Pub Date : 2023-01-03eCollection Date: 2023-01-01DOI: 10.12688/openresafrica.13566.1
Thomas Kariuki, Judith Omumbo, Kabura Ciugu, Elizabeth Marincola
The evidence is clear that climate change is the greatest challenge facing mankind today. Africa is disproportionately burdened by multiple direct and cascading impacts of the climate crisis. Global investments for climate change adaptation, however, have not prioritized Africa adequately and there is a significant knowledge gap in understanding the context and science of climate change and sustainable solutions for the continent's adaptation. Solutions for adaptation and resilience are made complex by an urgent need for accelerated economic growth, rapid population expansion and urbanization, habitat and biodiversity loss and dwindling financing. There are also challenges in matching policies, wavering commitments and actions with good science that focuses on sustainable lives, livelihoods and ecosystem preservation. The solutions must come from where the impacts are felt. The Science for Africa Foundation supports African researchers and institutions to lead in the science that addresses African priority development areas and has set climate change as a strategic priority. This call to action, by the SFA Foundation, outlines key areas that its strategy addresses through programs that support African scientific excellence, leadership and the best of Africa's research to understand the science of climate change and its impacts; collate and assess evidence for policy; grow high level technical capacity on the continent; and create innovative priority actions for Africa.
{"title":"The interconnected global emergencies of climate change, food security and health: a call to action by the Science for Africa Foundation.","authors":"Thomas Kariuki, Judith Omumbo, Kabura Ciugu, Elizabeth Marincola","doi":"10.12688/openresafrica.13566.1","DOIUrl":"10.12688/openresafrica.13566.1","url":null,"abstract":"<p><p>The evidence is clear that climate change is the greatest challenge facing mankind today. Africa is disproportionately burdened by multiple direct and cascading impacts of the climate crisis. Global investments for climate change adaptation, however, have not prioritized Africa adequately and there is a significant knowledge gap in understanding the context and science of climate change and sustainable solutions for the continent's adaptation. Solutions for adaptation and resilience are made complex by an urgent need for accelerated economic growth, rapid population expansion and urbanization, habitat and biodiversity loss and dwindling financing. There are also challenges in matching policies, wavering commitments and actions with good science that focuses on sustainable lives, livelihoods and ecosystem preservation. The solutions must come from where the impacts are felt. The Science for Africa Foundation supports African researchers and institutions to lead in the science that addresses African priority development areas and has set climate change as a strategic priority. This call to action, by the SFA Foundation, outlines key areas that its strategy addresses through programs that support African scientific excellence, leadership and the best of Africa's research to understand the science of climate change and its impacts; collate and assess evidence for policy; grow high level technical capacity on the continent; and create innovative priority actions for Africa.</p>","PeriodicalId":74358,"journal":{"name":"Open research Africa","volume":"6 ","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2023-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9958300/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10794259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-01DOI: 10.12688/openresafrica.13983.1
Elizabeth Nthambi Ndunda, Moses Mutiso Mwanza
Pollution of our environment as a result of industrialization and other human activities is a growing concern due to the harmful effects of most chemicals that are released into the environment. Of particular interest are the persistent organic pollutants (POPs) that are reported to be toxic and build up in the environment due to their persistence. Among the POPs are polychlorinated biphenyls (PCBs), which were widely used in the past in various applications ranging from additives in pesticides to dielectric fluids in electrical equipment. As a way of protecting the one health trilogy (environment, human and animal health), their determination in the environment is a paramount call that has seen researchers continue to provide advanced technologies towards achieving this goal. These technologies involve the conventional gold standard gas chromatography systems coupled to sensitive detectors that can detect trace level concentrations. They have come in handy in monitoring of PCBs but their application for routing monitoring may not be sustainable because of the cost of operation associated with them and the need for experts to run the equipment. As a result, there is need for affordable systems that are still able to achieve the required sensitivity for routine monitoring and real-time data acquisition. Sensor systems fit very well in this category since they can be miniaturized for affordability and portray many other desirable features. PCBs as environmentally relevant environmental pollutants have received minimal attention with regards to sensor development and this review highlights the efforts that have been made so far. It provides in-depth discussions on electrochemical sensors and the various modifications that have been employed to date to achieve detection of PCBs at low concentrations as well as the future prospects in remote and routine monitoring.
