Multivariate skew-normal distribution for modelling skewed spatial data.

Multivariate spatial data are commonly modelled using the shared spatial component and multivariate intrinsic conditional autoregressive (MICAR) models where the spatial random variables are assumed to be normally distributed. However, the normality assumption may not be always right as the spatially structured component may show non-normal distributions. We present, multivariate skew-normal spatial distribution in the modelling of multivariate conditional autoregressive models.

Benchmarking circularity in supply chains: A systematic literature review.

The challenges posed by unsustainable practices in today's economy underscore the urgent need for a transition toward a circular economy (CE) and a holistic supply chain (SC) perspective. Benchmarking plays a pivotal role in managing circular SCs, offering a metric to gauge progress. However, the lack of consensus on the optimal benchmarking approach hampers effective implementation of circular business practices.

Assessment of weight gain in adult patients living with HIV receiving first-line dolutegravir-based or efavirenz-based ART regimens in routine care clinics in Tshwane district, South Africa: An observational study.

Introduction: Although dolutegravir (DTG) is deemed stable, safe, cost-effective, and clinically beneficial, it also carries the risk of side effects, including observed weight gain among patients on DTG-based antiretroviral therapy (ART) regimens. We compared weight changes among adults (≥18 years) initiating tenofovir disoproxil fumarate, lamivudine, and dolutegravir (TLD) or tenofovir disoproxil fumarate, emtricitabine, and efavirenz (TEE) regimens and those switching from TEE to TLD (TEE-to-TLD switchers) in three large primary care facilities in South Africa METHODS: We conducted a retrospective longitudinal record review using patient medical records, extracting relevant demographic and clinical data from October 2018 to June 2021 from randomly selected adults who initiated TLD or TEE (initiators) and adult TEE-to-TLD switchers. We assessed weight, body mass index (BMI), and percentage weight changes for both groups and fitted linear regression and generalized linear models to determine factors associated with weight and BMI change and percentage weight change ≥10%, respectively, among treatment initiators.

Assessment of the performance of the plasma separation card for HIV-1 viral load monitoring in South Africa.

Unlabelled: Scaling up of newer innovations that address the limitations of the dried blood spot and the logistics of plasma monitoring is needed. We employed a multi-site, cross-sectional assessment of the plasma separation card (PSC) on blood specimens collected from all consenting adults, assenting young and pediatric patients living with HIV from 10 primary healthcare clinics in South Africa. Venous blood for EDTA-plasma samples was collected and analyzed according to the standard of care assay, while collected capillary blood for the PSC samples was analyzed using the Roche COBAS AmpliPrep/Cobas TaqMan (CAP/CTM) HIV-1 Test at the National Reference laboratories.

A framework for modelling and designing transparency systems: A case of a Vietnamese pork supply chain.

The three major meat supply chains in emerging markets are traditional wet markets, integrated supply chains, and the more recent collaborative supply chains. Customers in these markets are increasingly demanding safe and high-quality meat, which requires more transparency in the supply chain. This paper presents a generic framework for modelling and designing transparency systems in meat supply chains, with special attention to the needs of emerging markets like Vietnam where all the three supply chain types co-exist.

Resistance is common in paediatric patients failing ART in South Africa.

Background: Minimal data exist on HIV drug resistance patterns and prevalence among paediatric patients failing ART in resource-limited settings. We assessed levels of HIV drug resistance in children with virological failure.

Methods: This cross-sectional study, performed from March 2017 to March 2019 in South Africa, enrolled HIV-positive children aged ≤19 years, receiving ART through public health facilities with recent evidence suggestive of virological failure (at least one viral load ≥1000 copies/mL), across 45 randomly selected high-volume clinics from all nine provinces.

Syphilis screening coverage and positivity by HIV treatment status among South African pregnant women enrolled in the 2019 antenatal HIV sentinel survey.

We describe coverage of maternal syphilis screening, syphilis positivity, coverage of treatment and their association with maternal HIV infection and antiretroviral treatment (ART) status among pregnant women attending South African antenatal clinics. The 2019 antenatal care sentinel survey was a cross-sectional survey conducted from 1 October to 15 November 2019 at 1589 sentinel sites in all nine provinces of the country and aimed to enrol 36,000 pregnant women ages 15-49 years regardless of HIV, ART or syphilis status. Data collection procedures included obtaining written informed consent, a brief interview, medical record review and blood specimen collection.

Progress towards the UNAIDS 95-95-95 targets among pregnant women in South Africa: Results from the 2017 and 2019 national Antenatal HIV Sentinel Surveys.

Objectives: The UNAIDS 95-95-95 global targets for epidemic control aim to ensure by 2030 that 95% of HIV-positive people know their HIV status, 95% of people diagnosed with HIV receive sustained antiretroviral therapy (ART), and 95% of people on ART have viral suppression. While data on the first and second 95 targets are routinely reported nationally, data on the third 95 target are not available for pregnant women in South Africa. The lack of data on the third 95 target limits the inclusion of low viral suppression as one of the contributing factors in MTCT root cause analyses.

