Publisher Correction: Computer-aided interpretation of chest radiography reveals the spectrum of tuberculosis in rural South Africa

The original version of this Article contained errors in the affiliations of members of the Vukuzazi Team. Anand Ramnanan, Anele Mkhwanazi, Antony Rapulana, Anupa Singh, Ashentha Govender, Ayanda Zungu, Bongani Magwaza, Bongumenzi Ndlovu, Clive Mavimbela, Costa Criticos, Day Munatsi, Dilip Kalyan, Doctar Mlambo, Fezeka Mfeka, Freddy Mabetlela, Gregory Ording-Jespersen, Hannah Keal, Hlengiwe Dlamini, Hlengiwe Khathi, Hlobisile Chonco, Hlobisile Gumede, Hlolisile Khumalo, Hloniphile Ngubane, Hollis Shen, Innocentia Mpofana, Jaco Dreyer, Jade Cousins, Kandaseelan Chetty, Kayleen Brien, Khadija Khan, Khanyisani Buthelezi, Kimeshree Perumal, Kobus Herbst, Lindani Mthembu, Logan Pillay, Mandisi Dlamini, Mandlakayise Zikhali, Mbali Mbuyisa, Mbuti Mofokeng, Melusi Sibiya, Mlungisi Dube, Mpumelelo Steto, Mzamo Buthelezi, Nagavelli Padayachi, Nceba Gqaleni, Ngcebo Mhlongo, Nokukhanya Ntshakala, Nomathamsanqa Majozi, Nombuyiselo Zondi, Nomfundo Luthuli, Nomfundo Ngema, Nompilo Buthelezi, Nonceba Mfeka, Nondumiso Khuluse, Nondumiso Mabaso, Nondumiso Zitha, Nonhlanhla Mfekayi, Nonhlanhla Mzimela, Nozipho Mbonambi, Ntombiyenhlanhla Mkhwanazi, Ntombiyenkosi Ntombela, Pamela Ramkalawon, Phakamani Mkhwanazi, Philippa Mathews, Phumelele Mthethwa, Phumla Ngcobo, Raynold Zondo, Rochelle Singh, Rose Myeni, Sanah Bucibo, Sandile Mthembu, Sashin Harilall, Senamile Makhari, Seneme Mchunu, Senzeni Mkhwanazi, Sibahle Gumbi, Siboniso Nene, Sibusiso Mhlongo, Sibusiso Mkhwanazi, Sibusiso Nsibande, Simphiwe Ntshangase, Siphephelo Dlamini, Sithembile Ngcobo, Siyabonga Nsibande, Siyabonga Nxumalo, Sizwe Ndlela, Skhumbuzo Mthombeni, Smangaliso Zulu, Sphiwe Clement Mthembu, Sphiwe Ntuli, Talente Ntimbane, Thabile Zondi, Thandeka Khoza, Thengokwakhe Nkosi, Thokozani Bhengu, Thokozani Simelane, Tshwaraganang Modise, Tumi Madolo, Welcome Petros Mthembu, Xolani Mkhize, Zamashandu Mbatha, Zinhle Buthelezi, Zinhle Mthembu and Zizile Sikhosana were incorrectly associated with “Digital Health & Machine Learning, Hasso Plattner Institute for Digital Engineering, Berlin, Germany” and the affiliation “Africa Health Research Institute, KwaZulu-Natal, South Africa” was inadvertently omitted. This has now been corrected in both the PDF and HTML versions of the Article

Computer-aided interpretation of chest radiography reveals the spectrum of tuberculosis in rural South Africa.

