Implementation of DNA markers to produce genomically - Enhanced EPDs in nellore cattle

Background: The sequencing and publication of the cattle genome and the identification of single nucleotide polymorphism (SNP) molecular markers have provided new tools for animal genetic evaluation and genomic-enhanced selection. These new tools aim to increase the accuracy and scope of selection while decreasing generation interval. The objective of this study was to evaluate the enhancement of accuracy caused by the use of genomic information (Clarifide® - Pfizer) on genetic evaluation of Brazilian Nellore cattle. Review: The application of genome-wide association studies (GWAS) is recognized as one of the most practical approaches to modern genetic improvement. Genomic selection is perhaps most suited to the improvement of traits with low heritability in zebu cattle. The primary interest in livestock genomics has been to estimate the effects of all the markers on the chip, conduct cross-validation to determine accuracy, and apply the resulting information in GWAS either alone [9] or in combination with bull test and pedigree-based genetic evaluation data. The cost of SNP50K genotyping however limits the commercial application of GWAS based on all the SNPs on the chip. However, reasonable predictability and accuracy can be achieved in GWAS by using an assay that contains an optimally selected predictive subset of markers, as opposed to all the SNPs on the chip. The best way to integrate genomic information into genetic improvement programs is to have it included in traditional genetic evaluations. This approach combines traditional expected progeny differences based on phenotype and pedigree with the genomic breeding values based on the markers. Including the different sources of information into a multiple trait genetic evaluation model, for within breed dairy cattle selection, is working with excellent results. However, given the wide genetic diversity of zebu breeds, the high-density panel used for genomic selection in dairy cattle (Ilumina Bovine SNP50 array) appears insufficient for across-breed genomic predictions and selection in beef cattle. Today there is only one breed-specific targeted SNP panel and genomic predictions developed using animals across the entire population of the Nellore breed (www.pfizersaudeanimal.com), which enables genomically - enhanced selection. Genomic profiles are a way to enhance our current selection tools to achieve more accurate predictions for younger animals. Material and Methods: We analyzed the age at first calving (AFC), accumulated productivity (ACP), stayability (STAY) and heifer pregnancy at 30 months (HP30) in Nellore cattle fitting two different animal models; 1) a traditional single trait model, and 2) a two-trait model where the genomic breeding value or molecular value prediction (MVP) was included as a correlated trait. All mixed model analyses were performed using the statistical software ASREML 3.0. Results: Genetic correlation estimates between AFC, ACP, STAY, HP30 and respective MVPs ranged from 0.29 to 0.46. Results also showed an increase of 56%, 36%, 62% and 19% in estimated accuracy of AFC, ACP, STAY and HP30 when MVP information was included in the animal model. Conclusion: Depending upon the trait, integration of MVP information into genetic evaluation resulted in increased accuracy of 19% to 62% as compared to accuracy from traditional genetic evaluation. GE-EPD will be an effective tool to enable faster genetic improvement through more dependable selection of young animals.

An efficient implementation of tabu search in feeder reconfiguration of distribution systems

This paper presents an efficient tabu search algorithm (TSA) to solve the problem of feeder reconfiguration of distribution systems. The main characteristics that make the proposed TSA particularly efficient are a) the way in which the neighborhood of the current solution was defined; b) the way in which the objective function value was estimated; and c) the reduction of the neighborhood using heuristic criteria. Four electrical systems, described in detail in the specialized literature, were used to test the proposed TSA. The result demonstrate that it is computationally very fast and finds the best solutions known in the specialized literature. © 2012 IEEE.

