Population genetics of a lethally managed medium-sized predator

Globally, levels of human–wildlife conflict are increasing as a direct consequence of the expansion of people into natural areas resulting in competition with wildlife for food and other resources. By being forced into increasingly smaller pockets of suitable habitat, many animal species are at risk of becoming susceptible to loss of genetic diversity, inbreeding depression and the associated inability to adapt to environmental changes. Predators are often lethally controlled due to their threat to livestock. Predators such as jackals (black backed, golden and side striped; Canis mesomelas, C. aureus and C. adustus, respectively), red foxes (Vulpes vulpes) and coyotes (C. latrans) are highly adaptable and may respond to ongoing persecution through compensatory reproduction such as reproducing at a younger age, producing larger litters and/or compensatory immigration including dispersal into vacant territories. Despite decades of lethal management, jackals are problematic predators of livestock in South Africa and, although considered a temporary measure, culling of jackals is still common. Culling may affect social groups, kinship structure, reproductive strategies and sex-biased dispersal in this species. Here, we investigated genetic structure, variation and relatedness of 178 culled jackals on private small-livestock farms in the central Karoo of South Africa using 13 microsatellites. Genetic variation was moderate to high and was similar per year and per farm. An absence of genetic differentiation was observed based on STRUCTURE, principal component analysis and AMOVA. Relatedness was significantly higher within farms (r = 0.189) than between farms (r = 0.077), a result corroborated by spatial autocorrelation analysis. We documented 18 occurrences of dispersal events where full siblings were detected on different farms (range: 0.78–42.93 km). Distance between identified parent–offspring varied from 0 to 36.49 km. No evidence for sex-biased dispersal was found. Our results suggest that in response to ongoing lethal management, this population is most likely able to maintain genetic diversity through physiological and behavioural compensation mechanisms.APPENDIX S1. Supplementary methods.SUPPLEMENTARY TABLES. TABLE S1. Primer details for microsatellite loci used to genotype black-backed jackals (Canis Mesomelas). TABLE S2. Per-locus summary statistics as calculated in Cervus v3.0.7. The non-exclusion probabilities and combined non-exclusion probabilities (final row, italics) are relevant indicators of the power of the loci for parentage and sibship analyses. TABLE S3. Summary statistics for 20 sampling localities (farms) with >1 sample and for all farms pooled. Produced using the basicStats command of the diveRsity package v1.9.90 in R v3.6.2 and RStudio v1.2.5033. Standard deviation was calculated across loci in Microsoft Excel (stdev.s). Sampling localities with only one sample are not shown. TABLE S4. Summary statistics per year and for all years pooled. Produced using the basicStats command of the diveRsity package v1.9.90 in R v3.6.2 and RStudio v1.2.5033. Standard deviation was calculated across loci in Microsoft Excel (STDEV.S). TABLE S5. Pairwise FST values between farms with the full dataset (below diagonal) and associated significance at a level of 0.05 (above diagonal), where significant values are indicated by a “+” and non-significant values by a “−”. Calculated in Arlequin 3.5.2.2. TABLE S6. Pairwise FST values