Building awareness and capacity of bioinformatics and open science skills in Kenya: a sensitize, train, hack, and collaborate model.

We have applied the sensitize-train-hack-community model to build awareness of and capacity in bioinformatics in Kenya. Open science is the practice of science openly and collaboratively, with tools, techniques, and data freely shared to facilitate reuse and collaboration. Open science is not a mandatory curriculum course in schools, whereas bioinformatics is relatively new in some African regions. Open science tools can significantly enhance bioinformatics, leading to increased reproducibility. However, open science and bioinformatics skills, especially blended, are still lacking among students and researchers in resource-constrained regions. We note the need to be aware of the power of open science among the bioinformatics community and a clear strategy to learn bioinformatics and open science skills for use in research. Using the OpenScienceKE framework-Sensitize, Train, Hack, Collaborate/Community-the BOSS (Bioinformatics and Open Science Skills) virtual events built awareness and empowered researchers with the skills and tools in open science and bioinformatics. Sensitization was achieved through a symposium, training through a workshop and train-the-trainer program, hack through mini-projects, community through conferences, and continuous meet-ups. In this paper, we discuss how we applied the framework during the BOSS events and highlight lessons learnt in planning and executing the events and their impact on the outcome of each phase. We evaluate the impact of the events through anonymous surveys. We show that sensitizing and empowering researchers with the skills works best when the participants apply the skills to real-world problems: project-based learning. Furthermore, we have demonstrated how to implement virtual events in resource-constrained settings by providing Internet and equipment support to participants, thus improving accessibility and diversity.

Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta).

Cassava (Manihot esculenta Crantz) is a vital tropical root crop providing essential dietary energy to over 800 million people in tropical and subtropical regions. As a climate-resilient crop, its significance grows as the human population expands. However, yield improvement faces challenges from biotic and abiotic stress and limited breeding. Advanced sequencing and assembly techniques enabled the generation of a highly accurate, nearly complete, haplotype-resolved genome of the African cassava cultivar TMEB117. It is the most accurate cassava genome sequence to date with a base-level accuracy of QV > 64, N50 > 35 Mbp, and 98.9% BUSCO completeness. Over 60% of the genome comprises repetitive elements. We predicted over 45,000 gene models for both haplotypes. This achievement offers valuable insights into the heterozygosity genome organization of the cassava genome, with improved accuracy, completeness, and phased genomes. Due to its high susceptibility to African Cassava Mosaic Virus (ACMV) infections compared to other cassava varieties, TMEB117 provides an ideal reference for studying virus resistance mechanisms, including epigenetic variations and smallRNA expressions.

Severe malnutrition in children in Papua New Guinea: effect of a multi-faceted intervention to improve quality of care and nutritional outcomes.

BACKGROUND AND AIMS: Severe malnutrition remains a major problem in Papua New Guinea; it is associated with 11% of paediatric hospital admissions and 33% of all child deaths, with a case fatality rate around 20%. This article aims to evaluate the effectiveness of a multi-faceted intervention for improving care for children with severe malnutrition. METHODS: Severe malnutrition was defined as weight-for-age (WFA) <-3 Z-scores with severe wasting or mid upper arm circumference <115 mm or generalised oedema owing to malnutrition. The intervention included training for health-care workers on WHO guidelines for severe malnutrition, ward-round checklists, posters and support for nurses to provide better patient nutrition. Three point prevalence surveys were conducted; one before the intervention and two afterwards at 3-month intervals. The main outcomes were weight change since admission, energy intake and the proportion of the calculated required energy intake in the previous 24 hours. Each stage of the WHO guidelines for severe malnutrition management was assessed for adherence. RESULTS: There were significant improvements in the WHO steps for the management of severe malnutrition. At pre-intervention baseline, children received a median of 356 ml/day (IQR 178-450): 31% (95% CI 21-48) of their estimated daily energy requirements for weight. In the first follow-up survey, children received a median of 820 (IQR 600-1110) ml/day: 98% (95% CI 67-100) of daily energy requirements; and in the second follow-up survey they received 780 (IQR 480-900) ml/day: 86% (95% CI 46-100%) of daily requirement (P<0.001 both for volume received and percentage of energy requirements). Median weight gain prior to the intervention was 1.55 g/kg/day (IQR -4.3-6.0) which increased to 5.56 g/kg/day (IQR -3.7-12.0) and 10.19 g/kg/day (IQR 0-16.0) in the first and second follow-up surveys, respectively (P=0.013). CONCLUSION: Implementation of a multi-faceted intervention to improve the management of children with severe malnutrition was associated with improved quality of care and improved weight gain.