Computer-aided digital chest radiograph interpretation (CAD) can facilitate high-throughput screening for tuberculosis (TB), but its use in population-based active case-finding programs has been limited. In an HIV-endemic area in rural South Africa, we used a CAD algorithm (CAD4TBv5) to interpret digital chest x-rays (CXR) as part of a mobile health screening effort. Participants with TB symptoms or CAD4TBv5 score above the triaging threshold were referred for microbiological sputum assessment. During an initial pilot phase, a low CAD4TBv5 triaging threshold of 25 was selected to maximize TB case finding. We report the performance of CAD4TBv5 in screening 9,914 participants, 99 (1.0%) of whom were found to have microbiologically proven TB. CAD4TBv5 was able to identify TB cases at the same sensitivity but lower specificity as a blinded radiologist, whereas the next generation of the algorithm (CAD4TBv6) achieved comparable sensitivity and specificity to the radiologist. The CXRs of people with microbiologically confirmed TB spanned a range of lung field abnormality, including 19 (19.2%) cases deemed normal by the radiologist. HIV serostatus did not impact CAD4TB's performance. Notably, 78.8% of the TB cases identified during this population-based survey were asymptomatic and therefore triaged for sputum collection on the basis of CAD4TBv5 score alone. While CAD4TBv6 has the potential to replace radiologists for triaging CXRs in TB prevalence surveys, population-specific piloting is necessary to set the appropriate triaging thresholds. Further work on image analysis strategies is needed to identify radiologically subtle active TB

Global network of computational biology communities: ISCB's regional student groups breaking barriers [version 1; peer review: Not peer reviewed]

Regional Student Groups (RSGs) of the International Society for Computational Biology Student Council (ISCB-SC) have been instrumental to connect computational biologists globally and to create more awareness about bioinformatics education. This article highlights the initiatives carried out by the RSGs both nationally and internationally to strengthen the present and future of the bioinformatics community. Moreover, we discuss the future directions the organization will take and the challenges to advance further in the ISCB-SC main mission: “Nurture the new generation of computational biologists”.Fil: Shome, Sayane. University of Iowa; Estados UnidosFil: Parra, Rodrigo Gonzalo. European Molecular Biology Laboratory; Alemania. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Fatima, Nazeefa. Uppsala Universitet; SueciaFil: Monzon, Alexander Miguel. Università di Padova; ItaliaFil: Cuypers, Bart. Universiteit Antwerp; BélgicaFil: Moosa, Yumna. University of KwaZulu Natal; SudáfricaFil: Da Rocha Coimbra, Nilson. Universidade Federal de Minas Gerais; BrasilFil: Assis, Juliana. Universidade Federal de Minas Gerais; BrasilFil: Giner Delgado, Carla. Universitat Autònoma de Barcelona; EspañaFil: Dönertaş, Handan Melike. European Molecular Biology Laboratory. European Bioinformatics Institute; Reino UnidoFil: Cuesta Astroz, Yesid. Universidad de Antioquia; Colombia. Universidad Ces. Facultad de Medicina.; ColombiaFil: Saarunya, Geetha. University of South Carolina; Estados UnidosFil: Allali, Imane. Universite Mohammed V. Rabat; Otros paises de África. University of Cape Town; SudáfricaFil: Gupta, Shruti. Jawaharlal Nehru University; IndiaFil: Srivastava, Ambuj. Indian Institute of Technology Madras; IndiaFil: Kalsan, Manisha. Jawaharlal Nehru University; IndiaFil: Valdivia, Catalina. Universidad Andrés Bello; ChileFil: Olguín Orellana, Gabriel José. Universidad de Talca; ChileFil: Papadimitriou, Sofia. Vrije Unviversiteit Brussel; Bélgica. Université Libre de Bruxelles; BélgicaFil: Parisi, Daniele. Katholikie Universiteit Leuven; BélgicaFil: Kristensen, Nikolaj Pagh. Technical University of Denmark; DinamarcaFil: Rib, Leonor. Universidad de Copenhagen; DinamarcaFil: Guebila, Marouen Ben. University of Luxembourg; LuxemburgoFil: Bauer, Eugen. University of Luxembourg; LuxemburgoFil: Zaffaroni, Gaia. University of Luxembourg; LuxemburgoFil: Bekkar, Amel. Universite de Lausanne; SuizaFil: Ashano, Efejiro. APIN Public Health Initiatives; NigeriaFil: Paladin, Lisanna. Università di Padova; ItaliaFil: Necci, Marco. Università di Padova; ItaliaFil: Moreyra, Nicolás Nahuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentin

Case report: mechanisms of HIV elite control in two African women

Background The majority of people living with HIV require antiretroviral therapy (ART) for controlling viral replication, however there are rare HIV controllers who spontaneously and durably control HIV in the absence of treatment. Understanding what mediates viral control in these individuals has provided us with insights into the immune mechanisms that may be important to induce for a vaccine or functional cure for HIV. To date, few African elite controllers from high incidence settings have been described. We identified virological controllers from the CAPRISA 002 cohort of HIV-1 subtype C infected women in KwaZulu Natal, South Africa, two (1%) of whom were elite controllers. We examined the genetic, clinical, immunological and virological characteristics of these two elite HIV controllers in detail, to determine whether they exhibit features of putative viral control similar to those described for elite controllers reported in the literature. Case presentation In this case report, we present clinical features, CD4+ T cell and viral load trajectories for two African women over 7 years of HIV infection. Viral load became undetectable 10 months after HIV infection in Elite Controller 1 (EC1), and after 6 weeks in Elite Controller 2 (EC2), and remained undetectable for the duration of follow-up, in the absence of ART. Both elite controllers expressed multiple HLA Class I and II haplotypes previously associated with slower disease progression (HLA-A*74:01, HLA-B*44:03, HLA-B*81:01, HLA-B*57:03, HLA-DRB1*13). Fitness assays revealed that both women were infected with replication competent viruses, and both expressed higher mRNA levels of p21, a host restriction factor associated with viral control. HIV-specific T cell responses were examined using flow cytometry. EC1 mounted high frequency HIV-specific CD8+ T cell responses, including a B*81:01-restricted Gag TL9 response. Unusually, EC2 had evidence of pre-infection HIV-specific CD4+ T cell responses. Conclusion We identified some features typical of elite controllers, including high magnitude HIV-specific responses and beneficial HLA. In addition, we made the atypical finding of pre-infection HIV-specific immunity in one elite controller, that may have contributed to very early viral control. This report highlights the importance of studying HIV controllers in high incidence settings

The met and unmet health needs for HIV, hypertension, and diabetes in rural KwaZulu-Natal, South Africa: analysis of a cross-sectional multimorbidity survey.

BACKGROUND: The convergence of infectious diseases and non-communicable diseases in South Africa is challenging to health systems. In this analysis, we assessed the multimorbidity health needs of individuals and communities in rural KwaZulu-Natal and established a framework to quantify met and unmet health needs for individuals living with infectious and non-communicable diseases. METHODS: We analysed data collected between May 25, 2018, and March 13, 2020, from participants of a large, community-based, cross-sectional multimorbidity survey (Vukuzazi) that offered community-based HIV, hypertension, and diabetes screening to all residents aged 15 years or older in a surveillance area in the uMkhanyakude district in KwaZulu-Natal, South Africa. Data from the Vukuzazi survey were linked with data from demographic and health surveillance surveys with a unique identifier common to both studies. Questionnaires were used to assess the diagnosed health conditions, treatment history, general health, and sociodemographic characteristics of an individual. For each condition (ie, HIV, hypertension, and diabetes), individuals were defined as having no health needs (absence of condition), met health needs (condition that is well controlled), or one or more unmet health needs (including diagnosis, engagement in care, or treatment optimisation). We analysed met and unmet health needs for individual and combined conditions and investigated their geospatial distribution. FINDINGS: Of 18 041 participants who completed the survey (12 229 [67·8%] were female and 5812 [32·2%] were male), 9898 (54·9%) had at least one of the three chronic diseases measured. 4942 (49·9%) of these 9898 individuals had at least one unmet health need (1802 [18·2%] of 9898 needed treatment optimisation, 1282 [13·0%] needed engagement in care, and 1858 [18·8%] needed a diagnosis). Unmet health needs varied by disease; 1617 (93·1%) of 1737 people who screened positive for diabetes, 2681 (58·2%) of 4603 people who screened positive for hypertension, and 1321 (21·7%) of 6096 people who screened positive for HIV had unmet health needs. Geospatially, met health needs for HIV were widely distributed and unmet health needs for all three conditions had specific sites of concentration; all three conditions had an overlapping geographical pattern for the need for diagnosis. INTERPRETATION: Although people living with HIV predominantly have a well controlled condition, there is a high burden of unmet health needs for people living with hypertension and diabetes. In South Africa, adapting current, widely available HIV care services to integrate non-communicable disease care is of high priority. FUNDING: Fogarty International Center and the National Institutes of Health, the Bill & Melinda Gates Foundation, the South African Department of Science and Innovation, the South African Medical Research Council, the South African Population Research Infrastructure Network, and the Wellcome Trust. TRANSLATION: For the isiZulu translation of the abstract see Supplementary Materials section