{"title":"Towards miniaturized electrochemical sensors for monitoring of polychlorinated biphenyls.","authors":"Elizabeth Nthambi Ndunda, Moses Mutiso Mwanza","doi":"10.12688/openresafrica.13983.1","DOIUrl":"https://doi.org/10.12688/openresafrica.13983.1","url":null,"abstract":"<p><p>Pollution of our environment as a result of industrialization and other human activities is a growing concern due to the harmful effects of most chemicals that are released into the environment. Of particular interest are the persistent organic pollutants (POPs) that are reported to be toxic and build up in the environment due to their persistence. Among the POPs are polychlorinated biphenyls (PCBs), which were widely used in the past in various applications ranging from additives in pesticides to dielectric fluids in electrical equipment. As a way of protecting the one health trilogy (environment, human and animal health), their determination in the environment is a paramount call that has seen researchers continue to provide advanced technologies towards achieving this goal. These technologies involve the conventional gold standard gas chromatography systems coupled to sensitive detectors that can detect trace level concentrations. They have come in handy in monitoring of PCBs but their application for routing monitoring may not be sustainable because of the cost of operation associated with them and the need for experts to run the equipment. As a result, there is need for affordable systems that are still able to achieve the required sensitivity for routine monitoring and real-time data acquisition. Sensor systems fit very well in this category since they can be miniaturized for affordability and portray many other desirable features. PCBs as environmentally relevant environmental pollutants have received minimal attention with regards to sensor development and this review highlights the efforts that have been made so far. It provides in-depth discussions on electrochemical sensors and the various modifications that have been employed to date to achieve detection of PCBs at low concentrations as well as the future prospects in remote and routine monitoring.</p>","PeriodicalId":74358,"journal":{"name":"Open research Africa","volume":"6 ","pages":"5"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10192943/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10350374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-09-30eCollection Date: 2022-01-01DOI: 10.12688/openresafrica.13495.1
Gideon Nsubuga, David Patrick Kateete, Sharley Melissa Aloyo, Lwanga Newton Kigingi, Nasinghe Emmanuel, Kezimbira Dafala, Moses Levi Ntayi, Moses L Joloba, Kamulegeya Rogers
Biorepositories are essential because they guarantee the proper storage and distribution of biospecimens and their associated data for current and future research. In Eastern and Central Africa, the Integrated Biorepository of H3Africa Uganda (IBRH3AU) at Makerere University in Uganda was the first of its kind. It is strategically located at Makerere University College of Health Sciences, which is home to some of Uganda's most relevant and impactful infectious and non-infectious disease research. Since its inception as a pilot project in 2012, the IBRH3AU biorepository has grown into a state-of-the-art facility serving the H3Africa consortium and the rest of the scientific community. IBRH3AU has built a solid infrastructure over the past ten years with cutting-edge methods and technologies for the collection, processing, quality control, handling, management, storage and shipment of biospecimens. H3Africa researchers, local researchers, postgraduate and postdoctoral students, and the greater scientific community in Eastern and Central Africa and beyond have benefited from IBRH3AU's exceptional biobanking services.
{"title":"Biobanking in East and Central Africa: A case of the Integrated Biorepository of H3Africa Uganda.","authors":"Gideon Nsubuga, David Patrick Kateete, Sharley Melissa Aloyo, Lwanga Newton Kigingi, Nasinghe Emmanuel, Kezimbira Dafala, Moses Levi Ntayi, Moses L Joloba, Kamulegeya Rogers","doi":"10.12688/openresafrica.13495.1","DOIUrl":"10.12688/openresafrica.13495.1","url":null,"abstract":"<p><p>Biorepositories are essential because they guarantee the proper storage and distribution of biospecimens and their associated data for current and future research. In Eastern and Central Africa, the Integrated Biorepository of H3Africa Uganda (IBRH3AU) at Makerere University in Uganda was the first of its kind. It is strategically located at Makerere University College of Health Sciences, which is home to some of Uganda's most relevant and impactful infectious and non-infectious disease research. Since its inception as a pilot project in 2012, the IBRH3AU biorepository has grown into a state-of-the-art facility serving the H3Africa consortium and the rest of the scientific community. IBRH3AU has built a solid infrastructure over the past ten years with cutting-edge methods and technologies for the collection, processing, quality control, handling, management, storage and shipment of biospecimens. H3Africa researchers, local researchers, postgraduate and postdoctoral students, and the greater scientific community in Eastern and Central Africa and beyond have benefited from IBRH3AU's exceptional biobanking services.</p>","PeriodicalId":74358,"journal":{"name":"Open research Africa","volume":"5 ","pages":"33"},"PeriodicalIF":0.0,"publicationDate":"2022-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10175960/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9876112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-08-09DOI: 10.12688/openresafrica.13457.1
B. Gachie, Jean Chepngetich, Brenda Muriithi, Kelvin Thiong’o, J. Gathirwa, F. Kimani, P. Mwitari, G. Magoma, Daniel Kiboi
Background: Lumefantrine (LM), piperaquine (PQ), and amodiaquine (AQ) are the essential long-acting partner drugs in the artemisinin-based combination therapies (ACTs) treatment regimens globally. Understanding the resistance mechanisms to partner drugs remains critical for tracking resistant parasites. Cysteine desulfurase IscS (nfs1), one of the proteins involved in the iron-sulfur (FeS) biogenesis pathway, has been implicated in mediating malaria parasite drug resistance. Methods: Using the rodent malaria parasites Plasmodium berghei ANKA in mice, we assessed whether the nfs1 gene is associated with LM, PQ, and AQ resistance. By means of PCR and sequencing analysis, we probed for single nucleotide polymorphisms (SNPs) within the nfs1 gene. Using qPCR, we then measured the expression of the nfs1 gene in resistant parasites relative to the drug-sensitive parent parasites. Results: Our analyses of nfs1 reveal a non-synonymous Gln142Arg mutation in the LM and PQ-resistant parasites. This mutation was not detected in the AQ-resistant parasites. The mRNA quantification of the nfs1 gene reveals significant downregulation in both LM and PQ-resistant parasites compared to the drug-sensitive wild-type (WT) parasites. Conversely, nfs1 expression was upregulated in the AQ-resistant schizont stage compared to the WT parasites. Conclusion: Our data suggest that LM and PQ selection pressure induces nonsynonymous mutation and nfs1 downregulation of its expression in Plasmodium berghei. Collectively, these findings provide a premise for investigating LM and PQ resistance mechanisms in both P. berghei and P. falciparum.
