Scielo RSS <![CDATA[South African Journal of Science]]> http://www.scielo.org.za/rss.php?pid=0038-235320190002&lang= vol. 115 num. 3-4 lang. <![CDATA[SciELO Logo]]> http://www.scielo.org.za/img/en/fbpelogp.gif http://www.scielo.org.za <![CDATA[<b>Time to say...</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532019000200001&lng=&nrm=iso&tlng= <![CDATA[<b>State of African research: Snapshot of abstracts for the 2018 Women in Science Without Borders indaba</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532019000200002&lng=&nrm=iso&tlng= <![CDATA[<b>'Gender shouldn't matter because we are all scientists here': A narration of the panel discussion at the 2nd International Women in Science Without Borders conference</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532019000200003&lng=&nrm=iso&tlng= <![CDATA[<b>A global approach to the gender gap in mathematical, computing and natural sciences: How to measure it, how to reduce it?</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532019000200004&lng=&nrm=iso&tlng= <![CDATA[<b>A gender perspective on career challenges experienced by African scientists</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532019000200005&lng=&nrm=iso&tlng= Empirical knowledge of the career challenges that confront African scientists, and women scientists in particular, holds an important key to achieving future success in the science systems of the continent. In this article, we address a lack of evidence generally on the careers of scientists in Africa, by providing the first continent-wide description of the challenges they face, and how these challenges differ between women and men. Our analysis of questionnaire-survey data on approximately 5000 African scientists from 30 countries shows that women are not more challenged than men by a variety of career-related issues, with the exception of balancing work and family, which the majority of women, regardless of age and region, experience. Contrary to expectations, women are not only less likely than men to report a lack of funding as having impacted negatively on their careers, but have been more successful at raising research funding in the health sciences, social sciences and humanities. These results, as well as those from a comparison of women according to age and region, are linked to existing scholarship, which leads us to recommend priorities for future interventions aimed at effectively ensuring the equal and productive participation of women in the science systems of Africa. These priorities are addressing women's work-family role conflict; job security among younger women scientists; and women in North African and Western African countriesSignificance: •This study is the first to describe, on a multinational scale, the career challenges that confront African scientists, and women scientists in particular. •Contrary to expectations, we found that African women scientists do not report experiencing career challenges to a larger extent than men do, and have been more successful at raising research funding in three of the six major scientific fields. •However, the findings highlight the significance of the challenge that balancing work and family poses to the majority of African women scientists <![CDATA[<b>Assessing the potential effects of nevirapine in South African surface water on fish growth: A chronic exposure of <i>Oreochromis mossambicus</i></b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532019000200006&lng=&nrm=iso&tlng= Aquatic environments around the world have become mixtures of different types of pollutants, including pharmaceuticals. The presence of pharmaceuticals in aquatic environments has raised concerns regarding the possibility of unintended effects on aquatic animals. South Africa is currently the largest consumer of HIV antiretroviral drugs (ARVs) worldwide. Nevirapine (NVP), a first-line ARV, has been associated with serious liver toxicity in humans and has been repeatedly detected in South African surface water. We investigated the potential effect of NVP on the growth of larvae and juveniles of the Mozambique tilapia (Oreochromis mossambicus) through a chronic laboratory exposure. Larval and early juvenile stages were exposed to the highest reported environmental relevant concentration of NVP in South African surface water (1.48 µg/L) for 60 days in a static renewal system. Body mass and total length measurements were recorded and analysed for individuals aged 1, 5, 30 and 60 days. In total, 455 fish were assessed. The growth parameters of larvae exposed to NVP were not statistically significantly different (p>0.05) from those of control larvae. However, the juveniles exposed to NVP showed a slightly lower mean growth rate between the 30th and 60th day compared with the control fish. These results suggest that the concentration of NVP in South African surface water has no significant detrimental effects on fish growth during the first 2 months of their life. Further studies to investigate the effects on all life stages of fish are needed as it is evident that the growth rate of exposed fish could be affected after this stage.Significance: •This study was the first to investigate the effect of an antiretroviral drug in surface water on fish