Search results for "selection"
showing 10 items of 1940 documents
Effects of different simplified milk recording methods on genetic evaluation with Test-Day animal model
2007
The aims of the present study were to compare estimated breeding values (EBV) for milk yield using different testing schemes with a test-day animal model and to evaluate the effect of different testing schemes on the ranking of top sheep. Alternative recording schemes that use less information than that currently obtained with a monthly test-day schedule were employed to estimate breeding values. A random regression animal mixed model that used a spline function of days in milk was fitted. EBVs obtained with alternative recording schemes showed different degrees of Spearman correlation with EBVs obtained using the monthly recording scheme. These correlations ranged from 0.77 to 0.92. A redu…
Bayesian Model Averaging and Weighted Average Least Squares: Equivariance, Stability, and Numerical Issues
2011
This article is concerned with the estimation of linear regression models with uncertainty about the choice of the explanatory variables. We introduce the Stata commands bma and wals which implement, respectively, the exact Bayesian Model Averaging (BMA) estimator and the Weighted Average Least Squares (WALS) estimator developed by Magnus et al. (2010). Unlike standard pretest estimators which are based on some preliminary diagnostic test, these model averaging estimators provide a coherent way of making inference on the regression parameters of interest by taking into account the uncertainty due to both the estimation and the model selection steps. Special emphasis is given to a number pra…
Detecting global and local hippocampal shape changes in Alzheimer's disease using statistical shape models.
2012
Item does not contain fulltext The hippocampus is affected at an early stage in the development of Alzheimer's disease (AD). With the use of structural magnetic resonance (MR) imaging, we can investigate the effect of AD on the morphology of the hippocampus. The hippocampal shape variations among a population can be usually described using statistical shape models (SSMs). Conventional SSMs model the modes of variations among the population via principal component analysis (PCA). Although these modes are representative of variations within the training data, they are not necessarily discriminative on labeled data or relevant to the differences between the subpopulations. We use the shape des…
Molecular evolutionary analysis of type-1 human astroviruses identifies putative sites under selection pressure on the capsid protein
2017
Human astroviruses (HAstV) are important enteric pathogens that can be classified into eight sero/genotypes (HAstV-1 to -8). Although the various HAstV types show global spread, type-1 strains tend to be predominant. Molecular analysis of the genomic region encoding the capsid protein (ORF2) has revealed discrete sequence variation, with different lineages within each HAstV type and at least three major lineages have been identified within HAstV-1. Longitudinal epidemiological surveillance has revealed temporal shift of the various HAstV-1 lineages. Metadata analysis of HAstV-1 sequences available in the databases also revealed temporal shifts of the circulation of HAstV-1 lineages, suggest…
Evolution of Snake Venom Disintegrins by Positive Darwinian Selection
2008
PII-disintegrins, cysteine-rich polypeptides broadly distributed in the venoms of geographically diverse species of vipers and rattlesnakes, antagonize the adhesive functions of beta(1) and beta(3) integrin receptors. PII-disintegrins evolved in Viperidae by neofunctionalization of disintegrin-like domains of duplicated PIII-snake venom hemorrhagic metalloproteinase (SVMP) genes recruited into the venom proteome before the radiation of the advanced snakes. Minimization of the gene (loss of introns and coding regions) and the protein structures (successive loss of disulfide bonds) underpins the postduplication divergence of disintegrins. However, little is known about the underlying genetic …
Genomic determinants of protein folding thermodynamics in prokaryotic organisms.
2004
Here we investigate how thermodynamic properties of orthologous proteins are influenced by the genomic environment in which they evolve. We performed a comparative computational study of 21 protein families in 73 prokaryotic species and obtained the following main results. (i) Protein stability with respect to the unfolded state and with respect to misfolding are anticorrelated. There appears to be a trade-off between these two properties, which cannot be optimized simultaneously. (ii) Folding thermodynamic parameters are strongly correlated with two genomic features, genome size and G+C composition. In particular, the normalized energy gap, an indicator of folding efficiency in statistical…
Discrimination and selection of new potential antibacterial compounds using simple topological descriptors.
2003
Abstract The aim of the work was to discriminate between antibacterial and non-antibacterial drugs by topological methods and to select new potential antibacterial agents from among new structures. The method used for antibacterial activity selection was a linear discriminant analysis (LDA). It is possible to obtain a QSAR interpretation of the information contained in the discriminant function. We make use of the pharmacological distribution diagrams (PDDs) as a visualizing technique for the identification and selection of new antibacterial agents.
Computational Methods in Developing Quantitative Structure-Activity Relationships (QSAR): A Review
2006
Virtual filtering and screening of combinatorial libraries have recently gained attention as methods complementing the high-throughput screening and combinatorial chemistry. These chemoinformatic techniques rely heavily on quantitative structure-activity relationship (QSAR) analysis, a field with established methodology and successful history. In this review, we discuss the computational methods for building QSAR models. We start with outlining their usefulness in high-throughput screening and identifying the general scheme of a QSAR model. Following, we focus on the methodologies in constructing three main components of QSAR model, namely the methods for describing the molecular structure …
Modeling of the role of conformational dynamics in kinetics of the antigen-antibody interaction in heterogeneous phase.
2012
[EN] A novel approach that may potentially be used to study biomolecular interactions including the simultaneous determination of structural and kinetic binding parameters is described in this Article for the first time. It allows a rigid distinction between the possible reaction mechanisms of biomolecular recognition, induced fit and conformational selection. The relative importance of the two pathways is determined not by comparing rate constants but the structural aspects of the interaction instead. So the exact location of antigen molecules with respect to the capture antibody is depicted experimentally, avoiding the use of X-ray crystallography. The proposed pattern is applied to study…
A supramolecular system that strictly follows the binding mechanism of conformational selection
2020
Induced fit and conformational selection are two dominant binding mechanisms in biology. Although induced fit has been widely accepted by supramolecular chemists, conformational selection is rarely studied with synthetic systems. In the present research, we report a macrocyclic host whose binding mechanism is unambiguously assigned to conformational selection. The kinetic and thermodynamic aspects of this system are studied in great detail. It reveals that the kinetic equation commonly used for conformational selection is strictly followed here. In addition, two mathematical models are developed to determine the association constants of the same guest to the two host conformations. A “confo…