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.

Algoritmo Q-learning como estratégia de exploração e/ou explotação para metaheurísticas GRASP e algoritmo genético

Techniques of optimization known as metaheuristics have achieved success in the resolution of many problems classified as NP-Hard. These methods use non deterministic approaches that reach very good solutions which, however, don t guarantee the determination of the global optimum. Beyond the inherent difficulties related to the complexity that characterizes the optimization problems, the metaheuristics still face the dilemma of xploration/exploitation, which consists of choosing between a greedy search and a wider exploration of the solution space. A way to guide such algorithms during the searching of better solutions is supplying them with more knowledge of the problem through the use of a intelligent agent, able to recognize promising regions and also identify when they should diversify the direction of the search. This way, this work proposes the use of Reinforcement Learning technique - Q-learning Algorithm - as exploration/exploitation strategy for the metaheuristics GRASP (Greedy Randomized Adaptive Search Procedure) and Genetic Algorithm. The GRASP metaheuristic uses Q-learning instead of the traditional greedy-random algorithm in the construction phase. This replacement has the purpose of improving the quality of the initial solutions that are used in the local search phase of the GRASP, and also provides for the metaheuristic an adaptive memory mechanism that allows the reuse of good previous decisions and also avoids the repetition of bad decisions. In the Genetic Algorithm, the Q-learning algorithm was used to generate an initial population of high fitness, and after a determined number of generations, where the rate of diversity of the population is less than a certain limit L, it also was applied to supply one of the parents to be used in the genetic crossover operator. Another significant change in the hybrid genetic algorithm is the proposal of a mutually interactive cooperation process between the genetic operators and the Q-learning algorithm. In this interactive/cooperative process, the Q-learning algorithm receives an additional update in the matrix of Q-values based on the current best solution of the Genetic Algorithm. The computational experiments presented in this thesis compares the results obtained with the implementation of traditional versions of GRASP metaheuristic and Genetic Algorithm, with those obtained using the proposed hybrid methods. Both algorithms had been applied successfully to the symmetrical Traveling Salesman Problem, which was modeled as a Markov decision process

Diagnóstico operacional de lagoas de estabilização

This work intends to develop an approach based through scientific criteria in the operational diagnosis of ponds of stabilization, starting from analyses accomplished in loco and in laboratory of 78 systems of sewer treatment through ponds of stabilization in the State of Rio Grande do Norte. The objectives of the research are: to map, to evaluate and to diagnose the operational acting of the ponds of stabilization of the state of Rio Grande do Norte, through visits in loco and analyses laboratory; to build a SIG, through the map rain, locate the points of releases of sewages of the systems of existent ponds in Rio Grande do Norte, as well as operational data and his/her respective efficiency diagnosis in the removal of BOD and Coliforms Termotolerantes; to evaluate, in real scale, three systems of ponds of stabilization of RN in the operational efficiency for the parameters BOD5, COD, pH, Temperature, OD and Coliforms Termotolerantes. Of 78 ETEs of appraised RN just, 9% or 7 had maximum concepts in what concerns the removal of BOD and Coliforms Termotolerantes and 41% or 32, they had the worst concepts in term of operational efficiency. The flowing concentrations ETEs of RN of BOD and Coliforms were of 410mg/L and 2,50x107UFC/100ml, the predominant configuration is of the type F1+M1+M2, the relationship BOD/COD revealed for the sewer tributary characteristic biodegradable high. For the study of case of 3 ETEs, the best operational efficiencies in decreasing order were: Cidade (Municipal district), it Roça (State) and São Miguel (SAAE). The removals of final BOD were 51,6mg/L; 108,27mg/L and 62,6mg/L, tends efficiency of 82%; 74% and 81%. In term of coliforms removal in the final effluentes were 1,90x103UFC/100ml; 1,50x104UFC/100ml and 3,10x104UFC/100ml, tends efficiencies of 99,99%; 99,95% and 99,90%. In what it concerns the practice of agricultural reúso of cultures consumed raw, none of 3 ETEs assisted the parameters of the Resolution CONAMA 357/05, for other reúso practices, all assisted the categories B and C of OMS. For release in body receiving ETE Cidade just, they assist the demands of the resolution of CONAMA 357/05, by study of purification solemnity of the receiving body. The maintenance lack and operation; exclusive operator in ETEs and operation knowledge was the contributory factors for the operational fall in appraised ETEs of RN

Best practices for the implantation of ISO 14001 norms: a study of change management in two industrial companies in the Midwest region of the state of São Paulo - Brazil

Among the difficulties found in the implementation of ISO 14001 systems, resistance to change can always be found. It is mainly a consequence of the hurry to change, loss of focus, concentration of decision making at the level of top management, arbitrary imposition of objectives and results, faulty communication, and the absence of motivational and financial incentive for change.Therefore, the main objective of this paper is to present best practices with respect to the management of organizational change due to the implementation of ISO 14001 norms in two industrial companies in the Midwest region of the State of São Paulo - Brazil. (C) 2008 Elsevier Ltd. All rights reserved.