between farms with relatives removed (below diagonal) and associated significance at a level of 0.05 (above diagonal), where significant values are indicated by a “+” and non-significant values by a “−”. Calculated in Arlequin 3.5.2.2. TABLE S7. Comparison of mean pairwise relatedness (r) between years and mean individual inbreeding coefficients (F) between years. P-values for the Wilcoxon tests for difference in means are shown on the inside of the table (bordered by grey), with P-values for inbreeding comparisons shown below the diagonal (bottom left) and P-values for relatedness comparisons shown above the diagonal (top right). The mean F for each year is shown in the left-most column “outside” the main table, with the mean r for each year shown in the top row “outside” the main table. The numbers in parentheses after each year are the number of observations/data points for that year (number of samples for F and number of pairwise relatedness comparisons for r).SUPPLEMENTARY FIGURES. FIGURE S1. STRUCTURE HARVESTER results for (a) Delta K values and (b) probability (-LnPr) of K = 1–27 averaged over 20 runs and (c) genetic differentiation between the jackal sample locations (farms) based on STRUCTURE analysis (performed with K = 2–6) of 1 = GV, 2 = BB, 3 = BR, 4 = BD, 5 = DS, 6 = GG, 7 = HK, 8 = KD, 9 = KW, 10 = KK, 11 = KT, 12 = NG, 13 = ND, 14 = OG, 15 = RV, 16 = RE, 17 = RT, 18 = RD, 19 = SG, 20 = SK, 21 = VR, 22 = WK, 23 = CL, 24 = KR, 25 = WB and 26 = TD. FIGURE S2. STRUCTURE HARVESTER results for (a) Delta K values and (b) probability (-LnPr) of K = 1–27 averaged over 20 runs and (c) genetic differentiation between the jackal sample locations (farms) based on STRUCTURE analysis (performed with K = 2–6 and K = 14) of 1 = GV, 2 = BB, 3 = BD, 4 = DS, 5 = GG, 6 = HK, 7 = KW, 8 = KT, 9 = NG, 10 = ND, 11 = OG, 12 = RV, 13 = RE, 14 = RD, 15 = SG, 16 = SK, 17 = VR, 18 = WK and 19 = CL. After removing relatives, some localities had no samples, hence fewer sampling localities as compared to the full dataset. Note: The Evanno method (DeltaK) does not evaluate K = 1. FIGURE S3. Principal component analysis (PCA) of the different jackal sampling locations (farms) with related individuals removed. FIGURE S4. Plot comparing the relatedness estimates using six estimators and simulated individuals of known relatedness. Di, Dyadic likelihood estimator “DyadML”; LL, Lynch-Li estimator; LR, Lynch and Ritland estimator; QG, Queller and Goodnight estimator; Tri, Triadic likelihood estimator “TrioML”; W, Wang estimator. Plot produced with ggplot2 3.3.0 (Wickham, 2016). FIGURE S5. Results of the spatial autocorrelation analysis for A females and B males. The blue line indicates the autocorrelation coefficient of the data, with the 95% confidence interval at each distance class indicated by the black error bars, as determined by 1000 bootstrap resampling replicates. The red dashed lines indicate the 95% confidence interval around the null hypothesis (no spatial structure, i.e. rauto = 0), as determined by permutation (999 steps). Thus, if the error bars around the blue line do not overlap with the red dashed lines in a distance class, then genotypes were more (positive rauto) or less (negative rauto) similar than expected under the null hypothesis in that distance class. Such cases are indicated with an asterisk (*).The National Zoological Gardens, Pretoria and the University of South Africa.https://zslpublications.onlinelibrary.wiley.com/journal/14697998hj2023BiochemistryGeneticsMicrobiology and Plant Patholog

