Genome-Wide Association Studies for Growth Curves in Meat Rabbits Through the Single-Step Nonlinear Mixed Model

Growth is a complex trait with moderate to high heritability in livestock and must be described by the longitudinal data measured over multiple time points. Therefore, the used phenotype in genome-wide association studies (GWAS) of growth traits could be either the measures at the preselected time point or the fitted parameters of whole growth trajectory. A promising alternative approach was recently proposed that combined the fitting of growth curves and estimation of single-nucleotide polymorphism (SNP) effects into single-step nonlinear mixed model (NMM). In this study, we collected the body weights at 35, 42, 49, 56, 63, 70, and 84 days of age for 401 animals in a crossbred population of meat rabbits and compared five fitting models of growth curves (Logistic, Gompertz, Brody, Von Bertalanffy, and Richards). The logistic model was preferably selected and subjected to GWAS using the approach of single-step NMM, which was based on 87,704 genome-wide SNPs. A total of 45 significant SNPs distributed on five chromosomes were found to simultaneously affect the two growth parameters of mature weight (A) and maturity rate (K). However, no SNP was found to be independently associated with either A or K. Seven positional genes, including KCNIP4, GBA3, PPARGC1A, LDB2, SHISA3, GNA13, and FGF10, were suggested to be candidates affecting growth performances in meat rabbits. To the best of our knowledge, this is the first report of GWAS based on single-step NMM for longitudinal traits in rabbits, which also revealed the genetic architecture of growth traits that are helpful in implementing genome selection.

Fusing a Bayesian case velocity model with random forest for predicting COVID-19 in the U.S.

Predictions of COVID-19 case growth and mortality are critical to the decisions of political leaders, businesses, and individuals grappling with the pandemic. This predictive task is challenging due to the novelty of the virus, limited data, and dynamic political and societal responses. We embed a Bayesian nonlinear mixed model and a random forest algorithm within an epidemiological compartmental model for empirically grounded COVID-19 predictions. The Bayesian case model fits a location-specific curve to the velocity (first derivative) of the transformed cumulative case count, borrowing strength across geographic locations and incorporating prior information to obtain a posterior distribution for case trajectory. The compartmental model uses this distribution and predicts deaths using a random forest algorithm trained on COVID-19 data and population-level characteristics, yielding daily projections and interval estimates for infections and deaths in U.S. states. We evaluate forecasting accuracy on a two-week holdout set, finding that the model predicts COVID-19 cases and deaths well, with a mean absolute scaled error of 0.40 for cases and 0.32 for deaths throughout the two-week evaluation period. The substantial variation in predicted trajectories and associated uncertainty between states is illustrated by comparing three unique locations: New York, Ohio, and Mississippi. The sophistication and accuracy of this COVID-19 model offer reliable predictions and uncertainty estimates for the current trajectory of the pandemic in the U.S. and provide a platform for future predictions as shifting political and societal responses alter its course.

Skill Transference of a Probe-Tube Placement Training Simulator

Probe-tube placement is a necessary step in hearing aid verification which needs ample hands-on experience and confidence before performing in clinic. To improve the methods of training in probe-tube placement, a manikin-based training simulator was developed consisting of a 3D-printed head, a flexible silicone ear, and a mounted optical tracking system. The system is designed to provide feedback to the user on the depth and orientation of the probe tube, and the time required to finish the task. Although a previous validation study was performed to determine its realism and teachability with experts, further validation is required before implementation into educational settings.This study aimed to examine the skill transference of a newly updated probe-tube placement training simulator to determine if skills learned on this simulator successfully translate to clinical scenarios.All participants underwent a pretest in which they were evaluated while performing a probe-tube placement and real-ear-to-coupler difference (RECD) measurement on a volunteer. Participants were randomized into one of two groups: the simulator group or the control group. During a two-week training period, all participants practiced their probe-tube placement according to their randomly assigned group. After two weeks, each participant completed a probe-tube placement on the same volunteer as a posttest scenario.Twenty-five novice graduate-level student clinicians.Participants completed a self-efficacy questionnaire and an expert observer completed a questionnaire evaluating each participant’s performance during the pre- and posttest sessions. RECD measurements were taken after placing the probe tube and foam tip in the volunteer’s ear. Questionnaire results were analyzed through nonparametric t-tests and analysis of variance, whereas RECD results were analyzed using a nonlinear mixed model method.Results suggested students in the simulator group were less likely to contact the tympanic membrane when placing a probe tube, appeared more confident, and had better use of the occluding foam tip, resulting in more improved RECD measurements.The improved outcomes for trainees in the simulator group suggest that supplementing traditional training with the simulator provides useful benefits for the trainees, thereby encouraging its usage and implementation in educational settings.