Is There Risk Compensation among HIV Infected Youth and Adults 15 Years and Older on Antiretroviral Treatment in South Africa? Findings from the 2017 National HIV Prevalence, Incidence, Behaviour and Communication Survey.

In this paper, risk compensation among individuals on antiretroviral therapy (ART), using the 2017 South African national survey on HIV, is explored. A multi-stage stratified cluster random sampling approach was used to realize 11,130 participants 15 years and older. Logistic regression analysis assessed the association between multiple sexual partners, condom use at last sexual encounter, consistency of condom usage and potential explanatory variables using HIV status and ART exposure as a mediator variable.

Association between viral suppression during the third trimester of pregnancy and unintended pregnancy among women on antiretroviral therapy: Results from the 2019 antenatal HIV Sentinel Survey, South Africa.

Objectives: About half of the pregnancies among women living with HIV (WLWH) receiving antiretroviral therapy (ART) in sub-Saharan African countries are reported to be unintended. Unintended pregnancy is associated with late initiation of antenatal care (ANC), and may delay provision of viral load monitoring services, antenatal adherence counselling and support, and other services that promote sustained viral suppression throughout pregnancy. This study examines the association between unsuppressed viral load during the third trimester of pregnancy and unintended pregnancy among women who initiated ART before pregnancy.

The prevalence of unintended pregnancy and its association with HIV status among pregnant women in South Africa, a national antenatal survey, 2019.

To describe the prevalence of unintended pregnancy and its association with HIV status among pregnant women in South Africa. A cross-sectional survey was conducted between October and mid-November 2019 among pregnant women aged 15-49 years in 1589 selected public antenatal care facilities. Pregnancy intention was assessed using two questions from the London Measure of Unplanned Pregnancy.

A Comparison of Bayesian Spatial Models for HIV Mapping in South Africa.

Despite making significant progress in tackling its HIV epidemic, South Africa, with 7.7 million people living with HIV, still has the biggest HIV epidemic in the world. The Government, in collaboration with developmental partners and agencies, has been strengthening its responses to the HIV epidemic to better target the delivery of HIV care, treatment strategies and prevention services.

Coverage of maternal viral load monitoring during pregnancy in South Africa: Results from the 2019 national Antenatal HIV Sentinel Survey.

Objectives: South Africa has made remarkable progress in increasing the coverage of antiretroviral therapy (ART) among pregnant women; however, viral suppression among pregnant women receiving ART is reported to be low. Access to routine viral load testing is crucial to identify women with unsuppressed viral load early in pregnancy and to provide timely intervention to improve viral suppression. This study aimed to determine the coverage of maternal viral load monitoring nationally, focusing on viral load testing, documentation of viral load test results, and viral suppression (viral load < 50 copies/mL).

Recent HIV infection among pregnant women in the 2017 antenatal sentinel cross-sectional survey, South Africa: Assay-based incidence measurement.

Introduction: New HIV infection during pre-conception and pregnancy is a significant contributor of mother-to-child transmission of HIV in South Africa. This study estimated HIV incidence (defined as new infection within the last one year from the time of the survey which included both new infections occurred during pregnancy or just before pregnancy) among pregnant women and described the characteristics of recently infected pregnant women at national level.

Methods: Between 1 October and 15 November 2017, we conducted a national cross-sectional survey among pregnant women aged 15-49 years old attending antenatal care at 1,595 public facilities.

Application of machine learning to improve dairy farm management: A systematic literature review.

In recent years, several researchers and practitioners applied machine learning algorithms in the dairy farm context and discussed several solutions to predict various variables of interest, most of which were related to incipient diseases. The objective of this article is to identify, assess, and synthesize the papers that discuss the application of machine learning in the dairy farm management context. Using a systematic literature review (SLR) protocol, we retrieved 427 papers, of which 38 papers were determined as primary studies and thus were analysed in detail.

Population prevalence of sexually transmitted infections in a high HIV burden district in KwaZulu-Natal, South Africa: Implications for HIV epidemic control.

Background: Sexually transmitted infections (STIs) and Human immunodeficiency virus (HIV) share a complex bidirectional relationship, however, population prevalence and the association between the presence of STIs and HIV in a high HIV burden district in KwaZulu-Natal, South Africa is not known.

Methods: A total of 9812 participants aged 15-49 years were enrolled in a cross-sectional population-based household survey. Participants completed a structured questionnaire and provided first-pass urine (males) or self-collected vulvo-vaginal swabs (females) for the detection of STIs.

Identification of potential vulnerable points and paths of contamination in the Dutch broiler meat trade network.

