Mines ParisTech

About: Mines ParisTech is a education organization based out in Paris, France. It is known for research contribution in the topics: Finite element method & Microstructure. The organization has 6564 authors who have published 11676 publications receiving 359898 citations. The organization is also known as: École nationale supérieure des mines de Paris & École des mines de Paris.

The inference of protein–protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships

Abstract: Motivation: The prediction of protein--protein interactions is currently an important issue in bioinformatics. The mirror tree method uses evolutionary information to predict protein--protein interactions. However, it has been recognized that predictions by the mirror tree method lead to many false positives. The incentive of our study was to solve this problem by improving the method of extracting the co-evolutionary information regarding the protein pairs. Results: We developed a novel method to predict protein--protein interactions from co-evolutionary information in the framework of the mirror tree method. The originality is the use of the projection operator to exclude the information about the phylogenetic relationships among the source organisms from the distance matrix. Each distance matrix was transformed into a vector for the operation. The vector is referred to as a 'phylogenetic vector'. We have proposed three ways to extract the phylogenetic information: (1) using the 16S rRNA from the same source organisms as the proteins under consideration, (2) averaging the phylogenetic vectors and (3) analyzing the principal components of the phylogenetic vectors. We examined the performance of the proposed methods to predict interacting protein pairs from Escherichia coli, using experimentally verified data. Our method was successful, and it drastically reduced the number of false positives in the prediction. Availability: The R script for the prediction of protein--protein interactions reported in this manuscript is available at http://timpani.genome.ad.jp/~proj/ Contact: sato@kuicr.kyoto-u.ac.jp Supplementary information: The information is also available at the same site as the R script.

Chitosan-Supported Palladium Catalyst. 3. Influence of Experimental Parameters on Nitrophenol Degradation

Abstract: Glutaraldehyde cross-linked chitosan was loaded with palladium and then reduced by means of an in situ hydrogen generation procedure (Zn in sulfuric acid solution) to prepare a chitosan-supported palladium catalyst. This catalyst was successfully used to degrade nitrophenol in dilute solutions in the presence of sodium formate as the hydrogen donor. The optimum initial pH was below pH 4. The pH strongly increased during the reaction. The influence of the initial concentration of nitrophenol and sodium formate was studied in order to determine the minimum molar ratio between these compounds to achieve the complete conversion of the nitrogenous product. The pseudo-first-order equation was shown to fit degradation kinetics in most cases; however, in some cases it was necessary to use a variable-order equation in order to model the kinetics. Decreasing catalyst particle size increased degradation rate; the kinetic parameter varied linearly with the reciprocal of the diameter, indicating that film diffusion ma...

Constructive analysis of cyclic circuits

Abstract: Traditionally, circuits with combinational loops are found only in asynchronous designs. However, combinational loops can also be useful for synchronous circuit design. Combinational loops can arise from high-level language behavioral compiling, and can be used to reduce circuit size. We provide a symbolic algorithm that detects if a sequential circuit with combinational loops exhibits standard synchronous behavior, and if so, produces an equivalent circuit without combinational loops. We present applications to hardware and software synthesis from the Esterel synchronous programming language.