African Scientists Research Articles

African scientists call for more control of their continent’s genomic data

Voluntary guidelines aim to combat ‘helicopter’ science and ensure that studies benefit African citizens and scientists. Voluntary guidelines aim to combat ‘helicopter’ science and ensure that studies benefit African citizens and scientists.

The Collaborative African Genomics Network (CAfGEN): Applying Genomic technologies to probe host factors important to the progression of HIV and HIV-tuberculosis infection in sub-Saharan Africa.

Background: The Human Heredity and Health in Africa consortium (H3Africa) was conceived to facilitate the application of genomics technologies to improve health across Africa. Here, we describe how the Collaborative African Genomics Network (CAfGEN) of the H3Africa consortium is using genomics to probe host genetic factors important to the progression of HIV and HIV-tuberculosis (TB) coinfection in sub-Saharan Africa. Methods: CAfGEN is an H3Africa collaborative centre comprising expertise from the University of Botswana; Makerere University; Baylor College of Medicine Children's Clinical Centers of Excellence (COEs) in Botswana, Uganda, and Swaziland; as well as Baylor College of Medicine, Texas. The COEs provide clinical expertise for community engagement, participant recruitment and sample collection while the three University settings facilitate processing and management of genomic samples and provide infrastructure and training opportunities to sustain genomics research. Results: The project has focused on utilizing whole-exome sequencing to identify genetic variants contributing to extreme HIV disease progression phenotypes in children, as well as RNA sequencing and integrated genomics to identify host genetic factors associated with TB disease progression among HIV-positive children. These cohorts, developed using the COEs' electronic medical records, are exceptionally well-phenotyped and present an unprecedented opportunity to assess genetic factors in individuals whose HIV was acquired by a different route than their adult counterparts in the context of a unique clinical course and disease pathophysiology. Conclusions: Our approach offers the prospect of developing a critical mass of well-trained, highly-skilled, continent-based African genomic scientists. To ensure long term genomics research sustainability in Africa, CAfGEN contributes to a wide range of genomics capacity and infrastructure development on the continent, has laid a foundation for genomics graduate programs at its institutions, and continues to actively promote genomics research through innovative forms of community engagement brokered by partnerships with governments and academia to support genomics policy formulation.

A (Digital) Future for Saharan Rock Art?

First visited by westerners in the mid-nineteenth century, Saharan rock art has since received a great deal of attention. The richness and diversity of this region is recognised by the inclusion on the UNESCO World Heritage list of three properties: Tassili-n-Ajjer in Algeria, Tadrart Acacus in Libya, and Ennedi in Chad. The situation in many North African countries now makes this vast region very difficult to access: safety in the field is not guaranteed and few research funds are available. Today, a new generation of African and foreign scientists has no access to rock art sites in the north of the continent and the lack of fieldwork may entail a lack of safeguard and awareness. The growth of digital technologies over the last 15 years has revolutionised methods for recording rock art sites. Digital technologies are also used to mitigate the gap between artworks and accessibility in those countries where turmoil and social instability make fieldwork impossible. However, much of the documentation and most digital recordings of artworks currently available on the Internet lack an archaeological context. Equally, many of these websites barely mention methodological and theoretical aspects. It is also difficult to understand the extent of awareness among local communities in remote areas—sometimes suffering a digital and linguistic divide—and if (and how) they are genuinely able to exploit these digital resources. Here, I collate some examples from different parts of the Sahara illustrating that the recording, management and dissemination of rock art still present highs and lows. I argue that we should share theories and methods within the digital scientific community, with a view to adopting a shared nomenclature and a public thesaurus, making our cataloguing criteria explicit and, finally, developing an ethical code of conduct involving local communities.

Driving a greater understanding of non-communicable diseases in Africa through collaborative research: the experience of the GSK Africa NCD Open Lab

