AlphaSim: Software for Breeding Program Simulation

This paper describes AlphaSim, a software package for simulating plant and animal breeding programs. AlphaSim enables the simulation of multiple aspects of breeding programs with a high degree of flexibility. AlphaSim simulates breeding programs in a series of steps: (i) simulate haplotype sequences and pedigree; (ii) drop haplotypes into the base generation of the pedigree and select single-nucleotide polymorphism (SNP) and quantitative trait nucleotide (QTN); (iii) assign QTN effects, calculate genetic values, and simulate phenotypes; (iv) drop haplotypes into the burn-in generations; and (v) perform selection and simulate new generations. The program is flexible in terms of historical population structure and diversity, recent pedigree structure, trait architecture, and selection strategy. It integrates biotechnologies such as doubled-haploids (DHs) and gene editing and allows the user to simulate multiple traits and multiple environments, specify recombination hot spots and cold spots, specify gene jungles and deserts, perform genomic predictions, and apply optimal contribution selection. AlphaSim also includes restart functionalities, which increase its flexibility by allowing the simulation process to be paused so that the parameters can be changed or to import an externally created pedigree, trial design, or results of an analysis of previously simulated data. By combining the options, a user can simulate simple or complex breeding programs with several generations, variable population structures and variable breeding decisions over time. In conclusion, AlphaSim is a flexible and computationally efficient software package to simulate biotechnology enhanced breeding programs with the aim of performing rapid, low-cost, and objective in silico comparison of breeding technologies

The effect of Aloe ferox Mill. in the treatment of loperamide-induced constipation in Wistar rats

<p>Abstract</p> <p>Background</p> <p>Constipation is the most common gastrointestinal complaint all over the world and it is a risk factor of colorectal cancer. In this study, the efficacy of aqueous leaf extract of <it>Aloe </it><it>ferox </it>Mill. was studied against loperamide-induced constipation in Wistar rats.</p> <p>Methods</p> <p>Constipation was induced by oral administration of loperamide (3 mg/kg body weight) while the control rats received normal saline. The constipated rats were treated with 50, 100 and 200 mg/kg body weight/day of the extract for 7 days during which the feeding characteristics, body weight, fecal properties and gastrointestinal transit ratio were monitored.</p> <p>Results</p> <p>The extract improved intestinal motility, increased fecal volume and normalized body weight in the constipated rats, which are indications of laxative property of the herb with the 200 mg/kg body weight of the extract showing the best efficacy.</p> <p>Conclusion</p> <p>The effect of the extract compares favourably well with senokot, a standard laxative drug. These findings have therefore, lent scientific credence to the folkloric use of the herb as a laxative agent by the people of the Eastern Cape of South Africa.</p

Maternal morbidity in the first year after childbirth in Mombasa Kenya; a needs assessment

<p>Abstract</p> <p>Background</p> <p>In sub-Saharan Africa, few services specifically address the needs of women in the first year after childbirth. By assessing the health status of women in this period, key interventions to improve maternal health could be identified. There is an underutilised opportunity to include these interventions within the package of services provided for woman-child pairs attending child-health clinics.</p> <p>Methods</p> <p>This needs assessment entailed a cross-sectional survey with 500 women attending a child-health clinic at the provincial hospital in Mombasa, Kenya. A structured questionnaire, clinical examination, and collection of blood, urine, cervical swabs and Pap smear were done. Women's health care needs were compared between the early (four weeks to two months after childbirth), middle (two to six months) and late periods (six to twelve months) since childbirth.</p> <p>Results</p> <p>More than one third of women had an unmet need for contraception (39%, 187/475). Compared with other time intervals, women in the late period had more general health symptoms such as abdominal pain, fever and depression, but fewer urinary or breast problems. Over 50% of women in each period had anaemia (Hb <11 g/l; 265/489), with even higher levels of anaemia in those who had a caesarean section or had not received iron supplementation during pregnancy. Bacterial vaginosis was present in 32% (141/447) of women, while 1% (5/495) had syphilis, 8% (35/454) <it>Trichomonas vaginalis </it>and 11% (54/496) HIV infection.</p> <p>Conclusion</p> <p>Throughout the first year after childbirth, women had high levels of morbidity. Interface with health workers at child health clinics should be used for treatment of anaemia, screening and treatment of reproductive tract infections, and provision of family planning counselling and contraception. Providing these services during visits to child health clinics, which have high coverage both early and late in the year after childbirth, could make an important contribution towards improving women's health.</p