Evaluation of Three Amorphous Drug Delivery Technologies to Improve the Oral Absorption of Flubendazole

AbstractThis study investigates 3 amorphous technologies to improve the dissolution rate and oral bioavailability of flubendazole (FLU). The selected approaches are (1) a standard spray-dried dispersion with hydroxypropylmethylcellulose (HPMC) E5 or polyvinylpyrrolidone-vinyl acetate 64, both with Vitamin E d-α-tocopheryl polyethylene glycol succinate; (2) a modified process spray-dried dispersion (MPSDD) with either HPMC E3 or hydroxypropylmethylcellulose acetate succinate (HPMCAS-M); and (3) confining FLU in ordered mesoporous silica (OMS). The physicochemical stability and in vitro release of optimized formulations were evaluated following 2 weeks of open conditions at 25°C/60% relative humidity (RH) and 40°C/75% RH. All formulations remained amorphous at 25°C/60% RH. Only the MPSDD formulation containing HPMCAS-M and 3/7 (wt./wt.) FLU/OMS did not crystallize following 40°C/75% RH exposure. The OMS and MPSDD formulations contained the lowest and highest amount of hydrolyzed degradant, respectively. All formulations were dosed to rats at 20 mg/kg in suspension. One FLU/OMS formulation was also dosed as a capsule blend. Plasma concentration profiles were determined following a single dose. In vivo findings show that the OMS capsule and suspension resulted in the overall highest area under the curve and Cmax values, respectively. These results cross-evaluate various amorphous formulations and provide a link to enhanced biopharmaceutical performance