# Background The majority of premature deaths from non-communicable diseases (NCDs) occur in low-income countries. However, clinical research in these patient populations is generally lacking. Thus, many treatment paradigms for NCDs are either absent or extrapolated from populations with different genetics, health needs, and socio-economic circumstances. # Methods To evaluate the outcomes from the first call for proposals from the GSK Africa NCD Open Lab. Funding was offered to research projects aiming to improve understanding and generate new knowledge of NCDs in African populations. Proposals were sought for projects relating to cancer, cardiovascular disease, diabetes, chronic respiratory disease or chronic kidney diseases. The proposal had to be led by African scientists from Cameroon, The Gambia, Ghana, Kenya, Cote d'Ivoire, Malawi, Nigeria or Uganda and include a capacity building component. # Results The 155 eligible proposals covered oncology (31.0%), cardiovascular disease (27.1%), metabolic disorders such as diabetes (20.6%), chronic respiratory disease (9.7%) and chronic kidney disease (6.5%). Most applications were from Nigeria (37.8%), Kenya (17.3%) and Uganda (13.5%). Following initial review, 23 proposals were considered by a Scientific Advisory Board, and ten were invited to submit full applications. Five projects were funded in cardiovascular disease, the interaction between cardiovascular disease and HIV infection, breast cancer, asthma and chronic kidney disease/diabetes. Principal investigators were from Nigeria, Uganda and Malawi with collaborators from Cameroon, Ethiopia, Kenya, Mozambique, South Africa, the UK, USA and the Netherlands. All of the projects involved research capacity strengthening elements. # Conclusions These projects have the potential to improve the understanding of the aetiology and natural history of specific NCDs, while also informing the development of clinical guidelines for the effective management of disease. However, far more needs to be done to address capacity building and funding for NCD research in Africa.

Centre for Genomic Regulation - a hub for Integrative Biology in Barcelona.

Centre for Genomic Regulation - a hub for Integrative Biology in Barcelona.

Evaluating Climate Models with an African Lens

Abstract Climate models are becoming evermore complex and increasingly relied upon to inform climate change adaptation. Yet progress in model development is lagging behind in many of the regions that need the information most, including in Africa. Targeted model development for Africa is crucial and so too is targeted model evaluation. Assessment of model performance in specific regions often follows a “validation” approach, focusing on mean biases, but if models are to be improved, it is important to understand how they simulate regional climate dynamics: to move from validation to process-based evaluation. This evaluation may be different for every region and requires local weather and climate expertise: a “one size fits all” approach could overlook important, region-specific phenomena. So which are the important processes in African regions? And how might they be evaluated? This paper addresses these questions, drawing on the expertise of a team of scientists from Central, East, southern, and West Africa. For each region, the current understanding of climate models is reviewed, and an example of targeted evaluation is provided, including analysis of moist circulations, teleconnections, and modes of variability. A pan-African perspective is also considered, to examine processes operating between regions. The analysis is based on the Met Office Unified Model, but it uses diagnostics that might be applied to other models. These examples are intended to prompt further discussion among climate modelers and African scientists about how to best evaluate models with an African lens, and promote the development of a model evaluation hub for Africa, to fast track understanding of model behavior for this important continent.

The Role of Professional Societies in STEM Diversity

The overall percentages of African American scientists indicate underrepresentation in most science, technology, engineering, and mathematics (STEM) disciplines and the percentages appear to be declining over the last three decades. We will share insights on how professional societies can directly impact the broadening of participation as well as the persistence of racial groups in the STEM fields and hence, strengthen and sustain the Nation's future workforce.

Technology generation to dissemination: lessons learned from the tef improvement project

Indigenous crops also known as orphan crops are key contributors to food security, which is becoming increasingly vulnerable with the current trend of population growth and climate change. They have the major advantage that they fit well into the general socio-economic and ecological context of developing world agriculture. However, most indigenous crops did not benefit from the Green Revolution, which dramatically increased the yield of major crops such as wheat and rice. Here, we describe the Tef Improvement Project, which employs both conventional- and molecular-breeding techniques to improve tef—an orphan crop important to the food security in the Horn of Africa, a region of the world with recurring devastating famines. We have established an efficient pipeline to bring improved tef lines from the laboratory to the farmers of Ethiopia. Of critical importance to the long-term success of this project is the cooperation among participants in Ethiopia and Switzerland, including donors, policy makers, research institutions, and farmers. Together, European and African scientists have developed a pipeline using breeding and genomic tools to improve the orphan crop tef and bring new cultivars to the farmers in Ethiopia. We highlight a new variety, Tesfa, developed in this pipeline and possessing a novel and desirable combination of traits. Tesfa’s recent approval for release illustrates the success of the project and marks a milestone as it is the first variety (of many in the pipeline) to be released.

Made in Denmark: Scientific mobilities and the place of pedagogy in global health

ABSTRACTTransnational Global Health programmes planned and financed in the North and executed in the Global South usually involve some transfer of capacity between sites or capacity building in place. Capacity investment in the form of skills, knowledge, experience and equipment is often assumed to ‘flow’ between countries, laboratories and institutions, following the trajectories of mobile subjects in the knowledge economy. Drawing on in-depth interviews with Danish and East African scientists, this paper considers the mobilities that underpin scientific capacity building, drawing attention to the paradoxical in ways in which these programmes produce stasis and fixity, as well as mobility and exchange.

