Approximate Bayesian feature selection on a large meta-dataset offers novel insights on factors that effect siRNA potency

Motivation: Short interfering RNA (siRNA)-induced RNA interference is an endogenous pathway in sequence-specific gene silencing. The potency of different siRNAs to inhibit a common target varies greatly and features affecting inhibition are of high current interest. The limited success in predicting siRNA potency being reported so far could originate in the small number and the heterogeneity of available datasets in addition to the knowledge-driven, empirical basis on which features thought to be affecting siRNA potency are often chosen. We attempt to overcome these problems by first constructing a meta-dataset of 6483 publicly available siRNAs (targeting mammalian mRNA), the largest to date, and then applying a Bayesian analysis which accommodates feature set uncertainty. A stochastic logistic regression-based algorithm is designed to explore a vast model space of 497 compositional, structural and thermodynamic features, identifying associations with siRNA potency

Design method improvement of oxidizing-reducing processes at iron-ore material sintering on basis of experimental study of solid fuel combustion in layer

There the study objects are the reducing reactions and the reducing reactions of iron oxides and the combustion process of solid fuel at the sintering. The study purposes are to refine the combustion mechanisms of fuel depending on the main variables of sintering process; to develop the design method for the evolution depth of reducing reactions and of oxidizing reactions of iron oxides at the sintering. The design procedure for the products from the sintering fuel combustion and for the decomposition degree of air moisture in the combustion zone has been created; the design procedure of running depth of reducing and oxidizing processes at the sintering has been developed. The mechanisms characterizing the influence of technology variables on the indicators of combustion process have been established; the data about the composition of combustion products have been obtained; the change character of FeO inclusion along the layer height has been established; the influence of air humidity on the gas formation has been assessed; the FeO quantity in the melting zone has been determined. The results have been used in the mathematical model at the analysis of machine operation of sintering factories at the Cherepovets Integrated Iron-and-Steel Works (IISW), at the Karaganda IISW, at the Novolipetsk IISW. The application field is the metallurgyAvailable from VNTIC / VNTIC - Scientific & Technical Information Centre of RussiaSIGLERURussian Federatio

Peptide Nanopores and Lipid Bilayers: Interactions by Coarse-Grained Molecular-Dynamics Simulations

A set of 49 protein nanopore-lipid bilayer systems was explored by means of coarse-grained molecular-dynamics simulations to study the interactions between nanopores and the lipid bilayers in which they are embedded. The seven nanopore species investigated represent the two main structural classes of membrane proteins (α-helical and β-barrel), and the seven different bilayer systems range in thickness from ∼28 to ∼43 Å. The study focuses on the local effects of hydrophobic mismatch between the nanopore and the lipid bilayer. The effects of nanopore insertion on lipid bilayer thickness, the dependence between hydrophobic thickness and the observed nanopore tilt angle, and the local distribution of lipid types around a nanopore in mixed-lipid bilayers are all analyzed. Different behavior for nanopores of similar hydrophobic length but different geometry is observed. The local lipid bilayer perturbation caused by the inserted nanopores suggests possible mechanisms for both lipid bilayer-induced protein sorting and protein-induced lipid sorting. A correlation between smaller lipid bilayer thickness (larger hydrophobic mismatch) and larger nanopore tilt angle is observed and, in the case of larger hydrophobic mismatches, the simulated tilt angle distribution seems to broaden. Furthermore, both nanopore size and key residue types (e.g., tryptophan) seem to influence the level of protein tilt, emphasizing the reciprocal nature of nanopore-lipid bilayer interactions