{"title":"Lumefantrine pressure selects nonsynonymous mutation in cysteine desulfurase IscS gene in the rodent malaria parasite Plasmodium berghei ANKA","authors":"B. Gachie, Jean Chepngetich, Brenda Muriithi, Kelvin Thiong’o, J. Gathirwa, F. Kimani, P. Mwitari, G. Magoma, Daniel Kiboi","doi":"10.12688/openresafrica.13457.1","DOIUrl":"https://doi.org/10.12688/openresafrica.13457.1","url":null,"abstract":"Background: Lumefantrine (LM), piperaquine (PQ), and amodiaquine (AQ) are the essential long-acting partner drugs in the artemisinin-based combination therapies (ACTs) treatment regimens globally. Understanding the resistance mechanisms to partner drugs remains critical for tracking resistant parasites. Cysteine desulfurase IscS (nfs1), one of the proteins involved in the iron-sulfur (FeS) biogenesis pathway, has been implicated in mediating malaria parasite drug resistance. Methods: Using the rodent malaria parasites Plasmodium berghei ANKA in mice, we assessed whether the nfs1 gene is associated with LM, PQ, and AQ resistance. By means of PCR and sequencing analysis, we probed for single nucleotide polymorphisms (SNPs) within the nfs1 gene. Using qPCR, we then measured the expression of the nfs1 gene in resistant parasites relative to the drug-sensitive parent parasites. Results: Our analyses of nfs1 reveal a non-synonymous Gln142Arg mutation in the LM and PQ-resistant parasites. This mutation was not detected in the AQ-resistant parasites. The mRNA quantification of the nfs1 gene reveals significant downregulation in both LM and PQ-resistant parasites compared to the drug-sensitive wild-type (WT) parasites. Conversely, nfs1 expression was upregulated in the AQ-resistant schizont stage compared to the WT parasites. Conclusion: Our data suggest that LM and PQ selection pressure induces nonsynonymous mutation and nfs1 downregulation of its expression in Plasmodium berghei. Collectively, these findings provide a premise for investigating LM and PQ resistance mechanisms in both P. berghei and P. falciparum.","PeriodicalId":74358,"journal":{"name":"Open research Africa","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47101070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-06-27DOI: 10.12688/openresafrica.13349.2
Joel L. Bargul, Denna M. Mkwashapi, I. Namagembe, Immaculate Nakityo, A. Nakimuli, J. Byamugisha, Daniel Semakula, J. Seeley, N. Sewankambo
Background: In this paper, we explain how three early career researchers actively engaged community members in their health research projects in Kenya, Tanzania and Uganda, and what was learnt from the experience. The research project in Kenya was on camel trypanosomiasis and the role of camel biting keds (or louse flies) in disease transmission. The project in Tanzania looked at the effect of human immunodeficiency virus and antiretroviral therapy on fertility and ascertained the trends in the use of family planning services amongst women of reproductive age. The focus of the project in Uganda was the implementation of maternal death surveillance and the response policy to determine the cause of maternal deaths and how they might be prevented. Methods: In the three different settings, efforts to ensure local community engagement provided a focus for the researchers to hone their skills in explaining research concepts and working in partnership with community members to co-develop ideas, their research methods and outputs. Results: Involvement of communities in scientific research, which entailed a two-way mutual engagement process, led to (i) generation of new research ideas that shaped the work, (ii) strengthened mutual trust, and (iii) promoted uptake of research findings. Conclusion: Our key findings strongly support the need for considering community engagement as one of the key components in research studies.
