ScriptLattes: an open-source knowledge extraction system from the Lattes platform

The Lattes platform is the major scientific information system maintained by the National Council for Scientific and Technological Development (CNPq). This platform allows to manage the curricular information of researchers and institutions working in Brazil based on the so called Lattes Curriculum. However, the public information is individually available for each researcher, not providing the automatic creation of reports of several scientific productions for research groups. It is thus difficult to extract and to summarize useful knowledge for medium to large size groups of researchers. This paper describes the design, implementation and experiences with scriptLattes: an open-source system to create academic reports of groups based on curricula of the Lattes Database. The scriptLattes system is composed by the following modules: (a) data selection, (b) data preprocessing, (c) redundancy treatment, (d) collaboration graph generation among group members, (e) research map generation based on geographical information, and (f) automatic report creation of bibliographical, technical and artistic production, and academic supervisions. The system has been extensively tested for a large variety of research groups of Brazilian institutions, and the generated reports have shown an alternative to easily extract knowledge from data in the context of Lattes platform. The source code, usage instructions and examples are available at http://scriptlattes.sourceforge.net/.

The genome of the blood fluke Schistosoma mansoni

Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affects 210 million people in 76 countries. Here we present analysis of the 363 megabase nuclear genome of the blood fluke. It encodes at least 11,809 genes, with an unusual intron size distribution, and new families of micro-exon genes that undergo frequent alternative splicing. As the first sequenced flatworm, and a representative of the Lophotrochozoa, it offers insights into early events in the evolution of the animals, including the development of a body pattern with bilateral symmetry, and the development of tissues into organs. Our analysis has been informed by the need to find new drug targets. The deficits in lipid metabolism that make schistosomes dependent on the host are revealed, and the identification of membrane receptors, ion channels and more than 300 proteases provide new insights into the biology of the life cycle and new targets. Bioinformatics approaches have identified metabolic chokepoints, and a chemogenomic screen has pinpointed schistosome proteins for which existing drugs may be active. The information generated provides an invaluable resource for the research community to develop much needed new control tools for the treatment and eradication of this important and neglected disease.

HiPP: A Novel Hierarchical Point Placement Strategy and its Application to the Exploration of Document Collections

Point placement strategies aim at mapping data points represented in higher dimensions to bi-dimensional spaces and are frequently used to visualize relationships amongst data instances. They have been valuable tools for analysis and exploration of data sets of various kinds. Many conventional techniques, however, do not behave well when the number of dimensions is high, such as in the case of documents collections. Later approaches handle that shortcoming, but may cause too much clutter to allow flexible exploration to take place. In this work we present a novel hierarchical point placement technique that is capable of dealing with these problems. While good grouping and separation of data with high similarity is maintained without increasing computation cost, its hierarchical structure lends itself both to exploration in various levels of detail and to handling data in subsets, improving analysis capability and also allowing manipulation of larger data sets.

Chicken skeletal muscle-associated macroarray for gene discovery

Macro- and microarrays are well-established technologies to determine gene functions through repeated measurements of transcript abundance. We constructed a chicken skeletal muscle-associated array based on a muscle-specific EST database, which was used to generate a tissue expression dataset of similar to 4500 chicken genes across 5 adult tissues (skeletal muscle, heart, liver, brain, and skin). Only a small number of ESTs were sufficiently well characterized by BLAST searches to determine their probable cellular functions. Evidence of a particular tissue-characteristic expression can be considered an indication that the transcript is likely to be functionally significant. The skeletal muscle macroarray platform was first used to search for evidence of tissue-specific expression, focusing on the biological function of genes/transcripts, since gene expression profiles generated across tissues were found to be reliable and consistent. Hierarchical clustering analysis revealed consistent clustering among genes assigned to 'developmental growth', such as the ontology genes and germ layers. Accuracy of the expression data was supported by comparing information from known transcripts and tissue from which the transcript was derived with macroarray data. Hybridization assays resulted in consistent tissue expression profile, which will be useful to dissect tissue-regulatory networks and to predict functions of novel genes identified after extensive sequencing of the genomes of model organisms. Screening our skeletal-muscle platform using 5 chicken adult tissues allowed us identifying 43 'tissue-specific' transcripts, and 112 co-expressed uncharacterized transcripts with 62 putative motifs. This platform also represents an important tool for functional investigation of novel genes; to determine expression pattern according to developmental stages; to evaluate differences in muscular growth potential between chicken lines, and to identify tissue-specific genes.

PK/DB: database for pharmacokinetic properties and predictive in silico ADME models

The study of pharmacokinetic properties (PK) is of great importance in drug discovery and development. In the present work, PK/DB (a new freely available database for PK) was designed with the aim of creating robust databases for pharmacokinetic studies and in silico absorption, distribution, metabolism and excretion (ADME) prediction. Comprehensive, web-based and easy to access, PK/DB manages 1203 compounds which represent 2973 pharmacokinetic measurements, including five models for in silico ADME prediction (human intestinal absorption, human oral bioavailability, plasma protein binding, bloodbrain barrier and water solubility).