Fruit and vegetable biodiversity for nutritionally diverse diets: Challenges, opportunities, and knowledge gaps

Planetary health brings together intrinsically linked issues of human health and natural systems. This paper reviews evidence of how agrobiodiversity underpins dietary diversity for current human populations in the context of fruits and vegetables, and ways to maintain and improve these for future generations. Both the conservation and sustainable use of fruit and vegetable biodiversity and the consumption of diverse diets are sub-optimal, and in many contexts getting worse. Agrobiodiversity and nutrition are linked through food availability, access, conservation and consumption, with potential win-wins but notable trade-offs for policy and action through time, place, agrobiodiversity use, and equity. We pinpoint research gaps and call for inclusive deliberation for action

Standards in semen examination:publishing reproducible and reliable data based on high-quality methodology

Biomedical science is rapidly developing in terms of more transparency, openness and reproducibility of scientific publications. This is even more important for all studies that are based on results from basic semen examination. Recently two concordant documents have been published: the 6th edition of the WHO Laboratory Manual for the Examination and Processing of Human Semen, and the International Standard ISO 23162:2021. With these tools, we propose that authors should be instructed to follow these laboratory methods in order to publish studies in peer-reviewed journals, preferable by using a checklist as suggested in an Appendix to this article.Peer reviewe

Effect of Hydrocortisone on Mortality and Organ Support in Patients With Severe COVID-19: The REMAP-CAP COVID-19 Corticosteroid Domain Randomized Clinical Trial.

Importance: Evidence regarding corticosteroid use for severe coronavirus disease 2019 (COVID-19) is limited. Objective: To determine whether hydrocortisone improves outcome for patients with severe COVID-19. Design, Setting, and Participants: An ongoing adaptive platform trial testing multiple interventions within multiple therapeutic domains, for example, antiviral agents, corticosteroids, or immunoglobulin. Between March 9 and June 17, 2020, 614 adult patients with suspected or confirmed COVID-19 were enrolled and randomized within at least 1 domain following admission to an intensive care unit (ICU) for respiratory or cardiovascular organ support at 121 sites in 8 countries. Of these, 403 were randomized to open-label interventions within the corticosteroid domain. The domain was halted after results from another trial were released. Follow-up ended August 12, 2020. Interventions: The corticosteroid domain randomized participants to a fixed 7-day course of intravenous hydrocortisone (50 mg or 100 mg every 6 hours) (n = 143), a shock-dependent course (50 mg every 6 hours when shock was clinically evident) (n = 152), or no hydrocortisone (n = 108). Main Outcomes and Measures: The primary end point was organ support-free days (days alive and free of ICU-based respiratory or cardiovascular support) within 21 days, where patients who died were assigned -1 day. The primary analysis was a bayesian cumulative logistic model that included all patients enrolled with severe COVID-19, adjusting for age, sex, site, region, time, assignment to interventions within other domains, and domain and intervention eligibility. Superiority was defined as the posterior probability of an odds ratio greater than 1 (threshold for trial conclusion of superiority >99%). Results: After excluding 19 participants who withdrew consent, there were 384 patients (mean age, 60 years; 29% female) randomized to the fixed-dose (n = 137), shock-dependent (n = 146), and no (n = 101) hydrocortisone groups; 379 (99%) completed the study and were included in the analysis. The mean age for the 3 groups ranged between 59.5 and 60.4 years; most patients were male (range, 70.6%-71.5%); mean body mass index ranged between 29.7 and 30.9; and patients receiving mechanical ventilation ranged between 50.0% and 63.5%. For the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively, the median organ support-free days were 0 (IQR, -1 to 15), 0 (IQR, -1 to 13), and 0 (-1 to 11) days (composed of 30%, 26%, and 33% mortality rates and 11.5, 9.5, and 6 median organ support-free days among survivors). The median adjusted odds ratio and bayesian probability of superiority were 1.43 (95% credible interval, 0.91-2.27) and 93% for fixed-dose hydrocortisone, respectively, and were 1.22 (95% credible interval, 0.76-1.94) and 80% for shock-dependent hydrocortisone compared with no hydrocortisone. Serious adverse events were reported in 4 (3%), 5 (3%), and 1 (1%) patients in the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively. Conclusions and Relevance: Among patients with severe COVID-19, treatment with a 7-day fixed-dose course of hydrocortisone or shock-dependent dosing of hydrocortisone, compared with no hydrocortisone, resulted in 93% and 80% probabilities of superiority with regard to the odds of improvement in organ support-free days within 21 days. However, the trial was stopped early and no treatment strategy met prespecified criteria for statistical superiority, precluding definitive conclusions. Trial Registration: ClinicalTrials.gov Identifier: NCT02735707

