Prototyping a Knowledge-Based System to Identify Botanical Extracts for Plant Health in Sub-Saharan Africa.
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ABSTRACT:
SUBMITTER: Silvie PJ
PROVIDER: S-EPMC8146496 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Sub-Saharan Africa represents 69% of the total number of individuals living with HIV infection worldwide and 72% of AIDS deaths globally. Pulmonary infection is a common and frequently fatal complication, though little is known regarding the lower airway microbiome composition of this population. Our objectives were to characterize the lower airway microbiome of Ugandan HIV-infected patients with pneumonia, to determine relationships with demographic, clinical, immunological, and microbiological variables and to compare the composition and predicted metagenome of these communities to a comparable cohort of patients in the US (San Francisco). Bronchoalveolar lavage samples from a cohort of 60 Ugandan HIV-infected patients with acute pneumonia were collected. Amplified 16S ribosomal RNA was profiled and aforementioned relationships examined. Ugandan airway microbiome composition and predicted metagenomic function were compared to US HIV-infected pneumonia patients. Among the most common bacterial pulmonary pathogens, Pseudomonas aeruginosa was most prevalent in the Ugandan cohort. Patients with a richer and more diverse airway microbiome exhibited lower bacterial burden, enrichment of members of the Lachnospiraceae and sulfur-reducing bacteria and reduced expression of TNF-alpha and matrix metalloproteinase-9. Compared to San Franciscan patients, Ugandan airway microbiome were significantly richer, and compositionally distinct with predicted metagenomes that encoded a multitude of distinct pathogenic pathways e.g secretion systems. Ugandan pneumonia-associated airway microbiome is compositionally and functionally distinct from those detected in comparable patients in developed countries, a feature which may contribute to adverse outcomes in this population. Please note that the data from the comparable cohort of patients in the USUS data was published as supplemental material of PMID: 22760045 but not submitted to GEO The 'patient_info.txt' contains 12 clinical, 7 immunological and 3 microbiological variables for each patient.
2014-02-20 | GSE52791 | GEO
Project description:Konzo, a disease characterized by sudden, irreversible spastic paraparesis, affecting up to 10% of the population in some regions of Sub-Saharan Africa during outbreaks and is strongly associated with dietary exposure to cyanogenic bitter cassava. The molecular mechanisms underlying the development of konzo, remain largely unknown. Here, through an analysis of 16 individuals with konzo and matched healthy controls from the same outbreak zones, we identified 117 differentially methylated loci involved in numerous biological processes that may identify cyanogenic- sensitive regions of the genome, providing the first study of epigenomic alterations associated with sub-lethal cyanide exposure and a clinical phenotype.
2022-12-31 | GSE180119 | GEO
Project description:Sub-Saharan Africa represents 69% of the total number of individuals living with HIV infection worldwide and 72% of AIDS deaths globally. Pulmonary infection is a common and frequently fatal complication, though little is known regarding the lower airway microbiome composition of this population. Our objectives were to characterize the lower airway microbiome of Ugandan HIV-infected patients with pneumonia, to determine relationships with demographic, clinical, immunological, and microbiological variables and to compare the composition and predicted metagenome of these communities to a comparable cohort of patients in the US (San Francisco). Bronchoalveolar lavage samples from a cohort of 60 Ugandan HIV-infected patients with acute pneumonia were collected. Amplified 16S ribosomal RNA was profiled and aforementioned relationships examined. Ugandan airway microbiome composition and predicted metagenomic function were compared to US HIV-infected pneumonia patients. Among the most common bacterial pulmonary pathogens, Pseudomonas aeruginosa was most prevalent in the Ugandan cohort. Patients with a richer and more diverse airway microbiome exhibited lower bacterial burden, enrichment of members of the Lachnospiraceae and sulfur-reducing bacteria and reduced expression of TNF-alpha and matrix metalloproteinase-9. Compared to San Franciscan patients, Ugandan airway microbiome were significantly richer, and compositionally distinct with predicted metagenomes that encoded a multitude of distinct pathogenic pathways e.g secretion systems. Ugandan pneumonia-associated airway microbiome is compositionally and functionally distinct from those detected in comparable patients in developed countries, a feature which may contribute to adverse outcomes in this population. Please note that the data from the comparable cohort of patients in the USUS data was published as supplemental material of PMID: 22760045 but not submitted to GEO The 'patient_info.txt' contains 12 clinical, 7 immunological and 3 microbiological variables for each patient. The G2 PhyloChip microarray platform (commercially available from Second Genome, Inc.) was used to profile bacteria in lower airway samples from 60 subjects
2014-02-20 | E-GEOD-52791 | biostudies-arrayexpress
Project description:Measurement of incidence rates of childhood cancer in Africa is difficult. The study 'Cancer of Childhood in sub Saharan Africa' [Stefan C, Bray F, Ferlay J, Parkin DM and Liu B (2017) Cancer of Childhood in sub-Saharan Africaecancer11(755)] brings together results from 16 population-based registries which, as members of the African Cancer Registry Network (AFCRN), have been evaluated as achieving adequate coverage of their target population. The cancers are classified according to the third revision of the International Classification of Childhood Cancer (ICCC-3) and recorded rates in Africa are compared with those in childhood populations in the UK, France, and the USA. It is clear that, in many centres, lack of adequate diagnostic and treatment facilities, leads to under-diagnosis (and enumeration) of leukaemias and brain cancers. However, for several childhood cancers, incidence rates in Africa are higher than those in high income countries. This applies to infection-related cancers such as Kaposi sarcoma, Burkitt lymphoma, Hodgkin lymphoma and hepatocellular carcinoma, and also to two common embryonal cancers-retinoblastoma and nephroblastoma. These (and other) observations are unlikely to be artefact, and are of considerable interest when considering possible aetiological factors, including ethnic differences in risk (and hence genetic/familial antecedents). The data reported are the most extensive so far available on the incidence of cancer in sub Saharan Africa, and clearly indicate the need for more resources to be devoted to cancer registration, especially in the childhood age range, as part of an overall programme to improve the availability of diagnosis and treatment of this group of cancers, many of which have-potentially-an excellent prognosis.