{"title":"Case studies from the experience of early career researchers in East Africa in building community engagement in research","authors":"Joel L. Bargul, Denna M. Mkwashapi, I. Namagembe, Immaculate Nakityo, A. Nakimuli, J. Byamugisha, Daniel Semakula, J. Seeley, N. Sewankambo","doi":"10.12688/openresafrica.13349.2","DOIUrl":"https://doi.org/10.12688/openresafrica.13349.2","url":null,"abstract":"Background: In this paper, we explain how three early career researchers actively engaged community members in their health research projects in Kenya, Tanzania and Uganda, and what was learnt from the experience. The research project in Kenya was on camel trypanosomiasis and the role of camel biting keds (or louse flies) in disease transmission. The project in Tanzania looked at the effect of human immunodeficiency virus and antiretroviral therapy on fertility and ascertained the trends in the use of family planning services amongst women of reproductive age. The focus of the project in Uganda was the implementation of maternal death surveillance and the response policy to determine the cause of maternal deaths and how they might be prevented. Methods: In the three different settings, efforts to ensure local community engagement provided a focus for the researchers to hone their skills in explaining research concepts and working in partnership with community members to co-develop ideas, their research methods and outputs. Results: Involvement of communities in scientific research, which entailed a two-way mutual engagement process, led to (i) generation of new research ideas that shaped the work, (ii) strengthened mutual trust, and (iii) promoted uptake of research findings. Conclusion: Our key findings strongly support the need for considering community engagement as one of the key components in research studies.","PeriodicalId":74358,"journal":{"name":"Open research Africa","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43800945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-06-20DOI: 10.12688/openresafrica.13372.1
Gabin Samba, A. Dassou, R. Idohou, Corinne M. Anagonou, A. Dansi
Background: Storage pests cause extensive damages to stored products and are responsible for huge post-harvest losses affecting the quality, quantity, and germination potential of stored grains and seeds. This study aimed to investigate the variability of traditional methods of storage and conservation of maize seeds practiced by farmers to propose alternative measures for a significant reduction of post-harvest losses of seeds. Methods : Using participatory research approaches, we surveyed farmers from 21 randomly selected villages in 5 districts in southern Benin. Data were collected on the storage structures of the 3 certified and most produced maize seeds varieties. The forms under which maize seeds are stored, as well as the damage caused by the major storage insects, were determined. Results: Results showed that most farmers store maize seeds in the form of grains and spathe. Following the laboratory observation of the three maize varieties studied, the DMR / QPM variety produced only in the district of Zagnanado has a low abundance of storage insects and a low rate of post-harvest losses. Sitophilus zeamais is the most abundant pest of the three maize seed varieties followed by Prostephanus truncatus. The variety 2000 SYN EE was the most attacked by storage insects. The most promising post-harvest agricultural practice is the storage of maize with spathe saved in jute bags, in granaries or cribs. Conclusions: Storage insects contribute to the depreciation of the quality of grains, loss of grain and reduction of their germinability in stock. Improving farmers' awareness of these post-harvest practices could help to reduce the damage of storage insects.
背景:储粮害虫对储粮产品造成广泛的危害,对储粮和种子的质量、数量和发芽潜力造成巨大的采后损失。本研究旨在调查农民使用的传统玉米种子储存和保存方法的可变性,以提出显著减少种子收获后损失的替代措施。方法:采用参与式研究方法,对贝宁南部5个区随机抽取的21个村庄的农民进行调查。收集了3个经认证和产量最高的玉米种子品种的储存结构数据。确定了玉米种子的贮藏形式,以及主要贮藏昆虫对玉米种子造成的危害。结果:结果表明,大多数农民以谷粒和芽的形式储存玉米种子。通过对所研究的三个玉米品种的实验室观察,仅在Zagnanado地区生产的DMR / QPM品种的贮藏昆虫丰度低,收获后损失率低。玉米象是3个玉米种子品种中数量最多的害虫,其次是长角螟。品种2000 SYN EE是贮藏昆虫侵害最多的品种。最有希望的收获后农业做法是将玉米用黄麻袋、粮仓或摇篮储存起来。结论:储粮昆虫是造成粮食品质下降、粮食损失和粮食发芽率降低的原因之一。提高农民对这些收获后做法的认识有助于减少贮藏昆虫的损害。
{"title":"Maize seeds storage systems and post-harvest losses in Benin: diversity, efficiency, storage insects, and implications for better products conservation","authors":"Gabin Samba, A. Dassou, R. Idohou, Corinne M. Anagonou, A. Dansi","doi":"10.12688/openresafrica.13372.1","DOIUrl":"https://doi.org/10.12688/openresafrica.13372.1","url":null,"abstract":"Background: Storage pests cause extensive damages to stored products and are responsible for huge post-harvest losses affecting the quality, quantity, and germination potential of stored grains and seeds. This study aimed to investigate the variability of traditional methods of storage and conservation of maize seeds practiced by farmers to propose alternative measures for a significant reduction of post-harvest losses of seeds. Methods : Using participatory research approaches, we surveyed farmers from 21 randomly selected villages in 5 districts in southern Benin. Data were collected on the storage structures of the 3 certified and most produced maize seeds varieties. The forms under which maize seeds are stored, as well as the damage caused by the major storage insects, were determined. Results: Results showed that most farmers store maize seeds in the form of grains and spathe. Following the laboratory observation of the three maize varieties studied, the DMR / QPM variety produced only in the