Pipeline for macro- and microarray analyses

The pipeline for macro- and microarray analyses (PMmA) is a set of scripts with a web interface developed to analyze DNA array data generated by array image quantification software. PMmA is designed for use with single- or double-color array data and to work as a pipeline in five classes (data format, normalization, data analysis, clustering, and array maps). It can also be used as a plugin in the BioArray Software Environment, an open-source database for array analysis, or used in a local version of the web service. All scripts in PMmA were developed in the PERL programming language and statistical analysis functions were implemented in the R statistical language. Consequently, our package is a platform-independent software. Our algorithms can correctly select almost 90% of the differentially expressed genes, showing a superior performance compared to other methods of analysis. The pipeline software has been applied to 1536 expressed sequence tags macroarray public data of sugarcane exposed to cold for 3 to 48 h. PMmA identified thirty cold-responsive genes previously unidentified in this public dataset. Fourteen genes were up-regulated, two had a variable expression and the other fourteen were down-regulated in the treatments. These new findings certainly were a consequence of using a superior statistical analysis approach, since the original study did not take into account the dependence of data variability on the average signal intensity of each gene. The web interface, supplementary information, and the package source code are available, free, to non-commercial users at http://ipe.cbmeg.unicamp.br/pub/PMmA.

Object-oriented Programming Applied to the Development of Structural Analysis and Optimization Software

This paper presents the development of a two-dimensional interactive software environment for structural analysis and optimization based on object-oriented programming using the C++ language. The main feature of the software is the effective integration of several computational tools into graphical user interfaces implemented in the Windows-98 and Windows-NT operating systems. The interfaces simplify data specification in the simulation and optimization of two-dimensional linear elastic problems. NURBS have been used in the software modules to represent geometric and graphical data. Extensions to the analysis of three-dimensional problems have been implemented and are also discussed in this paper.

Vocalization data mining for estimating swine stress conditions

This study aimed to identify differences in swine vocalization pattern according to animal gender and different stress conditions. A total of 150 barrow males and 150 females (Dalland® genetic strain), aged 100 days, were used in the experiment. Pigs were exposed to different stressful situations: thirst (no access to water), hunger (no access to food), and thermal stress (THI exceeding 74). For the control treatment, animals were kept under a comfort situation (animals with full access to food and water, with environmental THI lower than 70). Acoustic signals were recorded every 30 minutes, totaling six samples for each stress situation. Afterwards, the audios were analyzed by Praat® 5.1.19 software, generating a sound spectrum. For determination of stress conditions, data were processed by WEKA® 3.5 software, using the decision tree algorithm C4.5, known as J48 in the software environment, considering cross-validation with samples of 10% (10-fold cross-validation). According to the Decision Tree, the acoustic most important attribute for the classification of stress conditions was sound Intensity (root node). It was not possible to identify, using the tested attributes, the animal gender by vocal register. A decision tree was generated for recognition of situations of swine hunger, thirst, and heat stress from records of sound intensity, Pitch frequency, and Formant 1.

Uso do software Estradas para determinação do espaçamento entre desaguadouros em estradas não pavimentadas do interior de Goiás

Estradas não pavimentadas correspondem a aproximadamente 90% da malha rodoviária brasileira. Estas, na maioria das vezes, são construídas sem a realização de estudos prévios, estando sujeitas a vários tipos de problemas. Um dos principais fatores de deterioração dessas vias é a ineficiência do sistema de drenagem. Neste trabalho simulou-se o espaçamento entre desaguadouros em estradas não pavimentadas, utilizando-se um software desenvolvido com base num modelo matemático de dimensionamento de sistemas de drenagem em estradas não pavimentadas. Utilizaram-se valores de erodibilidade, tensão crítica de cisalhamento e massa específica para diferentes solos de estradas, localizadas no Estado de Goiás. Simularam-se cenários considerando alterações na declividade (1, 5, 10 e 15%) e na seção transversal do canal com relações entre altura e largura de 1:1, 1:2, 1:5 e 1:10. O modelo respondeu sensivelmente às alterações na declividade, na seção transversal do canal e nas de resistência do solo. Os espaçamentos obtidos indicaram que, estradas com declividades inferiores a 5%, mesmo com elevados valores de erodibilidade permitiram espaçamentos viáveis em aspectos construtivos. No entanto, para as declividades de 10 e 15%, os espaçamentos, na maioria dos casos, apresentaram dimensões reduzidas, tornando-se impraticáveis, sendo necessário, nestes casos, proteção do canal ou alteração de suas características hidráulicas.