Comparison of selective genotyping strategies for prediction of breeding values in a population undergoing selection

Genomewide marker information can improve the reliability of breeding value predictions for young selection candidates in genomic selection. However, the cost of genotyping limits its use to elite animals, and how such selective genotyping affects predictive ability of genomic selection models is an open question. We performed a simulation study to evaluate the quality of breeding value predictions for selection candidates based on different selective genotyping strategies in a population undergoing selection. The genome consisted of 10 chromosomes of 100 cM each. After 5,000 generations of random mating with a population size of 100 (50 males and 50 females), generation G(0) (reference population) was produced via a full factorial mating between the 50 males and 50 females from generation 5,000. Different levels of selection intensities (animals with the largest yield deviation value) in G(0) or random sampling (no selection) were used to produce offspring of G(0) generation (G(1)). Five genotyping strategies were used to choose 500 animals in G(0) to be genotyped: 1) Random: randomly selected animals, 2) Top: animals with largest yield deviation values, 3) Bottom: animals with lowest yield deviations values, 4) Extreme: animals with the 250 largest and the 250 lowest yield deviations values, and 5) Less Related: less genetically related animals. The number of individuals in G(0) and G(1) was fixed at 2,500 each, and different levels of heritability were considered (0.10, 0.25, and 0.50). Additionally, all 5 selective genotyping strategies (Random, Top, Bottom, Extreme, and Less Related) were applied to an indicator trait in generation G(0), and the results were evaluated for the target trait in generation G(1), with the genetic correlation between the 2 traits set to 0.50. The 5 genotyping strategies applied to individuals in G(0) (reference population) were compared in terms of their ability to predict the genetic values of the animals in G(1) (selection candidates). Lower correlations between genomic-based estimates of breeding values (GEBV) and true breeding values (TBV) were obtained when using the Bottom strategy. For Random, Extreme, and Less Related strategies, the correlation between GEBV and TBV became slightly larger as selection intensity decreased and was largest when no selection occurred. These 3 strategies were better than the Top approach. In addition, the Extreme, Random, and Less Related strategies had smaller predictive mean squared errors (PMSE) followed by the Top and Bottom methods. Overall, the Extreme genotyping strategy led to the best predictive ability of breeding values, indicating that animals with extreme yield deviations values in a reference population are the most informative when training genomic selection models.

Implementation of two-stage Hopfield model and its application in nonlinear systems

This paper presents an efficient neural network for solving constrained nonlinear optimization problems. More specifically, a two-stage neural network architecture is developed and its internal parameters are computed using the valid-subspace technique. The main advantage of the developed network is that it treats optimization and constraint terms in different stages with no interference with each other. Moreover, the proposed approach does not require specification of penalty or weighting parameters for its initialization.

Hardware implementation of an analog neural nonderivative optimizer

Analog neural systems that can automatically find the minimum value of the outputs of unknown analog systems, described by convex functions, are studied. When information about derivative or gradient are not used, these systems are called analog nonderivative optimizers. An electronic circuit for the analog neural nonderivative optimizer proposed by Teixeira and Zak, and its simulation with software PSPICE, is presented. With the simulation results and hardware implementation of the system, the validity of the proposed optimizer can be verified. These results are original, from the best of the authors knowledge.

Assessment of cytokine values in serum by RT-PCR in HIV-1 infected individuals with and without highly active anti-retroviral therapy (HAART)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Determination and padronization of normal values of bone mineral density (BMD) of the acessory carpus bone in young Thoroughbred horse using optical densitometry in radiographic image

Em 12 fêmeas e 12 machos da raça Puro Sangue Inglês com idade média de 12 meses, avaliou-se os valores normais da densidade mineral óssea do carpo acessório em milímetros de alumínio (mmAl) até o momento do fechamento completo da epífise distal do rádio, por meio do método de densitometria óptica em imagens radiográficas. A avaliação foi realizada por meio de um programa computacional (software) especialmente desenvolvido para medida de densidade óptica em filmes de raios-X, o qual contém a imagem radiográfica do osso carpo acessório, região de partes moles adjacente ao carpo acessório e os degraus de uma escala de alumínio (phatom), que permitiu a medida de densidade mineral óssea, sendo esta a média aritmética da região de interesse determinada no osso carpo acessório correspondente ao valor em milímetros da escala. Os valores da densidade mineral óssea em mmAl do acessório do carpo em função da idade não apresentaram diferenças entre os sexos (p=0,86) permitindo que uma equação de reta fosse ajustada para ambos os sexos (densidade mineral óssea (DMO) mmAl = 3.109 + 0,056 x idade em meses), na faixa etária estudada.