growth. •Chronic exposure to the highest environmentally relevant concentration of nevirapine in South African waters did not affect the growth of early life stages of Mozambique tilapia. •The levels of antiretrovirals in aquatic systems should be monitored closely as their consumption is likely to increase in the future <![CDATA[<b>Reclassification of early stage breast cancer into treatment groups by combining the use of immunohistochemistry and microarray analysis</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532019000200007&lng=&nrm=iso&tlng= Immunohistochemistry (IHC) is routinely used to approximate breast cancer intrinsic subtypes, which were initially discovered by microarray analysis. However, IHC assessment of oestrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor-2 (HER2) status, is a poor surrogate of molecular subtype. Therefore, MammaPrint/BluePrint (MP/BP) microarray gene expression profiling is increasingly used to stratify breast cancer patients into different treatment groups. In this study, ER/PR status, as reported by standard IHC and single-gene mRNA analysis using TargetPrint, was compared with molecular subtyping to evaluate the combined use of MP/BP in South African breast cancer patients. Pathological information of 74 ER/PR positive, HER2 negative tumours from 73 patients who underwent microarray testing, were extracted from a central breast cancer genomics database. The IHC level was standardised by multiplying the intensity score (0-3) by the reported proportion of positively stained nuclei, giving a score of 0-300. Comparison between mRNA levels and IHC determination of ER/PR status demonstrated a significant correlation (p<0.001) for both receptors (ER: 0.34 and PR: 0.54). Concordance was shown in 61 (82%) cases and discordance in 13 (18%) of the 74 tumours tested. Further stratification by MP/BP identified 49 (66.2%) Luminal A, 21 (28.4%) Luminal B and 4 (5.4%) Basal-like tumours. Neither IHC nor TargetPrint could substitute BP subtyping, which measures the functional integrity of ER and can identify patients with false-positive tumours who are resistant to hormone therapy. These findings support the implementation of a pathology-supported genetic testing approach combining IHC and microarray gene profiling for definitive prognostic and predictive treatment decision-making in patients with early stage breast cancer.Significance: •Single-gene genomic oestrogen and progesterone receptor reporting adds limited additional information to the molecular stratification of breast cancer tumours and does not supersede the immunohistochemistry results. •Neither single-gene genomic mRNA nor immunohistochemistry reporting of oestrogen and progesterone receptor status can replace the combined use of MammaPrint/BluePrint genomic molecular subtyping. •Reliable distinction between Luminal A and B type tumours is not possible using immunohistochemistry or single-gene genomic mRNA assessment of oestrogen/progesterone and HER2 receptor status. •Combining immunohistochemistry and microarray gene profiling enables the identification of endocrine treatment resistant hormone-positive tumours lacking ERα function (Basal-like), despite positive expression at the protein and single-gene RNA level <![CDATA[<b>Parental care or opportunism in South African Triassic cynodonts?</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532019000200008&lng=&nrm=iso&tlng= Immunohistochemistry (IHC) is routinely used to approximate breast cancer intrinsic subtypes, which were initially discovered by microarray analysis. However, IHC assessment of oestrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor-2 (HER2) status, is a poor surrogate of molecular subtype. Therefore, MammaPrint/BluePrint (MP/BP) microarray gene expression profiling is increasingly used to stratify breast cancer patients into different treatment groups. In this study, ER/PR status, as reported by standard IHC and single-gene mRNA analysis using TargetPrint, was compared with molecular subtyping to evaluate the combined use of MP/BP in South African breast cancer patients. Pathological information of 74 ER/PR positive, HER2 negative tumours from 73 patients who underwent microarray testing, were extracted from a central breast cancer genomics database. The IHC level was standardised by multiplying the intensity score (0-3) by the reported proportion of positively stained nuclei, giving a score of 0-300. Comparison between mRNA levels and IHC determination of ER/PR status demonstrated a significant correlation (p<0.001) for both receptors (ER: 0.34 and PR: 0.54). Concordance was shown in 61 (82%) cases and discordance in 13 (18%) of the 74 tumours tested. Further stratification by MP/BP identified 49 (66.2%) Luminal A, 21 (28.4%) Luminal B and 4 (5.4%) Basal-like tumours. Neither IHC nor TargetPrint could substitute BP subtyping, which measures the functional integrity of ER and can identify patients with false-positive tumours who are resistant to hormone therapy. These findings support the implementation of a pathology-supported genetic testing approach combining IHC and microarray gene profiling for definitive prognostic and predictive treatment decision-making in patients with early stage