Similarity-Based Diff, Three-Way Diff and Merge

Semi-structured documents and data pervade modern workflows in all areas. Collaborative work and version management rely on effective, automatic difference analysis and three-way difference analysis tools. In our effort to develop a three-way difference analysis for tree-structured documents we developed a kernel three-way difference algorithm which extends the equality-based procedures, such as GNU diff3, by considering the similarity of documents in the difference analysis as well as to ignore the order of data if that is semantically suitable. As a result we obtain difference analysis algorithms that can be more fine-tuned to the application domain. Moreover, the equality-based counter-parts of our three-way difference analysis algorithms has the idempotency property, which the current three-way diff algorithms lacks.     

Stereochemistry of the N-glycosylation sites in glycoproteins

The stereochemical features displayed by the N-glycosidic linkagein crystalline N-linked glycoproteins are analyzed. From thestatistical analysis of 44 different glycosylation sites belongingto 26 glycoproteins of the Brookhaven Protein Data Bank, a meanstandard geometry for the GlcNAc moiety, along with a rationalizationof its confornia-tional behavior, can be proposed. As for theglycopeptide linkage, the distribution of observed conformationshas been analyzed on the basis of molecular mechanics calculations.The rotamer distribution of the Asn side chains conforms tothat observed on non-glycosylated structures, and it agreeswith the pattern of flexible conformations gathered from NMRmeasurements. In characterizing the protein-glycan interactions,some hydrogen bonds occur. Stacking between the amphiphilicmoiety of the glycan and some surrounding aromatic, or at leasthydrophobic, amino acid residues is also found. When lookingat the secondary structure of the glycosylated peptide, only25% of the glycosylation sites correspond to situations whereAsn is located at the top of a ß-turn. Other typesof secondary structure exist which fulfil the spatial requirementof having the glycan exposed at the surface of the protein.These data can be compared with the most recent studies on thepeptide conformation which would be required for glycosylation.     

The Active XML project: an overview

This paper provides an overview of the Active XML project developed at INRIA over the past five years. Active XML (AXML, for short), is a declarative framework that harnesses Web services for distributed data management, and is put to work in a peer-to-peer architecture. The model is based on AXML documents, which are XML documents that may contain embedded calls to Web services, and on AXML services, which are Web services capable of exchanging AXML documents. An AXML peer is a repository of AXML documents that acts both as a client by invoking the embedded service calls, and as a server by providing AXML services, which are generally defined as queries or updates over the persistent AXML documents. The approach gracefully combines stored information with data defined in an intensional manner as well as dynamic information. This simple, rather classical idea leads to a number of technically challenging problems, both theoretical and practical. In this paper, we describe and motivate the AXML model and language, overview the research results obtained in the course of the project, and show how all the pieces come together in our implementation. The first and third authors were partially funded by the European Project Edos. Work done when the second and third authors were at INRIA. Work done when the second and third authors were at INRIA.     

Validation of the performance of a GMO multiplex screening assay based on microarray detection

A new screening method for the detection and identification of GMO, based on the use of multiplex PCR followed by microarray, has been developed and is presented. The technology is based on the identification of quite ubiquitous GMO genetic target elements first amplified by PCR, followed by direct hybridisation of the amplicons on a predefined microarray (DualChip^® GMO, Eppendorf, Germany). The validation was performed within the framework of a European project (Co-Extra, contract no 007158) and in collaboration with 12 laboratories specialised in GMO detection. The present study reports the strategy and the results of an ISO complying validation of the method carried out through an inter-laboratory study. Sets of blind samples were provided consisting of DNA reference materials covering all the elements detectable by specific probes present on the array. The GMO concentrations varied from 1% down to 0.045%. In addition, a mixture of two GMO events (0.1% RRS diluted in 100% TOPAS19/2) was incorporated in the study to test the robustness of the assay in extreme conditions. Data were processed according to ISO 5725 standard. The method was evaluated with predefined performance criteria with respect to the EC CRL method acceptance criteria. The overall method performance met the acceptance criteria; in particular, the results showed that the method is suitable for the detection of the different target elements at 0.1% concentration of GMO with a 95% accuracy rate. This collaborative trial showed that the method can be considered as fit for the purpose of screening with respect to its intra- and inter-laboratory accuracy. The results demonstrated the validity of combining multiplex PCR with array detection as provided by the DualChip^® GMO (Eppendorf, Germany) for the screening of GMO. The results showed that the technology is robust, practical and suitable as a screening tool.     

Pyrene-adamantane-β-cyclodextrin: An efficient host–guest system for the biofunctionalization of SWCNT electrodes

The design of nanostructured biological architectures based on host–guest interactions between β-cyclodextrin and adamantane was investigated on SWCNT coatings using glucose oxidase (GOX) as biomolecule model. β-Cyclodextrin tagged GOX was immobilized on adamantane functionalized carbon nanotubes, deposited on platinum electrodes. Different functionalization techniques to attach “pyrene adamantane” on nanotubes were studied and compared in terms of the performances of the subsequently constructed glucose biosensors. The best results were obtained by dipping the nanotube deposit into a pyrene-adamantane solution followed by electropolymerization of the adsorbed pyrene monolayer. The constructed biosensor exhibited a good linear response toward glucose concentrations between 2 × 10⁻⁷ M and 1.6 × 10⁻³ M. The maximum current density and glucose sensitivity were 154.9 μA cm⁻² and 14.4 mA M⁻¹ cm⁻², respectively.     

Characterization of multi-walled carbon nanotube electrodes functionalized by electropolymerized tris(pyrrole-ether bipyridine) ruthenium (II)

We synthesized new electropolymerizable [Ru(bpy)_nL_m](PF₆)₂ (L = 4,4 bis(3-pyrrol-1-ylpropyloxy)bipyridyl) derivatives. The introduction of electron donating ether groups in the bipyridine ligand induced a negative shift of the Ru(III)/(II) redox couple. The electrochemical behavior of complex Ru1 (n = 2, m = 1) and complex Ru2 (n = 0, m = 3) were compared using platinum and Multi-Walled Carbon Nanotube (MWCNT) electrode. Higher polymerization yields and surface concentrations were obtained at MWCNT electrodes. Furthermore, MWCNT electrodes increase polymer permeability and decrease the charge trapping phenomenon involved in the oxidation and reduction of the polypyrrolic skeleton of the Ru(II) functionalized polymers.     

Cross-Linking Organic and Polyoxometalate Chemistries

This paper is a choral personal account on a longstanding and fruitful collaboration of organic and inorganic chemists to develop new hybrid polyoxometallic systems. .We explain our motivation and the context of our work that led to polyoxometalates with highly functional and reactive organic groups. Our approach yielded catalytically, biologically, and photochemically active systems.