Questioning the implementation of habitat corridors: a case study in interior São Paulo using ants as bioindicators

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A new implementation of population based incremental learning method for optimizations in electromagnetics

To enhance the global search ability of population based incremental learning (PBIL) methods, it is proposed that multiple probability vectors are to be included on available PBIL algorithms. The strategy for updating those probability vectors and the negative learning and mutation operators are thus re-defined correspondingly. Moreover, to strike the best tradeoff between exploration and exploitation searches, an adaptive updating strategy for the learning rate is designed. Numerical examples are reported to demonstrate the pros and cons of the newly implemented algorithm.

Estimates of genetic parameters, and cluster and principal components analyses of breeding values related to egg production traits in a White Leghorn population

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

An implementation of modified scatter search algorithm to transmission expansion planning

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

An analog implementation of radial basis neural networks (RBNN) using BiCMOS technology

This paper describes a analog implementation of radial basis neural networks (RBNN) in BiCMOS technology. The RBNN uses a gaussian function obtained through the characteristic of the bipolar differential pair. The gaussian parameters (gain, center and width) is changed with programmable current source. Results obtained with PSPICE software is showed.

Virtual instrumentation applied to the implementation of IEEE STD 1459-2000 power definitions

This paper discusses the utilization of Virtual Instrumentation to the implementation and evaluation of different power definitions, so that classical formulations and new definitions can be compared without the necessity of acquiring different power meters or analyzers. Accordingly, the definitions of IEEE Standard 1459-2000 for the measurement of power quantities under distorted and unbalanced situations, have been digitally implemented. Thus, several power and power factor components related to the decomposition of the measured voltage and current signals have been obtained. The proposed PC-based Virtual Instrument uses a high performance acquisition board and isolated sensors and transducers. All digital algorithms and routines have been implemented by means of a graphical development system. Regarding to the implementation of STD 1459, this paper also proposes several different algorithms to the required decompositions of voltage, current and power components. © 2005 IEEE.

Estimation of variance components and prediction of breeding values in rubber tree breeding using the REML/BLUP procedure

The present paper deals with estimation of variance components, prediction of breeding values and selection in a population of rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Müell.-Arg.] from Rio Branco, State of Acre, Brazil. The REML/BLUP (restricted maximum likelihood/best linear unbiased prediction) procedure was applied. For this purpose, 37 rubber tree families were obtained and assessed in a randomized complete block design, with three unbalanced replications. The field trial was carried out at the Experimental Station of UNESP, located in Selvíria, State of Mato Grosso do Sul, Brazil. The quantitative traits evaluated were: girth (G), bark thickness (BT), number of latex vessel rings (NR), and plant height (PH). Given the unbalanced condition of the progeny test, the REML/BLUP procedure was used for estimation. The narrow-sense individual heritability estimates were 0.43 for G, 0.18 for BT, 0.01 for NR, and 0.51 for PH. Two selection strategies were adopted: one short-term (ST - selection intensity of 8.85%) and the other long-term (LT - selection intensity of 26.56%). For G, the estimated genetic gains in relation to the population average were 26.80% and 17.94%, respectively, according to the ST and LT strategies. The effective population sizes were 22.35 and 46.03, respectively. The LT and ST strategies maintained 45.80% and 28.24%, respectively, of the original genetic diversity represented in the progeny test. So, it can be inferred that this population has potential for both breeding and ex situ genetic conservation as a supplier of genetic material for advanced rubber tree breeding programs. Copyright by the Brazilian Society of Genetics.

A new implementation of Population Based Incremental Learning method for optimization studies in electromagnetics

To enhance the global search ability of Population Based Incremental Learning (PBIL) methods, It Is proposed that multiple probability vectors are to be Included on available PBIL algorithms. As a result, the strategy for updating those probability vectors and the negative learning and mutation operators are redefined as reported. Numerical examples are reported to demonstrate the pros and cons of the newly Implemented algorithm. ©2006 IEEE.