Children's daily travel to school in Johannesburg-Soweto, South Africa: geography and school choice in the Birth to Twenty cohort study

This paper has two aims: to explore approaches to the measurement of children’s daily travel to school in a context of limited geospatial data availability, and to provide data regarding school choice and distance travelled to school in Soweto-Johannesburg, South Africa. The paper makes use of data from the Birth to Twenty cohort study (n=1428) to explore three different approaches to estimating school choice and travel to school. Firstly, straight-line distance between home and school is calculated. Secondly, census geography is used to determine whether a child's home and school fall in the same area. Thirdly, distance data are used to determine whether a child attends the nearest school. Each of these approaches highlights a different aspect of mobility, and all provide valuable data. Overall, primary school aged children in Soweto-Johannesburg are shown to be travelling substantial distances to school on a daily basis. Over a third travel more than 3km, one-way, to school, 60% attend schools outside of the suburb in which they live, and only 18% attend their nearest school. These data provide evidence for high levels of school choice in Johannesburg-Soweto, and that families and children are making substantial investments in pursuit of high quality educational opportunities. Additionally, these data suggest that two patterns of school choice are evident: one pattern involving travel of substantial distances and requiring a higher level of financial investment, and a second pattern, involving choice between more local schools, requiring less travel and a more limited financial investment

The development of computational biology in South Africa: successes achieved and lessons learnt

Bioinformatics is now a critical skill in many research and commercial environments as biological data are increasing in both size and complexity. South African researchers recognized this need in the mid-1990s and responded by working with the government as well as international bodies to develop initiatives to build bioinformatics capacity in the country. Significant injections of support from these bodies provided a springboard for the establishment of computational biology units at multiple universities throughout the country, which took on teaching, basic research and support roles. Several challenges were encountered, for example with unreliability of funding, lack of skills, and lack of infrastructure. However, the bioinformatics community worked together to overcome these, and South Africa is now arguably the leading country in bioinformatics on the African continent. Here we discuss how the discipline developed in the country, highlighting the challenges, successes, and lessons learnt

Prevalence of DDC genotypes in patients with aromatic L-amino acid decarboxylase (AADC) deficiency and in silico prediction of structural protein changes

Aromatic L-amino acid decarboxylase (AADC) deficiency is a rare autosomal recessive genetic disorder affecting the biosynthesis of dopamine, a precursor of both norepinephrine and epinephrine, and serotonin. Diagnosis is based on the analysis of CSF or plasma metabolites, AADC activity in plasma and genetic testing for variants in the DDC gene. The exact prevalence of AADC deficiency, the number of patients, and the variant and genotype prevalence are not known. Here, we present the DDC variant (n = 143) and genotype (n = 151) prevalence of 348 patients with AADC deficiency, 121 of whom were previously not reported. In addition, we report 26 new DDC variants, classify them according to the ACMG/AMP/ACGS recommendations for pathogenicity and score them based on the predicted structural effect. The splice variant c.714+4A>T, with a founder effect in Taiwan and China, was the most common variant (allele frequency = 32.4%), and c.[714+4A>T];[714+4A>T] was the most common genotype (genotype frequency = 21.3%). Approximately 90% of genotypes had variants classified as pathogenic or likely pathogenic, while 7% had one VUS allele and 3% had two VUS alleles. Only one benign variant was reported. Homozygous and compound heterozygous genotypes were interpreted in terms of AADC protein and categorized as: i) devoid of full-length AADC, ii) bearing one type of AADC homodimeric variant or iii) producing an AADC protein population composed of two homodimeric and one heterodimeric variant. Based on structural features, a score was attributed for all homodimers, and a tentative prediction was advanced for the heterodimer. Almost all AADC protein variants were pathogenic or likely pathogenic

Prevalence of DDC genotypes in patients with aromatic L-amino acid decarboxylase (AADC) deficiency and in silico prediction of structural protein changes

