Technical Report: CSVM Ecosystem

The CSVM format is derived from CSV format and allows the storage of tabular like data with a limited but extensible amount of metadata. This approach could help computer scientists because all information needed to uses subsequently the data is included in the CSVM file and is particularly well suited for handling RAW data in a lot of scientific fields and to be used as a canonical format. The use of CSVM has shown that it greatly facilitates: the data management independently of using databases; the data exchange; the integration of RAW data in dataflows or calculation pipes; the search for best practices in RAW data management. The efficiency of this format is closely related to its plasticity: a generic frame is given for all kind of data and the CSVM parsers don't make any interpretation of data types. This task is done by the application layer, so it is possible to use same format and same parser codes for a lot of purposes. In this document some implementation of CSVM format for ten years and in different laboratories are presented. Some programming examples are also shown: a Python toolkit for using the format, manipulating and querying is available. A first specification of this format (CSVM-1) is now defined, as well as some derivatives such as CSVM dictionaries used for data interchange. CSVM is an Open Format and could be used as a support for Open Data and long term conservation of RAW or unpublished data.Comment: 31 pages including 2p of Anne

The French research system : which evolution and which borders ?

We analyse the French Research System with the study of the contracts between the CNRS (Centre National de la Recherche Scientifique) and the companies and test the hypothesis of small world in science. Our working material is the data base of the contracts of the units of the CNRS with economic partners, which has been collecting information since 1986 to 2006. This first application of Network methods and tools to the CNRS contracts allows us to obtain some results: at first, the major firms’s scientific network is not "scale-free" as if competition and strategy between the most large firms dominate the behaviour in R&D investments and management of contracts with public research units. However, in second part, we demonstrate that every discipline network is a "small world", i.e. , that it exists several scientific communities in which the diffusion of information is free and easy, even if its forwards through any actors (some labs or some firms). Probably, there are several "small worlds" in this database as in the scientific collaboration networks. Is seems that the industrial research does not disturb too much the properties of scientific network, as it’s well known in the literature of Sciences Studies

Technical report: CSVM dictionaries

CSVM (CSV with Metadata) is a simple file format for tabular data. The possible application domain is the same as typical spreadsheets files, but CSVM is well suited for long term storage and the inter-conversion of RAW data. CSVM embeds different levels for data, metadata and annotations in human readable format and flat ASCII files. As a proof of concept, Perl and Python toolkits were designed in order to handle CSVM data and objects in workflows. These parsers can process CSVM files independently of data types, so it is possible to use same data format and parser for a lot of scientific purposes. CSVM-1 is the first version of CSVM specification, an extension of CSVM-1 for implementing a translation system between CSVM files is presented in this paper. The necessary data used to make the translation are also coded in another CSVM file. This particular kind of CSVM is called a CSVM dictionary, it is also readable by the current CSVM parser and it is fully supported by the Python toolkit. This report presents a proposal for CSVM dictionaries, a working example in chemistry, and some elements of Python toolkit usable to handle these files

Technical Report: CSVM format for scientific tabular data

The CSVM (CSV with metadata data) is issued from CSV format and used for storing experimental data, models, specifications. CSVM allows the storage of tabular data with a limited but extensible amount of metadata. This increases the exchange and long term use of RAW data because all information needed to use subsequently the data are included in the CSVM file. Basic CSVM files are readable by current tools (i.e. spreadsheets) for handling tables. Using full possibilities of concept, it is possible to deviate from a strict table and annotate also inside the data block. CSVM file are pure ASCII files and could provide a template for implementing best practices in handling raw data at a laboratory level, in exchange between data sources, in long term resources, or in collaborative processes particularly when different scientific fields are implied. In this document we describe the first (CSVM-1) release of CSVM format

Controlled release properties and final macroporosity of a pectin microspheres–calcium phosphate composite bone cement

The use of calcium phosphate cements (CPC) is restricted by their lack of macroporosity and poor drug release properties. To overcome these two limitations, incorporating degradable polymer microparticles into CPC is an attractive option, as polymer microparticles could help to control drug release and induce macroporosity after degradation. Although few authors have yet tested synthetic polymers, the potentiality of polysaccharides’ assuming this role has never been explored. Low-methoxy amidated pectins (LMAP) constitute valuable candidates because of their biocompatibility and ionic and pH sensitivity. In this study, the potentiality of a LMAP with a degree of esterification (DE) of 30 and a degree of amidation (DA) of 19 was explored. The aim of this study was to explore the influence of LMAP microspheres within the composite on the cement properties, drug release ability and final macroporosity after microspheres degradation. Three LMAP incorporation ratios, 2%, 4% and 6% w/w were tested, and ibuprofen was chosen as the model drug. In comparison with the CPC reference, the resulting composites presented reduced setting times and lowered the mechanical properties, which remained acceptable for an implantation in moderate-stress-bearing locations. Sustained release of ibuprofen was obtained on at least 45 days, and release rates were found to be controlled by the LMAP ratio, which modulated drug diffusion. After 4 months of degradation study, the resulting CPC appeared macroporous, with a maximum macroporosity of nearly 30% for the highest LMAP incorporation ratio, and interconnectivity between pores could be observed. In conclusion, LMAP appear as interesting candidates to generate macroporous bone cements with tailored release properties and macroporosity by adjusting the pectin content within the composites

Highly Efficient Access to Original Polycyclic Pyrrolopiperazine Scaffolds by a Three-Component Reaction with 1,3-Dicarbonyls.

International audienceMolecular sieves have been found to promote a new fast, environmentally friendly and experimentally simple mul- ticomponent domino reaction from 1,3-dicarbonyls for the synthe- sis of pyrrolopiperazine and azasteroid-like scaffolds, of potential synthetic and biological interests

A blaVIM-2 Plasmid Disseminating in Extensively Drug-Resistant Clinical Pseudomonas aeruginosa and Serratia marcescens Isolates

Infections caused by carbapenem-resistant Enterobacteriaceae isolates are an issue of major global concern (1). Genes coding for metallo-β-lactamases (MβLs) identified in clinical isolates are associated with mobile elements and subject to horizontal genetic transfer (HGT) events (2–6). VIM-2 is present on numerous plasmids, but only pNOR-2000 from Pseudomonas aeruginosa COL-1 from France (7, 8) and pLD209 from Pseudomonas putida LD209 from Argentina (9) have been completely sequenced. Here, we report the complete sequence and characterization of plasmid pDCPR1 harboring a blaVIM-2 gene cassette in a Tn402-type class 1 integron, which was isolated from two extensively drug-resistant strains: P. aeruginosa 802 (from a burn patient at the Hospital Municipal de Quemados, Argentina, 2005) and S. marcescens 68313 (Sanatorio Sagrado Corazón, Argentina, 2012).Fil: Vilacoba, Elisabet. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Quiroga, Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Pistorio, Mariano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Famiglietti, Angela María Rosa. Universidad de Buenos Aires. Facultad de Medicina. Hospital de Clínicas General San Martín; ArgentinaFil: Rodriguez, Hernan Bernardo. Universidad de Buenos Aires. Facultad de Medicina. Hospital de Clínicas General San Martín; ArgentinaFil: Kovensky, Jaime. Ciudad Autónoma de Buenos Aires. Hospital Municipal de Quemados; ArgentinaFil: Deraspe, Maxime. Université du Québec a Montreal; Canadá. Laval University; CanadáFil: Raymond, Frédéric. Université du Québec a Montreal; Canadá. Laval University; CanadáFil: Roy, Paul H.. Université du Québec a Montreal; Canadá. Laval University; CanadáFil: Centron, Daniela. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; Argentin