Spatial heterogeneity in projected leprosy trends in India

Background: Leprosy is caused by infection with Mycobacterium leprae and is characterized by peripheral nerve damage and skin lesions. The disease is classified into paucibacillary (PB) and multibacillary (MB) leprosy. The 2012 London Declaration formulated the following targets for leprosy control: (1) global interruption of transmission or elimination by 2020, and (2) reduction of grade-2 disabilities in newly detected cases to below 1 per million population at a global level by 2020. Leprosy is treatable, but diagnosis, access to treatment and treatment adherence (all necessary to curtail transmission) represent major challenges. Globally, new case detection rates for leprosy have remained fairly stable in the past decade, with India responsible for more than half of cases reported annually. Methods: We analyzed publicly available data from the Indian Ministry of Health and Family Welfare, and fit linear mixed-effects regression models to leprosy case detection trends reported at the district level. We assessed correlation of the new district-level case detection rate for leprosy with several state-level regressors: TB incidence, BCG coverage, fraction of cases exhibiting grade 2 disability at diagnosis, fraction of cases in children, and fraction multibacillary. Results: Our analyses suggest an endemic disease in very slow decline, with substantial spatial heterogeneity at both district and state levels. Enhanced active case finding was associated with a higher case detection rate. Conclusions: Trend analysis of reported new detection rates from India does not support a thesis of rapid progress in leprosy control

HIV care coverage among HIV-positive adolescent girls and young women in South Africa: Results from the HERStory Study

Background. Health service coverage cascades measure the proportion of a population in need of a service that experienced a positive health outcome from the service, and enable tracking of progress in achieving universal health coverage and inequities in care coverage.Objectives. To investigate HIV care coverage among HIV-positive adolescent girls and young women (AGYW) living in six South African districts, compare coverage by age and socioeconomic status (SES), and investigate other associated factors including participation in a combination HIV prevention intervention.Methods. The HERStory Study was an evaluation of the combination intervention, comprising a representative household survey of AGYW aged 15 - 24 years living in six intervention districts. From September 2017 to November 2018, biological, sociodemographic and behavioural data were collected. HIV-positive status, initiation of antiretroviral therapy (ART) and viral suppression were determined through laboratory tests (enzyme-linked immunosorbent assay for HIV antibodies, antiretroviral (ARV) metabolites and viral load (VL) testing). Viral suppression was defined as a VL <1 000 copies/mL. Knowledge of HIV-positive status was self-reported, and participants testing positive for ARV metabolites were assumed to have known their HIV-positive status. Unconditional HIV care cascades were created, stratified by age and SES. We used Pearson’s χ2 tests corrected for survey-based analysis to describe factors associated with knowledge of HIV status, and being on ART.Results. Of the 4 399 participants, 568 were HIV-positive (12.4%), of whom 60.8% (95% confidence interval (CI) 57.1 - 64.5) knew their status, 50.6% (95% CI 46.6 - 54.0) were on ART, and 62.1% (95% CI 58.4 - 65.9) were virally suppressed. Most participants (84.9%) were in the lower SES group, and they had better coverage than the higher SES group: 61.9% (95% CI 58.3 - 65.4) knew their status, 52.1% (95% CI 48.4 - 55.9) were on ART, and 64.9% (95% CI 61.3 - 68.4) were virally suppressed, compared with 55.0% (95% CI 42.1 - 68.0), 40.0% (95% CI 29.2 - 50.8), and 46.6% (95% CI 34.5 - 58.7), respectively. Participants aged 15 - 19 years had slightly inferior coverage to the 20 - 24-year-old group: 57.5% knew their status, 46.1% were on ART and 59.5% were virally suppressed, compared with 62.3%, 52.2% and 63.3%.Conclusions. These findings emphasise the need to close the gaps in HIV care coverage among AGYW, of whom only 61% knew their HIV-positive status and only 62% were virally suppressed. There is pro-poor inequality in HIV care coverage, with those in lower socioeconomic groups more likely to be virally suppressed

HIV care coverage among HIV-positive adolescent girls and young women in South Africa: Results from the HERStory Study