Biogenic nanoparticles application in agriculture for ROS mitigation and abiotic stress tolerance: A review

Plants have to face different abiotic stressors, such as extreme temperatures, drought, salinity, flood, and heavy metals, which negatively impact their growth and development, leading to lower agricultural productivity, food security concerns, and financial losses. Nanotechnology has emerged as a solution to mitigate these negative effects, improving resource use efficiency, reducing pollution, preventing plant diseases, and enhancing sustainability. Nanoparticles (NPs) apllication to agricultural crops addresses nutrient deficiencies, enhances stress tolerance, and improves crop yield and quality. Sustainable and environment friendly methods for synthesizing NPs have been developed over the last few decades. NPs possess distinct qualities and can serve as powerful sensors, controlling critical physiological and biochemical processes in plants. Furthermore, NPs offer unique mechanisms for adapting to changing climatic conditions. Abiotic stress generates reactive oxygen species (ROS), which cause oxidative stress and impairs redox homeostasis. The roles of ROS in signaling cascades and stress tolerance are gaining recognition. This review explores the potential of plant-based metallic and metallic oxide NPs to mitigate the harmful consequences of abiotic stresses induced excessive ROS. We have critically discussed green/biological synthesis methods of NPs, their potential roles in agriculture, and the mechanisms by which plant-based NPs can counteract ROS harmful effects on plant metabolism. Utilizing nanotechnology paves the way for sustainable crop cultivation, ensuring increased crop yields and enhanced environmental resilience

Convergence of HIV and non-communicable disease epidemics: geospatial mapping of the unmet health needs in an HIV hyperendemic community in South Africa

Introduction As people living with HIV (PLHIV) are experiencing longer survival, the co-occurrence of HIV and non-communicable diseases has become a public health priority. In response to this emerging challenge, we aimed to characterise the spatial structure of convergence of chronic health conditions in an HIV hyperendemic community in KwaZulu-Natal, South Africa.Methods In this cross-sectional study, we used data from a comprehensive population-based disease survey conducted in KwaZulu-Natal, South Africa, which collected data on HIV, diabetes and hypertension. We implemented a novel health needs scale to categorise participants as: diagnosed and well-controlled (Needs Score 1), diagnosed and suboptimally controlled (Score 2), diagnosed but not engaged in care (Score 3) or undiagnosed and uncontrolled (Score 4). Scores 2–4 were indicative of unmet health needs. We explored the geospatial structure of unmet health needs using different spatial clustering methods.Results The analytical sample comprised 18 041 individuals. We observed a similar spatial structure for HIV among those with combined needs Score 2–3 (diagnosed but uncontrolled) and Score 4 (undiagnosed and uncontrolled), with most PLHIV with unmet needs clustered in the southern urban and peri-urban areas. Conversely, a high prevalence of need Scores 2 and 3 for diabetes and hypertension was mostly distributed in the more rural central and northern part of the surveillance area. A high prevalence of need Score 4 for diabetes and hypertension was mostly distributed in the rural southern part of the surveillance area. Multivariate clustering analysis revealed a significant overlap of all three diseases in individuals with undiagnosed and uncontrolled diseases (unmet needs Score 4) in the southern part of the catchment area.Conclusions In an HIV hyperendemic community in South Africa, areas with the highest needs for PLHIV with undiagnosed and uncontrolled disease are also areas with the highest burden of unmet needs for other chronic health conditions, such as diabetes and hypertension. Our study has revealed remarkable differences in the distribution of health needs across the rural to urban continuum even within this relatively small study site. The identification and prioritisation of geographically clustered vulnerable communities with unmet health needs for both HIV and non-communicable diseases provide a basis for policy and implementation strategies to target communities with the highest health needs

Genome Detective: An Automated System for Virus Identification from High-throughput sequencing data.

