Plant-antivenom: Database of anti-venom medicinal plants

Plant-antivenom is a computational Websystem about medicinal plants with anti-venom properties. The system consists of a database of these plants, including scientific publications on this subject and amino acid sequences of active principles from venomous animals. The system relates these data allowing their integration through different search applications. For the development of the system, the first surveys were conducted in scientific literature, allowing the creation of a publication database in a library for reading and user interaction. Then, classes of categories were created, allowing the use of tags and the organization of content. This database on medicinal plants has information such as family, species, isolated compounds, activity, inhibited animal venoms, among others. Provision is made for submission of new information by registered users, by the use of wiki tools. Content submitted is released in accordance to permission rules defined by the system. The database on biological venom protein amino acid sequences was structured from the essential information from National Center for Biotechnology Information (NCBI). Plant-antivenom`s interface is simple, contributing to a fast and functional access to the system and the integration of different data registered on it. Plant-antivenom system is available on the Internet at http://gbi.fmrp.usp.br/plantantivenom.

The Object Management Group Ontology Definition Metamodel

Report of a submission being made to a major international software engineering standards group, the Object Management Group which ties together OMG standards with World-Wide Web Consortium and International Standards Organization standards. Major industry bodies including IBM are collaborating, and the submission has the support of 24 companies. OMG, W3C and ISO standards strongly influence the industry, especially in combination. Colomb was a major contributor, responsible for 30% of the submission, and the primary author of the paper.

MDA-based re-engineering with Object-Z

This paper describes a practical application of MDA and reverse engineering based on a domain-specific modelling language. A well defined metamodel of a domain-specific language is useful for verification and validation of associated tools. We apply this approach to SIFA, a security analysis tool. SIFA has evolved as requirements have changed, and it has no metamodel. Hence, testing SIFA’s correctness is difficult. We introduce a formal metamodelling approach to develop a well-defined metamodel of the domain. Initially, we develop a domain model in EMF by reverse engineering the SIFA implementation. Then we transform EMF to Object-Z using model transformation. Finally, we complete the Object-Z model by specifying system behavior. The outcome is a well-defined metamodel that precisely describes the domain and the security properties that it analyses. It also provides a reliable basis for testing the current SIFA implementation and forward engineering its successor.

An integrated database on ticks and tick-borne zoonoses in the tropics and subtropics with special reference to developing and emerging countries

Tick-borne zoonoses (TBZ) are emerging diseases worldwide. A large amount of information (e.g. case reports, results of epidemiological surveillance, etc.) is dispersed through various reference sources (ISI and non-ISI journals, conference proceedings, technical reports, etc.). An integrated database-derived from the ICTTD-3 project (http://www.icttd.nl)-was developed in order to gather TBZ records in the (sub-)tropics, collected both by the authors and collaborators worldwide. A dedicated website (http://www.tickbornezoonoses.org) was created to promote collaboration and circulate information. Data collected are made freely available to researchers for analysis by spatial methods, integrating mapped ecological factors for predicting TBZ risk. The authors present the assembly process of the TBZ database: the compilation of an updated list of TBZ relevant for (sub-)tropics, the database design and its structure, the method of bibliographic search, the assessment of spatial precision of geo-referenced records. At the time of writing, 725 records extracted from 337 publications related to 59 countries in the (sub-)tropics, have been entered in the database. TBZ distribution maps were also produced. Imported cases have been also accounted for. The most important datasets with geo-referenced records were those on Spotted Fever Group rickettsiosis in Latin-America and Crimean-Congo Haemorrhagic Fever in Africa. The authors stress the need for international collaboration in data collection to update and improve the database. Supervision of data entered remains always necessary. Means to foster collaboration are discussed. The paper is also intended to describe the challenges encountered to assemble spatial data from various sources and to help develop similar data collections.

Influence of differently oriented dentin surfaces and the regional variation of specimens on adhesive layer thickness and bond strength

Statement of the Problem: Adhesive systems can spread differently onto a substrate and, consequently, influence bonding. Purpose: The purpose of this study was to evaluate the effect of differently oriented dentin surfaces and the regional variation of specimens on adhesive layer thickness and microtensile bond strength (MTBS). Materials and Methods: Twenty-four molars were sectioned mesiodistally to expose flat buccal and lingual halves. Standardized drop volumes of adhesive systems (Single Bond [SB] and Prime & Bond 2.1 [PB2.1]) were applied to dentin according to the manufacturer`s instructions. Teeth halves were randomly divided into groups: 1A-SB/parallel to gravity; 1B-SB/perpendicular to gravity; 2A-PB2.1/parallel to gravity; and 2B-PB2.1/perpendicular to gravity. The bonded assemblies were stored in 37 degrees C distilled water for 24 hours and then sectioned to obtain dentin sticks (0.8 mm(2)). The adhesive layer thickness was determined in a light microscope (x200), and after 48 hours the specimens were subjected to MTBS test. Data were analyzed by one-way and two-way analysis of variance and Student-Newman-Keuls tests. Results: Mean values (MPa +/- SD) of MTBS were: 39.1 +/- 12.9 (1A); 32.9 +/- 12.4 (1B); 52.9 +/- 15.2 (2A); and 52.3 +/- 16.5 (2B). The adhesive systems` thicknesses (mu m +/- SD) were: 11.2 +/- 2.9 (1A); 18.1 +/- 7.3 (1B); 4.2 +/- 1.8 (2A); and 3.9 +/- 1.3 (2B). No correlation between bond strength and adhesive layer thickness for both SB and PB2.1 (r = -0.224, p = 0.112 and r = 0.099, p = 0.491, respectively) was observed. Conclusions: The differently oriented dentin surfaces and the regional variation of specimens on the adhesive layer thickness are material-dependent. These variables do not influence the adhesive systems` bond strength to dentin. CLINICAL SIGNIFICANCE Adhesive systems have different viscosities and spread differently onto a substrate, influencing the bond strength and also the adhesive layer thickness. Adhesive thickness does not influence dentin bond strength, but it may impair adequate solvent evaporation, polymer conversion, and may also determine water sorption and adhesive degradation over time. In the literature, many studies have shown that the adhesive layer is a permeable membrane and can fail over timebecause ofits continuous plasticizing and degradation when in contact with water. Therefore, avoiding thick adhesive layers may minimize these problems and provide long-term success for adhesive restorations.