Aromatic L-amino acid decarboxylase (AADC) deficiency is a rare autosomal recessive genetic disorder affecting the biosynthesis of dopamine, a precursor of both norepinephrine and epinephrine, and serotonin. Diagnosis is based on the analysis of CSF or plasma metabolites, AADC activity in plasma and genetic testing for variants in the DDC gene. The exact prevalence of AADC deficiency, the number of patients, and the variant and genotype prevalence are not known. Here, we present the DDC variant (n = 143) and genotype (n = 151) prevalence of 348 patients with AADC deficiency, 121 of whom were previously not reported. In addition, we report 26 new DDC variants, classify them according to the ACMG/AMP/ACGS recommendations for pathogenicity and score them based on the predicted structural effect. The splice variant c.714+4A>T, with a founder effect in Taiwan and China, was the most common variant (allele frequency = 32.4%), and c.[714+4A>T];[714+4A>T] was the most common genotype (genotype frequency = 21.3%). Approximately 90% of genotypes had variants classified as pathogenic or likely pathogenic, while 7% had one VUS allele and 3% had two VUS alleles. Only one benign variant was reported. Homozygous and compound heterozygous genotypes were interpreted in terms of AADC protein and categorized as: i) devoid of full-length AADC, ii) bearing one type of AADC homodimeric variant or iii) producing an AADC protein population composed of two homodimeric and one heterodimeric variant. Based on structural features, a score was attributed for all homodimers, and a tentative prediction was advanced for the heterodimer. Almost all AADC protein variants were pathogenic or likely pathogenic

The impact of educational attainment on household poverty in South Africa: A case study of Limpopo province

Poverty is a phenomenon that is multidimensional in nature and its meaning varies from one individual to another (Alkire and Foster 2011; Batana 2013; Bossert, Chakravarty, and D'Ambrosio 2013; Jansen et al. 2015). It can be seen as a failure to attain certain capabilities, absolute or relative,2 or a lack of income to meet a certain standard of living in a given society (Jansen et al. 2015). It can be chronic or temporary3, is often linked with underdevelopment, economic exclusion and vulnerabilities, and sometimes closely correlated with inequality (Mbuli 2008; Van der Berg 2008; Jansen et al. 2015). The definition of poverty employed determines its measurement

Biallelic MED27 variants lead to variable ponto-cerebello-lental degeneration with movement disorders.

MED27 is a subunit of the Mediator multiprotein complex, which is involved in transcriptional regulation. Biallelic MED27 variants have recently been suggested to be responsible for an autosomal recessive neurodevelopmental disorder with spasticity, cataracts and cerebellar hypoplasia. We further delineate the clinical phenotype of MED27-related disease by characterizing the clinical and radiological features of 57 affected individuals from 30 unrelated families with biallelic MED27 variants. Using exome sequencing and extensive international genetic data sharing, 39 unpublished affected individuals from 18 independent families with biallelic missense variants in MED27 have been identified (29 females, mean age at last follow-up 17 ± 12.4 years, range 0.1-45). Follow-up and hitherto unreported clinical features were obtained from the published 12 families. Brain MRI scans from 34 cases were reviewed. MED27-related disease manifests as a broad phenotypic continuum ranging from developmental and epileptic-dyskinetic encephalopathy to variable neurodevelopmental disorder with movement abnormalities. It is characterized by mild to profound global developmental delay/intellectual disability (100%), bilateral cataracts (89%), infantile hypotonia (74%), microcephaly (62%), gait ataxia (63%), dystonia (61%), variably combined with epilepsy (50%), limb spasticity (51%), facial dysmorphism (38%) and death before reaching adulthood (16%). Brain MRI revealed cerebellar atrophy (100%), white matter volume loss (76.4%), pontine hypoplasia (47.2%) and basal ganglia atrophy with signal alterations (44.4%). Previously unreported 39 affected individuals had seven homozygous pathogenic missense MED27 variants, five of which were recurrent. An emerging genotype-phenotype correlation was observed. This study provides a comprehensive clinical-radiological description of MED27-related disease, establishes genotype-phenotype and clinical-radiological correlations and suggests a differential diagnosis with syndromes of cerebello-lental neurodegeneration and other subtypes of 'neuro-MEDopathies'

The origins and rise of the Victorian brown coal industry 1835-1935

© 1966 Andrew D. SpaullThis history thesis was written at a time when the Victorian brown coal industry approaches its jubilee. It is also a period when the industry, together with the power and fuel industry, faces a new era of challenge and expansion. With this in mind, I have attempted to analyse, firstly, the various forces behind the establishment of a brown coal industry. Often these forces have been neglected or taken for granted, generally on the basis, that here was an expensive mineral resource open for exploitation. This particular reasoning is far from accurate, as I will attempt to show by a detailed study of the course and tempo of developments before the formal establishment of the industry. The second concern has been an attempt to capture and assess the problems of the industry in its gradual rise to the eventual position of a modern and vital Victorian industry