Quantitative RT-PCR analysis of differentially expressed genes in Quercus suber in response to Phytophthora cinnamomi infection

cDNA-AFLP methodology was used to gain insight into gene fragments differentially present in the mRNA profiles of Quercus suber roots infected with zoospores of Phytophthora cinnamomi at different post challenge time points. Fifty-three transcript-derived fragments (TDFs) were identified and sequenced. Six candidate genes were selected based on their expression patterns and homology to genes known to play a role in defence. They encode a cinnamyl alcohol dehydrogenase2 (QsCAD2), a protein disulphide isomerase (QsPDI), a CC-NBS-LRR resistance protein (QsRPc), a thaumatin-like protein (QsTLP), a chitinase (QsCHI) and a 1,3-β-glucanase (QsGlu). Evaluation of the expression of these genes by quantitative polymerase chain reaction (qPCR) revealed that transcript levels of QsRPc, QsCHI, QsCAD2 and QsPDI increased during the first 24 h post-inoculation, while those of thaumatin-like protein decreased. No differential expression was observed for 1,3-β-glucanase (QsGlu).Four candidate reference genes, polymerase II (QsRPII), eukaryotic translation initiation factor 5A (QsEIF-5A), β-tubulin (QsTUB) and a medium subunit family protein of clathrin adaptor complexes (QsCACs) were assessed to determine the most stable internal references for qRT-PCR normalization in the Phytophthora-Q. suber pathosystem in root tissues. Those found to be more stable, QsRPII and QsCACs, were used as internal reference in the present work.Knowledge on the Quercus defence mechanisms against biotic stress is scarce. This study provides an insight into the gene profiling of a few important genes of Q. suber in response to P. cinnamomi infection contributing to the knowledge of the molecular interactions involving Quercus and root pathogens that can be useful in the future to understand the mechanisms underlying oak resistance to soil-borne oomycetes.Peer Reviewe

Annual Wellness Visits and Influenza Vaccinations among Older Adults in the US

Objectives Investigate whether combinations of sociodemographic factors, chronic conditions, and other health indicators pose barriers for older adults to access Annual Wellness Visits (AWVs) and influenza vaccinations. Methods Data on 4999 individuals aged ≥65 years from the 2012 wave of the Health and Retirement Study linked with Medicare claims were analyzed. Conditional Inference Tree (CIT) and Random Forest (CIRF) analyses identified the most important predictors of AWVs and influenza vaccinations. Multivariable logistic regression (MLR) was used to quantify the associations. Results Two-year uptake was 22.8% for AWVs and 65.9% for influenza vaccinations. For AWVs, geographical region and wealth emerged as the most important predictors. For influenza vaccinations, number of somatic conditions, race/ethnicity, education, and wealth were the most important predictors. Conclusions The importance of geographic region for AWV utilization suggests that this service was unequally adopted. Non-Hispanic black participants and/or those with functional limitations were less likely to receive influenza vaccination

Effect on postpartum hemorrhage of prophylactic oxytocin (10 IU) by injection by community health officers in Ghana: a community-based, cluster-randomized trial.

BACKGROUND: Oxytocin (10 IU) is the drug of choice for prevention of postpartum hemorrhage (PPH). Its use has generally been restricted to medically trained staff in health facilities. We assessed the effectiveness, safety, and feasibility of PPH prevention using oxytocin injected by peripheral health care providers without midwifery skills at home births. METHODS AND FINDINGS: This community-based, cluster-randomized trial was conducted in four rural districts in Ghana. We randomly allocated 54 community health officers (stratified on district and catchment area distance to a health facility: ≥10 km versus <10 km) to intervention (one injection of oxytocin [10 IU] one minute after birth) and control (no provision of prophylactic oxytocin) arms. Births attended by a community health officer constituted a cluster. Our primary outcome was PPH, using multiple definitions; (PPH-1) blood loss ≥500 mL; (PPH-2) PPH-1 plus women who received early treatment for PPH; and (PPH-3) PPH-2 plus any other women referred to hospital for postpartum bleeding. Unsafe practice is defined as oxytocin use before delivery of the baby. We enrolled 689 and 897 women, respectively, into oxytocin and control arms of the trial from April 2011 to November 2012. In oxytocin and control arms, respectively, PPH-1 rates were 2.6% versus 5.5% (RR: 0.49; 95% CI: 0.27-0.88); PPH-2 rates were 3.8% versus 10.8% (RR: 0.35; 95% CI: 0.18-0.63), and PPH-3 rates were similar to those of PPH-2. Compared to women in control clusters, those in the intervention clusters lost 45.1 mL (17.7-72.6) less blood. There were no cases of oxytocin use before delivery of the baby and no major adverse events requiring notification of the institutional review boards. Limitations include an unblinded trial and imbalanced numbers of participants, favoring controls. CONCLUSION: Maternal health care planners can consider adapting this model to extend the use of oxytocin into peripheral settings including, in some contexts, home births. TRIAL REGISTRATION: ClinicalTrials.gov NCT01108289 Please see later in the article for the Editors' Summary