breast cancer.Significance: •Single-gene genomic oestrogen and progesterone receptor reporting adds limited additional information to the molecular stratification of breast cancer tumours and does not supersede the immunohistochemistry results. •Neither single-gene genomic mRNA nor immunohistochemistry reporting of oestrogen and progesterone receptor status can replace the combined use of MammaPrint/BluePrint genomic molecular subtyping. •Reliable distinction between Luminal A and B type tumours is not possible using immunohistochemistry or single-gene genomic mRNA assessment of oestrogen/progesterone and HER2 receptor status. •Combining immunohistochemistry and microarray gene profiling enables the identification of endocrine treatment resistant hormone-positive tumours lacking ERα function (Basal-like), despite positive expression at the protein and single-gene RNA level <![CDATA[<b>Alpha and sigma taxonomy of <i>Lystrosaurus murrayi </i>and <i>L. declivis</i>, Triassic dicynodonts (Therapsida) from the Karoo Basin, South Africa</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532019000200009&lng=&nrm=iso&tlng= Immunohistochemistry (IHC) is routinely used to approximate breast cancer intrinsic subtypes, which were initially discovered by microarray analysis. However, IHC assessment of oestrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor-2 (HER2) status, is a poor surrogate of molecular subtype. Therefore, MammaPrint/BluePrint (MP/BP) microarray gene expression profiling is increasingly used to stratify breast cancer patients into different treatment groups. In this study, ER/PR status, as reported by standard IHC and single-gene mRNA analysis using TargetPrint, was compared with molecular subtyping to evaluate the combined use of MP/BP in South African breast cancer patients. Pathological information of 74 ER/PR positive, HER2 negative tumours from 73 patients who underwent microarray testing, were extracted from a central breast cancer genomics database. The IHC level was standardised by multiplying the intensity score (0-3) by the reported proportion of positively stained nuclei, giving a score of 0-300. Comparison between mRNA levels and IHC determination of ER/PR status demonstrated a significant correlation (p<0.001) for both receptors (ER: 0.34 and PR: 0.54). Concordance was shown in 61 (82%) cases and discordance in 13 (18%) of the 74 tumours tested. Further stratification by MP/BP identified 49 (66.2%) Luminal A, 21 (28.4%) Luminal B and 4 (5.4%) Basal-like tumours. Neither IHC nor TargetPrint could substitute BP subtyping, which measures the functional integrity of ER and can identify patients with false-positive tumours who are resistant to hormone therapy. These findings support the implementation of a pathology-supported genetic testing approach combining IHC and microarray gene profiling for definitive prognostic and predictive treatment decision-making in patients with early stage breast cancer.Significance: •Single-gene genomic oestrogen and progesterone receptor reporting adds limited additional information to the molecular stratification of breast cancer tumours and does not supersede the immunohistochemistry results. •Neither single-gene genomic mRNA nor immunohistochemistry reporting of oestrogen and progesterone receptor status can replace the combined use of MammaPrint/BluePrint genomic molecular subtyping. •Reliable distinction between Luminal A and B type tumours is not possible using immunohistochemistry or single-gene genomic mRNA assessment of oestrogen/progesterone and HER2 receptor status. •Combining immunohistochemistry and microarray gene profiling enables the identification of endocrine treatment resistant hormone-positive tumours lacking ERα function (Basal-like), despite positive expression at the protein and single-gene RNA level <![CDATA[<b>In search of a place in history for mathematics: A lecture series in South Africa</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532019000200010&lng=&nrm=iso&tlng= This Commentary was invited by the South African Journal of Science and emanates from a seminar presented by Dr Tomoko Kitagawa entitled 'The History of Mathematics: An Interdisciplinary Work in Humanities' given at the Department of Historical and Heritage Studies of the University of Pretoria on 20 September 2018. Dr Kitagawa received her PhD from Princeton University and went on to teach history at Harvard University. Prior to her appointment at Harvard, she also worked for the Ministry of Foreign Affairs of Japan. She is an author of five books in Japanese, including a national bestseller, and was also selected as one of the 100 most influential people in Japan in 2012 and one of the 100 most amazing women in Japan in 2015. <![CDATA[<b>Managing South African biodiversity research data: Meeting the challenges of rapidly developing information technology</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532019000200011&lng=&nrm=iso&tlng= This Commentary was invited by the South African Journal of Science and emanates from a seminar presented by Dr Tomoko Kitagawa entitled 'The History of Mathematics: An Interdisciplinary Work in Humanities' given at the Department of Historical and Heritage Studies of the University of