Selection of anthracnose resistant common beans using detached leaves in partially controlled environment

The objectives of this study were to evaluate the possibility of selecting anthracnose resistant common bean plants using detached primary leaves in partially controlled environment of a greenhouse and identify differences in the reaction of genotypes to anthracnose. The common bean cultivars Ouro Negro, OuroVermelho, ManteigãoFosco 11, Rudá, Rudá-R, VP8, BRSMG Madrepérola, Pérola, MeiaNoite and BRSMG Talismãwere characterizedfor resistance to the races 65, 81 and 453 of Colletotrichum lindemuthianum and the method of detached primary leaves was compared to the method with the traditional inoculation of plants at the phenological stage V2. The lines Rudá, Rudá-R and Pérola were inoculated with the races 65 and 453 of C. lindemuthianum, aiming to assess the rate of coincidence of anthracnose severity by both inoculation methods. In general, the two methods presented similar results for the reaction of the cultivars. The use of detached primary leaves of common bean plants in the partially controlled environment was feasible for selection of plants resistant to anthracnose and has the advantages of low-needed infrastructure and reduction of resources, space and time.

Is the International Business Environment the actual context for international business research?

The International Business Environment (IBE) has been argued to be the essential context for international business (IB) studies and the distinguishing factor from other management studies and studies of large enterprises. Two content analysis show that many papers published in top tier IB journals either lack reference to any dimension of the IBE or tend to be uni-or bi-dimensional when addressing the IBE; it is not a surprise that the cultural dimension is the most often used. We suggest that: (a) there is need to developed more uni-and multi-dimensional environmental constructs; (b) a more holistic view of the IBE provides richer insights on the actual complexity underlying IB research. Future studies that provide more comprehensive models of the IBE that overcome the usual broad classifications of the international environment as undefined and uncontrollable factors are warranted to advance conceptual and empirical research.

Dinâmica da acumulação de capacidades inovadoras: evidências de empresas de software no Rio de janeiro e em São Paulo

São escassos estudos sobre a dinâmica da acumulação de capacidades inovadoras. Este artigo examina o tema em oito empresas de software em São Paulo e Rio de Janeiro, encontrando: diferenças inter e intraempresariais em termos da direção e taxa de acumulação de capacidade para funções tecnológicas específicas; acúmulo de capacidade tecnológica mais rápido em empresas mais jovens; e decréscimo das taxas de acumulação tecnológica à medida que as empresas se aproximam de níveis mais inovadores de capacidades, demonstrando a potencialidade para aceleração do processo. Tais evidências são relevantes para o entendimento da acumulação tecnológica e fornecem uma noção do tempo necessário para se obterem benefícios de esforços de aprendizagem e construção de capacidade inovadora.

Atratividade de projetos de software livre: importância teórica e estratégias para administração

Milhares de Projetos de Software Livre (PSL) foram e continuam sendo criados na Internet. Esse cenário aumenta as oportunidades de colaboração tanto quanto acirra a concorrência por usuários e contribuidores, que elevariam esses projetos a níveis superiores aos que seriam alcançados por seus fundadores sozinhos. E dado que o aprimoramento por meio de colaboração é o principal objetivo dos fundadores de PSL, a importância de entender e administrar a capacidade de atrair usuários e contribuidores fica estabelecida. Para auxiliar pesquisadores e fundadores nesse desafio, o conceito de atratividade é introduzido neste artigo, que desenvolve um ferramental teórico-gerencial sobre as causas, indicadores e consequências da atratividade, viabilizando sua administração estratégica.

Knowledge cities: a taxonomy for analyzing software and information service clusters

Software and information services (SIS) have become a field of increasing opportunities for international trade due to the worldwide diffusion of a combination of technological and organizational innovations. In several regions, the software industry is organized in clusters, usually referred to as "knowledge cities" because of the growing importance of knowledge-intensive services in their economy. This paper has two primary objectives. First, it raises three major questions related to the attractiveness of different cities in Argentina and Brazil for hosting software companies and to their impact on local development. Second, a new taxonomy is proposed for grouping clusters according to their dominant business segment, ownership pattern and scope of operations. The purpose of this taxonomy is to encourage further studies and provide an exploratory analytical tool for analyzing software clusters.

PROPOSTA DE INVESTIGAÇÃO SOBRE O USO DE SOFTWARE NO SUPORTE À INOVAÇÃO EM SERVIÇOS

RESUMOEste artigo examina os objetivos, instrumentos e características das inovações habilitadas por Tecnologias da Informação e Comunicação (TICs) no Brasil, enfatizando as tecnologias utilizadas, os canais habilitados pelas ferramentas digitais, os processos de aprendizado para inovação e as mudanças organizacionais necessárias para o uso de ferramentas avançadas. A metodologia consiste na adaptação de taxonomias existentes para os propósitos específicos da pesquisa e a realização de uma pesquisa de campo com o auxílio do software Atlas.ti. Os resultados mostram que as inovações habilitadas por TIC não constituem eventos isolados e pontuais, uma vez que alteram processos, formas de relacionamento com parceiros e clientes, e requerem uma maior integração de funções organizacionais. Importantes diferenças foram observadas em função do porte da empresa, da internacionalização das operações, da capacitação técnica e do grau de acesso a ferramentas proprietárias.

