A Causality Perspective of Genomic Breed Composition for Composite Animals.

Genomic breed composition (GBC) of an individual animal refers to the partition of its genome according to the inheritance from its ancestors or ancestral breeds. For crossbred or composite animals, knowing their GBC is useful to estimate heterosis, to characterize their actual inheritance from foundation breeds, and to make management decisions for crossbreeding programs. Various statistical approaches have been proposed to estimate GBC in animals, but the interpretations of estimates have varied with these methods. In the present study, we proposed a causality interpretation of GBC based on path analysis. We applied this method to estimating GBC in two composite breeds of beef cattle, namely Brangus and Beefmaster. Three SNP panels were used to estimate GBC: a 10K SNP panel consisting of 10,226 common SNPs across three GeneSeek Genomic Profiler (GGP) bovine SNP arrays (GGP 30K, GGP 40K, and GGP 50K), and two subsets (1K and 5K) of uniformly distributed SNPs. The path analysis decomposed the relationships between the ancestors and the composite animals into direct and indirect path effects, and GBC was measured by the relative ratio of the coefficients of direct (D-GBC) and combined (C-GBC) effects from each ancestral breed to the progeny, respectively. Estimated GBC varied only slightly between different genotyping platforms and between the three SNP panels. In the Brangus cattle, because the two ancestral breeds had a very distant relationship, the estimated D-GBC and C-GBC were comparable to each other in the path analysis, and they corresponded roughly to the estimated GBC from the linear regression and the admixture model. In the Beefmaster, however, the strong relationship in allelic frequencies between Hereford and Shorthorn imposed a challenge for the linear regression and the admixture model to estimated GBC reliably. Instead, D-GBC by the path analysis included only direct ancestral effects, and it was robust to bias due to high genomic correlations between reference (ancestral) breeds.

Quantification of deep medullary veins at 7 T brain MRI.

OBJECTIVES: Deep medullary veins support the venous drainage of the brain and may display abnormalities in the context of different cerebrovascular diseases. We present and evaluate a method to automatically detect and quantify deep medullary veins at 7 T. METHODS: Five participants were scanned twice, to assess the robustness and reproducibility of manual and automated vein detection. Additionally, the method was evaluated on 24 participants to demonstrate its application. Deep medullary veins were assessed within an automatically created region-of-interest around the lateral ventricles, defined such that all veins must intersect it. A combination of vesselness, tubular tracking, and hysteresis thresholding located individual veins, which were quantified by counting and computing (3-D) density maps. RESULTS: Visual assessment was time-consuming (2 h/scan), with an intra-/inter-observer agreement on absolute vein count of ICC = 0.76 and 0.60, respectively. The automated vein detection showed excellent inter-scan reproducibility before (ICC = 0.79) and after (ICC = 0.88) visually censoring false positives. It had a positive predictive value of 71.6 %. CONCLUSION: Imaging at 7 T allows visualization and quantification of deep medullary veins. The presented method offers fast and reliable automated assessment of deep medullary veins. KEY POINTS: • Deep medullary veins support the venous drainage of the brain • Abnormalities of these veins may indicate cerebrovascular disease and quantification is needed • Automated methods can achieve this and support human observers • The presented method provides robust and reproducible detection of veins • Intuitive quantification is provided via count and venous density maps.

Gold bugs and beyond: a review of iridescence and structural colour mechanisms in beetles (Coleoptera).

Members of the order Coleoptera are sometimes referred to as 'living jewels', in allusion to the strikingly diverse array of iridescence mechanisms and optical effects that have arisen in beetles. A number of novel and sophisticated reflectance mechanisms have been discovered in recent years, including three-dimensional photonic crystals and quasi-ordered coherent scattering arrays. However, the literature on beetle structural coloration is often redundant and lacks synthesis, with little interchange between the entomological and optical research communities. Here, an overview is provided for all iridescence mechanisms observed in Coleoptera. Types of iridescence are illustrated and classified into three mechanistic groups: multilayer reflectors, three-dimensional photonic crystals and diffraction gratings. Taxonomic and phylogenetic distributions are provided, along with discussion of the putative functions and evolutionary pathways by which iridescence has repeatedly arisen in beetles.