A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

Strain-specific genomic diversity in the Mycobacterium tuberculosis complex (MTBC) is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Several systems have been proposed to classify MTBC strains into distinct lineages and families. Here, we investigate single-nucleotide polymorphisms (SNPs) as robust (stable) markers of genetic variation for phylogenetic analysis. We identify ~92k SNP across a global collection of 1,601 genomes. The SNP-based phylogeny is consistent with the gold-standard regions of difference (RD) classification system. Of the ~7k strain-specific SNPs identified, 62 markers are proposed to discriminate known circulating strains. This SNP-based barcode is the first to cover all main lineages, and classifies a greater number of sublineages than current alternatives. It may be used to classify clinical isolates to evaluate tools to control the disease, including therapeutics and vaccines whose effectiveness may vary by strain type

A manual for large-scale sample collection, preservation, tracking, DNA extraction, and variety identification analysis

Several alternative options have been used for varietal identification. However most of the traditional methods have inherent uncertainty levels and estimates often have wide confidence intervals. In an attempt to circumvent traditional survey-based measurement errors in varietal identification, DNA-based varietal identification has been implemented in the Cassava Monitoring Survey (CMS) of Nigeria — a large adoption study involving 2500 cassava farming households. The DNA fingerprinting technique offers a reliable method to accurately identify varieties grown by farmers and increases accuracy and credibility in the interpretation of adoption rates and associated economic and policy analyses. Unlike phenotype-based methods, DNA is not affected by environmental conditions or plant growth stage and is more abundant than morphological descriptors. However, undertaking a credible DNA-based varietal identification is not a trivial matter because of the logistical challenges involving sample collection and tracking by a large team of field enumerators. This manual presents the detailed steps required for undertaking reliable DNA-fingerprinting-based identification of cassava varieties. In particular, the manual gives detailed information on the establishment of a sample tracking system, preparation of a readily available and cheap sample collection kit, field sample collection methodology, preparation of samples for DNA isolation, and development of a pipeline for variety identification analysis. This manual is part of the outputs of the CMS project funded by the CGIAR Research Program on Roots, Tubers and Bananas (RTB), the Bill & Melinda Gates Foundation, and the International Institute of Tropical Agriculture (IITA)

Determinants of under-five mortality in Gilgel Gibe Field Research Center, Southwest Ethiopia

Background: In developing countries like Ethiopia where there is no vital events registration system and laboratory diagnosis is lacking, causes of death in under-five children and its determinants could not be well known. The objective of this study was to investigate causes of death and its determinants in under-five children in Gilgel Gibe Field Research Center. Methods: A case-control study was conducted from December 12 to 27, 2005. Cases of under-five children who died between August 27, 2004 and September 22, 2005 and controls of alive children with the same age (+/-2 months) as cases were identified by a survey as the study population. Data were collected by trained enumerators using structured questionnaire adopted from World Health Organization (WHO). Causes of death were determined using the expert algorithm based on verbal autopsy data. Results: Neonatal and infant mortality rates were respectively 38 and 76.4 per 1000 live births. The two most common causes of death during neonatal period were prematurity (26.4%) and pneumonia (22.6%). Whereas the top causes of death in post-neonatal period were pneumonia (42%), malaria (37%) and acute diarrheal diseases (30%). Maternal education, practice and perception of mothers on the severity of illness and benefits of modern treatment were found to be independent predictor of child survival. Conclusion: Neonatal causes, pneumonia, malaria and diarrheal diseases were the major killers of under-five children in Ethiopia. In this study, practice of mothers and perceived benefits on the modern treatment are identified as the key predictors of child survival which are amenable to future intervention.The Ethiopian Journal of Health Development Vol. 21 (2) 2007: pp. 117-12

Cassava farmers' preferences for varieties and seed dissemination system in Nigeria: gender and regional perspectives

The Cassava Monitoring Survey (CMS) project was funded by the CGIAR-RTB Program and the Bill & Melinda Gates Foundation. The main goal was to carry out a study on cassava adoption and diffusion patterns in Nigeria. This includes explaining why farmers are adopting certain varieties and describing preference differences across regions and gender. This specific study and report is part of Component IV of the broader CMS Project, and it covered gender-differentiated, end-user surveys on varietal and trait preferences. The objective of this component was to use qualitative methods to probe deeper into some of the information that was obtained in the quantitative survey on gender-based trait preferences and seed dissemination pathways

Capacity of health facilities for diagnosis and treatment of HIV/AIDS in Ethiopia

