The dissertation consists of four separate studies that have focused on different aspects of the relationship between the management of sports related injuries and utilisation of best practices before sports, during sports and after sports-related injuries. Background: Participation in sports has an associated risk of injury which is defined by the type of sport and level of participation. Any injury affects the athletes‘ health status. To mitigate this risk, international sporting organizations provide guidelines, and mandates the proper evaluation and care for athletes before, during and after training or participation in competition. Despite the availability of guidelines describing best medical care practices for managing athletes, inappropriate management practices are reported globally. The barriers to best medical practice vary. While these barriers have been investigated in a variety of sports in developed countries, similar investigations have not been extensively conducted in developing countries, where the demands are different. Therefore, the overall aim of this thesis was to explore barriers to best medical practices in a variety of sports in Uganda. Methodology: The research was conducted as four studies. The first study used a descriptive case study approach. The data were collected on a sample of injured athletes (n=75) from four sports in Uganda (football/soccer, athletics, basketball and rugby) to describe the medical care practices of the sports resource providers. The current prevention, emergency care, intermediate treatment, rehabilitation services and return-to-sports strategies were all documented in a period of six months. The gaps in best practices were observed, and further investigated in the next three studies. Firstly, a validated questionnaire was used to establish the level of knowledge and practices of various components/themes of athletes‘ well-being and best practices among the stakeholders. Secondly, the current standards of the sports arenas and medical and high-performance facilities were examined using a validated checklist. The last study was a semi-structured interview which assessed the available national health care policies to support sports best practice strategies in Uganda Findings: The overall results of the first study showed there was a significant lack of compliance to best medical care practices in all the phases of athletes‘ health care. The barriers to best practice were confirmed as: (i) the lack of adequate knowledge and awareness on various best practice strategies, (ii) the sports and health facilities were below the required standards and, (iii) there were no national health sports care policies to support and facilitate the implementation of best practices in Uganda. Conclusion: (i) A holistic approach may be required to address the best medical care practice barriers in Uganda to improve on the health and safety of athletes. (ii) The knowledge of stakeholders should be improved and awareness created about best medical practices in sports in Uganda. (iii) There is a critical need to develop a national sports health care policy. (iv) The facilities for sports and health care of athletes urgently need improvement and supported.

Whole-Genome Sequencing (WGS) is ushering a new era in healthcare and research in identifying genetic variation in all populations. However, the African populations are still under-represented. Since African populations are being the most genetically diverse with high heterogeneity rate, we need to benchmark the Whole Genome Sequence (WGS) analysis pipeline to ensure reliable mutation detection. Therefore, it is essential to ensure that all steps of WGS downstream analysis are accurate, mainly the variant calling (VC). Current VC tools may produce falsepositive/negative results; such result may produce misleading conclusions in prioritisation of mutation, clinical relevancy and actionability of genes. With such many VC tools, two questions have arisen. Firstly, which tool has a high rate of sensitivity and precision in low either high coverage African sequences, given they have high genetic diversity and heterogeneity? Secondly, does the improvement of the VC result will advance the accuracy of detecting mutation and incidental finding (actionable genes) in African populations? In this project, a total of 100 DNA sequence samples was simulated (of which every 50 samples mimicked the genetics background of African and European, respectively) at different coverage (high and low). In particular, the sensitivity to discover polymorphisms was done by nine different VC tools. These tools were assessed in term of false positive/negative call rate given the simulated golden variants. Combining our result on sensitivity and positive predictive value (PPV). Lofreq performs best in African population data (sens=0.85, PPV=0.983, F-score=0.91) on high/low coverage data; as a result, we chose Lofreq to perform variant calling, and Gene-based annotation is performed to conduct in-sillico predication of mutation on publicly available data (the African Genome Variation and 1000 Genome Project). In doing so, we have leveraged WGS to examine and validate four of burden diseases in the African content, such as communicable diseases: HIV/AIDS, Malaria, Tuberculosis (TB), and Non-communicable diseases: such as Sickle cell disease, these diseases have uniquely shaped ethnic-specific and continental genomics variation and therefore provides unprecedented opportunities to map disease genes across the African continent. Moreover, the current actionable gene recommended by The American College of Medical Genetics and Genomics (ACMG) in the African population and update on additional African-specific actionable genes. Our result suggests African and African diaspora ethnic groups, particularly Bantu and Khoesan ethnics have gene diversity, high proportion of derived allele at low minor allele frequency (0.0 − 01) and the highest proportion of pathogenic variants within HIV, TB, Malaria, Sickle-Cell disease, while non-African ethnic groups including Latin America, Afro-Asiatic European related ethnic groups have high proportion of pathogenic variants within current actionable gene list. Overall, given the observed highest genetic diversity found in African ethnics and African diaspora related ethnics at these four Africa burden diseases and current actionable gene associated, our results support (1) the use of personalised medicine as beneficial to both African continent and worldwide; (2) a recommendation for African-specific actionable list of genes to further improve African and diaspora healthcare.

