Selection Scheme (selection + scheme)

Distribution by Scientific Domains

Selected Abstracts

Analysis of single-locus tests to detect gene/disease associations,

Kathryn Roeder
Abstract A goal of association analysis is to determine whether variation in a particular candidate region or gene is associated with liability to complex disease. To evaluate such candidates, ubiquitous Single Nucleotide Polymorphisms (SNPs) are useful. It is critical, however, to select a set of SNPs that are in substantial linkage disequilibrium (LD) with all other polymorphisms in the region. Whether there is an ideal statistical framework to test such a set of ,tag SNPs' for association is unknown. Compared to tests for association based on frequencies of haplotypes, recent evidence suggests tests for association based on linear combinations of the tag SNPs (Hotelling T2 test) are more powerful. Following this logical progression, we wondered if single-locus tests would prove generally more powerful than the regression-based tests? We answer this question by investigating four inferential procedures: the maximum of a series of test statistics corrected for multiple testing by the Bonferroni procedure, TB, or by permutation of case-control status, TP; a procedure that tests the maximum of a smoothed curve fitted to the series of of test statistics, TS; and the Hotelling T2 procedure, which we call TR. These procedures are evaluated by simulating data like that from human populations, including realistic levels of LD and realistic effects of alleles conferring liability to disease. We find that power depends on the correlation structure of SNPs within a gene, the density of tag SNPs, and the placement of the liability allele. The clearest pattern emerges between power and the number of SNPs selected. When a large fraction of the SNPs within a gene are tested, and multiple SNPs are highly correlated with the liability allele, TS has better power. Using a SNP selection scheme that optimizes power but also requires a substantial number of SNPs to be genotyped (roughly 10,20 SNPs per gene), power of TP is generally superior to that for the other procedures, including TR. Finally, when a SNP selection procedure that targets a minimal number of SNPs per gene is applied, the average performances of TP and TR are indistinguishable. Genet. Epidemiol. © 2005 Wiley-Liss, Inc. [source]

Ab initio QM/MM dynamics of H3O+ in water

Pathumwadee Intharathep
Abstract A molecular dynamics (MD) simulation based on a combined ab initio quantum mechanics/molecular mechanics (QM/MM) method has been performed to investigate the solvation structure and dynamics of H3O+ in water. The QM region is a sphere around the central H3O+ ion, and contains about 6,8 water molecules. It is treated at the Hartree-Fock (HF) level, while the rest of the system is described by means of classical pair potentials. The Eigen complex (H9O) is found to be the most prevalent species in the aqueous solution, partly due to the selection scheme of the center of the QM region. The QM/MM results show that the Eigen complex frequently converts back and forth into the Zundel (H5O) structure. Besides the three nearest-neighbor water molecules directly hydrogen-bonded to H3O+, other neighbor waters, such as a fourth water molecule which interacts preferentially with the oxygen atom of the hydronium ion, are found occasionally near the ion. Analyses of the water exchange processes and the mean residence times of water molecules in the ion's hydration shell indicate that such next-nearest neighbor water molecules participate in the rearrangement of the hydrogen bond network during fluctuative formation of the Zundel ion and, thus, contribute to the Grotthuss transport of the proton. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006 [source]

Prediction of experimentally unknown re distances of organic molecules from Dunning basis set extrapolations for ab initio post-HF calculations

Alexander Neugebauer
Abstract An approach to estimate equilibrium re bond lengths of organic molecules which contain standard bonding situations for CC, CH, CO and CN distances from only one equation is presented. For this, optimizations of molecular geometries using correlated post-Hartree,Fock and density functional methods have been performed. A selection scheme was developed to determine the most reliable methodology for prediction of equilibrium re distances of covalent bonds from a set of investigated theoretical methods. Consequently, distances computed in the CCSD(T) procedure via exponential extrapolation from a consecutive set of Dunning cc-pVXZ basis sets by use of Eqn (2) are accurate up to ±,0.0005,Å in comparison to experimentally available re distances. Applications for predictions of the experimentally unknown re distances of methanol, methylamine and methylenimine are presented. Additionally the estimation of re distances of larger, chemically more interesting molecules is possible by lower order calculations (e.g. DFT B3LYP/cc-pVDZ) via linear correlation statistics using the results from our re reference model system via Eqn (3). Copyright © 2006 John Wiley & Sons, Ltd. [source]

A compact dual-element antenna array for adaptive MIMO system

Xuan Wang
Abstract A novel compact dual-element antenna array is proposed for adaptive MIMO system. By four embedded PIN diodes in the feeding network, the antenna array has three different working states. It can operate as a dual-element antenna array or work as a single antenna while the unselected antenna is terminated to a lumped matched resistor. As a dual-element antenna array, it has a ,10 dB impedance bandwidth of 595 MHz covering UMTS band with mutual coupling lower than ,15 dB in the whole band. The measured radiation patterns show that the radiation property of the selected antenna keeps steady no matter the other antenna is selected or not. The proposed antenna array can achieve antenna selection scheme to adapt to the time-varying channel conditions. © 2008 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 348,351, 2009; Published online in Wiley InterScience ( DOI 10.1002/mop.24044 [source]

Alternative formulation and applications aspects of the generalized projection method for array antenna synthesis

E. Botha
Abstract An array synthesis technique is formulated, which implements the method of generalized projections in the array excitation space. This permits the use of relaxation in the overall recursion relation that is not possible with previous formulations, resulting in accelerated convergence for slowly converging problems. Weighted least squares is introduced as a backward operator in an integral way that enhances the method. Means are described for determining starting points that assist the synthesis algorithm in avoiding so-called traps. The results obtained for a diverse selection of applications of the method are discussed. These demonstrate the effects on convergence of the use of relaxation, different pattern sampling angle selection schemes, and different starting point selection schemes. © 2009 Wiley Periodicals, Inc. Int J RF and Microwave CAE, 2009. [source]