district of Zagnanado has a low abundance of storage insects and a low rate of post-harvest losses. Sitophilus zeamais is the most abundant pest of the three maize seed varieties followed by Prostephanus truncatus. The variety 2000 SYN EE was the most attacked by storage insects. The most promising post-harvest agricultural practice is the storage of maize with spathe saved in jute bags, in granaries or cribs. Conclusions: Storage insects contribute to the depreciation of the quality of grains, loss of grain and reduction of their germinability in stock. Improving farmers' awareness of these post-harvest practices could help to reduce the damage of storage insects.","PeriodicalId":74358,"journal":{"name":"Open research Africa","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46131586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-06-09DOI: 10.12688/openresafrica.13406.1
Benard W. Kulohoma, Ibrahim Ng'eno
The clinical importance of non-malaria febrile acute illness (NM-AFI) in patients with a negative parasitological test has become apparent, with the progressive reduction in malaria transmission in endemic regions. Bacterial pathogens, for example Streptococcus pneumoniae and Haemophilus influenzae, which contribute disproportionally to febrile illness, are now preventable by vaccines. However, there are no vaccines, and little is known about viral NM-AFI prevalence, proliferation, virulence, and transmission chains between hosts. Although the predominant viral causes of NM-AFI are established, it is unclear if there are other NM-AFI associated emerging infectious viral pathogens that previously remained undetectable by conventional diagnostic strategies, for example severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Presumptive broad-spectrum antibiotic prescriptions to aparasitaemic patients not only drive drug resistance, but also lead to poor treatment outcomes. We hypothesized that insights on NM-AFI etiology, and consequently case management, could be improved by exploiting viral sequence diversity to identify viral pathogens present within metagenomics samples. We exploited simulated and existing infectious disease (Ebola, hepatitis C, chikungunya, and mosquito-borne arboviruses) metagenomic datasets to determine the composition of viral pathogens present, by implementing profile Hidden Markov Models derived from Swiss-Prot viral reference sequences for accurate pathogen detection and classification. Our analysis identified a combination of sequences from multiple viral etiological agents within the same disease sample. This approach provides a granular perspective of multiple viral etiological agents present within a single intra-host disease episode. It highlights prevalent viral strains that can subsequently be routinely detected using directed diagnostic tests to improve disease surveillance in endemic regions.
{"title":"NOMAD: metagenomic characterisation of the viral pathogen composition in outbreaks of non-malaria acute febrile illness cases","authors":"Benard W. Kulohoma, Ibrahim Ng'eno","doi":"10.12688/openresafrica.13406.1","DOIUrl":"https://doi.org/10.12688/openresafrica.13406.1","url":null,"abstract":"The clinical importance of non-malaria febrile acute illness (NM-AFI) in patients with a negative parasitological test has become apparent, with the progressive reduction in malaria transmission in endemic regions. Bacterial pathogens, for example Streptococcus pneumoniae and Haemophilus influenzae, which contribute disproportionally to febrile illness, are now preventable by vaccines. However, there are no vaccines, and little is known about viral NM-AFI prevalence, proliferation, virulence, and transmission chains between hosts. Although the predominant viral causes of NM-AFI are established, it is unclear if there are other NM-AFI associated emerging infectious viral pathogens that previously remained undetectable by conventional diagnostic strategies, for example severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Presumptive broad-spectrum antibiotic prescriptions to aparasitaemic patients not only drive drug resistance, but also lead to poor treatment outcomes. We hypothesized that insights on NM-AFI etiology, and consequently case management, could be improved by exploiting viral sequence diversity to identify viral pathogens present within metagenomics samples. We exploited simulated and existing infectious disease (Ebola, hepatitis C, chikungunya, and mosquito-borne arboviruses) metagenomic datasets to determine the composition of viral pathogens present, by implementing profile Hidden Markov Models derived from Swiss-Prot viral reference sequences for accurate pathogen detection and classification. Our analysis identified a combination of sequences from multiple viral etiological agents within the same disease sample. This approach provides a granular perspective of multiple viral etiological agents present within a single intra-host disease episode. It highlights prevalent viral strains that can subsequently be routinely detected using directed diagnostic tests to improve disease surveillance in endemic regions.","PeriodicalId":74358,"journal":{"name":"Open research Africa","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49091256","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-04-08eCollection Date: 2022-01-01DOI: 10.12688/openresafrica.13383.1
Ismail B Ahmed, Eucharia O Nwaichi, Ejikeme Ugwoha, John N Ugbebor, Samuel B Arokoyu
