Genomic prediction in a multiploid crop: genotype by environment interaction and allele dosage effects on predictive ability in banana

Open Access Journal; Published online: 2 March 2018Improving the efficiency of selection in conventional crossbreeding is a major priority in banana (Musa spp.) breeding. Routine application of classical marker assisted selection (MAS) is lagging in banana due to limitations in MAS tools. Genomic selection (GS) based on genomic prediction models can address some limitations of classical MAS, but the use of GS in banana has not been reported to date. The aim of this study was to evaluate the predictive ability of six genomic prediction models for 15 traits in a multi-ploidy training population. The population consisted of 307 banana genotypes phenotyped under low and high input field management conditions for two crop cycles. The single nucleotide polymorphism (SNP) markers used to fit the models were obtained from genotyping by sequencing (GBS) data. Models that account for additive genetic effects provided better predictions with 12 out of 15 traits. The performance of BayesB model was superior to other models particularly on fruit filling and fruit bunch traits. Models that included averaged environment data were more robust in trait prediction even with a reduced number of markers. Accounting for allele dosage in SNP markers (AD-SNP) reduced predictive ability relative to traditional bi-allelic SNP (BA-SNP), but the prediction trend remained the same across traits. The high predictive values (0.47– 0.75) of fruit filling and fruit bunch traits show the potential of genomic prediction to increase selection efficiency in banana breeding

Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda

Background International and global organisations advocate targeting interventions to areas of high HIV prevalence (ie, hotspots). To better understand the potential benefits of geo-targeted control, we assessed the extent to which HIV hotspots along Lake Victoria sustain transmission in neighbouring populations in south-central Uganda. Methods We did a population-based survey in Rakai, Uganda, using data from the Rakai Community Cohort Study. The study surveyed all individuals aged 15–49 years in four high-prevalence Lake Victoria fishing communities and 36 neighbouring inland communities. Viral RNA was deep sequenced from participants infected with HIV who were antiretroviral therapy-naive during the observation period. Phylogenetic analysis was used to infer partial HIV transmission networks, including direction of transmission. Reconstructed networks were interpreted through data for current residence and migration history. HIV transmission flows within and between high-prevalence and low-prevalence areas were quantified adjusting for incomplete sampling of the population. Findings Between Aug 10, 2011, and Jan 30, 2015, data were collected for the Rakai Community Cohort Study. 25 882 individuals participated, including an estimated 75·7% of the lakeside population and 16·2% of the inland population in the Rakai region of Uganda. 5142 participants were HIV-positive (2703 [13·7%] in inland and 2439 [40·1%] in fishing communities). 3878 (75·4%) people who were HIV-positive did not report antiretroviral therapy use, of whom 2652 (68·4%) had virus deep-sequenced at sufficient quality for phylogenetic analysis. 446 transmission networks were reconstructed, including 293 linked pairs with inferred direction of transmission. Adjusting for incomplete sampling, an estimated 5·7% (95% credibility interval 4·4–7·3) of transmissions occurred within lakeside areas, 89·2% (86·0–91·8) within inland areas, 1·3% (0·6–2·6) from lakeside to inland areas, and 3·7% (2·3–5·8) from inland to lakeside areas. Interpretation Cross-community HIV transmissions between Lake Victoria hotspots and surrounding inland populations are infrequent and when they occur, virus more commonly flows into rather than out of hotspots. This result suggests that targeted interventions to these hotspots will not alone control the epidemic in inland populations, where most transmissions occur. Thus, geographical targeting of high prevalence areas might not be effective for broader epidemic control depending on underlying epidemic dynamics. Funding The Bill & Melinda Gates Foundation, the National Institute of Allergy and Infectious Diseases, the National Institute of Mental Health, the National Institute of Child Health and Development, the Division of Intramural Research of the National Institute for Allergy and Infectious Diseases, the World Bank, the Doris Duke Charitable Foundation, the Johns Hopkins University Center for AIDS Research, and the President's Emergency Plan for AIDS Relief through the Centers for Disease Control and Prevention

General anaesthetic and airway management practice for obstetric surgery in England: a prospective, multi-centre observational study

There are no current descriptions of general anaesthesia characteristics for obstetric surgery, despite recent changes to patient baseline characteristics and airway management guidelines. This analysis of data from the direct reporting of awareness in maternity patients' (DREAMY) study of accidental awareness during obstetric anaesthesia aimed to describe practice for obstetric general anaesthesia in England and compare with earlier surveys and best-practice recommendations. Consenting patients who received general anaesthesia for obstetric surgery in 72 hospitals from May 2017 to August 2018 were included. Baseline characteristics, airway management, anaesthetic techniques and major complications were collected. Descriptive analysis, binary logistic regression modelling and comparisons with earlier data were conducted. Data were collected from 3117 procedures, including 2554 (81.9%) caesarean deliveries. Thiopental was the induction drug in 1649 (52.9%) patients, compared with propofol in 1419 (45.5%). Suxamethonium was the neuromuscular blocking drug for tracheal intubation in 2631 (86.1%), compared with rocuronium in 367 (11.8%). Difficult tracheal intubation was reported in 1 in 19 (95%CI 1 in 16-22) and failed intubation in 1 in 312 (95%CI 1 in 169-667). Obese patients were over-represented compared with national baselines and associated with difficult, but not failed intubation. There was more evidence of change in practice for induction drugs (increased use of propofol) than neuromuscular blocking drugs (suxamethonium remains the most popular). There was evidence of improvement in practice, with increased monitoring and reversal of neuromuscular blockade (although this remains suboptimal). Despite a high risk of difficult intubation in this population, videolaryngoscopy was rarely used (1.9%)

