Latent Classes of Anthropometric Growth in Early Childhood Using Uni- and Multivariate approaches in a South African Birth Cohort.

Background: Conventional methods for modelling longitudinal growth data focus on the analysis of mean longitudinal trends or the identification of abnormal growth based on cross-sectional standardized z-scores. Latent Class Mixed Modelling (LCMM) considers the underlying heterogeneity in growth profiles and allows for the identification of groups of subjects that follow similar longitudinal trends.

Methods: LCMM was used to identify underlying latent profiles of growth for univariate responses of standardized height, standardized weight, standardized body mass index and standardized weight-for-length/height measurements and multivariate response of joint standardized height and standardized weight measurements from birth to five years for a sample of 1143 children from a South African birth cohort, the Drakenstein Child Health Study (DCHS).

Multivariate approach for longitudinal analysis of brain metabolite levels from ages 5-11 years in children with perinatal HIV infection.

Treatment guidelines recommend that children with perinatal HIV infection (PHIV) initiate antiretroviral therapy (ART) early in life and remain on it lifelong. As part of a longitudinal study examining the long-term consequences of PHIV and early ART on the developing brain, 89 PHIV children and a control group of 85 HIV uninfected children (HIV-) received neuroimaging at ages 5, 7, 9 and 11 years, including single voxel magnetic resonance spectroscopy (MRS) in three brain regions, namely the basal ganglia (BG), midfrontal gray matter (MFGM) and peritrigonal white matter (PWM). We analysed age-related changes in absolute metabolite concentrations using a multivariate approach traditionally applied to ecological data, the Correlated Response Model (CRM) and compared these to results obtained from a multilevel mixed effect modelling (MMEM) approach.

Simulation of African and non-African low and high coverage whole genome sequence data to assess variant calling approaches.

Current variant calling (VC) approaches have been designed to leverage populations of long-range haplotypes and were benchmarked using populations of European descent, whereas most genetic diversity is found in non-European such as Africa populations. Working with these genetically diverse populations, VC tools may produce false positive and false negative results, which may produce misleading conclusions in prioritization of mutations, clinical relevancy and actionability of genes. The most prominent question is which tool or pipeline has a high rate of sensitivity and precision when analysing African data with either low or high sequence coverage, given the high genetic diversity and heterogeneity of this data.

A broad survey of DNA sequence data simulation tools.

In silico DNA sequence generation is a powerful technology to evaluate and validate bioinformatics tools, and accordingly more than 35 DNA sequence simulation tools have been developed. With such a diverse array of tools to choose from, an important question is: Which tool should be used for a desired outcome? This question is largely unanswered as documentation for many of these DNA simulation tools is sparse. To address this, we performed a review of DNA sequence simulation tools developed to date and evaluated 20 state-of-art DNA sequence simulation tools on their ability to produce accurate reads based on their implemented sequence error model.

Control of gastrointestinal nematodes in goats on pastures in South Africa using nematophagous fungi Duddingtonia flagrans and selective anthelmintic treatments.

The effectiveness of selective anthelmintic treatments and use of nematophagous fungi Duddingtonia flagrans in reducing levels of gastrointestinal nematodes in goats was investigated at Onderstepoort, South Africa. Nineteen (19) naturally infected indigenous male goats, aged 10 months, were separated into four groups and grazed in separate previously ungrazed paddocks for two worm seasons (February 2002-March 2003). Two groups of goats were fed D.