Pretoria on 20 September 2018. Dr Kitagawa received her PhD from Princeton University and went on to teach history at Harvard University. Prior to her appointment at Harvard, she also worked for the Ministry of Foreign Affairs of Japan. She is an author of five books in Japanese, including a national bestseller, and was also selected as one of the 100 most influential people in Japan in 2012 and one of the 100 most amazing women in Japan in 2015. <![CDATA[<b>Communication on rhino poaching: Precautionary lessons about backfires and boomerangs</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532019000200012&lng=&nrm=iso&tlng= This Commentary was invited by the South African Journal of Science and emanates from a seminar presented by Dr Tomoko Kitagawa entitled 'The History of Mathematics: An Interdisciplinary Work in Humanities' given at the Department of Historical and Heritage Studies of the University of Pretoria on 20 September 2018. Dr Kitagawa received her PhD from Princeton University and went on to teach history at Harvard University. Prior to her appointment at Harvard, she also worked for the Ministry of Foreign Affairs of Japan. She is an author of five books in Japanese, including a national bestseller, and was also selected as one of the 100 most influential people in Japan in 2012 and one of the 100 most amazing women in Japan in 2015. <![CDATA[<b>A call to embrace adaptive management for effective elephant conservation in Zimbabwe</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532019000200013&lng=&nrm=iso&tlng= This Commentary was invited by the South African Journal of Science and emanates from a seminar presented by Dr Tomoko Kitagawa entitled 'The History of Mathematics: An Interdisciplinary Work in Humanities' given at the Department of Historical and Heritage Studies of the University of Pretoria on 20 September 2018. Dr Kitagawa received her PhD from Princeton University and went on to teach history at Harvard University. Prior to her appointment at Harvard, she also worked for the Ministry of Foreign Affairs of Japan. She is an author of five books in Japanese, including a national bestseller, and was also selected as one of the 100 most influential people in Japan in 2012 and one of the 100 most amazing women in Japan in 2015. <![CDATA[<b>A fair individualised university researcher rating system? A rejoinder to the current NRF debate</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532019000200014&lng=&nrm=iso&tlng= This Commentary was invited by the South African Journal of Science and emanates from a seminar presented by Dr Tomoko Kitagawa entitled 'The History of Mathematics: An Interdisciplinary Work in Humanities' given at the Department of Historical and Heritage Studies of the University of Pretoria on 20 September 2018. Dr Kitagawa received her PhD from Princeton University and went on to teach history at Harvard University. Prior to her appointment at Harvard, she also worked for the Ministry of Foreign Affairs of Japan. She is an author of five books in Japanese, including a national bestseller, and was also selected as one of the 100 most influential people in Japan in 2012 and one of the 100 most amazing women in Japan in 2015. <![CDATA[<b>On defining droughts: Response to 'The ecology of drought - a workshop report'</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532019000200015&lng=&nrm=iso&tlng= This Commentary was invited by the South African Journal of Science and emanates from a seminar presented by Dr Tomoko Kitagawa entitled 'The History of Mathematics: An Interdisciplinary Work in Humanities' given at the Department of Historical and Heritage Studies of the University of Pretoria on 20 September 2018. Dr Kitagawa received her PhD from Princeton University and went on to teach history at Harvard University. Prior to her appointment at Harvard, she also worked for the Ministry of Foreign Affairs of Japan. She is an author of five books in Japanese, including a national bestseller, and was also selected as one of the 100 most influential people in Japan in 2012 and one of the 100 most amazing women in Japan in 2015. <![CDATA[<b>The decline of the Knysna elephants: Pattern and hypotheses</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532019000200016&lng=&nrm=iso&tlng= Understanding and identifying drivers of local population declines are important in mitigating future risks and optimising conservation efforts. The Knysna elephants have, after being afforded protection since the early 1900s, declined to near extinction today. We propose three hypotheses as to why the Knysna elephant population declined. The refugee hypothesis suggests that anthropogenic activities forced the elephants to take refuge in the forest and that the low-quality food acted as the primary driver of decline. The illegal killing hypothesis suggests that the elephants adapted to the forest and its immediate fynbos habitat, with the decline being a consequence of illegal kills. The stochastic founder population hypothesis postulates that the population size and structure left it vulnerable to demographic stochasticity. We critically reviewed available evidence for these hypotheses and found that, although the historical elephant range