Petroleum hydrocarbon spill on land pollutes soil and reduces its ecosystem. Hydrocarbon transport in the soil is aided by several biological, physical, and chemical processes. However, pore characteristics play a major role in the distribution within the soil matrix. Restoring land use after spills necessitates remediation using cost-effective technologies. Several remediation technologies have been demonstrated at different scales, and research is ongoing to improve their performances towards the reduction of treatment costs. The process of removing the contaminants in the soil is through one or a combination of containment, separation, and degradation methods under the influence of biological, physical, chemical, and electrically-dominated processes. Generally, performance improvement is achieved through the introduction of products/materials and/or energy. Nevertheless, the technologies can be categorized based on effectiveness period as short, medium, and long term. The treatment cost of short, medium, and long-term technologies are usually in the range of $39 - 331/t (/tonne), $22 - 131/t, and $8 - 131/t, respectively. However, the total cost depends on other factors such as site location, capital cost, and permitting. This review compiles cost-saving strategies reported for different techniques used in remediating petroleum hydrocarbon polluted soil. We discuss the principles of contaminant removal, performance enhancing methods, and the cost-effectiveness analysis of selected technologies.
{"title":"Cost reduction strategies in the remediation of petroleum hydrocarbon contaminated soil.","authors":"Ismail B Ahmed, Eucharia O Nwaichi, Ejikeme Ugwoha, John N Ugbebor, Samuel B Arokoyu","doi":"10.12688/openresafrica.13383.1","DOIUrl":"10.12688/openresafrica.13383.1","url":null,"abstract":"<p><p>Petroleum hydrocarbon spill on land pollutes soil and reduces its ecosystem. Hydrocarbon transport in the soil is aided by several biological, physical, and chemical processes. However, pore characteristics play a major role in the distribution within the soil matrix. Restoring land use after spills necessitates remediation using cost-effective technologies. Several remediation technologies have been demonstrated at different scales, and research is ongoing to improve their performances towards the reduction of treatment costs. The process of removing the contaminants in the soil is through one or a combination of containment, separation, and degradation methods under the influence of biological, physical, chemical, and electrically-dominated processes. Generally, performance improvement is achieved through the introduction of products/materials and/or energy. Nevertheless, the technologies can be categorized based on effectiveness period as short, medium, and long term. The treatment cost of short, medium, and long-term technologies are usually in the range of $39 - 331/t (/tonne), $22 - 131/t, and $8 - 131/t, respectively. However, the total cost depends on other factors such as site location, capital cost, and permitting. This review compiles cost-saving strategies reported for different techniques used in remediating petroleum hydrocarbon polluted soil. We discuss the principles of contaminant removal, performance enhancing methods, and the cost-effectiveness analysis of selected technologies.</p>","PeriodicalId":74358,"journal":{"name":"Open research Africa","volume":"5 ","pages":"21"},"PeriodicalIF":0.0,"publicationDate":"2022-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9718438/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9194865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-01-01DOI: 10.12688/openresafrica.13397.1
Erick K Serem, Joel L Bargul, Moses M Ngari, Osman A Abdullahi, David M Mburu
Background: Animal African trypanosomosis (AAT) is a veterinary disease caused by trypanosomes transmitted cyclically by tsetse flies. AAT causes huge agricultural losses in sub-Saharan Africa. Both tsetse flies and trypanosomosis (T&T) are endemic in the study area inhabited by smallholder livestock farmers at the livestock-wildlife interface around Arabuko-Sokoke Forest Reserve (ASFR) in Kilifi County on the Kenyan coast. We assessed farmers' knowledge, perceptions and control practices towards T&T. Methods: A cross-sectional study was conducted during November and December 2017 to collect data from 404 randomly selected cattle-rearing households using a structured questionnaire. Descriptive statistics were used to determine farmers' knowledge, perceptions, and control practices towards T&T. Demographic factors associated with knowledge of T&T were assessed using a logistic regression model. Results: Participants consisted of 53% female, 77% married, 30% elderly (>55 years), and the majority (81%) had attained primary education or below. Most small-scale farmers (98%) knew the tsetse fly by its local name, and 76% could describe the morphology of the adult tsetse fly by size in comparison to the housefly's ( Musca domestica). Only 16% of the farmers knew tsetse flies as vectors of livestock diseases. Higher chances of adequate knowledge on T&T were associated with the participants' (i) age of 15-24 years (aOR 2.88 (95% CI 1.10-7.52), (ii) level of education including secondary (aOR 2.46 (95% CI 1.43-4.24)) and tertiary (aOR 3.80 (95% CI 1.54-9.37)), and (iii) employment status: self-employed farmers (aOR 6.54 (95% CI 4.36-9.80)). Conclusions: Our findings suggest that small-scale farmers around ASFR have limited knowledge of T&T. It is envisaged that efforts geared towards training of the farmers would bridge this knowledge gap and sharpen the perceptions and disease control tactics to contribute to the prevention and control of T&T.
