An environment for knowledge discovery in biology

This paper describes a data mining environment for knowledge discovery in bioinformatics applications. The system has a generic kernel that implements the mining functions to be applied to input primary databases, with a warehouse architecture, of biomedical information. Both supervised and unsupervised classification can be implemented within the kernel and applied to data extracted from the primary database, with the results being suitably stored in a complex object database for knowledge discovery. The kernel also includes a specific high-performance library that allows designing and applying the mining functions in parallel machines. The experimental results obtained by the application of the kernel functions are reported. © 2003 Elsevier Ltd. All rights reserved.

Chemical transfer of warning information in non-injured fish

In this study we describe pacus, Piaractus mesopotamicus, detecting the presence of a predator by conspecific alerting pheromone. Moreover, we investigate whether this chemical information indicates the presence of a specific predator, or whether it indicates general disturbance. We exposed groups of pacus to the view of a predator fish (trahira, Hoplias malabaricus), a non-predator fish (piracanjuba, Brycon orbignyanus) or an aquarium without any fish (control), and then we transferred their water to isolated conspecifics. We set up six trials of each condition in which we analysed the dispersion and the distance from the visual stimulus in water-donor fish and the distance from the chemical stimulus in water-receiver pacus. This study showed that pacus visually identified the presence of another fish and recognised it as predator or non-predator. This is interpreted as an innate response. Such heterospecific detection affects the behaviour of pacus, which release chemicals that induce conspecifics to adopt a similar behavioural response. At least two chemicals might be involved, one of them possibly an alerting pheromone.

Measuring and analyzing color and texture information in anatomical leaf cross sections: An approach using computer vision to aid plant species identification

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Reliability of Web-Based Information in Inquiry Projects

This case study aims at identifying how a community of secondary school students selects web-based information and factors associated with the reliability of online reference sources during their collaborative inquiry (co-inquiry) projects. This study, conducted in a public secondary school in Brazil, focused on information literacy skills for collaborative open learning (colearning). The research is based on qualitative content analysis implemented on the online platform weSPOT. Although students are mindful of the importance of comparing different sources of information they seem not to be aware of reliability in online environments. Teacher's guidance is essential to support co-learners in developing competences, particularly related to critical thinking.

The utility of open-access biodiversity information in representing anurans in the Brazilian Atlantic Forest and Cerrado

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Estatuto biológico do processamento de informação mental

Raciocinando no contexto do programa neomecanicista para a Biologia, estudamos a natureza do processamento de informação no sistema vivo em geral, e no cérebro humano em particular, onde uma aplicação do modelo da Auto-Organização nos conduz à hipótese do Supercódigo. Este seria um programa mental, molecularmente codificado, responsável pelas competências inatas, como a competência lingüística. Fazemos também uma comparação entre nossa hipótese e a da Linguagem do Pensamento, proposta por Jerry Fodor.

Duration of spermatogenesis in the bullfrog (Lithobates catesbeianus)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Contributions and perspectives of chicken genomics in Brazil: from biological model to export commodity

Chicken is one of the most important sources of animal protein for human consumption, and breeding programmes have been responsible for constant improvements in production efficiency and product quality. Furthermore, chicken has largely contributed to fundamental discoveries in biology for the last 100 years. In this article we review recent developments in poultry genomics and their contribution to adding functional information to the already existing structural genomics, including the availability of the complete genome sequence, a comprehensive collection of mRNA sequences ( ESTs), microarray platforms, and their use to complement QTL mapping strategies in the identification of genes that underlie complex traits. Efforts of the Brazilian Poultry Genomics Programme in this area resulted in generation of a resource population, which was used for identification of Quantitative Trait Loci ( QTL) regions, generation of ESTs and candidate gene studies that contributed to furthering our understanding of the complex biological processes involved in growth and muscular development in chicken.

Postural control in children: Coupling to dynamic somatosensory information

The purpose of this investigation was to determine whether the coupling between dynamic somatosensory information and body sway is similar in children and adults. Thirty children (4-, 6-, and 8-year-olds) and 10 adults stood upright, with feet parallel, and lightly contacting the fingertip to a rigid metal plate that moved rhythmically at 0.2, 0.5, and 0.8 Hz. Light touch to the moving contact surface induced postural sway in all participants. The somatosensory stimulus produced a broadband frequency response in children, while the adult response was primarily at the driving frequency. Gain, as a function of frequency, was qualitatively the same in children and adults. Phase decreased less in 4-year-olds than other age groups, suggesting a weaker coupling to position information in the sensory stimulus. Postural sway variability was larger in children than adults. These findings suggest that, even as young as age 6, children show well-developed coupling to the sensory stimulus. However, unlike adults, this coupling is not well focused at the frequency specified by the somatosensory signal. Children may be unable to uncouple from sensory information that is less relevant to the task, resulting in a broadband response in their frequency spectrum. Moreover, higher sway variability may not result from the sensory feedback process, but rather from the children's underdeveloped ability to estimate an internal model of body orientation.

