Exploration of data for analysis using boundary line methodology

The boundary line model has been proposed for interpretation of the plot of a biological response (such as crop yield) against a potentially-limiting variable from observations in a large set of scenarios across which other factors show uncontrolled variation. Under this model the upper bound of the distribution of data represents the limiting effect of the potential factor on the response. Methods have been proposed to fit this model, but we propose that an initial exploratory data analysis step is needed to evaluate evidence that (i) the model is plausible and (ii) that any limiting upper bound is exhibited by the data set (which could, in principle, not include any cases where the factor is limiting). We propose a statistic based on the density of observations in upper sections of early convex hull peels of the data plot. We evaluate this approach using various data sets, some of which have been used for boundary line analysis in previous studies

Linkages between soil, crop, livestock, and human selenium status in Sub-Saharan Africa: a scoping review.

Selenium (Se) is essential for human health, however, data on population Se status and agriculture-nutrition-health linkages are limited in sub-Saharan Africa (SSA). The scoping review aims to identify linkages between Se in soils/crops, dietary Se intakes, and livestock and human Se status in SSA. Online databases, organisational websites and grey literature were used to identify articles. Articles were screened at title, abstract and full text levels using eligibility criteria. The search yielded 166 articles from which 112 were excluded during abstract screening and 54 full text articles were assessed for eligibility. The scoping review included 34 primary studies published between 1984 and 2021. The studies covered Se concentrations in soils (n = 7), crops (n = 9), animal tissues (n = 2), livestock (n = 3), and human Se status (n = 15). The evidence showed that soil/crop Se concentrations affected Se concentration in dietary sources, dietary Se intake and biomarkers of Se status. Soil types are a primary driver of human Se status and crop Se concentration correlates positively with biomarkers of Se dietary status. Although data sets of Se concentrations exist across the food system in SSA, there is limited evidence on linkages across the agriculture-nutrition nexus. Extensive research on Se linkages across the food chain is warranted

Do agronomic approaches aligned to regenerative agriculture improve the micronutrient concentrations of edible portions of crops? A scoping review of evidence

Regenerative Agriculture (RA) is used to describe nature-based agronomic approaches that aim to build soil health and crop resilience, minimize negative environmental outcomes, and improve farmer livelihoods. A benefit that is increasingly attributed to crops grown under RA practices is improved nutritional content. However, we do not know the extent to which RA influences crop nutritional quality and under what management approaches and context, can such effects be realized. A scoping review of recent literature (Web of Science, 2000-2021) was carried out to assess the evidence that RA approaches improve crop micronutrient quality. Papers included combinations of agronomic approaches that could be defined as Regenerative: "Organic Inputs" including composts and manures, cover crops, crop rotations, crop residues and biochars; "Reduced Tillage", "Intercropping", "Biostimulants" e.g. arbuscular mycorrhizal fungi; plant growth promoting bacteria, and "Irrigation", typically deficit-irrigation and alternate wetting and drying. The crop types reviewed were predetermined covering common sources of food and included: Tomato (Solanum lycopersicum L.), Wheat (Triticum aestivum L.), Rice (Oryza sativa L.), Maize (Zea mays L.), Pulses (Fabaceae), Alliums (Allium spp.), and "other" crop types (30 types). This scoping review supports a potential role for RA approaches in increasing the concentrations of micronutrients in the edible portions of several crop types under specific practices, although this was context specific. For example, rice grown under increased organic inputs showed significant increases in grain zinc (Zn) concentration in 15 out of 16 studies. The vitamin C concentration of tomato fruit increased in similar to 50% of studies when plants were grown under increased organic inputs, and in 76% of studies when plants were grown under deficit irrigation. Overall, the magnitude and reproducibility of the effects of RA practices on most crop nutritional profiles were difficult to assess due to the diversity of RA approaches, geographical conditions, and the limited number of studies for most crops in each of these categories. Future research with appropriate designs, improved on-farm surveillance and nutritional diagnostics are needed for better understanding the potential role of RA in improving the quality of food, human nutrition, and health

