"Life is so easy on ART, once you accept it": Acceptance, denial and linkage to HIV care in Shiselweni, Swaziland.

BACKGROUND: Timely uptake of antiretroviral therapy, adherence and retention in care for people living with HIV (PLHIV) can improve health outcomes and reduce transmission. Médecins Sans Frontières and the Swaziland Ministry of Health provide community-based HIV testing services (HTS) in Shiselweni, Swaziland, with high HTS coverage but sub-optimal linkage to HIV care. This qualitative study examined factors influencing linkage to HIV care for PLHIV diagnosed by community-based HTS. METHODS: Participants were sampled purposively, exploring linkage experiences among both genders and different age groups. Interviews were conducted with 28 PLHIV (linked and not linked) and 11 health practitioners. Data were thematically analysed to identify emergent patterns and categories using NVivo 10. Principles of grounded theory were applied, including constant comparison of findings, raising codes to a conceptual level, and inductively generating theory from participant accounts. RESULTS: The process of HIV status acceptance or denial influenced the accounts of patients' health seeking and linkage to care. This process was non-linear and varied temporally, with some experiencing non-acceptance for an extended period of time. Non-acceptance was linked to perceptions of HIV risk, with those not identifying as at risk less likely to expect and therefore be prepared for a positive result. Status disclosure was seen to support linkage, reportedly occurring after the acceptance of HIV status. HIV status acceptance motivated health seeking and tended to be accompanied by a perceived need for, and positive value placed on, HIV health care. CONCLUSIONS: The manner in which PLHIV process a positive result can influence their engagement with HIV treatment and care. Thus, there is a need for individually tailored approaches to HTS, including the potential for counselling over multiple sessions if required, supporting status acceptance, and disclosure. This is particularly relevant considering 90-90-90 targets and the need to better support PLHIV to engage with HIV treatment and care following diagnosis

METAREP: JCVI metagenomics reports—an open source tool for high-performance comparative metagenomics

Summary: JCVI Metagenomics Reports (METAREP) is a Web 2.0 application designed to help scientists analyze and compare annotated metagenomics datasets. It utilizes Solr/Lucene, a high-performance scalable search engine, to quickly query large data collections. Furthermore, users can use its SQL-like query syntax to filter and refine datasets. METAREP provides graphical summaries for top taxonomic and functional classifications as well as a GO, NCBI Taxonomy and KEGG Pathway Browser. Users can compare absolute and relative counts of multiple datasets at various functional and taxonomic levels. Advanced comparative features comprise statistical tests as well as multidimensional scaling, heatmap and hierarchical clustering plots. Summaries can be exported as tab-delimited files, publication quality plots in PDF format. A data management layer allows collaborative data analysis and result sharing

"I don't want them to know": how stigma creates dilemmas for engagement with Treat-all HIV care for people living with HIV in Eswatini.

"Treat-all" programmes aim to improve clinical outcomes and to reduce HIV transmission through regular HIV testing and immediate offer of antiretroviral therapy (ART) for those diagnosed HIV-positive, irrespective of immunological status and symptoms of disease. Global narratives on the benefits of Treat-all anticipate reduced HIV-related stigma and increased "normalisation" of HIV with Treat-all implementation, whereby HIV is remoulded as a manageable, chronic condition where stigmatising symptoms can be concealed. Drawing on Goffman's stigma work, we aimed to investigate how stigma may influence the engagement of clinically asymptomatic people living with HIV (PLHIV) with Treat-all HIV care in Shiselweni, Eswatini (formerly Swaziland). This longitudinal research comprised 106 interviews conducted from August 2016 to September 2017, including repeated interviews with 30 PLHIV, and one-off interviews with 20 healthcare workers. Data were analysed thematically using NVivo 11, drawing upon principles of grounded theory to generate findings inductively from participants' accounts. Stigma was pervasive within the narratives of PLHIV, framing their engagement with treatment and care. Many asymptomatic PLHIV were motivated to initiate ART in order to maintain a "discreditable" status, by preventing the development of visible and exposing symptoms. However, engagement with treatment and care services could itself be exposing. PLHIV described the ways in which these "invisibilising" benefits and exposing risks of ART were continually assessed and navigated over time. Where the risk of exposure was deemed too great, this could lead to intermittent treatment-taking, and disengagement from care. Addressing HIV related stigma is crucial to the success of Treat-all, and should thus be a core component of HIV responses

"Is it making any difference?" A qualitative study examining the treatment-taking experiences of asymptomatic people living with HIV in the context of Treat-all in Eswatini.