Students' preferred teaching techniques for biochemistry in biomedicine and medicine courses

The aim of this study was to investigate the students' preferred teaching techniques, such as traditional blackboard, power-point, or slide-projection, for biochemistry discipline in biomedicine and medicine courses from São Paulo State University, UNESP, Botucatu, São Paulo, Brazil. Preferences for specific topic and teaching techniques were determined from questionnaires on a Liquert scale from 1 to 5 (strongly disagree; disagree; neither agree, nor disagree; agree; strongly agree) distributed at the end of biochemistry discipline to 180 biomedical students (30 students/year) and 540 medical students (90 students/year), during the years 2000-2005. Despite of the different number of hours applied to the course topics for the two groups of students, the majority of undergraduates from biomedicine and medicine preferred metabolic topics. Although the perception of a medical student is expected to be different than that of a biomedical student, as the aims of the two programs are different, 92.4% of students from each course agreed or strongly agreed with the biochemistry topics, and 92.1% thought highly on this subject. The majority of students, a number of 139 undergraduates from biomedicine and 419 from medicine course, preferred traditional blackboard teaching than slide-projection, or power-point class. In conclusion, it is imperative that the health courses reflect on sophisticated technology and data presentation with high density of information in biochemistry discipline. The traditional classes with blackboard presentation were most favored by students from biomedicine and medicine courses. The use of students' preferred teaching techniques might turn biochemistry more easily understood for biomedical and medical students. © 2007 by The International Union of Biochemistry and Molecular Biology.

The role of prophage in plant-pathogenic bacteria

A diverse set of phage lineages is associated with the bacterial plant-pathogen genomes sequenced to date. Analysis of 37 genomes revealed 5,169 potential genes (approximately 4.3 Mbp) of phage origin, and at least 50 had no function assigned or are nonessential to phage biology. Some phytopathogens have transcriptionally active prophage genes under conditions that mimic plant infection, suggesting an association between plant disease and prophage transcriptional modulation. The role of prophages within genomes for cell biology varies. For pathogens such as Pectobacterium, Pseudomonas, Ralstonia, and Streptomyces, involvement of prophage in disease symptoms has been demonstrated. In Xylella and Xanthomonas, prophage activity is associated with genome rearrangements and strain differentiation. For other pathogens, prophage roles are yet to be established. This review integrates available information in a unique interface (http://propnav.esalq.usp.br) that may be assessed to improve research in prophage biology and its association with genome evolution and pathogenicity. © Copyright ©2013 by Annual Reviews. All rights reserved.

Cadmium stress antioxidant responses and root-to-shoot communication in grafted tomato plants

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A Learning Function for Parameter Reduction in Spiking Neural Networks with Radial Basis Function

Spiking neural networks - networks that encode information in the timing of spikes - are arising as a new approach in the artificial neural networks paradigm, emergent from cognitive science. One of these new models is the pulsed neural network with radial basis function, a network able to store information in the axonal propagation delay of neurons. Learning algorithms have been proposed to this model looking for mapping input pulses into output pulses. Recently, a new method was proposed to encode constant data into a temporal sequence of spikes, stimulating deeper studies in order to establish abilities and frontiers of this new approach. However, a well known problem of this kind of network is the high number of free parameters - more that 15 - to be properly configured or tuned in order to allow network convergence. This work presents for the first time a new learning function for this network training that allow the automatic configuration of one of the key network parameters: the synaptic weight decreasing factor.

Assessment of the potential genotoxic risk of medicinal Tamarindus indica fruit pulp extract using in vivo assays

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Dysglycemias in pregnancy: from diagnosis to treatment. Brazilian consensus statement

There is an urgent need to find consensus on screening, diagnosing and treating all degrees of DYSGLYCEMIA that may occur during pregnancies in Brazil, considering that many cases of DYSGLYCEMIA in pregnant women are currently not diagnosed, leading to maternal and fetal complications. For this reason the Brazilian Diabetes Society (SBD) and the Brazilian Federation of Gynecology and Obstetrics Societies (FEBRASGO), got together to introduce this proposal. We present here a joint consensus regarding the standardization of clinical management for pregnant women with any degree of Dysglycemia, on the basis of current information, to improve medical assistance and to avoid related complications of Dysglycemia in pregnancy to the mother and the fetus. This consensus aims to standardize the diagnosis among general practitioners, endocrinologists and obstetricians allowing the dissemination of information in basic health units, public and private services, that are responsible for screening, diagnosing and treating disglycemic pregnant patients.