Huntington disease (HD) is a devastating neurodegenerative condition characterised by a triad of symptoms: behavioural/psychiatric changes, cognitive decline and movement disorder. The dominantly inherited disease-causing mutation is an expanded trinucleotide (CAG) repeat in the Huntingtin(HTT) gene. Clinical symptoms are believed to be the result of degeneration of specific neuronal populations that are susceptible to the presence of a toxic expanded protein product. The disease is incurable and following the onset of symptoms, is progressively debilitating over 10-20 years and eventually fatal. Although typical epidemiological studies of prevalence are challenging for a genetic disorder such as HD, family studies and various other methods of ascertainment have been used to estimate its occurrence in different populations. Prevalence is therefore known to vary geographically; population-specific haplotypes have been hypothesised to be the basis of this variation between ethnic groups. High prevalence estimates for populations with European ancestry led to the supposition that the HD mutation was introduced to different regions by Europeans. In South Africa, a survey in the 1970s estimated that the prevalence of HD in the white and coloured subpopulations was similar at 2 per 100 000 individuals; while that in the black subpopulation was significantly lower, at less than 0.01 per 100 000 individuals. Molecular genetic analyses have since revealed links between the white and coloured subpopulations which would explain the similarity in prevalence; however, our knowledge of the genetics of HD in the black subpopulation, has been sorely lacking. This study provides, for the first time, a comprehensive analysis of the HTT gene in an African population. An evaluation of the normal distribution of CAG-tract sizes highlighted significant differences between the subpopulations. Haplotype analysis identified population-specific disease-associated haplotypes, confirming distinct origins of the HD mutation in the different subpopulations. In a coloured family with the rare juvenile form of the disease, DNA sequencing revealed no novel variants within the immediate vicinity of the CAG-tract that could be associated with the observed instability. This indicates that genome-wide analyses may be more useful in identifying factors related to repeat instability and future investigations are planned for a cohort of South African patients affected by juvenile onset HD.

Sickle Cell Disease (SCD) is a growing global problem with firm roots in sub-Saharan Africa (SSA) representing over 3/4 of the global burden of the disease. The prevalence of the sickle mutation (HbS) in SSA has been amplified by the partial resistance to Plasmodium falciparum malaria, which is endemic along tropical equatorial Africa. Several genetic variants have since been associated with fetal hemoglobin (HbF), the disease-ameliorating globin protein, including variants at three principal loci; BCL11A, HBS1L-MYB intergenic polymorphisms (HMIP1/2) and the β-globin gene cluster, which together account for 10 - 20% HbF variance in SCD patients. Similarly, numerous signalling pathways have been implicated in the regulation of γ-globin expression, however, a complete understanding of the regulation of HbF remains elusive. The overall aims of this project were: 1a) to investigate the known variants in key HbF-promoting loci such as BCL11A erythroid-specific enhancer, BCL11A, HBS1L-MYB intergenic polymorphism (HMIP1/2), the β-globin gene cluster, as well as the influence of the co-inheritance of 3.7kb alpha globin gene deletion in a cohort of SCD patients from Cameroon; and 1b) to validate novel HbF-promoting loci reported in 2 genome-wide association studies (GWAS) carried out in a population of Sardinians (Italy) and SCD patients from Tanzania and explore the influence of known promoter variants in SAR1 associated with HbF in African American patients amongst Cameroonian SCD patients; 2) to investigate the molecular mechanisms of hydroxyurea (HU)-induced production of HbF using a primary erythroid cell model from hematopoietic stem cells (HSCs) derived from umbilical cord blood and lastly, 3) to investigate the prevalence of SCD-related polymorphisms; β-globin gene haplotype, HbS mutation and malaria-resistance variants in 3 SCD-unaffected (HbAA) cohorts from South Africa, Zimbabwe and Malawi.