In the footsteps of Einstein, Sagan and Barnard: Identifying South Africa’s most visible scientists


 
 
 Highly visible scientists are increasingly recognised as influential leaders with a special role to play in making science part of mainstream society. Through consultation with a panel of 45 experts working at the science–media interface, we sought to identify the most visible scientists currently living and working in South Africa. In total, 211 scientists – less than 1% of the scientific workforce of the country – were identified as visible in the public sphere. The demographic profile and institutional spread of South Africa’s visible scientists suggest that more should be done to increase the diversity of scientists who are publicly visible. Although only 8% of South Africans are white, 78% of the group of visible scientists were white, and 63% of the visible scientists were men. Only 17 black women were identified as publicly visible scientists. While visible scientists were identified at 42 different research institutions, more than half of the visible scientists were associated with just four universities. Recent controversies surrounding the two most visible South African scientists identified via this study, and the potential implications for fellow scientists’ involvement in public engagement, are briefly discussed.
 
 
 
 
 Significance: 
 
 
 
 This is the first study to identify highly visible scientists in South Africa.
 The study has meaningful policy implications for mobilising scientists towards public science engagement.
 It is an important contribution towards the new public engagement framework of the Department of Science and Technology.
 
 
 

African scientists get their own open-access publishing platform

African scientists get their own open-access publishing platform

The past is a key to the future: Lessons paleoecological data can provide for management of the African Great Lakes

Abstract Rapid ecological changes in the African Great Lakes (AGL) present lake managers with extraordinary challenges to understand the changes' underlying causes and forecast what they portend for the future. Monitoring and experimental data from the AGL are essential but are limited in duration and continuity. The magnitude of change suggests that a centennial-millennial timescale perspective is needed to identify drivers of change and prepare for changes yet to come. In this review I propose that paleoecological and paleolimnological approaches can provide this perspective. AGL paleorecords have documented the impacts of excess sedimentation, external nutrient loading, and climate change, and can demonstrate the specific ecosystem responses associated with these various drivers. Paleorecords can help us understand how multiple stressors interact and in some cases can falsify specific cause-and-effect hypotheses when the putative causes can be shown to have occurred after the effect started. The number of useful AGL paleorecords is still quite small. Replication is needed to test if patterns seen and hypotheses inferred from single localities are robust for an entire lake, and to understand regional variability within and between lakes. Because many paleorecord methods are quite inexpensive it would be highly desirable if these approaches were incorporated into the routine tool kit of local AGL scientists working in tandem with fisheries and water-quality scientists. Training African lake scientists and conservation biologists to analyze paleorecords should be a high priority for AGL stakeholders interested in the long-term prognoses for the economic and biodiversity resources that they oversee.

Africa and health: a Commission to accelerate success

The final results of a 4-year project to analyse the challenges and opportunities for health in sub-Saharan Africa are now published as a Lancet Commission—The Path to Longer and Healthier Lives for All Africans by 2030—led by African physicians, health scientists, and policy makers. 1 Agyepong IA Sewankambo N Binagwaho A et al. The path to longer and healthier lives for all Africans by 2030: the Lancet Commission on the future of health in sub-Saharan Africa. Lancet. 2017; (published online Sept 13.)http://dx.doi.org/10.1016/S0140-6736(17)31509-X Summary Full Text Full Text PDF PubMed Scopus (113) Google Scholar Their conclusion is one of qualified optimism, grounded in a rigorous appraisal of new evidence and past experience. The vision of the Commission is that Africans should expect the same opportunities for health by 2030 as all other peoples. But that hopeful message is based on a further proposition—that more of the same, in terms of policies and programmes, is not enough. The path to longer and healthier lives for all Africans by 2030: the Lancet Commission on the future of health in sub-Saharan AfricaSub-Saharan Africa's health challenges are numerous and wide-ranging. Most sub-Saharan countries face a double burden of traditional, persisting health challenges, such as infectious diseases, malnutrition, and child and maternal mortality, and emerging challenges from an increasing prevalence of chronic conditions, mental health disorders, injuries, and health problems related to climate change and environmental degradation. Although there has been real progress on many health indicators, life expectancy and most population health indicators remain behind most low-income and middle-income countries in other parts of the world. Full-Text PDF

Forging a Laboring Race: The African American Worker in the Progressive Imagination