Genome Detective is an easy to use web-based software application that assembles the genomes of viruses quickly and accurately. The application uses a novel alignment method that constructs genomes by reference-based linking of de-novo contigs by combining amino-acids and nucleotide scores. The software was optimized using synthetic datasets to represent the great diversity of virus genomes. The application was then validated with next generation sequencing data of hundreds of viruses. User time is minimal and it is limited to the time required to upload the data

Genome Detective: an automated system for virus identification from high-throughput sequencing data

SUMMARY: Genome Detective is an easy to use web-based software application that assembles the genomes of viruses quickly and accurately. The application uses a novel alignment method that constructs genomes by reference-based linking of de novo contigs by combining amino-acids and nucleotide scores. The software was optimized using synthetic datasets to represent the great diversity of virus genomes. The application was then validated with next generation sequencing data of hundreds of viruses. User time is minimal and it is limited to the time required to upload the data. AVAILABILITY AND IMPLEMENTATION: Available online: http://www.genomedetective.com/app/typingtool/virus/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.status: publishe

Genome Detective: an automated system for virus identification from high-throughput sequencing data

Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2018-10-24T16:33:26Z No. of bitstreams: 1 Vilsker M Genome...2018.pdf: 188021 bytes, checksum: 6e033cec3fa3935db76c651a7ee16c6f (MD5)Approved for entry into archive by Ana Maria Fiscina Sampaio ([email protected]) on 2018-10-24T17:02:13Z (GMT) No. of bitstreams: 1 Vilsker M Genome...2018.pdf: 188021 bytes, checksum: 6e033cec3fa3935db76c651a7ee16c6f (MD5)Made available in DSpace on 2018-10-24T17:02:13Z (GMT). No. of bitstreams: 1 Vilsker M Genome...2018.pdf: 188021 bytes, checksum: 6e033cec3fa3935db76c651a7ee16c6f (MD5) Previous issue date: 2018South African Medical Research Council (MRC-RFA-UFSP-01-2013/UKZN HIVEPI), a Royal Society Newton Advanced Fellowship (TdO), the VIROGENESIS project receives funding from the European Union’s Horizon 2020 Research and Innovation Program (under Grant Agreement no. 634650) and the National Institutes of Health Common Fund, grant number U24HG006941Emweb bvba. Herent, Belgium.University of KwaZulu-Natal. School of Laboratory Medicine and Medical Sciences. Nelson R Mandela School of Medicine. College of Health Sciences. KwaZulu-Natal Research Innovation and Sequencing Platform. Durban, South Africa.The Dutch National Institute for Public Health and the Environment. Bilthoven, The Netherlands.University of KwaZulu-Natal. School of Laboratory Medicine and Medical Sciences. Nelson R Mandela School of Medicine. College of Health Sciences. KwaZulu-Natal Research Innovation and Sequencing Platform. Durban, South Africa / Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Belo Horizonte, MG, Brasil / Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Hematologia, Genética e Biologia Computacional. Salvador, BA, Brasil.Emweb bvba. Herent, Belgium.Emweb bvba. Herent, Belgium.Emweb bvba. Herent, Belgium.Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Belo Horizonte, MG, Brasil / Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Hematologia, Genética e Biologia Computacional. Salvador, BA, Brasil / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brasil.Rega Institute for Medical Research. KU Leuven. Department of Microbiology and Immunology. Clinical and Epidemiological Virology. Leuven, Belgium.Rega Institute for Medical Research. KU Leuven. Department of Microbiology and Immunology. Clinical and Epidemiological Virology. Leuven, Belgium / Universidade Nova de Lisboa. Instituto de Higiene e Medicina Tropical. Health and Tropical Medicine. Unidade de Microbiologia. Lisbon, Portugal.Emweb bvba. Herent, Belgium.University of KwaZulu-Natal. School of Laboratory Medicine and Medical Sciences. Nelson R Mandela School of Medicine. College of Health Sciences. KwaZulu-Natal Research Innovation and Sequencing Platform. Durban, South Africa.Genome Detective is an easy to use web-based software application that assembles the genomes of viruses quickly and accurately. The application uses a novel alignment method that constructs genomes by reference-based linking of de novo contigs by combining amino-acids and nucleotide scores. The software was optimized using synthetic datasets to represent the great diversity of virus genomes. The application was then validated with next generation sequencing data of hundreds of viruses. User time is minimal and it is limited to the time required to upload the data