| S-EPMC5533598 | biostudies-other
Project description:One challenge to achieving Millennium Development Goals was inequitable access to quality health services. In order to achieve the Sustainable Development Goals, interventions need to reach underserved populations. Analyzing health indicators in small geographic units aids the identification of hotspots where coverage lags behind neighboring areas. The purpose of these analyses is to identify areas of low coverage or high need in order to inform effective resource allocation to reduce child health inequity between and within countries. Using data from The Demographic and Health Survey Program surveys conducted in 27 selected African countries between 2010 and 2014, we computed estimates for six child health indicators for subnational regions. We calculated Global Moran's I statistics and used Local Indicator of Spatial Association analysis to produce a spatial layer showing spatial associations. We created maps to visualize sub-national autocorrelation and spatial clusters. The Global Moran's I statistic was positive for each indicator (range: 0.41 to 0.68), and statistically significant (p <0.05), suggesting spatial autocorrelation across national borders, and highlighting the need to examine health indicators both across countries and within them. Patterns of substantial differences among contiguous subareas were apparent; the average intra-country difference for each indicator exceeded 20 percentage points. Clusters of cross-border associations were also apparent, facilitating the identification of hotspots and informing the allocation of resources to reduce child health inequity between and within countries. This study exposes differences in health indicators in contiguous geographic areas, indicating that specific regional and subnational, in addition to national, strategies to improve health and reduce health inequalities are warranted.
| S-EPMC6114521 | biostudies-literature
Project description:Schistosomiasis remains a global health problem with an estimated 250 million people in 78 countries infected, of whom 85% live in Sub-Saharan Africa. Preventive chemotherapy remains the key public health strategy to combat schistosomiasis worldwide. Recently the WHO emphasized on the use of integrative approaches in the control and elimination of schistosomiasis. However, a detailed understanding of sociocultural factors that may influence the uptake of the intended health activities and services is vital. Thus, our study sought to understand the knowledge, attitudes, perceptions, beliefs and practices about schistosomiasis in various communities in Sub-Saharan Africa.A systematic search of literature for the period 2006-2016 was done on Medline, PubMed, CINAHL, Psych info and Google Scholar using the following key words "Schistosomiasis, S. mansoni, S. haematobium, knowledge, attitudes, perceptions, beliefs and practices in Sub-Saharan Africa" in combination with Bolean operators (OR, AND). In this context, we reviewed studies conducted among school children, community members and caregivers of preschool children. Thematic analysis was utilised for the overall synthesis of the selected studies. This was done after reading the articles in depth. Themes were identified and examined for similarities, differences and contradictions.Gaps in schistosomiasis related knowledge and sociocultural barriers towards the uptake of preventive and treatment services among communities in Sub-Saharan Africa were identified. In addition to limited knowledge and negative attitudes, risky water related practices among community members, school children and caregivers of preschool children were identified as key factors promoting transmission of the disease.The study concluded that a comprehensive health education programme using contextual and standardised training tools may improve peoples' knowledge, attitudes and practices in relation to schistosomiasis prevention and control. Findings also highlight the significance of including caregivers in the planning and implementation schistosomiasis control programs targeting pre-school children.
| S-EPMC5773048 | biostudies-literature
Project description:A characteristic of Plasmodium falciparum infections is the gradual acquisition of clinical immunity resulting from repeated exposures to the parasite. While the molecular basis of protection against clinical malaria remains unresolved, its effects on epidemiological patterns are well recognized. Accumulating epidemiological data constitute a valuable resource that must be intensively explored and interpreted as to effectively inform control planning.Here we apply a mathematical model to clinical data from eight endemic regions in sub-Saharan Africa. The model provides a quantitative framework within which differences in age distribution of clinical disease are assessed in terms of the parameters underlying transmission. The shorter infectious periods estimated for clinical infections induce a regime of bistability of endemic and malaria-free states in regions of mesoendemic transmission. The two epidemiological states are separated by a threshold that provides a convenient measure for intervention design. Scenarios of eradication and resurgence are simulated.In regions that support mesoendemic transmission, intervention success depends critically on reducing prevalence below a threshold which separates endemic and malaria-free regimes.