Patterns and Predictors ofStaphylococcus aureusCarriage during the First Year of Life: a Longitudinal Study

ABSTRACTWe sought here to investigate the patterns ofStaphylococcus aureuscarriage in the first year of life, its determinants, and the dynamics of transmission between mothers and infants. A prospective longitudinal cohort study ofS. aureuscarriage among mothers and their infants was performed, including monthly screenings from pregnancy/birth through the first year of the infant’s life. Medical and lifestyle data were collected. InfantS. aureuscarriage was detected from rectal and nasal swabs, and maternal carriage was detected from nasal and vaginal swabs. Multivariate analysis and a nonlinear mixed model (NLMIXED) were used to determine the predictors of carriage andS. aureuspersistence. Of the 671 women recruited, 130 women carriedS. aureusat recruitment (19.3%); they and their 132 infants were included in the study. A total of 93% of the infants acquiredS. aureussometime during the first year of life; 64% of these infants acquired the maternal strain, mostly (66%) during the first month of life. We observed that 70 women (52.50%) and 17 infants (14%) carriedS. aureuspersistently. Early acquisition ofS. aureuscarriage was associated with longer duration of initial carriage and was the most significant predictor ofS. aureuspersistence, while day care center attendance was negatively associated with persistent carriage. Methicillin-resistantS. aureuswas carried by two infants for only 1 month each and not by any of the mothers. Early acquisition ofS. aureus, mostly from the mother, is thus an important determinant of carriage persistence in infancy.

Usual diet quality among 8- to 12-year-old Brazilian children

Nutritional surveys are important information sources for public policy in the food and nutrition field. They focus on assessing usual dietary patterns, because health outcomes result from the long-term intake. Here we aimed to evaluate diet quality adjusted for day-to-day variance among Brazilian children. Data were collected between March 2013 and August 2015. The sample included 8- to 12-year-old children (n = 1,357) from public schools from all administrative regions of a Brazilian city. One 24-h dietary recall (24HR) was collected for the whole sample and two 24HR for two non-consecutive days of the same week for a subsample. The Healthy Eating Index-2010 (HEI-2010) was adapted to Brazilian food habits and the Brazilian dietary guidelines were used to evaluate diet quality. Statistical analysis included a multipart, nonlinear mixed model with correlated random effects proposed by the U.S. National Cancer Institute to correct diet quality for day-to-day variance. The adapted HEI-2010 total score was 51.8. Children with poorer diet quality (< 10th percentile) scored less than 41.1, and children with higher diet quality (> 90th percentile) scored more than 62.4. The overall adequacy of adapted HEI-2010 components was low. Higher adequacy percentages were identified for total protein foods (94.9%), greens (62.3%), and seafood and plant proteins (52.2%). Seven components showed less than 10% of adequacy: refined grains, fatty acids, dairy, sodium, total vegetable, whole grains, and empty calories. This study identified the main inadequacies among children’s diet quality, which can guide promotion actions for healthy eating.

Reaction rate coefficient k20 and temperature coefficient Θ in organic waste thermal disintegration

It was described the test of sewage sludge and organic fraction of municipal mixed solid waste thermal disintegration process. The waste activated sludge used during the tests was collected from the secondary settlement tank in a mechanical-biological wastewater treatment plant. The biowaste used in the studies was collected from an area of new buildings. It was noticed from means values of Soluble Chemical Oxygen Demand (SCOD) plot that both heating temperature and time, influence the amount of dissolved COD. The observations indicate that changes of SCOD can be described by an increasing, differentiable function of time and the rate of change of the soluble COD in the hydrolysates, in time is proportional to the difference of the maximum values of SCOD and its value in time, which leads to the relationship of the first-order ordinary differential equation. The process effectiveness depending on the temperature was described with the mathematical model including Van't Hoff-Arrhenius equation. Inspection of the data and some preliminary fits indicates, that for the description of changes in SCOD terms of time and temperature were adopted the form of nonlinear mixed model. Values of k20 indicator and Θ parameter depend on the substrate type. For waste activated sludge thermal disintegration, value of reaction speed indicator k20 was 0.028 h-1 (0,67 d-1), and value of temperature indicator equalled Θ = 1.024. For thermal disintegration of biological waste, value of reaction speed indicator k20 was 0.016 h-1 (0,38 d-1), and value of temperature indicator equalled Θ = 1.016.