ProbFAST: Probabilistic Functional Analysis System Tool

Background: The post-genomic era has brought new challenges regarding the understanding of the organization and function of the human genome. Many of these challenges are centered on the meaning of differential gene regulation under distinct biological conditions and can be performed by analyzing the Multiple Differential Expression (MDE) of genes associated with normal and abnormal biological processes. Currently MDE analyses are limited to usual methods of differential expression initially designed for paired analysis. Results: We proposed a web platform named ProbFAST for MDE analysis which uses Bayesian inference to identify key genes that are intuitively prioritized by means of probabilities. A simulated study revealed that our method gives a better performance when compared to other approaches and when applied to public expression data, we demonstrated its flexibility to obtain relevant genes biologically associated with normal and abnormal biological processes. Conclusions: ProbFAST is a free accessible web-based application that enables MDE analysis on a global scale. It offers an efficient methodological approach for MDE analysis of a set of genes that are turned on and off related to functional information during the evolution of a tumor or tissue differentiation. ProbFAST server can be accessed at http://gdm.fmrp.usp.br/probfast.

Sentidos de biblioteca escolar no discurso da Ciência da Informação

This paper approaches the meaning of school library through a multidisciplinary perspective including the Information Science, the French Discourse Analysis and Education. It aims to understand how the imaginary about this institution is constructed, in the area of Information Science, and to reflect on how this symbol is influenced by the social, historical and ideological conditions of discourse production and by memory. To develop these questions, first of all, it accomplishes a brief review of the literature concerning the French Discourse Analysis; then it analyzes discourses about the school library in nineteen scientific documents ( articles and works presented at scientific events), and also the different meanings of this information unit, its objectives and its ways of constituting the social imaginary. It is concluded that the information professionals could and should collaborate to the spreading of new practices and meaning in the school library.

Sociedade e gestão do risco: o aquífero Guarani em Ribeirão Preto-SP, Brasil

Contemporary society creates risks of all kinds, changing the meaning of this term. Although it may be associated with natural hazards, it gradually assumes a stronger relation with human actions, especially due to the use of technology. The use of land for agricultural and urban activities creates the possibility of contamination in the recharge area of the Guarani aquifer in the municipality of Ribeirao Preto, state of Sao Paulo, Brazil. This city is one of the most important in the state with high economic development. Besides this, it is located in the recharge area of the main reservoir of underground water of South Cone. This paper aims to discuss the management of groundwater use in Ribeirao Preto and reflects the risk that contamination and overexploitation might cause to the main city's water supply.

Distinct conformational properties determined by implicit and explicit representation of protein-solvent interactions. An analytical and computer simulation study

In the protein folding problem, solvent-mediated forces are commonly represented by intra-chain pairwise contact energy. Although this approximation has proven to be useful in several circumstances, it is limited in some other aspects of the problem. Here we show that it is possible to achieve two models to represent the chain-solvent system. one of them with implicit and other with explicit solvent, such that both reproduce the same thermodynamic results. Firstly, lattice models treated by analytical methods, were used to show that the implicit and explicitly representation of solvent effects can be energetically equivalent only if local solvent properties are time and spatially invariant. Following, applying the same reasoning Used for the lattice models, two inter-consistent Monte Carlo off-lattice models for implicit and explicit solvent are constructed, being that now in the latter the solvent properties are allowed to fluctuate. Then, it is shown that the chain configurational evolution as well as the globule equilibrium conformation are significantly distinct for implicit and explicit solvent systems. Actually, strongly contrasting with the implicit solvent version, the explicit solvent model predicts: (i) a malleable globule, in agreement with the estimated large protein-volume fluctuations; (ii) thermal conformational stability, resembling the conformational hear resistance of globular proteins, in which radii of gyration are practically insensitive to thermal effects over a relatively wide range of temperatures; and (iii) smaller radii of gyration at higher temperatures, indicating that the chain conformational entropy in the unfolded state is significantly smaller than that estimated from random coil configurations. Finally, we comment on the meaning of these results with respect to the understanding of the folding process. (C) 2009 Elsevier B.V. All rights reserved.

Language, discourse and politics

After discussing the meaning of the word politics, this paper shows that there are four possible approaches to the issue of the relationships between language, discourse and politics: a) the intrinsic political nature of language; b) the relations of power between discourses and their political dimension; c) the relations of power between languages and the political dimension of their usage and; d) linguistic policies. This paper addresses only the first two of these items. Languages have an intrinsically political nature because they subject their speakers to their order. The acts of silencing operationalized in discourse manifest a relation of power. The spread of discourses in the social space is also subject to the order of power. The use of language may be the space of pertinence, but is also that of exclusion, separation and even the elimination of the other. Therefore, language is not a neutral communication tool, but it is permeated by politics, by power. Because of the dislocations that it produces, literature is a form of swindling language, unveiling the powers that are imprinted on it.