Low-Level Fluoride Exposure Increases Insulin Sensitivity in Experimental Diabetes

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

Caracterização funcional do fator da tradução eIF5A por meio de interações genéticas

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

O esquecido de si, Dante Milano: rastros de uma poética do esquecimento

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Análise do transcriptoma de folhas de cana-de-açúcar submetidas à prolongada limitação hídrica usando RNA-Seq

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Introdução a ontologias e suas aplicações

Different vocabularies and contexts are barriers to the communication between people or software systems. It is necessary a common understanding in the domain that is talked about, so it can be obtained a correct interpretation of the information. An ontology formally models the structure of a domain and turn explicit the shared understanding in the form of concepts and relations that emerge from its observation. Constitutes a sort of framework used in the mapping to the meaning of the information that is talked about. The formal accuracy in which they are defined, by means of axioms, allow machine processing, implicating in systems interoperability. Structured this way, the knowledge is easily transferred between people or systems from different contexts. Ontologies present several applications nowadays. They are considered the infra-structure to the Semantic Web, which is composed by Web resources with embedded meaning. Thereby, the automatic execution of complex tasks is allowed, with the benefit from the effective communication between Web software agents. Among other applications, they also have been used to structure the knowledge generated from several areas, like Biology and Software Engineering.

OntoSDM: an approach to improve quality on spatial data mining algorithms

The increase in new electronic devices had generated a considerable increase in obtaining spatial data information; hence these data are becoming more and more widely used. As well as for conventional data, spatial data need to be analyzed so interesting information can be retrieved from them. Therefore, data clustering techniques can be used to extract clusters of a set of spatial data. However, current approaches do not consider the implicit semantics that exist between a region and an object’s attributes. This paper presents an approach that enhances spatial data mining process, so they can use the semantic that exists within a region. A framework was developed, OntoSDM, which enables spatial data mining algorithms to communicate with ontologies in order to enhance the algorithm’s result. The experiments demonstrated a semantically improved result, generating more interesting clusters, therefore reducing manual analysis work of an expert.

Framework para integração semântica de dados geoespaciais: integração de dados geológicos

Pós-graduação em Ciência da Computação - IBILCE

Estudo de transcriptomas por RNAseq em tecidos de cabeça e glândula salivar de Rhodnius montenegrensis e Rhodnius robustus (Hemiptera, Reduviidade, Triatominae)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Ontologias no processo de indexação automática de documentos textuais

Pós-graduação em Ciência da Informação - FFC

Adaptação do comportamento animal e mundos emergentes

Discutimos as implicações da noção de adaptação que é uma noção chave para a teoria da evolução clássica. Em lugar de obstinar-se em considerar os organismos como coleção de traços adaptados, propomos buscar estudar a evolução por meio de um quadro teórico onde prevalece uma outra ontologia que destaca o fato de que os organismos e as circunstâncias são totalmente integrados. A etapa preliminar necessária para esta reconsideração consiste em passar de uma lógica prescritiva para uma lógica proscritiva. Isto é, da idéia de que tudo que não é permitido, é proibido; à idéia que o que não é proibido, é permitido. Propomos que a idéia de que os sistemas vivos especificam o mundo no qual eles vivem pode modificar nossa maneira de encarar os processos adaptativos.

