Adding gene transcripts into genomic prediction improves accuracy and reveals sampling time dependence.

Recent developments allowed generating multiple high-quality 'omics' data that could increase the predictive performance of genomic prediction for phenotypes and genetic merit in animals and plants. Here, we have assessed the performance of parametric and nonparametric models that leverage transcriptomics in genomic prediction for 13 complex traits recorded in 478 animals from an outbred mouse population. Parametric models were implemented using the best linear unbiased prediction, while nonparametric models were implemented using the gradient boosting machine algorithm.

Genome-wide association study in thoroughbred horses naturally infected with cyathostomins.

Cyathostomins are considered one of the most important parasites of horses. A group of horses within a herd can be responsible for eliminating the majority of parasite eggs. This phenotype might be explained by genetic factors.

Prediction performance of linear models and gradient boosting machine on complex phenotypes in outbred mice.

We compared the performance of linear (GBLUP, BayesB, and elastic net) methods to a nonparametric tree-based ensemble (gradient boosting machine) method for genomic prediction of complex traits in mice. The dataset used contained genotypes for 50,112 SNP markers and phenotypes for 835 animals from 6 generations. Traits analyzed were bone mineral density, body weight at 10, 15, and 20 weeks, fat percentage, circulating cholesterol, glucose, insulin, triglycerides, and urine creatinine.

Risk prediction in surgery using case-based reasoning and agent-based modelization.

Managing the risks arising from the actions and conditions of the various elements that make up an operating room is a major concern during a surgical procedure. One of the main challenges is to define alert thresholds in a non-deterministic context where unpredictable adverse events occur. In response to this problematic, this paper presents an architecture that couples a Multi-Agent System (MAS) with Case-Based Reasoning (CBR).

Fine mapping of genomic regions associated with female fertility in Nellore beef cattle based on sequence variants from segregating sires.

Background: Impaired fertility in cattle limits the efficiency of livestock production systems. Unraveling the genetic architecture of fertility traits would facilitate their improvement by selection. In this study, we characterized SNP chip haplotypes at QTL blocks then used whole-genome sequencing to fine map genomic regions associated with reproduction in a population of Nellore () heifers.

Dual-purpose Guzerá cattle exhibit high dairy performance under heat stress.

The present study evaluated the heat stress response pattern of dual-purpose Guzerá cattle for test-day (TD) milk yield records of first lactation and estimated genetic parameters and trends related to heat stress. A total of 31,435 TD records from 4,486 first lactations of Guzerá cows, collected between 1986 and 2012, were analysed. Two random regression models considered days in milk (DIM) and/or temperature × humidity-dependent (THI) covariate.

Accounting for population structure in selective cow genotyping strategies.

The objective of the present study was to investigate the impact of considering population structure in cow genotyping strategies over the accuracy and bias of genomic predictions. A small dairy cattle population was simulated to address these objectives. Based on four main traditional designs (random, top-yield, extreme-yield and top-accuracy cows), different numbers (1,000; 2,000 and 5,000) of cows were sampled and included in the reference population.

Correction: Enriched Air Nitrox Breathing Reduces Venous Gas Bubbles after Simulated SCUBA Diving: A Double-Blind Cross-Over Randomized Trial.

[This corrects the article DOI: 10.1371/journal.pone.

Enriched Air Nitrox Breathing Reduces Venous Gas Bubbles after Simulated SCUBA Diving: A Double-Blind Cross-Over Randomized Trial.

Objective: To test the hypothesis whether enriched air nitrox (EAN) breathing during simulated diving reduces decompression stress when compared to compressed air breathing as assessed by intravascular bubble formation after decompression.

Methods: Human volunteers underwent a first simulated dive breathing compressed air to include subjects prone to post-decompression venous gas bubbling. Twelve subjects prone to bubbling underwent a double-blind, randomized, cross-over trial including one simulated dive breathing compressed air, and one dive breathing EAN (36% O2) in a hyperbaric chamber, with identical diving profiles (28 msw for 55 minutes).