The poultry meat supply chain is complex and therefore vulnerable to many potential contaminations that may occur. To ensure a safe product for the consumer, an efficient traceability system is required that enables a quick and efficient identification of the potential sources of contamination and proper implementation of mitigation actions. In this study, we explored the use of graph theory to construct a food supply chain network for the broiler meat supply chain in the Netherlands and tested it as a traceability system.

Awareness of HIV-positive status and linkage to treatment prior to pregnancy in the "test and treat" era: A national antenatal sentinel survey, 2017, South Africa.

Introduction: Knowledge of HIV status in South Africa (SA) is reported to be 90% among people living with HIV. National level estimates could mask population-specific levels, which are critical to monitor program coverage and potential impact. Using data from the 2017 national antenatal sentinel survey, we assessed knowledge of HIV-positive status, initiation of antiretroviral therapy (ART), and socio-demographic characteristics associated with knowledge of HIV-positive status prior to the current pregnancy among women attending antenatal care.

Evaluating DREAMS HIV prevention interventions targeting adolescent girls and young women in high HIV prevalence districts in South Africa: protocol for a cross-sectional study.

Background: Young women in sub-Saharan Africa remain at the epicentre of the HIV epidemic, with surveillance data indicating persistent high levels of HIV incidence. In South Africa, adolescent girls and young women (AGYW) account for a quarter of all new HIV infections. Determined, Resilient, Empowered, AIDS-free, Mentored and Safe (DREAMS) is a strategy introduced by the United States President's Emergency Plan for AIDS Relief (PEPFAR) aimed at reducing HIV incidence among AGYW in 10 countries in sub-Saharan Africa by 25% in the programme's first year, and by 40% in the second year.

Viral suppression and factors associated with failure to achieve viral suppression among pregnant women in South Africa.

Objective: To describe viral load levels among pregnant women and factors associated with failure to achieve viral suppression (viral load ≤50 copies/ml) during pregnancy.

Design: Between 1 October and 15 November 2017, a cross-sectional survey was conducted among 15-49-year-old pregnant women attending antenatal care (ANC) at 1595 nationally representative public facilities.

Methods: Blood specimens were taken from each pregnant woman and tested for HIV.

Assessment of readiness to transition from antenatal HIV surveillance surveys to PMTCT programme data-based HIV surveillance in South Africa: The 2017 Antenatal Sentinel HIV Survey.

Objective: South Africa has used antenatal HIV surveys for HIV surveillance in pregnant women since 1990. We assessed South Africa's readiness to transition to programme data based antenatal HIV surveillance with respect to PMTCT uptake, accuracy of point-of-care rapid testing (RT) and selection bias with using programme data in the context of the 2017 antenatal HIV survey.

Methods: Between 1 October and 15 November 2017, the national survey was conducted in 1,595 public antenatal facilities selected using stratified multistage cluster sampling method.

Trends in HIV Prevention, Treatment, and Incidence in a Hyperendemic Area of KwaZulu-Natal, South Africa.

Importance: In Africa, the persistently high HIV incidence rate among young women is the major obstacle to achieving the goal of epidemic control.

Objective: To determine trends in coverage of HIV prevention and treatment programs and HIV incidence.

Design, Setting, And Participants: This cohort study consisted of 2 sequential, community-based longitudinal studies performed in the Vulindlela and Greater Edendale area in KwaZulu-Natal, South Africa.

Longitudinal adherence to maternal antiretroviral therapy and infant Nevirapine prophylaxis from 6 weeks to 18 months postpartum amongst a cohort of mothers and infants in South Africa.

Background: Despite improved policies to prevent mother-to-child HIV transmission (MTCT), adherence to maternal antiretroviral therapy (ART) and infant Nevirapine prophylaxis (NVP) is low in South Africa. We describe ART adherence amongst a cohort of HIV-positive mothers and HIV-exposed but uninfected infants from 6 weeks until 18 months post-delivery and identify risk factors for nonadherence.

Methods: Data were collected in 2012-2014 through a nationally representative survey of PMTCT effectiveness.

Does voluntary medical male circumcision protect against sexually transmitted infections among men and women in real-world scale-up settings? Findings of a household survey in KwaZulu-Natal, South Africa.

Introduction: Male circumcision (MC) confers partial protection to men against HIV and, in research settings, some sexually transmitted infections (STIs). It is also associated with protection from some STIs among female partners. However, real-world data on changes in STI transmission associated with large-scale public African medical male circumcision (MMC) conducted for HIV prevention are lacking and would improve estimates of the health impact of MMC.

Trends in Pretreatment HIV-1 Drug Resistance in Antiretroviral Therapy-naive Adults in South Africa, 2000-2016: A Pooled Sequence Analysis.

Background: South Africa has the largest public antiretroviral therapy (ART) programme in the world. We assessed temporal trends in pretreatment HIV-1 drug resistance (PDR) in ART-naïve adults from South Africa.

Methods: We included datasets from studies conducted between 2000 and 2016, with HIV-1 sequences from more than ten ART-naïve adults.