BACKGROUND. Health service coverage cascades measure the proportion of a population in need of a service that experienced a positive health outcome from the service, and enable tracking of progress in achieving universal health coverage and inequities in care coverage. OBJECTIVES. To investigate HIV care coverage among HIV-positive adolescent girls and young women (AGYW) living in six South African districts, compare coverage by age and socioeconomic status (SES), and investigate other associated factors including participation in a combination HIV prevention intervention. METHODS. The HERStory Study was an evaluation of the combination intervention, comprising a representative household survey of AGYW aged 15 - 24 years living in six intervention districts. From September 2017 to November 2018, biological, sociodemographic and behavioural data were collected. HIV-positive status, initiation of antiretroviral therapy (ART) and viral suppression were determined through laboratory tests (enzyme-linked immunosorbent assay for HIV antibodies, antiretroviral (ARV) metabolites and viral load (VL) testing). Viral suppression was defined as a VL <1 000 copies/mL. Knowledge of HIV-positive status was self-reported, and participants testing positive for ARV metabolites were assumed to have known their HIV-positive status. Unconditional HIV care cascades were created, stratified by age and SES. We used Pearson’s χ2 tests corrected for survey-based analysis to describe factors associated with knowledge of HIV status, and being on ART. RESULTS. Of the 4 399 participants, 568 were HIV-positive (12.4%), of whom 60.8% (95% confidence interval (CI) 57.1 - 64.5) knew their status, 50.6% (95% CI 46.6 - 54.0) were on ART, and 62.1% (95% CI 58.4 - 65.9) were virally suppressed. Most participants (84.9%) were in the lower SES group, and they had better coverage than the higher SES group: 61.9% (95% CI 58.3 - 65.4) knew their status, 52.1% (95% CI 48.4 - 55.9) were on ART, and 64.9% (95% CI 61.3 - 68.4) were virally suppressed, compared with 55.0% (95% CI 42.1 - 68.0), 40.0% (95% CI 29.2 - 50.8), and 46.6% (95% CI 34.5 - 58.7), respectively. Participants aged 15 - 19 years had slightly inferior coverage to the 20 - 24-year-old group: 57.5% knew their status, 46.1% were on ART and 59.5% were virally suppressed, compared with 62.3%, 52.2% and 63.3%. CONCLUSIONS. These findings emphasise the need to close the gaps in HIV care coverage among AGYW, of whom only 61% knew their HIVpositive status and only 62% were virally suppressed. There is pro-poor inequality in HIV care coverage, with those in lower socioeconomic groups more likely to be virally suppressed.The South African Medical Research Council (SAMRC), the Global Fund, the South African National Treasury and a CIPHER Growing the Leaders of Tomorrow grant from the International AIDS Society.http://www.samj.org.zadm2022Internal Medicin

Employing machine learning for reliable miRNA target identification in plants

<p>Abstract</p> <p>Background</p> <p>miRNAs are ~21 nucleotide long small noncoding RNA molecules, formed endogenously in most of the eukaryotes, which mainly control their target genes post transcriptionally by interacting and silencing them. While a lot of tools has been developed for animal miRNA target system, plant miRNA target identification system has witnessed limited development. Most of them have been centered around exact complementarity match. Very few of them considered other factors like multiple target sites and role of flanking regions.</p> <p>Result</p> <p>In the present work, a Support Vector Regression (SVR) approach has been implemented for plant miRNA target identification, utilizing position specific dinucleotide density variation information around the target sites, to yield highly reliable result. It has been named as p-TAREF (plant-Target Refiner). Performance comparison for p-TAREF was done with other prediction tools for plants with utmost rigor and where p-TAREF was found better performing in several aspects. Further, p-TAREF was run over the experimentally validated miRNA targets from species like <it>Arabidopsis</it>, <it>Medicago</it>, Rice and Tomato, and detected them accurately, suggesting gross usability of p-TAREF for plant species. Using p-TAREF, target identification was done for the complete Rice transcriptome, supported by expression and degradome based data. miR156 was found as an important component of the Rice regulatory system, where control of genes associated with growth and transcription looked predominant. The entire methodology has been implemented in a multi-threaded parallel architecture in Java, to enable fast processing for web-server version as well as standalone version. This also makes it to run even on a simple desktop computer in concurrent mode. It also provides a facility to gather experimental support for predictions made, through on the spot expression data analysis, in its web-server version.</p> <p>Conclusion</p> <p>A machine learning multivariate feature tool has been implemented in parallel and locally installable form, for plant miRNA target identification. The performance was assessed and compared through comprehensive testing and benchmarking, suggesting a reliable performance and gross usability for transcriptome wide plant miRNA target identification.</p