Harvesting nutrition : Grain legumes and nutritious diets in sub-Saharan Africa

Low quality diets is the number one risk factor for the global burden of disease. Agriculture is one of the sectors with strong potential to enhance the quality of diets; especially among rural populations in low and middle income countries where malnutrition levels are highest and agriculture is often still the most important source of food and income. In sub-Saharan Africa the availability of nutrient-dense foods such as legumes, dairy, meat, fruits, nuts and seeds has declined while the availability of grains less-dense in protein and micronutrients has increased. The protein and micronutrient intake from sub-Saharan African diets is often estimated to be inadequate. Grain legumes are appreciated for their contribution to dietary protein and micronutrient intake in addition to their benefits in replenishing soil fertility. This thesis describes the research conducted to investigate the potential of grain legume cultivation for nutritious diets of smallholder farming households in sub-Saharan Africa. The research was conducted both at crop level (Chapters 2 and 3) and at whole diet level (Chapters 4 and 5). The current and potential role of grain legumes on protein, both quantity and quality, and micronutrient adequacy in the diet of rural Ghanaian infants and young children was studied (Chapter 2). Energy and nutrient (including amino acids) intakes of breastfed children of 6-8 months (n=97), 9-11 months (n=97), 12-23 months (n=114), and non-breastfed children of 12-23 months (n=29) were assessed using a repeated quantitative multi-pass 24-hour recall method. Food-based dietary guidelines that best cover nutrient adequacy within the constraints of the local current dietary patterns were modelled using the linear programming software Optifood (version 4.0.9, Optifood©). 60% of the children consumed legumes with an average portion size of 20 g per day contributing more than 10% of their total protein, folate, iron and niacin intake. The final food-based dietary guidelines included legumes and provided adequate protein and essential amino acids. Adding extra legumes to the food-based dietary guidelines, on top of the current dietary pattern, improved adequacy of calcium, iron, niacin and zinc but not reached sufficient amounts to meet requirements. Although legumes are often said to be the ‘meat of the poor’ and the current grain legume consumption among rural children does contribute to their protein intakes, the main nutritional benefit of increased legume consumption is improvement of micronutrient adequacy. Within the framework of a large agricultural legume cultivation project (N2Africa), we studied (Chapter 3) the potential to improve children’s dietary diversity by comparing N2Africa and non-N2Africa households in a cross-sectional quasi-experimental design, followed by structural equation modelling and focus group discussions in rural Ghana and Kenya. Participating in N2Africa was not associated with improved dietary diversity of children. However, for soybean in Kenya, structural equation modelling (combining data from N2Africa and non-N2Africa households) indicated that via production for own consumption the dietary diversity of children can be improved, but indicated no effect via income and food purchases and no effect for both pathways in Ghana. Results are possibly related to differences in the food environment between the two countries as was found in the focus group discussions. These findings confirm the importance of the food environment for translation of enhanced crop production into improved human nutrition. This study also showed that in a situation where rigorous study designs cannot be implemented, structural equation modelling is a useful option to analyse whether agriculture projects have the potential to improve nutrition and focus group discussions can provide valuable additional explanatory qualitative information. For a high quality diet, legumes need to be consumed in combination with other foods from different food groups. Therefore in Chapters 4 and 5, a systems approach was used studying the potential of legumes as well as all other foods cultivated to cover the food needs of households based on the food-based dietary guidelines developed for this thesis. In Chapter 4, the current situation was examined among 329 rural Ghanaian households. The food production of about 60% of the households did not cover their required quantities of grains and legumes and none covered their required quantities of vegetables. At nutrient level, the food production of over half the households supplied insufficient calcium (75.7%), vitamin A (100%), vitamin B12 (100%) and vitamin C (77.5%) to cover their requirements. The diversity of the production of a household was positively related with their food and nutrient coverage, but not with children’s dietary diversity and nutrient adequacy. These findings suggest that the promotion of FBDGs alone is insufficient to lead to improvements in diets. Additional strategies are needed to increase the food availability and accessibility of the households, especially that of fruits and vegetables and also of grain legumes. In Chapter 5, we used a farm-level systems approach to investigated the minimum farm size needed, the optimal crop combination to grow and the potential contribution of mainstream agricultural interventions to provide a nutritious diet and additional income in all seasons of the year for an average rural household in Northern Ghana. Linear programming was applied to model different scenarios and interventions. The food-based dietary guidelines developed for this thesis were used as well as data from other secondary sources for information on seasonal yields, waste factors, crop availability, crop land use and prices for all crops produced in Northern Ghana. Results indicate that 75% of the household had sufficient farm size (>1.43 ha) to produce their food needs for a nutritious diet. Agricultural interventions increasing the yields of grains and legumes decrease the farm size needed to about 1 ha (17% of households reported a farm size Overall the results of this thesis show that the main contribution of grain legumes to nutritious diets is in terms of micronutrients intake and not protein intake. Whether a grain legumes cultivation project, such as N2Africa, will result in dietary improvements depends on the characteristics of the food environment, as well as whether a nutrition goal is set and activities such as nutrition behaviour change communication and women’s empowerment are included. This thesis also shows that a mixed method design including pathway analysis is a good approach to study nutrition impact of agriculture interventions when RCTs are not possible. Finally, the thesis results show that investigating the gaps in food availability and food needs using a systems approach at farm level provides useful insights to be able to better coordinate and integrate nutrition across agricultural interventions and investments. For future agriculture and nutrition research: specialists from both disciplines should be involved from the start and be able to think outside of their discipline; a shift from research at crop level to whole diet level research is needed using a systems approach; economic and market knowledge are necessary; and testing the practical feasibility of research findings need to be planned and incorporated from the beginning. Let’s harvest nutrition!</p