背景:非洲动物锥虫病(AAT)是一种由采采蝇周期性传播的锥虫引起的兽医学疾病。AAT在撒哈拉以南非洲造成了巨大的农业损失。采采蝇和锥虫病(T&T)在肯尼亚海岸基利菲县阿拉布科-索科克森林保护区(ASFR)附近牲畜-野生动物交界的小农养殖户居住的研究区域流行。我们评估了农民对T&T的知识、认知和控制做法。方法:采用横断面研究方法,于2017年11月至12月随机抽取404户养牛户,采用结构化问卷收集数据。描述性统计用于确定农民对T&T的知识,观念和控制措施。使用逻辑回归模型评估与T&T知识相关的人口统计学因素。结果:参与者中53%为女性,77%为已婚,30%为老年人(>55岁),大多数(81%)为初等及以下文化程度。大多数小农(98%)知道采采蝇的当地名称,76%的人可以通过大小描述成年采采蝇与家蝇(Musca domestica)的形态。只有16%的农民知道采采蝇是牲畜疾病的媒介。对T&T有充分了解的机会与参与者(i) 15-24岁(aOR 2.88 (95% CI 1.10-7.52), (ii)教育水平包括中等教育(aOR 2.46 (95% CI 1.43-4.24))和高等教育(aOR 3.80 (95% CI 1.54-9.37)),以及(iii)就业状况:个体农场主(aOR 6.54 (95% CI 4.36-9.80))相关。结论:我们的研究结果表明,ASFR附近的小农对T&T的了解有限。据设想,旨在培训农民的努力将弥合这一知识差距,提高认识和疾病控制策略,从而有助于预防和控制T&T。
{"title":"Farmers' knowledge, perceptions, and practices on animal trypanosomosis and the tsetse fly vector: A cross-sectional study around Kenya's Arabuko-Sokoke Forest Reserve at the livestock-wildlife interface.","authors":"Erick K Serem, Joel L Bargul, Moses M Ngari, Osman A Abdullahi, David M Mburu","doi":"10.12688/openresafrica.13397.1","DOIUrl":"https://doi.org/10.12688/openresafrica.13397.1","url":null,"abstract":"<p><p><b>Background:</b> Animal African trypanosomosis (AAT) is a veterinary disease caused by trypanosomes transmitted cyclically by tsetse flies. AAT causes huge agricultural losses in sub-Saharan Africa. Both tsetse flies and trypanosomosis (T&T) are endemic in the study area inhabited by smallholder livestock farmers at the livestock-wildlife interface around Arabuko-Sokoke Forest Reserve (ASFR) in Kilifi County on the Kenyan coast. We assessed farmers' knowledge, perceptions and control practices towards T&T. <b>Methods:</b> A cross-sectional study was conducted during November and December 2017 to collect data from 404 randomly selected cattle-rearing households using a structured questionnaire. Descriptive statistics were used to determine farmers' knowledge, perceptions, and control practices towards T&T. Demographic factors associated with knowledge of T&T were assessed using a logistic regression model. <b>Results:</b> Participants consisted of 53% female, 77% married, 30% elderly (>55 years), and the majority (81%) had attained primary education or below. Most small-scale farmers (98%) knew the tsetse fly by its local name, and 76% could describe the morphology of the adult tsetse fly by size in comparison to the housefly's ( <i>Musca domestica</i>). Only 16% of the farmers knew tsetse flies as vectors of livestock diseases. Higher chances of adequate knowledge on T&T were associated with the participants' (i) age of 15-24 years (aOR 2.88 (95% CI 1.10-7.52), (ii) level of education including secondary (aOR 2.46 (95% CI 1.43-4.24)) and tertiary (aOR 3.80 (95% CI 1.54-9.37)), and (iii) employment status: self-employed farmers (aOR 6.54 (95% CI 4.36-9.80)). <b>Conclusions:</b> Our findings suggest that small-scale farmers around ASFR have limited knowledge of T&T. It is envisaged that efforts geared towards training of the farmers would bridge this knowledge gap and sharpen the perceptions and disease control tactics to contribute to the prevention and control of T&T.</p>","PeriodicalId":74358,"journal":{"name":"Open research Africa","volume":"5 ","pages":"22"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10439355/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10424253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-01-01DOI: 10.12688/openresafrica.13438.2
Imelda Namagembe, Jolly Beyeza-Kashesya, Joseph Rujumba, Dan K Kaye, Moses Mukuru, Noah Kiwanuka, Ashley Moffett, Annettee Nakimuli, Josaphat Byamugisha
Background: Preventable maternal and newborn deaths remain a global concern, particularly in low- and- middle-income countries (LMICs) Timely maternal death surveillance and response (MDSR) is a recommended strategy to account for such deaths through identifying contextual factors that contributed to the deaths to inform recommendations to implement in order to reduce future deaths. Implementation of MDSR is still suboptimal due to barriers such as inadequate skills and leadership to support MDSR. With the leadership of WHO and UNFPA, there is momentum to roll out MDSR, however, the barriers and enablers for implementation have received limited attention. These have implications for successful implementation. The aim of this study was: To