INTRODUCTION: Treat-all is being implemented in several African settings, in accordance with 2015 World Health Organisation guidelines. The factors known to undermine adherence to antiretroviral therapy (ART) may change in the context of Treat-all, where people living with HIV (PLHIV) increasingly initiate ART at earlier, asymptomatic stages of disease, soon after diagnosis. This paper aimed to examine the asymptomatic PLHIV's experiences engaging with early ART initiation under the Treat-all policy, including how they navigate treatment-taking over the longer term. METHODS: A longitudinal qualitative study was conducted within a Médecins Sans Frontières/Ministry of Health Treat-all pilot in Shiselweni, southern Eswatini. The Treat-all pilot began in October 2014, adopted into national policy in October 2016. Participants were recruited purposively to include newly diagnosed, clinically asymptomatic PLHIV with a range of treatment-taking experiences, and healthcare workers (HCW) with various roles. This analysis drew upon a sub-sample of 17 PLHIV who had been on ART for at least 12 months, with mean 20 months on ART at first interview, and who undertook three interviews each. Additionally, 20 HCWs were interviewed once. Interviews were conducted from August 2016 to September 2017. Data were analysed thematically using coding, drawing upon principles of grounded theory, and aided by Nvivo 11. RESULTS: It was important for PLHIV to perceive the need for treatment, and to have evidence of its effectiveness to motivate their treatment-taking, thereby supporting engagement with care. For some, coming to terms with a HIV diagnosis or re-interpreting past illnesses as signs of HIV could point to the need for ART to prevent health deterioration and prolong life. However, others doubted the accuracy of an HIV diagnosis and the need for treatment in the absence of symptoms or signs of ill health, with some experimenting with treatment-taking as a means of seeking evidence of their need for treatment and its effect. Viral load monitoring appeared important in offering a view of the effect of treatment on the level of the virus, thereby motivating continued treatment-taking. CONCLUSIONS: These findings highlight the importance of PLHIV perceiving need for treatment and having evidence of the difference that ART is making to them for motivating treatment-taking. Patient support should be adapted to address these concerns, and viral load monitoring made routinely available within Treat-all care, with communication of suppressed results emphasized to patients

Challenges and successes in the implementation of option B+ to prevent mother-to-child transmission of HIV in southern Swaziland.

BACKGROUND: Universal antiretroviral therapy (ART) for all pregnant/ breastfeeding women living with Human Immunodeficiency Virus (HIV), known as Prevention of mother-to child transmission of HIV (PMTCT) Option B+ (PMTCTB+), is being scaled up in most countries in Sub-Saharan Africa. In the transition to PMTCTB+, many countries face challenges with proper implementation of the HIV care cascade. We aimed to describe the feasibility of a PMTCTB+ approach in the public health sector in Swaziland. METHODS: Lifelong ART was offered to a cohort of HIV+ pregnant women aged ≥16 years at the first antenatal care (ANC1) visit in 9 public sector facilities, between 01/2013 and 06/2014. The study enrolment period was divided into 3 phases (early: 01-06/2013, mid: 07-12/2013 and late: 01-06/2014) to account for temporal trends. Kaplan-Meier estimates and Cox proportional-hazards regression models were applied for ART initiation and attrition analyses. RESULTS: Of 665 HIV+ pregnant women, 496 (74.6%) initiated ART. ART initiation increased in later study enrolment phases (mid: aHR: 1.41; later: aHR: 2.36), and decreased at CD4 ≥ 500 (aHR: 0.69). 52.9% were retained in care at 24 months. Attrition was associated with ANC1 in the third trimester (aHR: 2.37), attending a secondary care facility (aHR: 1.98) and ART initiation during later enrolment phases (mid aHR: 1.48; late aHR: 1.67). Of 373 women eligible, 67.3% received a first VL. 223/251 (88.8%) were virologically suppressed (< 1000 copies/mL). Of 670 infants, 53.6% received an EID test, 320/359 had a test result recorded and of whom 7 (2.2%) were HIV+. CONCLUSIONS: PMTCTB+ was found to be feasible in this setting, with high rates of maternal viral suppression and low transmission to the infant. High treatment attrition, poor follow-up of mother-baby pairs and under-utilisation of VL and EID testing are important programmatic challenges

Semi-natural habitats support biological control, pollination and soil conservation in Europe:A review

Semi-natural habitats are integral to most agricultural areas and have the potential to support ecosystem services, especially biological control and pollination by supplying resources for the invertebrates providing these services and for soil conservation by preventing erosion and run-off. Some habitats are supported through agri-environment scheme funding in the European Union, but their value for ecosystem service delivery has been questioned. An improved understanding of previous research approaches and outcomes will contribute to the development of more sustainable farming systems, improve experimental designs and highlight knowledge gaps especially for funders and researchers. Here we compiled a systematic map to allow for the first time a review of the quantity of evidence collected in Europe that semi-natural habitats support biological control, pollination and soil conservation. A literature search selected 2252 publications, and, following review, 270 met the inclusion criteria and were entered into the database. Most publications were of pest control (143 publications) with less on pollination (78 publications) or soil-related aspects (31). For pest control and pollination, most publications reported a positive effect of semi-natural habitats. There were weaknesses in the evidence base though because of bias in study location and the crops, whilst metrics (e.g. yield) valued by end users were seldom measured. Hedgerows, woodland and grassland were the most heavily investigated semi-natural habitats, and the wider landscape composition was often considered. Study designs varied considerably yet only 24% included controls or involved manipulation of semi-natural habitats. Service providers were commonly measured and used as a surrogate for ecosystem service delivery. Key messages for policymakers and funders are that they should encourage research that includes more metrics required by end users, be prepared to fund longer-term studies (61% were of only 1-year duration) and investigate the role of soils within semi-natural habitats in delivering ecosystem services