| S-EPMC2262141 | biostudies-other
Project description:ObjectiveTo examine knowledge of menstruation, HIV and STIs other than HIV across eight sites in SSA to develop effective programmatic interventions enabling adolescents to achieve positive SRH as their transition to adulthood.MethodsWe combine data from eight Health and Demographic Surveillance Sites across sub-Saharan Africa, from an adolescent-specific survey that included 7116 males and females age 10-19 years old. We provide pooled and site-specific estimates from multiple analytic models examining the how year-specific age, school attendance and work correlate with knowledge of menstruation, HIV knowledge and knowledge of sexually transmitted infections (STIs) other than HIV.ResultsMany adolescents lack knowledge of menstruation (37.3%, 95% CI 31.8, 43.1 do not know of menstruation) and STIs other than HIV (55.9%, 95% CI 50.4, 61.3 do not know of other STIs). In multivariate analysis, older age, being in school and wealth are significant positive correlates of STI knowledge. Older adolescent age, female sex and being in school are significant positive correlates of knowledge of menstruation. Knowledge of HIV is high (89.7%, 95% CI 8.3, 12.7 know of HIV) and relatively similar across adolescent age, sex, wealth and school and work attendance.ConclusionKnowledge of HIV is widespread across adolescents in these communities in sub-Saharan Africa, but knowledge of other dimensions of sexual and reproductive health - menstruation and other STIs in this study - is lacking especially for early adolescents (10- to 14-year olds). The dissemination of more comprehensive sexual and reproductive health information is needed within these and similar communities in SSA to help adolescents gain insight on how to make their own decisions towards positive adolescent sexual and reproductive health and protect them from risks.
| S-EPMC7612914 | biostudies-literature
Project description:AimHIV prevention measures in sub-Saharan Africa are still short of attaining the UNAIDS 90-90-90 fast track targets set in 2014. Identifying predictors for HIV status may facilitate targeted screening interventions that improve health care. We aimed at identifying HIV predictors as well as predicting persons at high risk of the infection.MethodWe applied machine learning approaches for building models using population-based HIV Impact Assessment (PHIA) data for 41,939 male and 45,105 female respondents with 30 and 40 variables respectively from four countries in sub-Saharan countries. We trained and validated the algorithms on 80% of the data and tested on the remaining 20% where we rotated around the left-out country. An algorithm with the best mean f1 score was retained and trained on the most predictive variables. We used the model to identify people living with HIV and individuals with a higher likelihood of contracting the disease.ResultsApplication of XGBoost algorithm appeared to significantly improve identification of HIV positivity over the other five algorithms by f1 scoring mean of 90% and 92% for males and females respectively. Amongst the eight most predictor features in both sexes were: age, relationship with family head, the highest level of education, highest grade at that school level, work for payment, avoiding pregnancy, age at the first experience of sex, and wealth quintile. Model performance using these variables increased significantly compared to having all the variables included. We identified five males and 19 females individuals that would require testing to find one HIV positive individual. We also predicted that 4·14% of males and 10.81% of females are at high risk of infection.ConclusionOur findings provide a potential use of the XGBoost algorithm with socio-behavioural-driven data at substantially identifying HIV predictors and predicting individuals at high risk of infection for targeted screening.
| S-EPMC8325403 | biostudies-literature
Project description:Background: This study aimed to gain an understanding of the challenges faced by people with hearing impairment (HI) in Cameroon, their understanding of the causes of HI, and how challenges could be remedied to improve the quality of life of persons with HI. Methods: Semi-structured one-on-one in-depth interviews and observation of participant behaviour when answering questions were used to collect data from 10 HI professionals (healthcare workers and educationists), and 10 persons affected by HI (including caregivers). Results: The results show that the different groups associate the causes of HI to genetics, environmental factors, and a spiritual curse. There were reported cases of stigma and discrimination of persons with HI, with people sometimes referring to HI as an "intellectual disorder." Interviewees also highlighted the difficulty persons with HI have in accessing education and healthcare services and suggested the need for the government and health researchers to develop strategies for the prevention and early diagnosis of HI. These strategies include (1) the awareness of the general population regarding HI, (2) the development of facilities for the proper management and new-born screening of HI, and (3) the implementation of a premarital screening to reduce the burden of HI of genetic origin. Conclusions: This study confirms the difficult social interaction and access to proper management faced by persons with HI in Cameroon and further highlights the need to educate populations on the causes of HI for a better acceptance of individuals with HI in the Cameroonian society.
| S-EPMC9397862 | biostudies-literature