Multicast packing problem: abordagem multiobjetivo

This work presents a algorithmic study of Multicast Packing Problem considering a multiobjective approach. The first step realized was an extensive review about the problem. This review serverd as a reference point for the definition of the multiobjective mathematical model. Then, the instances used in the experimentation process were defined, this instances were created based on the main caracteristics from literature. Since both mathematical model and the instances were definined, then several algoritms were created. The algorithms were based on the classical approaches to multiobjective optimization: NSGA2 (3 versions), SPEA2 (3 versions). In addition, the GRASP procedures were adapted to work with multiples objectives, two vesions were created. These algorithms were composed by three recombination operators(C1, C2 e C3), two operator for build solution, a mutation operator and a local search procedure. Finally, a long experimentation process was performed. This process has three stages: the first consisted of adjusting the parameters; the second was perfomed to indentify the best version for each algorithm. After, the best versions for each algorithm were compared in order to identify the best algorithm among all. The algorithms were evaluated based on quality indicators and Hypervolume Multiplicative Epsilon

Best site for embryo transfer: the upper or lower half of endometrial cavity?

BACKGROUND: the objective of the present study was to determine the importance of the site of embryo transfer (upper or lower half endometrial cavity) on implantation and clinical pregnancy rates. METHODS: A total of 400 transfers guided by ultrasound were randomly assigned to two groups according to the distance between the uterine fundus and the catheter tip at the time of embryo placement. Group I (n=200) consisted of transfers corresponding to a distance of <50% of the endometrial cavity length (ECL), i.e. transfer in upper half of the cavity; and group II (n=200) consisted of transfers corresponding to a distance of greater than or equal to50%, of the ECL, i.e. transfer in lower half of cavity. The Student's t-test, Mann-Whitney test and Fisher's exact test were used where appropriate. RESULTS: the general characteristics of the study population and the main transfer cycle characteristics had an equal distribution (P>0.05) between groups I and II. No significant difference in implantation or pregnancy rates was observed between groups I and II. CONCLUSION: the implantation or pregnancy rates were similar whether the embryos were deposited in the upper or lower half of the endometrial cavity.

Genetic and environmental factors that affect the best time of Thoroughbred horses in Brazil

On the basis of information provided by the Brazilian Association of Race Horse Breeders, we analysed the racing performance of 947 Thoroughbred horses in races held from 1985 to 1992. The performance was evaluated using the best, time of the animals. The variance component was obtained by the derivative-free restricted maximum likelihood method, and the model used contained fixed effects of the racing month and year, sex, race track, track condition, animal age, number of competitors in race, and distance, and the random animal effect. The low heritability estimate obtained (0.12) indicates that selection based on animal phenotypic value must induce small genetic changes in this trail.

A comparison of profilometer and AutoCAD software techniques in evaluation of implant angulation in vitro

Purpose: The aim of this study was to compare 2 different methods of assessment of implants at different inclinations (90 degrees and 65 degrees)-with a profilometer and AutoCAD software. Materials and Methods: Impressions (n = 5) of a metal matrix containing 2 implants, 1 at 90 degrees to the surface and 1 at 65 degrees to the surface, were obtained with square impression copings joined together with dental floss splinting covered with autopolymerizing acrylic resin, an open custom tray, and vinyl polysiloxane impression material. Measurement of the angles (in degrees) of the implant analogs were assessed by the same blinded operator with a profilometer and through analysis of digitized images by AutoCAD software. For each implant analog, 3 readings were performed with each method. The results were subjected to a nonparametric Kruskal-Wallis test, with P <= .05 considered significant. Results: For implants perpendicular to the horizontal surface of the specimen (90 degrees), there were no significant differences between the mean measurements obtained with the profilometer (90.04 degrees) and AutoCAD (89.95 degrees; P=.9142). In the analyses of the angled implants at 65 degrees in relation to the horizontal surface of the specimen, significant differences were observed (P=.0472) between the mean readings with the profilometer (65.73 degrees) and AutoCAD (66.25 degrees). Conclusions: The degrees of accuracy of implant angulation recording vary among the techniques available and may vary depending on the angle of the implant. Further investigation is needed to determine the best test conditions and the best measuring technique for determination of the angle of the implant in vitro.

Strand Analysis, a free online program for the computational identification of the best RNA interference (RNAi) targets based on Gibbs free energy

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

Catch-per-unit-effort: which estimator is best?

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Calculating the Best Dual Bound for Problems with Multiple Lagrangian Relaxations

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

On the entropy operator for the general SU(1,1) TFD formulation

In this Letter, an entropy operator for the general unitary SU(1, 1) TFD formulation is proposed and used to lead a bosonic system from zero to finite temperature. Namely, considering the closed bosonic string as the target system, the entropy operator is used to construct the thermal vacuum. The behaviour of such a state under the breve conjugation rules is analyzed and it was shown that the breve conjugation does not affect the thermal effects. From this thermal vacuum the thermal energy, the entropy and the free energy of the closed bosonic string are calculated and the appropriated thermal distribution for the system is found after the free energy minimization. (C) 2004 Elsevier B.V. All rights reserved.

Massive superstring vertex operator in D=10 superspace

Using the pure spinor formalism for the superstring, the vertex operator for the first massive states of the open superstring is constructed in a manifestly super-Poincare covariant manner. This vertex operator describes a massive spin-two multiplet in terms of ten-dimensional superfields.