Natural products biological screening and ligand-based virtual screening for the discovery of new antileishmanial agents

In the course of our research program to discover novel antileishmanial agents, a biological screening of natural products against Leishmania major promastigotes allowed the identification of a furoquinoline alkaloid (1) and a furanocoumarin (2) as new hits. Subsequently, an integrated ligand-based virtual screening approach was employed to search for new antileishmanial compounds using these naturally occurring molecules as templates. Fourteen out of 40 compounds selected from a database of about 800,000 compounds (extracted from ZINC, a free database for virtual screening) were experimentally confirmed to possess significant in vitro antileishmanial properties. The application of ligand-based virtual screening as a complementary approach to experimental natural product screening was a useful strategy to facilitate the identification of new promising lead candidates.

Elementary Petri net inside RFID distributed database (PNRD)

Usually, a Petri net is applied as an RFID model tool. This paper, otherwise, presents another approach to the Petri net concerning RFID systems. This approach, called elementary Petri net inside an RFID distributed database, or PNRD, is the first step to improve RFID and control systems integration, based on a formal data structure to identify and update the product state in real-time process execution, allowing automatic discovery of unexpected events during tag data capture. There are two main features in this approach: to use RFID tags as the object process expected database and last product state identification; and to apply Petri net analysis to automatically update the last product state registry during reader data capture. RFID reader data capture can be viewed, in Petri nets, as a direct analysis of locality for a specific transition that holds in a specific workflow. Following this direction, RFID readers storage Petri net control vector list related to each tag id is expected to be perceived. This paper presents PNRD cornerstones and a PNRD implementation example in software called DEMIS Distributed Environment in Manufacturing Information Systems.

Integration of Ligand- and Target-Based Virtual Screening for the Discovery of Cruzain Inhibitors

A myriad of methods are available for virtual screening of small organic compound databases. In this study we have successfully applied a quantitative model of consensus measurements, using a combination of 3D similarity searches (ROCS and EON), Hologram Quantitative Structure Activity Relationships (HQSAR) and docking (FRED, FlexX, Glide and AutoDock Vina), to retrieve cruzain inhibitors from collected databases. All methods were assessed individually and then combined in a Ligand-Based Virtual Screening (LBVS) and Target-Based Virtual Screening (TBVS) consensus scoring, using Receiving Operating Characteristic (ROC) curves to evaluate their performance. Three consensus strategies were used: scaled-rank-by-number, rank-by-rank and rank-by-vote, with the most thriving the scaled-rank-by-number strategy, considering that the stiff ROC curve appeared to be satisfactory in every way to indicate a higher enrichment power at early retrieval of active compounds from the database. The ligand-based method provided access to a robust and predictive HQSAR model that was developed to show superior discrimination between active and inactive compounds, which was also better than ROCS and EON procedures. Overall, the integration of fast computational techniques based on ligand and target structures resulted in a more efficient retrieval of cruzain inhibitors with desired pharmacological profiles that may be useful to advance the discovery of new trypanocidal agents.

Knowledge and attitude of parents or caretakers regarding transmissibility os caries disease

Dental caries is a transmissible infectious disease in which mutans streptococci are generally considered to be the main etiological agents. Although the transmissibility of dental caries is relatively well established in the literature, little is known whether information regarding this issue is correctly provided to the population. The present study aimed at evaluating, by means of a questionnaire, the knowledge and usual attitude of 640 parents and caretakers regarding the transmissibility of caries disease. Most interviewed adults did not know the concept of dental caries being an infectious and transmissible disease, and reported the habit of blowing and tasting food, sharing utensils and kissing the children on their mouth. 372 (58.1%) adults reported that their children had already been seen by a dentist, 264 (41.3%) answered that their children had never gone to a dentist, and 4 (0.6%) did not know. When the adults were asked whether their children had already had dental caries, 107 (16.7%) answered yes, 489 (76.4%) answered no, and 44 (6.9%) did not know. Taken together, these data reinforce the need to provide the population with some important information regarding the transmission of dental caries in order to facilitate a more comprehensive approach towards the prevention of the disease.