Can we talk about labor in the Progressive Era without talking about black bodies? Paul R. D. Lawrie's ardent new book shows exactly why we cannot, both in ways that are intentional and some that are not. Lawrie's study of eugenicists and social scientists in and out of government offices from the 1880s through World War I offers a disturbing accounting of entrepreneurial race scientists who found innumerable ways to quantify bigoted claims about black bodies. Even as most of their projects came to little, they produced, Lawrie says, “new forms of knowledge on race—the Negro as an embodied pathology—which would inform the discourse of American race relations for the foreseeable future” (p. 137). Eugenicists may have (mostly) failed because “expediency continued to trump long-term considerations of race betterment and national health,” but their ideas about biology and the nation's health and efficiency persisted (p. 92). By inserting “the black body” into Progressive Era thinking, Lawrie rightly implicates the American state, progressive politics, and industrial capitalism in race making. The Boasian environmentalism that progressives are so often credited with never completely overtook biological thinking in American social politics. Moreover, Lawrie's source base in federal and northern archives makes evident that racialist ideas circulated beyond the South. Lawrie wisely writes across the color line, noting the ways African American social scientists both challenged and furthered such thinking. The ability of Forging a Laboring Race to connect racist empiricism with state action and social politics is the book's greatest strength.

South African Ebola diagnostic response in Sierra Leone: A modular high biosafety field laboratory.

BackgroundIn August 2014, the National Institute for Communicable Diseases (NICD) in South Africa established a modular high-biosafety field Ebola diagnostic laboratory (SA FEDL) near Freetown, Sierra Leone in response to the rapidly increasing number of Ebola virus disease (EVD) cases.Methods and findingsThe SA FEDL operated in the Western Area of Sierra Leone, which remained a “hotspot” of the EVD epidemic for months. The FEDL was the only diagnostic capacity available to respond to the overwhelming demand for rapid EVD laboratory diagnosis for several weeks in the initial stages of the EVD crisis in the capital of Sierra Leone. Furthermore, the NICD set out to establish local capacity amongst Sierra Leonean nationals in all aspects of the FEDL functions from the outset. This led to the successful hand-over of the FEDL to the Sierra Leone Ministry of Health and Sanitation in March 2015. Between 25 August 2014 and 22 June 2016, the laboratory tested 11,250 specimens mostly from the Western Urban and Western Rural regions of Sierra Leone, of which 2,379 (21.14%) tested positive for Ebola virus RNA.ConclusionsThe bio-safety standards and the portability of the SA FEDL, offered a cost-effective and practical alternative for the rapid deployment of a field-operated high biocontainment facility. The SA FEDL teams demonstrated that it is highly beneficial to train the national staff in the course of formidable disease outbreak and accomplished their full integration into all operational and diagnostic aspects of the laboratory. This initiative contributed to the international efforts in bringing the EVD outbreak under control in Sierra Leone, as well as capacitating local African scientists and technologists to respond to diagnostic needs that might be required in future outbreaks of highly contagious pathogens.

Broadening Participation in the Sciences within and from Africa: Purpose, Challenges, and Prospects.

Many of Africa's challenges have scientific solutions, but there are fewer individuals engaged in scientific activity per capita on this continent than on any other. Only a handful of African scientists use their skills to capacity or are leaders in their disciplines. Underrepresentation of Africans in scientific practice, discourse, and decision making reduces the richness of intellectual contributions toward hard problems worldwide. This essay outlines challenges faced by teacher-scholars from sub-Saharan Africa as we build scientific expertise. Access to tertiary-level science is difficult and uneven across Africa, and the quality of training available varies from top-range to inadequate. Access to science higher education needs to increase, particularly for female students, first-generation literates, and rural populations. We make suggestions for collaborative initiatives involving stakeholders outside Africa and/or outside academia that could extend educational opportunities available to African students and increase the chance that Africa-based expertise is globally available.

H3Africa: An Africa exemplar? Exploring its framework on protecting human research participants.

The Human Heredity and Health in Africa (H3Africa) Consortium is a conglomeration of research and infrastructure projects spread throughout Africa whose aim is to apply genomic methodology to diseases affecting the people in the region. Its operation is innovative in the sense that it is doing something new; that is, filling a hitherto existing void in genomic research capability of African scientists and infusing resources and manpower to institutions and investigators across Africa. But aside from developing and sustaining capacity in genomic research and biorepositories, H3Africa is also invested in developing appropriate ethical regulatory regime to govern research in these areas. This latter concern -research ethics governance - is the major subject of this paper. Specifically, the paper discusses protection of research participants as envisaged by H3Africa in the area of consent, safeguarding privacy, maintaining confidentiality of health information and sharing of data/biospecimens. The ultimate goal is to determine whether H3Africa initiatives and processes are consistent or at odds with international guidelines and best practices.