Age-disparity, sexual connectedness and HIV infection in disadvantaged communities around Cape Town, South Africa: a study protocol

The original publication is available at http://www.biomedcentral.com/1471-2458/11/616Abstract: Background Crucial connections between sexual network structure and the distribution of HIV remain inadequately understood, especially in regard to the role of concurrency and age disparity in relationships, and how these network characteristics correlate with each other and other risk factors. Social desirability bias and inaccurate recall are obstacles to obtaining valid, detailed information about sexual behaviour and relationship histories. Therefore, this study aims to use novel research methods in order to determine whether HIV status is associated with age-disparity and sexual connectedness as well as establish the primary behavioural and socio-demographic predictors of the egocentric and community sexual network structures. Method/Design We will conduct a cross-sectional survey that uses a questionnaire exploring one-year sexual histories, with a focus on timing and age disparity of relationships, as well as other risk factors such as unprotected intercourse and the use of alcohol and recreational drugs. The questionnaire will be administered in a safe and confidential mobile interview space, using audio computer-assisted self-interview (ACASI) technology on touch screen computers. The ACASI features a choice of languages and visual feedback of temporal information. The survey will be administered in three peri-urban disadvantaged communities in the greater Cape Town area with a high burden of HIV. The study communities participated in a previous TB/HIV study, from which HIV test results will be anonymously linked to the survey dataset. Statistical analyses of the data will include descriptive statistics, linear mixed-effects models for the inter- and intra-subject variability in the age difference between sexual partners, survival analysis for correlated event times to model concurrency patterns, and logistic regression for association of HIV status with age disparity and sexual connectedness. Discussion This study design is intended to facilitate more accurate recall of sensitive sexual history data and has the potential to provide substantial insights into the relationship between key sexual network attributes and additional risk factors for HIV infection. This will help to inform the design of context-specific HIV prevention programmes.Publishers' versio

Health-seeking behaviours of older black women living with non-communicable diseases in an urban township in South Africa

BACKGROUND: Various studies have shown that non-communicable diseases (NCDs) especially diabetes and hypertension are prevalent among older women living in South African urban areas, placing a heavy burden on the healthcare system. This study aimed to understand the health-seeking behaviour, healthcare practices and prevalence of traditional herbal medicine (THM) use among older women self-reporting NCDs from the Prospective Urban Rural Epidemiology study (PURE). METHOD: A homogenous purposive sampling of PURE participants was used to recruit women who were 50 years or older (n = 250). Descriptive statistics were used to examine the number of NCDs reported by the study sample, health seeking behaviour and practices as well as THM use. Logistic regression was also employed to investigate possible associations between reported conditions and THM use or medical pluralism. RESULTS: Within the study sample, 72 % self-reported an NCD. Of those with self-reported NCDs, 46 % had one, and 54 % had two or more NCDs. Those with NCDs usually visited public clinics (80 %), relied on doctors (90 %) and nurses (85 %) for health information, and mostly used conventional medicine (CM) to manage high blood pressure (81 %). About 30 % of those with NCDs indicated using THM, of whom 29 (53 %) reported practicing medical pluralism. Participants with dental problems (OR: 3.24, 95 % CI: 1.30–8.20), headaches (OR: 2.42, 95 % CI: 1.24–4.94), heart burn (OR: 2.30, 95 % CI: 1.18–4.48) and severe tiredness (OR: 2.05, 95 % CI: 1.08–3.99) were more likely to use THM. Anxiety and allergies increased the likelihood to practise medical pluralism by five and 20 times, respectively. CONCLUSION: Self-reported NCD with co-morbidities was prevalent among the participants in the study. Most of the study participants utilized state-owned clinics and hospitals for the management of their chronic conditions. THM use was not very common. However, among those who used THM, medical pluralism was prevalent. Family history was the most common reason for THM use, with many THM patrons utilizing these for treatment of a health condition. Older black women with anxiety and allergies were more likely to practise medical pluralism

High-Throughput Sequencing, Characterization and Detection of New and Conserved Cucumber miRNAs

Micro RNAS (miRNAs) are a class of endogenous small non coding RNAs involved in the post-transcriptional regulation of gene expression. In plants, a great number of conserved and specific miRNAs, mainly arising from model species, have been identified to date. However less is known about the diversity of these regulatory RNAs in vegetal species with agricultural and/or horticultural importance