Encefalite no litoral paulista: a emergência da epidemia e a reação da mídia impressa

No litoral sul do estado de São Paulo, ocorreu uma epidemia de encefalite pelo arbovírus Rocio de 1975 a 1978. As altas taxas de morbidade e mortalidade causaram impacto social. Neste trabalho, o objetivo foi apresentar um estudo sobre como a mídia impressa relatou os acontecimentos sociais relacionados ao surgimento da epidemia no primeiro semestre de 1975. Reportagens sobre a epidemia no litoral sul foram obtidas do banco de dados dos jornais A Tribuna, Folha de S.Paulo e Jornal da Tarde. Foram analisadas as notícias até o mês de julho de 1975, fase inicial e de maior impacto da epidemia. Com a identificação de casos de encefalite, de causa desconhecida, a Secretaria de Estado da Saúde desaconselhou a ida de turistas para o litoral, utilizando a mídia como veículo de divulgação. Diante das notícias, ocorreu a fuga dos turistas e, consequentemente, a crise do comércio. Observou-se a revolta dos comerciantes, que geraram embates contra a mídia, no que tange à forma de divulgação da epidemia. Alguns prefeitos alegaram inveracidade de notícias publicadas. A proibição feita pelas autoridades sanitárias foi relatada pela mídia de forma abrangente, englobando sujeitos envolvidos nesse discurso. Assim, foram reveladas ao público as tensões geradas entre os detentores do conhecimento científico e o poder econômico local. Os jornais realizaram cobertura abrangente, abordando vários temas, entretanto disseminaram incertezas e fizeram uso de imagens sensacionalistas, além de desarticular acontecimentos biológicos e sociais. Os temas chegaram aos leitores de forma fragmentada e com sentidos sociais comprometidos.

Validade científica de conhecimento epidemiológico gerado com base no estudo Saúde Bucal Brasil 2003

Problematiza-se a afirmação de que não são válidas as estimativas sobre as condições de saúde bucal da população brasileira geradas pelo SB Brasil 2003. Criticam-se os elementos que pretendem sustentar esse ponto de vista com base apenas em conceitos estatísticos, sem prova empírica. Identificam-se reduções decorrentes da abordagem epistemocêntrica que recusa peremptoriamente outras formas de conhecimento e não reconhece o caráter multidisciplinar da epidemiologia. Reconstituem-se informações sobre a realização do levantamento e seu impacto na produção de conhecimento. Faz-se uma analogia entre ciência e arte, argumentando-se que, nas imagens obtidas por ambas, os saberes gerados a partir do objeto cognoscível assumem feições variadas e, portanto, o reconhecimento de sua validade requer amplo domínio do objeto e operações com adequados critérios de valor. Conclui-se pela cientificidade, validade e relevância da produção acadêmica desenvolvida a partir da base de dados do levantamento SB Brasil 2003.

Kerteszia subgenus of Anopheles associated with the Brazilian Atlantic rainforest: current knowledge and future challenges

Background: The Atlantic rainforest ecosystem, where bromeliads are abundant, provides an excellent environment for Kerteszia species, because these anophelines use the axils of those plants as larval habitat. Anopheles (K.) cruzii and Anopheles (K.) bellator are considered the primary vectors of malaria in the Atlantic forest. Although the incidence of malaria has declined in some areas of the Atlantic forest, autochthonous cases are still registered every year, with Anopheles cruzii being considered to be a primary vector of both human and simian Plasmodium. Methods: Recent publications that addressed ecological aspects that are important for understanding the involvement of Kerteszia species in the epidemiology of malaria in the Atlantic rainforest in the Neotropical Region were analysed. Conclusion: The current state of knowledge about Kerteszia species in relation to the Atlantic rainforest ecosystem was discussed. Emphasis was placed on ecological characteristics related to epidemiological aspects of this group of mosquitoes. The main objective was to investigate biological aspects of the species that should be given priority in future studies

Students' collective knowledge construction in the virtual learning environment ""ToLigado - your school interactive newspaper""

Introduction. The ToLigado Project - Your School Interactive Newspaper is an interactive virtual learning environment conceived, developed, implemented and supported by researchers at the School of the Future Research Laboratory of the University of Sao Paulo, Brazil. Method. This virtual learning environment aims to motivate trans-disciplinary research among public school students and teachers in 2,931 schools equipped with Internet-access computer rooms. Within this virtual community, students produce collective multimedia research documents that are immediately published in the portal. The project also aims to increase students' autonomy for research, collaborative work and Web authorship. Main sections of the portal are presented and described. Results. Partial results of the first two years' implementation are presented and indicate a strong motivation among students to produce knowledge despite the fragile hardware and software infrastructure at the time. Discussion. In this new environment, students should be seen as 'knowledge architects' and teachers as facilitators, or 'curiosity managers'. The ToLigado portal may constitute a repository for future studies regarding student attitudes in virtual learning environments, students' behaviour as 'authors', Web authorship involving collective knowledge production, teachers' behaviour as facilitators, and virtual learning environments as digital repositories of students' knowledge construction and social capital in virtual learning communities.

Influence of the technological innovation degree on knowledge creation: Evidence from a Brazilian firm

The aim of this paper is to analyze the process of knowledge creation when developing high technology products in projects having various innovation degrees. The main contribution to the literature is the systematization of an approach to analyze knowledge creation during the product innovation process. Three innovation projects developed by a company specialized in industrial automation systems were investigated using case studies. The knowledge creation processes, which took place in these three projects, were analyzed comparatively. As a distinctive result of this paper, the main features of the knowledge creation processes influenced by a degree of technological innovation are identified.