The importance of haplotype length and heritability using genomic selection in dairy cattle

T.M. Villumsen
Summary Reliabilities for genomic estimated breeding values (GEBV) were investigated by simulation for a typical dairy cattle breeding setting. Scenarios were simulated with different heritabilites (h2) and for different haplotype sizes, and seven generations with only genotypes were generated to investigate reliability of GEBV over time. A genome with 5000 single nucleotide polymorphisms (SNP) at distances of 0.1 cM and 50 quantitative trait loci (QTL) was simulated, and a Bayesian variable selection model was implemented to predict GEBV. Highest reliabilities were obtained for 10 SNP haplotypes. At optimal haplotype size, reliabilities in generation 1 without phenotypes ranged from 0.80 for h2 = 0.02 to 0.93 for h2 = 0.30, and in the seventh generation without phenotypes ranged from 0.69 for h2 = 0.02 to 0.86 for h2 = 0.30. Reliabilities of GEBV were found sufficiently high to implement dairy selection schemes without progeny testing in which case a data time-lag of two to three generations may be present. Reliabilities were also relatively high for low heritable traits, implying that genomic selection could be especially beneficial to improve the selection on, e.g. health and fertility. [source]

A comparison of restricted selection procedures to control genetic gains

S. Ieiri
Summary Using Monte Carlo simulation, two schemes of restricted selection were compared under various combinations of genetic parameters and constraints on the genetic gains. The first selection scheme is the combination of best linear unbiased prediction (BLUP) evaluation and linear programming technique (BLUP + LP), and the second one is based on the restricted BLUP selection (RBLUP). Selection for two traits was supposed, in which animals were selected to maximize the genetic gain in trait 2 (,g2) under a proportional restriction on the genetic gain in trait 1 (,g1) to satisfy the intended ratio (,g1:,g2). Little differences were found between the two selection schemes with respect to the genetic gains averaged over replicates. However, in all the cases studied, the variance of genetic gains among replicates under BLUP + LP selection was smaller and less sensitive to the genetic parameters and the intended restriction than RBLUP selection. Under the situations of antagonistic selection, the difference tended to be larger. When the heritabilities of the two traits were different, RBLUP selection remarkably increased the variance of genetic gain in a trait with a higher heritability. These results suggest that BLUP + LP selection should always be preferable to RBLUP selection because of the smaller risk of selection. This choice is especially important for the situation where the genetic parameters act as limiting factors for the achievement of intended genetic gains. Zusammenfassung Unter Verwendung von Monte Carlo Simulation wurden zwei verschiedene Selektionsstrategien mit verschiedenen Kombinationen genetischer Parameter und Beschränkungen des genetischen Fortschritts verglichen. Die erste Selektionsstrategie stellt eine Kombination von BLUP-Schätzung und linearer Programmiertechnik (BLUP + LP) dar, die zweite Strategie basiert auf einer reduzierten BLUP-Selektion (RBLUP). Die Selektion wurde auf zwei Merkmalen basierend durchgeführt in welchen Tiere ausgewählt wurden, um den genetischen Fortschritt in Merkmal 2 zu maximieren (,g2) unter proportionaler Restriktion des genetischen Fortschritts in Merkmal 1 (,g1), um die beabsichtigte Beziehung zu erreichen (,g1:,g2). Kleine Unterschiede wurden zwischen den beiden Selektionsstrategien in Bezug auf den mittleren genetischen Fortschritt über Wiederholungen gefunden. Wie auch immer, in allen untersuchten Fällen war die Varianz des genetischen Fortschritts zwischen Wiederholungen mit der BLUP + LP-Selektion geringer und weniger abhängig in Bezug auf die genetischen Parameter und die beabsichtigte Restriktion im Vergleich zur RBLUP-Selektion. Unter den Gegebenheiten der gegenläufigen Selektion schien der Unterschied größer zu werden. Wenn die Heritabilitäten der beiden Merkmale unterschiedlich waren, stieg die Varianz des genetischen Fortschritts bei RBLUP in einem Merkmal mit höherer Heritabilität außergewöhnlich. Diese Ergebnisse deuten an, dass BLUP + LP-Selektion gegenüber RBLUP aufgrund des geringeren Selektionsrisikos stets bevorzugt werden sollte. Diese Wahl ist vornehmlich wichtig für die Situation, in der die genetischen Parameter ein limitierender Faktor zur Erreichung von genetischem Fortschritt sind. [source]

Effect of mate selection on fuzzy selective mating criteria in closed dairy multiple ovulation and embryo transfer nucleus programs

ABSTRACT In order to control rates of response and inbreeding, mate selection using fuzzy selective mating criteria (FMC) was investigated in adult multiple ovulation and embryo transfer nucleus schemes for dairy cattle. Stochastic simulation was used to model the closed nucleus scheme. This mate selection was examined in four alternative mating and male selection schemes: (i) a hierarchical scheme; (ii) a hierarchical sibship scheme (two males per sibship); (iii) a factorial scheme (two sires per dam); and (iv) a factorial sibship scheme (two males per sibship and two sires per dam). Genetic response and inbreeding rate tended to be reduced by increasing the trade-off parameter of FMC between the expected breeding value and inbreeding of progeny. Inbreeding rates in all schemes were reduced by reducing the variance of family size through selection and the average coancestry of mating pairs through mate allocation. [source]