84.9 (SD = 12.2) (n=181). Participants accessing the MTSS gained 2.42 (p<0.05) additional standard score points per term completed in the MTSS. Those entering nursery with the lowest vocabulary scores, made the most rapid progress (intercept –slope covariance -0.70). Discussion These results indicate that MTSS within schools can have a positive impact on children’s vocabulary development. Children entering nursery with the most significant needs can be supported to begin to close the gap and it is crucial that the universal tier of support is more than simply ‘business as usual’

Investigation of human C12orf65 and mtRF1, members of the mitochondria translation release factor family

PhD ThesisMitochondria contain their own DNA (mtDNA) and protein synthesis machinery. Human mtDNA encodes for two rRNAs, 22 tRNAs and 13 polypeptides. Those polypeptides are subunits of complexes involved in oxidative phosphorylation and their translation is driven by the mitoribosome. Translation consists of four phases - initiation, elongation, termination and mitoribosome recycling- with translation factors required at each step. My work focused on termination, which requires the action of release factors. In human mitochondria, there are four proteins in the release factor family: mRF1a, ICT1, mtRF1 and C12orf65. Termination occurs once a release factor recognises a stop codon (UAA or UAG) in the A site of the mitoribosome. This changes the mitoribosome conformation, inducing the polypeptide’s release. Only mtRF1a recognizes stop codons and terminates translation for all the 13 mtDNA-encoded polypeptides. However, all four members contain the GGQ motif involved in peptide release. ICT1 is a component of the mitoribosome large subunit. My research focused on the functions of mtRF1 and C12orf65 which are yet unknown, although it was observed that patients with C12orf65 pathogenic variants show impaired mitochondria translation. My research hypothesis was that C12orf65 and mtRF1 initiate termination in mitoribosomes that stall during translation. Stalling has multiple causes including mRNA pseudoknot structures, defective tRNA or insufficient amino acids. Release factors would recognise mRNA targets to the same effect as stop codons. To test this, I aimed to identify mRNA targets specific to mtRF1. I also aimed to detect proteins C12orf65 interacted with to confirm whether it was involved in termination. I used cross-linking and immunoprecipitation of the mitoribosome, BioID2 and CRISPR-Cas9 techniques. Thus, I obtained and characterized two BioID2 cell lines that helped locate C12orf65 interactors involved in translation. Moreover, I established a C12orf65 knockout cell line that presents a growth defect, further demonstrating C12orf65’s involvement in cell viability.European Union’s Horizon 2020 research and innovation programm

Subcritical Behaviour in Rotating Convection and Convectively-Driven Dynamos

PhD ThesisIn planets and stars, convection is thought to be key for generating and maintaining largescale magnetic fields. Many planets possess a hydromagnetic dynamo driven by convective motions, such as the geodynamo. However, a number of smaller planetary bodies, such as Mars, show evidence of once possessing a dynamo that suddenly ceased to exist. One suggested cause for the sudden cessation of the Martian dynamo is that it was operating in a subcritical parameter regime, that is, the dynamo continued to exist when its controlling parameter decreased below the critical value for linear onset, before eventually collapsing towards the non-magnetic trivial state. This thesis aims to explore subcritical behaviour in dynamo action and convection in order to better understand the dynamic processes that affect planetary dynamos. In the first part of this thesis, we focus upon the simpler problem of rotating convection in the absence of a magnetic field. In two-dimensional rotating convection, localised states, known as ‘convectons’, have previously been observed for moderate rotation rates. Convectons are associated with systematic shear flows which locally reduce the inhibiting nature of rotation on convection, potentially promoting subcritical behaviour. We study convectons in 2D Boussinesq convection in a rotating plane layer and perform parametric surveys in both a fully-truncated model with restricted symmetries, and a model where the full horizontal structure is allowed. We successfully obtain rotating convectons for rapid rotation and explore their bifurcation structure, stability and key features. In particular, we show that convectons are typically associated with a full local reduction in the effective rotation. In the second part of this thesis, we study dynamo action using 3D numerical simulations of planar Boussinesq convection at rapid rotation, focussing again on subcritical behaviour. We first generate a large-scale magnetic field in the supercritical regime that significantly influences convective motions. Subcritical solutions are then found by tracking this solution branch into the subcritical regime. Here the dynamo is sustained for convective driving below the critical value for the linear onset of non-magnetic convection. We show that increasing rotation leads to an extension of the subcritical range to an optimal value. At more rapid rotation, subcriticality is then hampered by the emergence of a large-scale convective mode. The inability of the large-scale mode to sustain dynamo action leads to an intermittent behaviour that appears to inhibit subcriticality. Finally, we study the key parameter regimes at which subcritical dynamos exist, such as an optimal magnetic Reynolds number

Citizen participation, collective action and digital media: Seeking spatial justice in Manizales, Colombia