Versatility and Stereotypy of Free-Tailed Bat Songs

In mammals, complex songs are uncommon and few studies have examined song composition or the order of elements in songs, particularly with respect to regional and individual variation. In this study we examine how syllables and phrases are ordered and combined, ie “syntax”, of the song of Tadarida brasiliensis, the Brazilian free-tailed bat. Specifically, we test whether phrase and song composition differ among individuals and between two regions, we determine variability across renditions within individuals, and test whether phrases are randomly ordered and combined. We report three major findings. First, song phrases were highly stereotyped across two regions, so much so that some songs from the two colonies were almost indistinguishable. All males produced songs with the same four types of syllables and the same three types of phrases. Second, we found that although song construction was similar across regions, the number of syllables within phrases, and the number and order of phrases in songs varied greatly within and among individuals. Last, we determined that phrase order, although diverse, deviated from random models. We found broad scale phrase-order rules and certain higher order combinations that were highly preferred. We conclude that free-tailed bat songs are composed of highly stereotyped phrases hierarchically organized by a common set of syntactical rules. However, within global species-specific patterns, songs male free-tailed bats dynamically vary syllable number, phrase order, and phrase repetitions across song renditions

Declining mortality following acute myocardial infarction in the Department of Veterans Affairs Health Care System

<p>Abstract</p> <p>Background</p> <p>Mortality from acute myocardial infarction (AMI) is declining worldwide. We sought to determine if mortality in the Veterans Health Administration (VHA) has also been declining.</p> <p>Methods</p> <p>We calculated 30-day mortality rates between 2004 and 2006 using data from the VHA External Peer Review Program (EPRP), which entails detailed abstraction of records of all patients with AMI. To compare trends within VHA with other systems of care, we estimated relative mortality rates between 2000 and 2005 for all males 65 years and older with a primary diagnosis of AMI using administrative data from the VHA Patient Treatment File and the Medicare Provider Analysis and Review (MedPAR) files.</p> <p>Results</p> <p>Using EPRP data on 11,609 patients, we observed a statistically significant decline in adjusted 30-day mortality following AMI in VHA from 16.3% in 2004 to 13.9% in 2006, a relative decrease of 15% and a decrease in the odds of dying of 10% per year (p = .011). Similar declines were found for in-hospital and 90-day mortality.</p> <p>Based on administrative data on 27,494 VHA patients age 65 years and older and 789,400 Medicare patients, 30-day mortality following AMI declined from 16.0% during 2000-2001 to 15.7% during 2004-June 2005 in VHA and from 16.7% to 15.5% in private sector hospitals. After adjusting for patient characteristics and hospital effects, the overall relative odds of death were similar for VHA and Medicare (odds ratio 1.02, 95% C.I. 0.96-1.08).</p> <p>Conclusion</p> <p>Mortality following AMI within VHA has declined significantly since 2003 at a rate that parallels that in Medicare-funded hospitals.</p

A Case Study for Large-Scale Human Microbiome Analysis Using JCVI’s Metagenomics Reports (METAREP)

As metagenomic studies continue to increase in their number, sequence volume and complexity, the scalability of biological analysis frameworks has become a rate-limiting factor to meaningful data interpretation. To address this issue, we have developed JCVI Metagenomics Reports (METAREP) as an open source tool to query, browse, and compare extremely large volumes of metagenomic annotations. Here we present improvements to this software including the implementation of a dynamic weighting of taxonomic and functional annotation, support for distributed searches, advanced clustering routines, and integration of additional annotation input formats. The utility of these improvements to data interpretation are demonstrated through the application of multiple comparative analysis strategies to shotgun metagenomic data produced by the National Institutes of Health Roadmap for Biomedical Research Human Microbiome Project (HMP) (http://nihroadmap.nih.gov). Specifically, the scalability of the dynamic weighting feature is evaluated and established by its application to the analysis of over 400 million weighted gene annotations derived from 14 billion short reads as predicted by the HMP Unified Metabolic Analysis Network (HUMAnN) pipeline. Further, the capacity of METAREP to facilitate the identification and simultaneous comparison of taxonomic and functional annotations including biological pathway and individual enzyme abundances from hundreds of community samples is demonstrated by providing scenarios that describe how these data can be mined to answer biological questions related to the human microbiome. These strategies provide users with a reference of how to conduct similar large-scale metagenomic analyses using METAREP with their own sequence data, while in this study they reveal insights into the nature and extent of variation in taxonomic and functional profiles across body habitats and individuals. Over one thousand HMP WGS datasets and the latest open source code are available at http://www.jcvi.org/hmp-metarep