L1pred: A Sequence-Based Prediction Tool for Catalytic Residues in Enzymes with the L1-logreg Classifier

To understand enzyme functions, identifying the catalytic residues is a usual first step. Moreover, knowledge about catalytic residues is also useful for protein engineering and drug-design. However, to experimentally identify catalytic residues remains challenging for reasons of time and cost. Therefore, computational methods have been explored to predict catalytic residues. Here, we developed a new algorithm, L1pred, for catalytic residue prediction, by using the L1-logreg classifier to integrate eight sequence-based scoring functions. We tested L1pred and compared it against several existing sequence-based methods on carefully designed datasets Data604 and Data63. With ten-fold cross-validation, L1pred showed the area under precision-recall curve (AUPR) and the area under ROC curve (AUC) of 0.2198 and 0.9494 on the training dataset, Data604, respectively. In addition, on the independent test dataset, Data63, it showed the AUPR and AUC values of 0.2636 and 0.9375, respectively. Compared with other sequence-based methods, L1pred showed the best performance on both datasets. We also analyzed the importance of each attribute in the algorithm, and found that all the scores contributed more or less equally to the L1pred performance

Synthetic Biology: Mapping the Scientific Landscape

This article uses data from Thomson Reuters Web of Science to map and analyse the scientific landscape for synthetic biology. The article draws on recent advances in data visualisation and analytics with the aim of informing upcoming international policy debates on the governance of synthetic biology by the Subsidiary Body on Scientific, Technical and Technological Advice (SBSTTA) of the United Nations Convention on Biological Diversity. We use mapping techniques to identify how synthetic biology can best be understood and the range of institutions, researchers and funding agencies involved. Debates under the Convention are likely to focus on a possible moratorium on the field release of synthetic organisms, cells or genomes. Based on the empirical evidence we propose that guidance could be provided to funding agencies to respect the letter and spirit of the Convention on Biological Diversity in making research investments. Building on the recommendations of the United States Presidential Commission for the Study of Bioethical Issues we demonstrate that it is possible to promote independent and transparent monitoring of developments in synthetic biology using modern information tools. In particular, public and policy understanding and engagement with synthetic biology can be enhanced through the use of online interactive tools. As a step forward in this process we make existing data on the scientific literature on synthetic biology available in an online interactive workbook so that researchers, policy makers and civil society can explore the data and draw conclusions for themselves

Non-Destructive Evaluation in Manufacturing using Spectroscopic Ellipsometry

The manufacture of optical coatings, computer disks, as well as advanced electronic multilayered devices and circuit structures requires high precision in the measurement and control of thicknesses and interfacial and surface roughnesses. Variable angle spectroscopic ellipsometry (VASE) is non-destructive and monolayer sensitive. VASE uses polarized light, and the technique can be applied in nearly any ambient, including air, vacuum, or corrosive environment. Applications to coated window glass, space protective coatings, semiconductor device, as well as sputtered media computer disk manufacturing are discussed. At the present time these NDE measurements are mainly ex situ, but in situ (during deposition) applications are being rapidly developed

Chevrel Phases: Genesis and Developments

International audienceThis chapter summarizes the important role played by Marcel Sergent in the discovery in the Rennes Laboratory of the Chevrel Phases, which stimulated considerable interest in the international solid-state chemistry community, because of their remarkable superconducting properties. After a brief general introduction to this topic, the seminal discoveries associated with these phases between 1970 and 1990 are described. After that their initial synthesis and structural determination was discovered, it was necessary to establish their critical superconducting transition temperature, the critical magnetic field, and the critical current density in wires, single crystals, and thin films. More recently their applications as battery materials, in catalysis, and their thermoelectric properties have been studied and are briefly described. These phases opened up the way not only to a rich solid-state chemistry but also to a rich solution chemistry, which complemented the classical field of transition metal carbonyl clusters. The basic cluster units of the Chevrel Phases continue to be studied in the Rennes Laboratory by the heirs of Marcel Sergent and more widely in the international community