Ph. D. Thesis.This thesis explores the possibilities and limitations of citizen participation and collective action for spatial justice across the online and offline spaces of the everyday. It uses the case study of Manizales, Colombia; a city that proclaims itself as innovative, socially inclusive and participatory. Two hypotheses informed the research design. One, that despite city’s efforts on digital innovation, local government in Manizales had yet to use the collaborative potential of digital media, in order to improve participatory and collaborative processes of city-making. And two, that there are significant differences in the perceptions from local government and social collectives, about the transforming potential of collective action and digital media uses for inclusion and participation. Consequently, the research questions explore the relationships between governmental initiatives and the everyday life of socio-territorial movements seeking spatial justice, as well as the ways in which citizens mobilise, the local roles of digital media in collective action, and the implications of the findings to transform debates about spatial justice in Manizales and beyond. Drawing on five months of place-based participant observation in Manizales, a year and a half of netnographic exercises (online participant observation), complemented by interviews and perception exercises, the thesis provides an empirical analysis that is grounded in the everyday processes of city-making, from the formal protocols to the informal and alternative. Three socio-territorial movements in the city served as the sub-cases of study, which included several individuals and collectives that became crucial participants in this research. Overall, this thesis highlights the importance of understanding local socio-political contexts in relation to processes and efforts around digital innovation for participation and collective action. Additionally, it argues that the expansion of urban planning, as a practice that embraces and makes the most of the chaos of participation – both online and offline, requires recognition and integration of city-making practices outside of hegemonic structures of power. Moreover, the findings reveal a case of urban contestation as an exercise of transgressive, rather than insurgent citizenship, which can enrich current debates about the Right to the City and practical approaches towards data and spatial justice in the city.Research Excellency Academy, School of Architecture Planning and Landscape at Newcastle Universit

Spatial optimisation for resilient infrastructure services

Ph. D. Thesis.Infrastructure networks provide crucial services to the functioning of human settlements. Extreme weather events, especially flooding, can lead to disruption or complete loss of these crucial infrastructure services, which can have significant impacts on people’s health and wellbeing, as well as being costly to repair. Urban areas concentrate infrastructure and people, and are consequently particularly sensitive to disruptions due to natural (and human-made) disasters. Flooding alone constituted 47% of all weather-related disasters between 1995 and 2015, causing enormous loss of lives and economic damages. Climate change is projected to further exacerbate the impacts that natural disasters have on cities. Choices about where to site infrastructure have a significant impact on the impacts of extreme weather events. For example, investments in flood risk management have typically focussed on prioritising interventions to protect people, houses and businesses. Protection of infrastructure services has either been a bonus benefit of flood defence protection of property, or been implemented by individual infrastructure operators. Spatial planning is a key process to influence the distribution of people and activities over broad spatial scales. However, decision-making processes to locate infrastructure services does not typically consider resilience issues at broad spatial scales which can lead to inefficient use of resources. Moreover, spatial planning typically requires consideration of multiple, sometimes competing, objectives with solutions that are not readily tractable. Balancing multiple trade-offs in spatial planning with multiple variables at high spatial resolution is computationally demanding. This research has developed a new framework for multi-objective Pareto-optimal location-allocation problems solving. The RAO (Resource Allocation Optimisation) framework developed here is a heuristic approach that makes use of a Genetic Algorithm (GA) to produce Pareto-optimal spatial plans that balance a typical tradeoff in spatial planning: the maximisation of accessibility of a given infrastructure service vs the minimisation of the costs of providing that service. The method is applied to two case studies: (i) Storage of temporary flood defences, and (ii) Location of healthcare facilities. The RAO is first applied to a flood risk management case study in the Humber Estuary, UK, to optimise the strategic allocation of storing space for emergency resources (like temporary flood barriers, portable generators, pumps etc.) by maximising the accessibility of warehouses (i.e. minimising travel times from storing locations to deployment sites) and minimising costs. The evaluation of costs involves both capital and operational costs such as the length of temporary defences needed, storage site locations, number of lorries and personnel to enable their deployment, and maintenance costs. A baseline is tested against a number of scenarios, including a flood disrupting road network and thereby deployment operations, as well as variable infrastructure and land use costs, different transportation and deployment strategies and changing the priority of protecting different critical infrastructures. Key findings show investment in strategically located warehouses decreases deployment time across the whole region by several hours, while prioritising the protection of the infrastructure assets serving larger shares of population can cut costs by 30%. Moreover, the analysis of the ensemble of all scenarios provides crucial insights for spatial planners. For example, storage sites in Hull or Hedon, and in the areas of Withernsea and Drax are robust choices under all scenarios. Meanwhile, the Humber Bridge is shown to play a crucial role in enabling regional coverage of temporary barriers. The second case study shows how emergency response strategies can be enhanced by optimal allocation of healthcare facilities at a regional scale. The RAO framework allocates healthcare facilities in Northland (New Zealand) balancing the trade-off between maximisation of accessibility (i.e. minimisation of travel times between households and GP clinics) and minimisation of costs (i.e. number of clinics and doctors). Results show how c.80% of Northland’s population lives within a 20 minutes drive from the closest GP, but this can be increased to 90% with strategic investment and relocation of doctors and clinics. By accounting for flood and landslide risk, the RAO is used to identify strategies that improve accessibility to healthcare services by up to 5% even during extreme events (when compared to the current business as usual service accessibility). Application to these two problems demonstrates that the RAO framework can identify optimal strategies to deploy finite resources to maximise the resilience of infrastructure services. Moreover, it provides an analytical appreciation of the sensitivity between planning tradeoffs and therefore the overall robustness of a strategy to uncertainty. The method is consequently of benefit to local authorities, infrastructure operators and agencies responsible for disaster management. Following successful application to regional scale case studies, it is recommended that future work scale the analysis to consider resource allocation to protect infrastructure at a national scaleEngineering and Physical Sciences Research Counci