Estimates of Dietary Mineral Micronutrient Supply from Staple Cereals in Ethiopia at a District Level

Recent surveys have revealed substantial spatial variation in the micronutrient composition of cereals in Ethiopia, where a single national micronutrient concentration values for cereal grains are of limited use for estimating typical micronutrient intakes. We estimated the district-level dietary mineral supply of staple cereals, combining district-level cereal production and crop mineral composition data, assuming cereal consumption of 300 g capita−1 day−1 proportional to district-level production quantity of each cereal. We considered Barley (Hordeum vulgare L.), maize (Zea mays L.), sorghum (Sorghum bicolor (L.) Moench), teff (Eragrostis tef (Zuccagni) Trotter), and wheat (Triticum aestivum L.) consumption representing 93.5% of the total cereal production in the three major agrarian regions. On average, grain cereals can supply 146, 23, and 7.1 mg capita−1 day−1 of Ca, Fe, and Zn, respectively. In addition, the Se supply was 25 µg capita−1 day−1. Even at district-level, cereals differ by their mineral composition, causing a wide range of variation in their contribution to the daily dietary requirements, i.e., for an adult woman: 1–48% of Ca, 34–724% of Fe, 17–191% of Se, and 48–95% of Zn. There was considerable variability in the dietary supply of Ca, Fe, Se, and Zn from staple cereals between districts in Ethiopi

Sub-sampling a large physical soil archive for additional analyses to support spatial mapping; a pre-registered experiment in the Southern Nations, Nationalities, and Peoples Region (SNNPR) of Ethiopia

The value of physical archives of soil material from field sampling activities has been widely recognized. If we want to use archive material for new destructive analyses to support a task, such as spatial mapping, then an efficient sub-sampling strategy is needed, both to manage analytical costs and to conserve the archive material. In this paper we present an approach to this problem when the objective is spatial mapping by ordinary kriging. Our objective was to subsample the physical archive from the Ethiopia Soil Information System (EthioSIS) survey of the Southern Nations, Nationalities and Peoples Region (SNNPR) for spatial mapping of two variables, concentrations of particular fractions of selenium and iodine in the soil, which had not been measured there. We used data from cognate parts of surrounding regions of Ethiopia to estimate variograms of these properties, and then computed prediction error variances for maps in SNNPR based on proposed subsets of the archive of different size, selected to optimize a spatial coverage criterion (with some close sample pairs included). On this basis a subsample was selected. This is a preregistered experiment in that we have proposed criteria for evaluating the success of our approach, and are publishing that in advance of receiving analytical data on the subsampled material from the laboratories where they are being processed. A subsequent short report will publish the outcome. The use of preregistered trials is widely recommended and used in areas of science including public health, and we believe that it is a sound strategy to promote reproducible research in soil science

Agronomic biofortification increases grain zinc concentration of maize grown under contrasting soil types in Malawi

Zinc (Zn) deficiency remains a public health problem in Malawi, especially among poor and marginalized rural populations, linked with low dietary intake of Zn due to consumption of staple foods that are low in Zn content. The concentration of Zn in staple cereal grain can be increased through application of Zn-enriched fertilizers, a process called agronomic biofortification or agro-fortification. Field experiments were conducted at three Agricultural Research Station sites to assess the potential of agronomic biofortification to improve Zn concentration in maize grain in Malawi as described in registered report published previously. The hypotheses of the study were (i) that application of Zn-enriched fertilizers would increase in the concentration of Zn in maize grain to benefit dietary requirements of Zn and (ii) that Zn concentration in maize grain and the effectiveness of agronomic biofortification would be different between soil types. At each site two different subsites were used, each corresponding to one of two agriculturally important soil types of Malawi, Lixisols and Vertisols. Within each subsite, three Zn fertilizer rates (1, 30, and 90 kg ha−1) were applied to experimental plots, using standard soil application methods, in a randomized complete block design. The experiment had 10 replicates at each of the three sites as informed by a power analysis from a pilot study, published in the registered report for this experiment, designed to detect a 10% increase in grain Zn concentration at 90 kg ha−1, relative to the concentration at 1 kg ha−1. At harvest, maize grain yield and Zn concentration in grain were measured, and Zn uptake by maize grain and Zn harvest index were calculated. At 30 kg ha−1, Zn fertilizer increased maize grain yields by 11% compared with nationally recommended application rate of 1 kg ha−1. Grain Zn concentration increased by 15% and uptake by 23% at the application rate of 30 kg ha−1 relative to the national recommendation rate. The effects of Zn fertilizer application rate on the response variables were not dependent on soil type. The current study demonstrates the importance of increasing the national recommendation rate of Zn fertilizer to improve maize yield and increase the Zn nutritional value of the staple crop