Background: There are dearth of literature on the capacity of the health system to diagnose and treat HIV/AIDS in Ethiopia. In this study we evaluated the capacity of health facilities for HIV/AIDS care, its spatial distribution and variations by regions and zones in Ethiopia. Methods: We analyzed the Service Provision Assessment plus (SPA+) survey data that were collected in 2014 in all regions of Ethiopia. We assessed structural, process and overall capacity of the health system based on the Donabedian quality of care model. We included 5 structural and 8 process indicators and overall capacity score was constructed by taking the average of all indicators. Multiple linear regression was done using STATA 14 to assess the association of the location and types of health facilities with overall capacity score. Maps displaying the average capacity score at Zonal level were produced using ArcGIS Desktop v10.3 (Environmental Systems Research Institute Inc., Redlands CA, USA). Results: A total of 873 health facilities were included in the analysis. Less than 5% of the private facilities provided antiretroviral therapy (ART); had national ART guideline, baseline CD4 count or viral load and tuberculosis screening mechanisms. Nearly one-third of the health centers (34.9%) provided ART. Public hospitals have better capacity score (77.1%) than health centers (45.9%) and private health facilities (24.8%). The overall capacity score for urban facilities (57.1%) was higher than that of the rural (38.2%) health facilities (β = 15.4, 95% CI: 11.7, 19.2). Health centers (β = − 21.4, 95% CI: -25.4, − 17.4) and private health facilities (β = − 50.9, 95% CI: -54.8, − 47.1) had lower overall capacity score than hospitals. Facilities in Somali (β = − 13.8, 95% CI: -20.6, − 7.0) and SNNPR (β = − 5.0, 95% CI: -9.8, − 0.1) regions had lower overall capacity score than facilities in the Oromia region. Zones located in emerging regions such as Gambella and Benishangul Gumz and in remote areas of Oromia and SNNPR had lower capacity score in terms of process indicators. Conclusions: There is a significant geographical heterogeneity on the capacity of health facilities for HIV/AIDS care and treatment in Ethiopia. Targeted capacity improvement initiatives are recommended with focus on health centers and private health facilities, and emerging Regions and the rural and remote areas

Sensitive electrochemical determination of ethambutol in pharmaceutical formulation and human urine at nickel nanoparticles/electrochemically reduced graphene oxide modified electrode

This paper describes the application of nickel nanoparticles decorated electrochemically reduced graphene oxide modified glassy carbon electrode (NiNPs/ERGO/GCE) for the determination of ethambutol (ETB), an anti-Mycobacterium tuberculosis drug. The modified electrode showed remarkable electrocatalytic properties accompanied with a significant enhancement in the peak current response towards ETB compared to the bare electrode. The results showed that the composite modified electrode played a significant catalytic role due to the synergetic effect of NiNPs and ERGO. The NiNPs/ERGO modified electrode demonstrated excellent square wave voltammetric response towards ETB determination at the NiNPs/ERGO/GCE in the range 0.05‒100 µM. The sensor demonstrated outstanding sensitivity towards ETB determination with limit of detection (LOD) and limit of quantification (LOQ) of 0.023 and 0.075 µM, respectively. The developed sensor was effectively validated for real sample study using drug formulation and urine samples which showed an acceptable recovery (99.6‒109%). The electrode also exhibited good precision (RSD < 1%, n = 20), reproducibility (RSD < 1.9%, n = 3), long-term stability (92% of its initial response after two weeks) and selectivity towards interfering substances in the determination of ethambutol.               KEY WORDS: Ethambutol, Glassy carbon electrode, Square wave voltammetry, Electrochemically reduced graphene oxide, Nickel nanoparticles Bull. Chem. Soc. Ethiop. 2019, 33(2), 215-228.DOI: https://dx.doi.org/10.4314/bcse.v33i2.

Accuracy on Diagnostic Performance of Point Of Care Liodetect® Tb-St Rapid Test for the Diagnosis of Pulmonary Tuberculosis in North West Ethiopia

Background: Tuberculosis (TB) is the leading cause of death due to a single infectious agent. To improve TB case detection and treatment in healthcare-disrupted urban and rural settings, an accurate point-of-care (POC) test that does not rely on sputum quality is urgently needed. Objective: To evaluate the accuracy of performance of a new rapid POC antibody-based detection test for the diagnosis of pulmonary TB. Methods: This prospective cross-sectional study was conducted from June 2018 to July 2019 in presumptive pulmonary TB (PTB) patients in Northwest Ethiopia. Sputum was routinely collected for diagnosis of TB with a Lowenstein Jensen (LJ) culture and an Xpert MTB/RIF test was compared with the LIODetect TB ST rapid point-of-care diagnostic test. Using LJ culture and Xpert MTB/RIF for M.tb detection as our reference standards. SPSS ver. 20 and Medcalc were used to analyze descriptive and diagnostic accuracy tests, respectively. Result: A total of 233 samples were analyzed.  The LIODetect TB-ST rapid test showed a sensitivity of 53.0%, specificity of 91.0%, positive predictive values (PPV) of 70.0 %, negative predicted values (NPV) of 83.1 % with overall accuracy of 80.3%when compared to the LJ culture as a reference method. Similarly, the same test showed sensitivity of 69.6%, specificity of 90.6%, PPV of 67.9%, NPV of 91.1%, and over all accuracy of 85.8% when compared to the Xpert MTB/RIF as a reference standard. Further, when exclusively evaluated in people living with HIV (PLWH), the LIODetect TB-ST rapid test diagnostic showed similar performance as  described above, with an overall accuracy of 83.7% and 86.1% when compared to LJ culture and the Xpert MTB/RIF test, respectively. Conclusion: The LIODetect TB-ST rapid test performance was optimal against the MTB/RIF test and LJ culture. This POC test also had optimal sensitivity and better specificity in both HIV negative people and People living with human immunodeficiency virus (PLWH). Thus, the LIODetect TB-ST rapid test could be a useful  as POC TB screening test in resource-limited urban/rural areas, where routine TB diagnosis using LJ and/or the Xpert MTB/RIF test can not be performed.