Studies on mosquitoes (Diptera: Culicidae) and anthropic environment: 1- Parity of blood seeking Anopheles (Kerteszia) in South-Eastern Brazil

Populations of Anopheles (Kerteszia) were sampled fortnightly over a one-year period (August 1991 to July 1992) at Ribeira Valley, S. Paulo State, Brazil. Indoor and outdoor collections were made on human bait at evening crepuscular period. The Polovodova technique for age grading was applied to 3,501 females of Anopheles cruzii and to 416 females of An. bellator. That sample represented 34.4% of the total number of mosquitoes collected. The most abundant species found was An. cruzii. However, An. bellator showed an endophagy that was almost three times greater than that of An. cruzii. The overall parous rate was 25.4% and uniparity was practically dominant one. A proportion of 26.9% of An. cruzii and 12.0% of An. bellator were found to be uniparous. Only three outdoor females of the former species (0.1%) showed biparity. Parity of An. cruzii was higher in females caught outdoors than in those caught indoors. Nevertheless, 497 nulliparous females examined (417 cruzii and 80 bellator) had ovaries that had advanced to Christophers and Mer stages III to V. These results imply that these females had already practised hematophagy. Relating these results to those from the parous females, a high statistical significance was found, leading to the conclusion that gonothophic discordance is a common pattern among these anophelines. Further, these results obtained with human bait catches strongly suggest that nearly 38.0% of these host-seeking females had already taken at least one previous blood-meal. So it is possible that enough time could thus be available for the plasmodian development in the vectors.

Studies on mosquitoes (Diptera: Culicidae) and anthropic environment: 2 - Immature stages research at a rice irrigation system location in South-Eastern Brazil

A relation between a rice irrigation system and mosquito breeding was established in a study undertaken at the Ribeira Valley Experimental Station, from January through December 1992. Flooding favoured Anopheles (Nyssorhynchus) and Culex (Melanoconion) species, while empty paddies condition were propitious to Aedes scapularis and Culex (Culex) species. Compared with a more primitive area of the same region, several species showed high a degree of adaptation to the anthropic environment. Among them, Anopheles albitarsis, a potential malaria vector that breeds in the irrigation system, has shown immature stage production thirteen times higher than at the natural breeding sites. In addition, Ae. scapularis, An. oswaldoi, Cx. bastagarius, and Cx. chidesteri presented high levels of synanthropy.

Studies on mosquitoes (Diptera: Culicidae) and anthropic environment: 3- Survey of adult stages at the rice irrigation system and the emergence of Anopheles albitarsis in South-Eastern, Brazil

A study of adult Culicidae ecology was carried out from January 1992 through January 1993 at the rice irrigation system of the Ribeira Valley Experimental Station. The adaptation of Anopheles albitarsis to the anthropic environment became evident through the adult collections made at its various habitats represented by the irrigation system and the edge of the residual pond, as well as at those made within the local patchy residual woods. Other potential disease vectors were prevalent in the irrigated system too. There were Aedes scapularis, Culex nigripalpus and Cx. ribeirensis that were collected at various habitats. Remarkable differences among their prevalences were obtained such as between the natural forest and anthropic environments. In the former An. albitarsis was practically non-existent, thus suggesting that it might be considered as eusynathropic. As the populations of other species seemed to increase in the anthropic environment, they may be regarded as hemisynanthropes. Observations suggest the hypothesis that the development of irrigated land may be a factor in the emergence of An. albitarsis, and some other species, as well as the possibility of an increase in the transmission of mosquito-borne diseases such as malaria.

Studies on mosquitoes (Diptera: Culicidae) and anthropic environment: 4 - Survey of resting adults and synanthropic behaviour in South-Eastern, Brazil

Resting adults Culicidae were collected from January 1992 through January 1993 in several habitats of the Ribeira Valley region. The diversity of species found among them suggested that the vegetation remaining within human settlements favored the survival and the population increase of some mosquitoes. Among there are: Ae. scapularis, Ae. serratus, Cx. (Culex), Cx. nigripalpus and Cx. (Melanoconion) such as Cx. ribeirensis. That preservation role may be attributed to the rearing of livestock and the consequent increase in the number of blood sources. These species may be classified as hemisynanthropes and Cx. oedipus apparently evolving to the eusynanthropic status. On the other hand, An. cruzii showed an asynanthropic behaviour, with a low degree of survival in the modified human environment. Epidemiological implications of the data are mentioned.

Studies on mosquitoes (Diptera: Culicidae) and anthropic environment: 6 - Breeding in empty conditions of rice fields in South-Eastern Brazil

Studies on culicid breeding in empty rice fields were carried out during the cultivation cycle from May to November 1993. This period corresponded to stages 1 and 2, when empty conditions prevailed. Breeding occurred in stage 1 and the first part of stage 2, corresponding respectively to fallow uncultivated and ploughing situations. No breeding was found to take place during the second part of stage 2 when transient floods and harrowing occurred. The predominant species were Aedes scapularis, Culex nigripalpus and Cx. mollis. The Pilosus Group of Culex (Melanoconion) was found at lower densities. Some epidemiological considerations are presented.