Global precedence changes by environment: A systematic review and meta-analysis on effect of perceptual field variables on global-local visual processing.

Perceptual organization and, in particular, visual processing have been debated for many years. The global precedence effect in local-global visual processing, as introduced by David Navon, refers to the condition that global aspects of a scene are processed more rapidly than are local details. This perceptual dynamic is influenced by many factors that can be divided into two major categories: subjective or internal factors (e.

miRNA target recognition using features of suboptimal alignments.

MicroRNAs (miRNAs) are a class of short RNA molecules that regulate gene expression by binding directly to messenger RNAs. Conventional approaches to miRNA target prediction estimate the accessibility of target sites and the strength of the binding miRNA by finding optimums of some energy models, which involves O(n3) computations. Alternatively, we narrow down potential binding sites of miRNAs to suboptimal hits of a pairwise alignment algorithm called Fitting Alignment in O(n2).

Effect of PITX2 knockdown on transcriptome of primary human trabecular meshwork cell cultures.

Purpose: To identify genes whose expressions in primary human trabecular meshwork (TM) cell cultures are affected by the transcription factor pituitary homeobox 2 (PITX2) and to identify genes that may have roles in glaucoma. Known glaucoma causing genes account for disease in a small fraction of patients, and we aimed at identification of other genes that may have subtle and accumulative effects not easily identifiable by a genetic approach.

Methods: Expression profiles derived using microarrays were compared between TM control cells and cells treated with PITX2 siRNAs using three protocols so as to minimize false positive and negative results.

Global haplotype partitioning for maximal associated SNP pairs.

Background: Global partitioning based on pairwise associations of SNPs has not previously been used to define haplotype blocks within genomes. Here, we define an association index based on LD between SNP pairs. We use the Fisher's exact test to assess the statistical significance of the LD estimator.

A tale of two symmetrical tails: structural and functional characteristics of palindromes in proteins.

Background: It has been previously shown that palindromic sequences are frequently observed in proteins. However, our knowledge about their evolutionary origin and their possible importance is incomplete.

Results: In this work, we tried to revisit this relatively neglected phenomenon.

Evolution of 'ligand-diffusion chreodes' on protein-surface models: a genetic-algorithm study.

Lattice models have been previously used to model ligand diffusion on protein surfaces. Using such models, it has been shown that the presence of pathways (or 'chreodes') of consecutive residues with certain properties can decrease the number of steps required for the arrival of a ligand at the active site. In this work, we show that, based on a genetic algorithm, ligand-diffusion pathways can evolve on a protein surface, when this surface is selected for shortening the travel length toward the active site.

Solvent accessibility, residue charge and residue volume, the three ingredients of a robust amino acid substitution matrix.

Cost measure matrices or different amino acid indices have been widely used for studies in many fields of biology. One major criticism of these studies might be based on the unavailability of an unbiased and yet effective amino acid substitution matrix. Throughout this study we have devised a cost measure matrix based on the solvent accessibility, residue charge, and residue volume indices.