Challenges facing young African scientists in their research careers: A qualitative exploratory study

Africa accounts for 14% of world's population, and the economies of most African countries are considered to be growing, but this is not reflected in the amount of research published by Africans. This study aimed at identifying the challenges that young African scientists face in their career development. This was a qualitative exploratory study involving young researchers who attended the Teaching and Research in Natural Sciences for Development (TReND) in Africa scientific writing and communication workshop, which was held in Malawi in September 2015. A semi-structured questionnaire was sent to all workshop participants who consented to taking part in the survey. In total, 28 questionnaires were sent via email and 15 were returned, representing a response rate of 53.6%. Data were analysed using thematic analysis. Young Africans develop their research interests various ways. The most common career-promoting factors identified by the study participants included formal classroom learning, aspirations to attain academic qualifications, work satisfaction, and the desire to fulfill parents' dreams. Challenges cited by survey respondents included a lack of mentorship, funds, and research and writing skills. Lack of interest in research by policymakers, lack of motivation by peers, and heavy workload (leaving little time for research) were also reported as challenges. Respondents suggested that grants specifically targeting young scientists would be beneficial. Participants also urged for the establishment of mentorship programmes, increasing motivation for research, and more frequent training opportunities. There is need for improved funding for institutional and research network strengthening in Africa, with particular attention given to expanding opportunities for young researchers.

One Health Research in Northern Tanzania - Challenges and Progress

East Africa has one of the world’s fastest growing human populations—many of whom are dependent on livestock—as well as some of the world’s largest wildlife populations. Humans, livestock, and wildlife often interact closely, intimately linking human, animal, and environmental health. The concept of One Health captures this interconnectedness, including the social structures and beliefs driving interactions between species and their environments. East African policymakers and researchers are recognising and encouraging One Health research, with both groups increasingly playing a leading role in this subject area. One Health research requires interaction between scientists from different disciplines, such as the biological and social sciences and human and veterinary medicine. Different disciplines draw on norms, methodologies, and terminologies that have evolved within their respective institutions and that may be distinct from or in conflict with one another. These differences impact interdisciplinary research, both around theoretical and methodological approaches and during project operationalisation. We present experiential knowledge gained from numerous ongoing projects in northern Tanzania, including those dealing with bacterial zoonoses associated with febrile illness, foodborne disease, and anthrax. We use the examples to illustrate differences between and within social and biological sciences and between industrialised and traditional societies, for example, with regard to consenting procedures or the ethical treatment of animals. We describe challenges encountered in ethical approval processes, consenting procedures, and field and laboratory logistics and offer suggestions for improvement. While considerable investment of time in sensitisation, communication, and collaboration is needed to overcome interdisciplinary challenges inherent in One Health research, this can yield great rewards in paving the way for successful implementation of One Health projects. Furthermore, continued investment in African institutions and scientists will strengthen the role of East Africa as a world leader in One Health research.

One Health Research in Northern Tanzania - Challenges and Progress.

East Africa has one of the world's fastest growing human populations—many of whom are dependent on livestock—as well as some of the world's largest wildlife populations. Humans, livestock, and wildlife often interact closely, intimately linking human, animal, and environmental health. The concept of One Health captures this interconnectedness, including the social structures and beliefs driving interactions between species and their environments. East African policymakers and researchers are recognising and encouraging One Health research, with both groups increasingly playing a leading role in this subject area. One Health research requires interaction between scientists from different disciplines, such as the biological and social sciences and human and veterinary medicine. Different disciplines draw on norms, methodologies, and terminologies that have evolved within their respective institutions and that may be distinct from or in conflict with one another. These differences impact interdisciplinary research, both around theoretical and methodological approaches and during project operationalisation. We present experiential knowledge gained from numerous ongoing projects in northern Tanzania, including those dealing with bacterial zoonoses associated with febrile illness, foodborne disease, and anthrax. We use the examples to illustrate differences between and within social and biological sciences and between industrialised and traditional societies, for example, with regard to consenting procedures or the ethical treatment of animals. We describe challenges encountered in ethical approval processes, consenting procedures, and field and laboratory logistics and offer suggestions for improvement. While considerable investment of time in sensitisation, communication, and collaboration is needed to overcome interdisciplinary challenges inherent in One Health research, this can yield great rewards in paving the way for successful implementation of One Health projects. Furthermore, continued investment in African institutions and scientists will strengthen the role of East Africa as a world leader in One Health research.