assess barriers and facilitators to implementation of MDSR at a busy urban National Referral Hospital as perceived by health workers, administrators, and other partners in Reproductive Health. Methods: Qualitative study using in-depth interviews (24), 4 focus-group discussions with health workers, 15 key-informant interviews with health sector managers and implementing partners in Reproductive-Health. We conducted thematic analysis drawing on the Theory of Planned Behaviour (TPB). Results: The major barriers to implementation of MDSR were: inadequate knowledge and skills; fear of blame / litigation; failure to implement recommendations; burn out because of workload and inadequate leadership- to support health workers. Major facilitators were involving all health workers in the MDSR process, eliminate blame, strengthen leadership, implement recommendations from MDSR and functionalize lower health facilities (especially Health Centre -IVs). Conclusions: The barriers of MDSR include knowledge and skills gaps, fear of blame and litigation, and other health system factors such as erratic emergency supplies, and leadership/governance challenges. Recommendation: Efforts to strengthen MDSR for impact should use health system responsiveness approach to address the barriers identified, constructive participation of health workers to harness the facilitators and addressing the required legal framework.
{"title":"Barriers and facilitators to maternal death surveillance and response at a busy urban National Referral Hospital in Uganda.","authors":"Imelda Namagembe, Jolly Beyeza-Kashesya, Joseph Rujumba, Dan K Kaye, Moses Mukuru, Noah Kiwanuka, Ashley Moffett, Annettee Nakimuli, Josaphat Byamugisha","doi":"10.12688/openresafrica.13438.2","DOIUrl":"https://doi.org/10.12688/openresafrica.13438.2","url":null,"abstract":"<p><p><b>Background:</b> Preventable maternal and newborn deaths remain a global concern, particularly in low- and- middle-income countries (LMICs) Timely maternal death surveillance and response (MDSR) is a recommended strategy to account for such deaths through identifying contextual factors that contributed to the deaths to inform recommendations to implement in order to reduce future deaths. Implementation of MDSR is still suboptimal due to barriers such as inadequate skills and leadership to support MDSR. With the leadership of WHO and UNFPA, there is momentum to roll out MDSR, however, the barriers and enablers for implementation have received limited attention. These have implications for successful implementation. The aim of this study was: To assess barriers and facilitators to implementation of MDSR at a busy urban National Referral Hospital as perceived by health workers, administrators, and other partners in Reproductive Health. <b>Methods:</b> Qualitative study using in-depth interviews (24), 4 focus-group discussions with health workers, 15 key-informant interviews with health sector managers and implementing partners in Reproductive-Health. We conducted thematic analysis drawing on the Theory of Planned Behaviour (TPB). <b>Results:</b> The major barriers to implementation of MDSR were: inadequate knowledge and skills; fear of blame / litigation; failure to implement recommendations; burn out because of workload and inadequate leadership- to support health workers. Major facilitators were involving all health workers in the MDSR process, eliminate blame, strengthen leadership, implement recommendations from MDSR and functionalize lower health facilities (especially Health Centre -IVs). <b>Conclusions:</b> The barriers of MDSR include knowledge and skills gaps, fear of blame and litigation, and other health system factors such as erratic emergency supplies, and leadership/governance challenges. <b>Recommendation</b>: Efforts to strengthen MDSR for impact should use health system responsiveness approach to address the barriers identified, constructive participation of health workers to harness the facilitators and addressing the required legal framework.</p>","PeriodicalId":74358,"journal":{"name":"Open research Africa","volume":"5 ","pages":"31"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10280031/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9712084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}