Anemia in children aged 6–59 months was significantly associated with maternal anemia status in rural Zimbabwe

Globally, anemia is a public health problem affecting mostly women of reproductive age (WRA, n = 452) and children aged 6–59 months (n = 452) from low- and lower-middle-income countries. This cross-sectional study assessed the prevalence and determinants of anemia in WRA and children aged 6–59 months in rural Zimbabwe. The venous blood sample was measured for hemoglobin utilizing a HemoCue machine. Anthropometric indices were assessed and classified based on World Health Organization standards. Socioeconomic characteristics were assessed. The median (±inter quartile range (IQR)) age of WRA was 29 ± 12 years and that for children was 29 ± 14 months. The prevalence of anemia was 29.6% and 17.9% in children and WRA, respectively, while the median (±IQR) hemoglobin levels were 13.4 ± 1.8 and 11.7 ± 1.5 g/dl among women and children, respectively. Multiple logistic regression analysis was used to assess determinants of anemia. Anemia in children was significantly associated with maternal anemia (odds ratio (OR) = 2.02; 95% CI 1.21–3.37; p = .007) and being a boy (OR = 0.63; 95% CI 0.41–0.95; p = .029), while anemia in WRA was significantly associated with the use of unimproved dug wells as a source of drinking water (OR = 0.36; 95% CI 0.20–0.66; p = .001) and lack of agricultural land ownership (OR = 0.51; 95% CI 0.31–0.85; p = .009). Anemia is a public health problem in the study setting. The positive association between maternal and child anemia reflects the possibility of cross-generational anemia. Therefore, interventions that focus on improving preconceptual and maternal nutritional status may help to reduce anemia in low-income settings

Anemia in children aged 6-59 months was significantly associated with maternal anemia status in rural Zimbabwe.

Globally, anemia is a public health problem affecting mostly women of reproductive age (WRA, n = 452) and children aged 6–59 months (n = 452) from low- and lower-middle-income countries. This cross-sectional study assessed the prevalence and determinants of anemia in WRA and children aged 6–59 months in rural Zimbabwe. The venous blood sample was measured for hemoglobin utilizing a HemoCue machine. Anthropometric indices were assessed and classified based on World Health Organization standards. Socioeconomic characteristics were assessed. The median (±inter quartile range (IQR)) age of WRA was 29 ± 12 years and that for children was 29 ± 14 months. The prevalence of anemia was 29.6% and 17.9% in children and WRA, respectively, while the median (±IQR) hemoglobin levels were 13.4 ± 1.8 and 11.7 ± 1.5 g/dl among women and children, respectively. Multiple logistic regression analysis was used to assess determinants of anemia. Anemia in children was significantly associated with maternal anemia (odds ratio (OR) = 2.02; 95% CI 1.21–3.37; p = .007) and being a boy (OR = 0.63; 95% CI 0.41–0.95; p = .029), while anemia in WRA was significantly associated with the use of unimproved dug wells as a source of drinking water (OR = 0.36; 95% CI 0.20–0.66; p = .001) and lack of agricultural land ownership (OR = 0.51; 95% CI 0.31–0.85; p = .009). Anemia is a public health problem in the study setting. The positive association between maternal and child anemia reflects the possibility of cross-generational anemia. Therefore, interventions that focus on improving preconceptual and maternal nutritional status may help to reduce anemia in low-income settings

