Accessing marker effects and heritability estimates from genome prediction by Bayesian regularized neural networks

Recently, there is an increasing interest on semi- and non-parametric methods for genome-enabled prediction, among which the Bayesian regularized artificial neural networks (BRANN) stand. We aimed to evaluate the predictive performance of BRANN and to exploit SNP effects and heritability estimates using two different approaches (relative importance-RI, and relative contribution-RC). Additionally, we aimed also to compare BRANN with the traditional RR-BLUP and BLASSO by using simulated datasets. The simplest BRANN (net1), RR-BLUP and BLASSO methods outperformed other more parameterized BRANN (net2, net3, … net6) in terms of predictive ability. For both simulated traits (Y1 and Y2) the net1 provided the best h2 estimates (0.33 for both, being the true h2=0.35), whereas RR-BLUP (0.18 and 0.22 for Y1 and Y2, respectively) and BLASSO (0.20 and 0.26 for Y1 and Y2, respectively) underestimated h2. The marker effects estimated from net1 (using RI and RC approaches) and RR-BLUP were similar, but the shrinkage strength was remarkable for BLASSO on both traits. For Y1, the correlation between the true fifty QTL effects and the effects estimated for the SNPs located in the same QTL positions were 0.61, 0.60, 0.60 and 0.55, for RI, RC, RR-BLUP and BLASSO; and for Y2, these correlations were 0.81, 0.81, 0.81 and 0.71, respectively. In summary, we believe that estimates of SNP effects are promising quantitative tools to bring discussions on chromosome regions contributing most effectively to the phenotype expression when using ANN for genomic predictions

University\u2014industry interactions in an immature system of innovation: Evidence from Minas Gerais, Brazil

This paper evaluates interactions between firms and universities in Minas Gerais, one of the Brazilian states. The heterogeneity in Minas Gerais replicates the heterogeneity that exists in Brazil as a whole. This paper adapts the pioneering Yale and Carnegie Mellon surveys (USA) to an immature national system of innovation. We found that, in immature systems of innovation, beyond their traditional functions, universities perform a dual role in their interactions with firms: they substitute for and complement the research and development done by the firms themselves. In addition, contrary to conventional wisdom, even in the so-called low-tech and medium-tech sectors, universities matter