Prevalence and factors associated with neonatal hypoglycemia in Northern Uganda: a community-based cross-sectional study

Background: Neonatal hypoglycemia is the most common endocrine abnormality in children, which is associated with increased morbidity and mortality. The burden and risk factors of neonatal hypoglycemia in rural communities in sub-Saharan Africa are unknown. Objective: To determine the prevalence and risk factors for neonatal hypoglycemia in Lira District, Northern Uganda. Methods: This was a community-based cross-sectional study, nested in a cluster randomized controlled trial designed to promote health facility births and newborn care practices in Lira District, Northern Uganda. This study recruited neonates born to mothers in the parent study. Random blood glucose was measured using an On Call® Plus glucometer (ACON Laboratories, Inc., 10125 Mesa Road, San Diego, CA, USA). We defined hypoglycemia as a blood glucose of < 47 mg/dl. To determine the factors associated with neonatal hypoglycemia, a multivariable linear regression mixed-effects model was used. Results: We examined 1416 participants of mean age 3.1 days (standard deviation (SD) 2.1) and mean weight of 3.2 kg (SD 0.5). The mean neonatal blood glucose level was 81.6 mg/dl (SD 16.8). The prevalence of a blood glucose concentration of < 47 mg/dl was 2.2% (31/1416): 95% CI 1.2%, 3.9%. The risk factors for neonatal hypoglycemia were delayed breastfeeding initiation [adjusted mean difference, − 2.6; 95% CI, − 4.4, − 0.79] and child age of 3 days or less [adjusted mean, − 12.2; 95% CI, − 14.0, − 10.4]. Conclusion: The incidence of neonatal hypoglycemia was low in this community and was predicted by delay in initiating breastfeeding and a child age of 3 days or less. We therefore suggest targeted screening and management of neonatal hypoglycemia among neonates before 3 days of age and those who are delayed in the onset of breastfeeding

[United States Soil Survey Report]

Text describes the area, climate, agricultural history and statistics, soil-survey methods and definitions, soils and crops, land uses and agricultural methods, irrigation, and morphology and genesis of soils of Comal and Hays Counties, Texas

The Veterans Aging Cohort Study Index is not associated with HIV-associated neurocognitive disorders in Uganda

The Veterans Aging Cohort Study (VACS) Index has been associated with HIV-associated neurocognitive disorder (HAND) in some populations but has not been studied in sub-Saharan Africa. We investigated whether the VACS Index is associated with HAND in a rural population in Rakai, Uganda. HIV-infected (HIV+) adults on antiretroviral therapy underwent a neurocognitive battery for determination of HAND stage using Frascati criteria. VACS component scores were recorded for all participants. Out of 156 study participants, HAND stages were 49% normal cognition, 15% asymptomatic neurocognitive impairment, 31% minor neurocognitive disorder, and 7% HIV-associated dementia. There was no significant association between VACS Index and any HAND stage. In this first study of the VACS Index in sub-Saharan Africa, we found no association between VACS Index score and HAND

Uptake and retention on HIV pre-exposure prophylaxis among key and priority populations in South-Central Uganda

Introduction Pre‐exposure prophylaxis (PrEP) programmes have been initiated in sub‐Saharan Africa to prevent HIV acquisition in key populations at increased risk. However, data on PrEP uptake and retention in high‐risk African communities are limited. We evaluated PrEP uptake and retention in HIV hyperendemic fishing villages and trading centres in south‐central Uganda between April 2018 and March 2019. Methods PrEP eligibility was assessed using a national risk screening tool. Programme data were used to evaluate uptake and retention over 12 months. Multivariable modified Poisson regression estimated adjusted prevalence ratios (aPR) and 95% Confidence intervals (CIs) of uptake associated with covariates. We used Kaplan–Meier analysis to estimate retention and multivariable Cox regression to estimate adjusted relative hazards (aRH) and 95% CIs of discontinuation associated with covariates. Results and discussion Of the 2985 HIV‐negative individuals screened; 2750 (92.1 %) were eligible; of whom 2,536 (92.2%) accepted PrEP. Male (aPR = 0.91, 95% CI = 0.85 to 0.97) and female (aPR = 0.85, 95% CI = 0.77 to 0.94) fisher folk were less likely to accept compared to HIV‐discordant couples. Median retention was 45.4 days for both men and women, whereas retention was higher among women (log rank, p &lt; 0.001) overall. PrEP discontinuation was higher among female sex workers (aRH = 1.42, 95% CI = 1.09 to 1.83) and female fisher folk (aRH = 1.99, 95% CI = 1.46 to 2.72), compared to women in discordant couples. Male fisher folk (aRH = 1.37, 95% CI = 1.07 to 1.76) and male truck drivers (aRH = 1.49, 95% CI = 1.14 to 1.94) were more likely to discontinue compared to men in discordant couples. Women 30 to 34 years tended to have lower discontinuation rates compared to adolescents 15 to 19 years (RH = 0.78 [95% CI = 0.63 to 0.96]). Conclusions PrEP uptake was high, but retention was very low especially among those at the highest risk of HIV: fisher folk, sex workers and truck drivers and adolescent girls. Research on reasons for PrEP discontinuation could help optimize retention