Virus-Host Coevolution: Common Patterns of Nucleotide Motif Usage in Flaviviridae and Their Hosts

Virus-host biological interaction is a continuous coevolutionary process involving both host immune system and viral escape mechanisms. Flaviviridae family is composed of fast evolving RNA viruses that infects vertebrate (mammals and birds) and/or invertebrate (ticks and mosquitoes) organisms. These host groups are very distinct life forms separated by a long evolutionary time, so lineage-specific anti-viral mechanisms are likely to have evolved. Flaviviridae viruses which infect a single host lineage would be subjected to specific host-induced pressures and, therefore, selected by them. In this work we compare the genomic evolutionary patterns of Flaviviridae viruses and their hosts in an attempt to uncover coevolutionary processes inducing common features in such disparate groups. Especially, we have analyzed dinucleotide and codon usage patterns in the coding regions of vertebrate and invertebrate organisms as well as in Flaviviridae viruses which specifically infect one or both host types. The two host groups possess very distinctive dinucleotide and codon usage patterns. A pronounced CpG under-representation was found in the vertebrate group, possibly induced by the methylation-deamination process, as well as a prominent TpA decrease. The invertebrate group displayed only a TpA frequency reduction bias. Flaviviridae viruses mimicked host nucleotide motif usage in a host-specific manner. Vertebrate-infecting viruses possessed under-representation of CpG and TpA, and insect-only viruses displayed only a TpA under-representation bias. Single-host Flaviviridae members which persistently infect mammals or insect hosts (Hepacivirus and insect-only Flavivirus, respectively) were found to posses a codon usage profile more similar to that of their hosts than to related Flaviviridae. We demonstrated that vertebrates and mosquitoes genomes are under very distinct lineage-specific constraints, and Flaviviridae viruses which specifically infect these lineages appear to be subject to the same evolutionary pressures that shaped their host coding regions, evidencing the lineage-specific coevolutionary processes between the viral and host groups

Drinking water quality from rural handpump-boreholes in Africa

Groundwater provides a vital source of drinking water for rural communities in many parts of Africa, particularly in the dry season when there are few safe alternative sources. This paper summarises results from a study (n = 428) assessing dry season water quality, both microbiological and inorganic chemistry, in handpump equipped boreholes (HPBs) across the Ethiopia Highlands (n = 142), Malawi (n = 162) and Uganda (n = 124) using a stratified, randomised sampling design. This study seeks to examine general water quality by randomly sampling rural groundwater supplies across larger areas with different geology and climate. The majority, 72%, of HPBs surveyed provide good quality dry season drinking water as defined by WHO drinking water quality criteria. Within this overall picture, the most notable constraints were from thermotolerant coliforms (TTCs), which exceeded the WHO drinking water guideline of zero colony forming units (cfu/100 ml) in 21% of sites (range 0–626 cfu/100 ml). TTC contamination was found to have a significant and positive correlation with annual average rainfall (ρ = 0.2, p = 0.00003). Across all three countries, WHO health based chemical drinking water quality values were exceeded at 9% of sites and were found for manganese (4%), fluoride (2.6%) and nitrate (2.5%); arsenic concentrations were below the guideline value of 10 μg l−1 (range 400 μg l−1) found in drinking water sources in Uganda challenges the decision by WHO not to formalise a health-based guideline for Mn. While the overall level of microbiological contamination from HPBs is low, results from this study strongly suggest that at a national and regional level, microbiological contamination rather than chemical contamination will provide a greater barrier to achieving targets set for improved drinking water quality under the UN-SDG 6. Efforts should be made to ensure that boreholes are properly sited and constructed effectively to reduce pathogen contamination