Mental retardation (MR) is a handicap with severe implications not only for thosethat suffer from this disability, but also for their families, society and the welfaresystems which support them. A large proportion of these individuals are afflictedwith the X-linked form of the condition. To date a total of 87 genes have beenimplicated in the pathogenesis of X-linked mental retardation (XLMR).

TBX3, a member of the developmentally important T-box transcription factor family, has been shown to be overexpressed and to behave as an oncogene in several cancers. Much of this work has, however, been performed in carcinomas of epithelial origin and little is known about the role ofTBX3 in sarcomas of mesenchymal origin. This study provides novel evidence to show that TBX3protein, but not mRNA, is upregulated in a number of transformed fibroblast and fibrosarcoma cell lines of mesenchymal origin. Fibro sarcoma is an aggressive soft-tissue sarcoma derived from fibroblasts and, while it occurs very rarely, there are no targeted therapy approaches and survival rates remain low. More work is clearly needed to characterise the molecular mechanisms involved infibrosarcoma development, to allow for more effective treatments to be identified. This study, therefore, aimed firstly to determine the role of TBX3 in transformed fibroblast and fibrosarcoma cells; secondly to investigate the signalling pathways responsible for the upregulation of TBX3; and lastly to identify target genes which mediate the role of TBX3 in these cells. To determine the function of TBX3 in transformed fibroblast and fibro sarcoma cells, cell culture models were generated in which TBX3 was stably knocked down in transformed CT-1 cells, as well as the naturally occurring aggressive HT1080 cell line, and the effect on key features of oncogenesis determined. In both cell lines, a substantial decrease in in vitro cell proliferation, measured using growth curve and BrdU incorporation assays, anchorage independence, measured using soft-agar assays, and migration, measured using scratch and transwell migration assays, was observed. Importantly, the knockdown of TBX3 was also able to significantly increase the in vivo tumour forming ability of HT1080 cells in a mouse model. A TBX3 overexpression cell culture model was also generated in the HT1080 cells and, despite their aggressive nature, increased TBX3 expression resulted in a reduced oncogenic phenotype, including markedly decreased in vivo tumour formation. These results were unexpected and demonstrate for the first time that TBX3 behaves as a tumour suppressor in transformed fibroblast and fibro sarcoma cells, suggesting it may function as either oncoprotein or tumour suppressor depending on cellular context. [Please note: the thesis file has been deferred until June 2018]