decline most likely resulted through the refugee hypothesis, the weak demographic and life-history information limits elimination of either of the other hypotheses. We touch on the implications for decision-makers and draw attention to information requirements.Significance: •We highlight the knowledge and management challenges which exist for small, threatened populations of which long-term demographic data are sparse. •We provide the first unbiased evaluation of multiple drivers that may have caused the decline of the Knysna elephants <![CDATA[<b>Exploring integrative research in the context of invasive alien plant management</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532019000200017&lng=&nrm=iso&tlng= Addressing complex challenges facing social-ecological systems (SES) requires the integration of knowledge from a diversity of disciplines and stakeholders. This requirement has resulted in the establishment of many integrative research programmes, both globally and locally, aimed at co-producing knowledge relevant to solving SES challenges. However, despite the increase in integrative projects, there has been little research on the nature and extent to which these projects acknowledge and integrate information from diverse disciplines or knowledge types. In this study, we explored the extent to which the integration of different disciplines has occurred, using a case study of the South African invasive species management programme, Working for Water (WfW). Here we provide an overview of the research produced under the auspices of WfW, and how it came to be. Additionally, we assess the extent to which research associated with the programme addressed the research priorities and how these priorities relate to one another. Findings show that WfW-associated research is primarily focused on the ecological processes and impacts associated with invasive alien plants and biological control. Social science and applied research are, however, under-represented, infrequent in nature and inadequately address the research priorities set in the programme. To address these shortcomings, we recommend the development of a detailed research strategy and action plan conducive to integrative research and transdisciplinary collaboration, and relevant to solving complex SES challenges such as those associated with biological invasions.Significance: •We provide a reference point by which we can assess research progress and guide integration of diverse knowledge systems. •The results can help guide research decision-making as it relates to invasive species management <![CDATA[<b>Leveraging media informatics for the surveillance and understanding of disease outbreaks</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532019000200018&lng=&nrm=iso&tlng= Syndromic disease surveillance mechanisms can be enhanced by incorporating mass media informatics for disease discourse and aberration detection and social psychology for understanding risk perceptions and the drivers of uptake and resistance. Using computerised text analysis, the coverage of the outbreak of Zika virus in Brazil in 2017/2018 in four newspapers - O Estado, O Globo, the Times of London and the New York Times - was examined and patterns were compared with Google Trends. Quantitative indicators showed waves of attention to Zika peaked in the same period but local newspapers, O Estado and O Globo, indicated lower levels of anxiety in the run up to the Olympics when compared with foreign media. The unusual surge in attention to dengue in early 2015 was an early indication to sound the alarm for extensive clinical investigations. This, together with the flagging of Zika by O Globo almost a year before the global alarm, indicates the suitability of this method for surveillance and detection of aberrations. Media attention waves are also significantly associated with Google Trends, indicating empirical equivalence. Qualitative indicators show the extra motivation over Google, World Wide Web or Twitter searches by highlighting public perceptions. Findings show the absence of a stable body of scientific knowledge at the outbreak and an ensuing crisis of understanding. Local concerns were about the economic crisis, religious beliefs, poverty and crime - all inhibitors to containment - while the global alarm was amplified by risk to tourists and athletes, and political disputes mixed with religious beliefs.Significance: •This study contributes to research on the use of longitudinal media data as surrogate sources for syndromic disease surveillance. •Mass media informatics provide empirical equivalence to Google Trends. •Clinical and non-clinical factors contributed to public anxiety over disease epidemics. •Lack of clinical knowledge at the onset of the crisis contributed to anxiety among scientists and the public <![CDATA[<b>Ostrich farmer characteristics predict conservation opportunity</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532019000200019&lng=&nrm=iso&tlng= Environmental sustainability rests on human choice and action. Understanding these may assist in determining the factors that predict or influence an individual's behaviour towards the environment. In South Africa, approximately 80% of the most threatened vegetation