Data from: Food and nutrient gaps in rural Northern Ghana: does production of smallholder farming households support adoption of food-based dietary guidelines?

Food-based dietary guidelines (FBDGs) provide guidance to policy makers, the private sector and consumers to redesign food systems and to improve diets of vulnerable populations. As appropriate FBDGs are based on the actual dietary patterns and their costs, it is assumed that the recommended foods are available, affordable and acceptable for the population under study. Using quantitative dietary intake data of young children in rural Northern Ghana, we developed local FBDGs and studied whether these are supported by the diversity and quantity of the production of a household among 329 households. We found that 40% of rural Northern Ghanaian infants and young children were stunted and their nutrient intakes were far below the recommendations: the probability of adequacy for most nutrient intakes was less than 50%. At household level, the developed FBDGs were, on average, unable to sufficiently cover the household requirements for fat (60.4% of recommended nutrient intake (RNI)), calcium (34.3% RNI), iron (60.3% RNI), vitamin A (39.1% RNI), vitamin B12 (2.3% RNI) and vitamin C (54.6% RNI). This implies that even when these FBDGs are fully adopted the requirements for these nutrients will not be met. In addition, the nutrient needs and food needs (according to the developed FBDGs) of a household were only marginally covered by their own food production. The food production of over half the households supplied insufficient calcium (75.7%), vitamin A (100%), vitamin B12 (100%) and vitamin C (77.5%) to cover their needs. The food production of about 60% of the households did not cover their required quantities of grains and legumes and none covered their required quantities of vegetables. Further analysis of the food gaps at district and national level showed that sufficient grains were available at both levels (267% and 148%, respectively) to meet requirements; availability of legumes was sufficient at district level (268%) but not at national level (52%); and vegetables were insufficient at both levels (2% and 49%, respectively). Diversifying household food production is often proposed as a means to increase the diversity of foods available and thereby increasing dietary diversity of rural populations. We found that the diversity of the production of a household was indeed positively related with their food and nutrient coverage. However, the diversity of the production of a household and their food and nutrient coverage were not related with children’s dietary diversity and nutrient adequacy. Our results show that the production of a households does not support the adoption of FBDGs in rural Northern Ghana, especially for vegetables. This suggests that the promotion of FBDGs through nutrition education or behaviour change communications activities alone is insufficient to lead to improvements in diets. Additional strategies are needed to increase the food availability and accessibility of the households, especially that of fruits and vegetables, such as diversification of the crops grown, increased production of specific crops and market-based strategies

Data from: Food and nutrient gaps in rural Northern Ghana: does production of smallholder farming households support adoption of food-based dietary guidelines?

Food-based dietary guidelines (FBDGs) provide guidance to policy makers, the private sector and consumers to redesign food systems and to improve diets of vulnerable populations. As appropriate FBDGs are based on the actual dietary patterns and their costs, it is assumed that the recommended foods are available, affordable and acceptable for the population under study. Using quantitative dietary intake data of young children in rural Northern Ghana, we developed local FBDGs and studied whether these are supported by the diversity and quantity of the production of a household among 329 households. We found that 40% of rural Northern Ghanaian infants and young children were stunted and their nutrient intakes were far below the recommendations: the probability of adequacy for most nutrient intakes was less than 50%. At household level, the developed FBDGs were, on average, unable to sufficiently cover the household requirements for fat (60.4% of recommended nutrient intake (RNI)), calcium (34.3% RNI), iron (60.3% RNI), vitamin A (39.1% RNI), vitamin B12 (2.3% RNI) and vitamin C (54.6% RNI). This implies that even when these FBDGs are fully adopted the requirements for these nutrients will not be met. In addition, the nutrient needs and food needs (according to the developed FBDGs) of a household were only marginally covered by their own food production. The food production of over half the households supplied insufficient calcium (75.7%), vitamin A (100%), vitamin B12 (100%) and vitamin C (77.5%) to cover their needs. The food production of about 60% of the households did not cover their required quantities of grains and legumes and none covered their required quantities of vegetables. Further analysis of the food gaps at district and national level showed that sufficient grains were available at both levels (267% and 148%, respectively) to meet requirements; availability of legumes was sufficient at district level (268%) but not at national level (52%); and vegetables were insufficient at both levels (2% and 49%, respectively). Diversifying household food production is often proposed as a means to increase the diversity of foods available and thereby increasing dietary diversity of rural populations. We found that the diversity of the production of a household was indeed positively related with their food and nutrient coverage. However, the diversity of the production of a household and their food and nutrient coverage were not related with children’s dietary diversity and nutrient adequacy. Our results show that the production of a households does not support the adoption of FBDGs in rural Northern Ghana, especially for vegetables. This suggests that the promotion of FBDGs through nutrition education or behaviour change communications activities alone is insufficient to lead to improvements in diets. Additional strategies are needed to increase the food availability and accessibility of the households, especially that of fruits and vegetables, such as diversification of the crops grown, increased production of specific crops and market-based strategies

Children's 24hour recall dietary intake data and calculated IDDS

Children's 24hour recall dietary intake data and calculated IDD

Anthropometry data

Anthropometry data (no more than 3 indirect indentifiers per subject are allowed to publish, sex is not included, if this data is needed please contact corresponding author