After anterior cruciate ligament reconstruction (ACL-R), persistent strength and biomechanical deviations remain. Reducing these by training may reduce risk of re-injury or osteoarthritis for these patients. A cross-sectional study investigated biomechanics of ACL-R male patients long-term (~5 years) post surgery. Fifteen ACL-R and fifteen healthy controls were tested in walking and running using motion capture. Devi- ations were found, primarily between-limbs, and also between groups. Largest deviations were lower knee angles and moments in the affected limb during running. However, these were not found during walking; thus, differences were highlighted by the higher-intensity task. During running, knee abduction moment was lower (more valgus) for the affected compared to unaffected and control limbs. The larger effects in moment show greater clinical potential than knee valgus angle. The ACL-R patients had lower impact foot strike during running than controls. The above results indicate chronic, clinical changes in joint loading. A randomised controlled intervention trial evaluated progressive eccentric cycling for ACL-R males, compared to concentric controls. This is one of the first trials of eccentric vs. concentric training for ACL-R, matched by rating of perceived exertion. Twenty-six adult males, 12 weeks post hamstring-graft ACL-R trained three times/week for 8 weeks under supervision. During training the eccentric group limb powers absorbed were higher than those produced by the concentric group, with a lower heart rate. For both groups, pain scores were low, and one of the patient-reported outcomes (IKDC) improved. Hamstring strength increased in the eccentric group by 15%, but this was not seen in the concentric group. For both groups, 60°/s quadriceps strength increased by a similar amount, approximately 28%. Biomechanically, eccentric training was more effective than matched concen- tric training at resolving knee (P=0.022, walk) and hip (P =0.010, run) flexion angle deviations in the affected limb. In both groups, knee extension moments increased, reducing asymmetries. Large knee abduction moment deviations at baseline were not reduced by either programme (P >0.05). At follow-up (~6 months), both groups showed similar return-to-sports progress; several patients passed using one criterion (IKDC), and none passed using a stricter four-criteria method (Univ. Delaware). Thus it can be concluded that for adult ACL-R males, eccentric cycle training is clinically acceptable, with similar or in some cases better outcomes than concentric cycle training. It improves patient-reported outcomes, strength recovery, biomechanical deviations, and return-to-sports measures.

In population groups where subjects do not lie still during Magnetic Resonance Spectroscopy (MRS) scans, real-time volume of interest (VOI), frequency, and main magnetic field (B0) shim correction may be necessary. This work demonstrates firstly that head movement causes significant B0 disruption in both single voxel spectroscopy and spectroscopic imaging.

Includes abstract.~Includes bibliographical references. / The first part of this thesis examines issues in the processing and analysis of continuous wave functional linear infrared spectroscopy (fNIRS) of the brain usung the DYNOT system. In the second part, the same sensorimotor experiment is carried out using functional magnetic resonance imaging (fMRI) and near infrared spectroscopy in eleven of the same subjects, to establish whether similar results can be obtained at the group level with each modality. Various techniques for motion artefact removal in fNIRS are compared. Imaging channels with negligible distance between source and detector are used to detect subject motion, and in data sets containing deliberate motion artefacts, independent component analysis and multiple-channel regression are found to improve the signal-to-noise ratio.

Executive function (EF), that shows rapid development in the preschool years, is foundational for cognitive development. Previous research has found aspects of physical development including gross motor skills and physical activity to be related to EF. However, evidence for these relationships in the preschool years, as well as in low- and middle-income countries is lacking. Therefore, this study aimed to investigate the relationships between EF (and related components of cognitive development) with physical activity and gross motor skills (GMS) in a sample of preschool children from urban and rural low-income settings in South Africa. Cognitive and physical outcomes were measured in a sample of preschool children (N=129; Mage = 50.7±8.3 months; 52.7% girls) from urban (Soweto) and rural (Bushbuckridge) low-income settings in South Africa. Cognitive components included EF, self-regulation (Early Years Toolbox, EYT), attention (adapted visual search task) and school readiness (Early Childhood Development Criteria Test). Physical outcomes included objectively measured physical activity (accelerometry), gross motor skills (Test for Gross Motor Development 2) and anthropometric measurements (height and weight). On average, children from both settings showed higher than expected scores for EF and self-regulation (based on Australian norms for the EYT), adequate gross motor proficiency and high volumes of physical activity (M total physical = 476 minutes per day). In contrast, a high proportion of children, particularly in the rural setting, demonstrated below average scores for school readiness. Investigations into the relationships revealed that EF was positively associated with self-regulation, attention and school readiness. Positive associations were also found between GMS and physical activity and, and physical activity and body mass index (BMI). And finally, that GMS, but not physical activity, was positively associated with all components of cognitive development. This study is the first to provide evidence for the importance of EF and the link between motor and cognitive development in preschool children from South African, low-income settings. Another key finding was that there may be factors promoting early EF skills in these settings but that these skills, although associated, are not transferring to school readiness. The lack of (or negative) associations between physical activity and cognition presents another key finding, further research is needed to identify whether there are specific amounts and types of physical activity that specifically benefit cognitive development.