types are in the hands of the private agricultural community. In the Little Karoo, which is situated in the Succulent Karoo biodiversity hotspot, unsustainable land-use practices including ostrich flock breeding threaten this region's lowland biodiversity. We interviewed ostrich farmers in the Oudtshoorn Basin to quantify latent variables thought to represent components of conservation opportunity: environmental attitude, conservation knowledge, conservation behaviour, and willingness to collaborate with agricultural, environmental and conservation organisations. Three groups of land managers were identified: (1) younger land managers (<31 years' farming experience) with bigger farms (≥2050 ha) who had above-average scores for all four indicators, (2) older farmers (≥31 years' farming experience) who had above-average scores for environmental attitude and conservation knowledge, average scores for environmental attitude, but low willingness to collaborate, and (3) a large group of younger farmers (<31 years' farming experience) with smaller properties (<2050 ha) who had low to average scores for all four indicators. Farmers in the first two groups represent the best opportunities for conservation, although different strategies would have to be employed to engage them given the current low willingness to collaborate among older farmers. Land managers were more willing to collaborate with agricultural than conservation organisations, pointing to a need to involve agricultural organisations in championing more environmentally sustainable ostrich breeding practices.Significance: •Achievement of biodiversity conservation targets requires stewardship in production landscapes outside protected areas, which necessitates identification of farmers who present conservation opportunity, i.e. who are willing and able to participate in conservation. •Plant biodiversity in the Little Karoo has been severely degraded through ostrich flock breeding, but ostrich farmers consider their practices to be ecologically sustainable. •In the Little Karoo, land managers with more years of farming experience, and younger farmers with larger properties, represented the greatest opportunity for interventions to promote more biodiversity-friendly ostrich farming practices <![CDATA[<b>An empirical investigation of alternative semi-supervised segmentation methodologies</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532019000200020&lng=&nrm=iso&tlng= Segmentation of data for the purpose of enhancing predictive modelling is a well-established practice in the banking industry. Unsupervised and supervised approaches are the two main types of segmentation and examples of improved performance of predictive models exist for both approaches. However, both focus on a single aspect - either target separation or independent variable distribution - and combining them may deliver better results. This combination approach is called semi-supervised segmentation. Our objective was to explore four new semi-supervised segmentation techniques that may offer alternative strengths. We applied these techniques to six data sets from different domains, and compared the model performance achieved. The original semi-supervised segmentation technique was the best for two of the data sets (as measured by the improvement in validation set Gini), but others outperformed for the other four data sets.Significance: •We propose four newly developed semi-supervised segmentation techniques that can be used as additional tools for segmenting data before fitting a logistic regression. •In all comparisons, using semi-supervised segmentation before fitting a logistic regression improved the modelling performance (as measured by the Gini coefficient on the validation data set) compared to using unsegmented logistic regression <![CDATA[<b>A bioinformatics pipeline for rare genetic diseases in South African patients</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532019000200021&lng=&nrm=iso&tlng= The research fields of bioinformatics and computational biology are growing rapidly in South Africa. Bioinformatics pipelines play an integral part in handling sequencing data, which are used to investigate the aetiology of common and rare diseases. Bioinformatics platforms for common disease aetiology are well supported and continuously being developed in South Africa. However, the same is not the case for rare diseases aetiology research. Investigations into the latter rely on international cloud-based tools for data analyses and ultimately confirmation of a genetic disease. However, these tools are not necessarily optimised for ethnically diverse population groups. We present an in-house developed bioinformatics pipeline to enable researchers to annotate and filter variants in either exome or amplicon next-generation sequencing data. This pipeline was developed using next-generation sequencing data of a predominantly African cohort of patients diagnosed with rare disease.Significance: •We demonstrate the feasibility of in-country development of ethnicity-sensitive, automated bioinformatics pipelines using free software in a South African context. •We provide a roadmap for development of similarly ethnicity-sensitive bioinformatics pipelines