Applying the Transdisciplinary Adaptive Systemic Approach to Securing the Long-Term Future of Grassland Ecosystems

Contemporary grasslands all exist as complex adaptive systems, specifically complex social-ecological systems – whether these are in protected areas or are part of private or communal agricultural landscapes. These systems are subject to the current planetary condition that includes rapidly growing human populations and demand for natural resources, the widespread use of pollutants, and climate change consequences. All complex adaptive systems have characteristics in common - they comprise multiple elements, which interact, and the multiple interactions cause intersecting feedback loops. As a result, a current system condition reflects its history, future condition is difficult to predict, and interventions have unpredictable outcomes – some positive others negative. The system itself produces emergent properties – new characteristics - through time, out of the multiple element interactions. As complex social-ecological systems, grasslands have all the interactive complexity of both society and ecosystems. This paper uses place-based landscape restoration interventions in the grasslands of the Tsitsa River Catchment, South Africa, and the Lake Tana basin, Ethiopia, to showcase the development and application of the Adaptive Systemic Approach – which we present as an advance in participatory sustainability science

Computational studies on heterogenization of homogeneous catalyst of iron(III), nickel(II) and copper(II) N,N′-disalicylidene-1,2-phenylenediamine complex

Density functional theory (DFT) calculations were carried out on iron(III), nickel(II) and copper(II) complexes of N,N′-ethylenebis(salicylimine) both at molecular level (isolated complexes) and encapsulated in a zeolite framework to investigate changes that occur in their geometrical and electronic parameters as well as in their reactivity and stability. The computational results showed that the zeolite encapsulated metal complexes have higher reactivity and less stability as compared to the isolated metal complexes.               KEY WORDS: Density functional theory, N,N′-ethylenebis(salicylimine), Computational studies, Heterogenization, Electronic parameters Bull. Chem. Soc. Ethiop. 2019, 33(1), 91-102DOI: https://dx.doi.org/10.4314/bcse.v33i1.

Multi-Level Analysis and Spatial Interpolation of Distributions and Predictors of Childhood Diarrhea in Nigeria.

Background: Diarrhea is one of the health problems contributing to Nigeria's under-5 mortality rate, ranked as the eighth highest globally. As our search is concerned, there is limited evidence on the spatial distribution of childhood diarrhea in Nigeria. Therefore, this study aimed to examine the spatial distribution and predictors of diarrhea among under-5 children in Nigeria. Materials and Methods: Using data from the child's recode file of the 2018 Nigeria Demographic and Health Survey, a sample of 28 583 children of women of reproductive age was considered as the sample size for this study. The outcome variable used in this study was childhood diarrhea. We employed both multilevel and spatial analyses to ascertain the factors associated with childhood diarrhea as well as its spatial clustering. Results: The regional distribution of the prevalence of diarrhea among children in Nigeria ranged from 0% to 62%. The hotspots for childhood diarrhea were in Yobe, Bauchi, Gombe, Kano, Sokoto, Imo, and Taraba. The likelihood of a child having diarrhea in Nigeria was higher among women whose partners have secondary education and above [aOR = 1.18; 95%CI = 1.05-1.33], women currently working [aOR = 1.24; 95%CI = 1.13-1.35], women practicing Islam [aOR = 1.24; 95%CI = 1.04-1.46], and women who were exposed to mass media [aOR = 1.29; 95%CI = 1.18-1.42], compared to women whose partners had no formal education, women not currently working, women practicing Christianity, and those who were not exposed to mass media. Children born to mothers who reside in North East [aOR = 2.55; 95%CI = 2.10-3.10], and communities with medium socioeconomic status [aOR = 1.44; 95%CI = 1.09-1.91] were more likely to experience diarrhea compared to those born to mothers residing in the North Central and in communities with low socioeconomic status. Conclusion: High proportions of childhood diarrhea among under-5 children in Nigeria were located in Yobe, Bauchi, Gombe, Kano, Sokoto, Imo, and Taraba. Policies and interventions that seek to reduce or eliminate diarrhea diseases among under-5 children in Nigeria should take a keen interest in the factors identified as predictors of childhood diarrhea in this study as this will help in achieving the aims of WASH, ORT corners, and SDG 3 by the year 2030