Ontologias no processo de indexação automática de documentos textuais

Pós-graduação em Ciência da Informação - FFC

Assessing the gain of biological data integration in gene networks inference

Background: A current challenge in gene annotation is to define the gene function in the context of the network of relationships instead of using single genes. The inference of gene networks (GNs) has emerged as an approach to better understand the biology of the system and to study how several components of this network interact with each other and keep their functions stable. However, in general there is no sufficient data to accurately recover the GNs from their expression levels leading to the curse of dimensionality, in which the number of variables is higher than samples. One way to mitigate this problem is to integrate biological data instead of using only the expression profiles in the inference process. Nowadays, the use of several biological information in inference methods had a significant increase in order to better recover the connections between genes and reduce the false positives. What makes this strategy so interesting is the possibility of confirming the known connections through the included biological data, and the possibility of discovering new relationships between genes when observed the expression data. Although several works in data integration have increased the performance of the network inference methods, the real contribution of adding each type of biological information in the obtained improvement is not clear. Methods: We propose a methodology to include biological information into an inference algorithm in order to assess its prediction gain by using biological information and expression profile together. We also evaluated and compared the gain of adding four types of biological information: (a) protein-protein interaction, (b) Rosetta stone fusion proteins, (c) KEGG and (d) KEGG+GO. Results and conclusions: This work presents a first comparison of the gain in the use of prior biological information in the inference of GNs by considering the eukaryote (P. falciparum) organism. Our results indicates that information based on direct interaction can produce a higher improvement in the gain than data about a less specific relationship as GO or KEGG. Also, as expected, the results show that the use of biological information is a very important approach for the improvement of the inference. We also compared the gain in the inference of the global network and only the hubs. The results indicates that the use of biological information can improve the identification of the most connected proteins.

The incorporeal order in Plato's Philebus

In this paper, I intend to analyze how Plato's Philebus takes up some specific topics of Platonic dialectic and employs them to understand how the cognitive soul can be affected by false pleasures, false opinions, and false images. This study aims to criticize certain modern readings of Platonism, chiefly esoteric theory based on Plato's unwritten doctrine, which stipulate a revision of the Platonic theory of forms and defend the emergence of a new ontology explained by two principles, the One and the unlimited Dyad of great and small, conceived both as formal principle and material principle.

Quantitative proteomic analysis and functional studies reveal that nucleophosmin is involved in cell death in glioblastoma cell line transfected with siRNA

Previously, we reported that nucleophosmin (NPM) was increased in glioblastoma multiforme (GBM). NPM is a phosphoprotein related to apoptosis, ribosome biogenesis, mitosis, and DNA repair, but details about its function remain unclear. We treated U87MG and A172 cells with small interference RNA (siRNA) and obtained a reduction of 80% in NPM1 expression. Knockdown at the protein level was evident after the 4th day and was maintained until the 7th day of transfection that was investigated by quantitative proteomic analysis using isobaric tags. The comparison of proteomic analysis of NPM1-siRNA against controls allowed the identification of 14 proteins, two proteins showed increase and 12 presented a reduction of expression levels. Gene ontology assigned most of the hypoexpressed proteins to apoptosis regulation, including GRP78. NPM1 silencing did not impair cell proliferation until the 7th day after transfection, but sensitized U87MG cells to temozolomide (TMZ), culminating with an increase in cell death and provoking at a later period a reduction of colony formation. In a large data set of GBM patients, both GRP78 and NPM1 genes were upregulated and presented a tendency to shorter overall survival time. In conclusion, NPM proved to participate in the apoptotic process, sensitizing TMZ-treated U87MG and A172 cells to cell death, and in association with upregulation of GRP78 may be helpful as a predictive factor of poor prognosis in GBM patients.

Trichoderma harzianum expressed sequence tags for identification of genes with putative roles in mycoparasitism against Fusarium solani

The plant pathogen Fusarium solani causes a disease root rot of common bean (Phaseolus vulgaris) resulting in great losses of yield in irrigated areas of the Southeast and Midwest regions of Brazil. Species of the genus Trichoderma have been used in the biological control of this pathogen as an alternative to chemical control. To gain new insights into the biocontrol mechanism used by Trichoderma harzianum against the phytopathogenic fungus, Fusarium solani, we performed a transcriptome analysis using expressed sequence tags (ESTs) and quantitative real-time PCR (RT-qPCR) approaches. A cDNA library from T. harzianum mycelium (isolate ALL42) grown on cell walls of F. solani (CWFS) was constructed and analyzed. A total of 2927 high quality sequences were selected from 3845 and 37.7% were identified as unique genes. The Gene Ontology analysis revealed that the majority of the annotated genes are involved in metabolic processes (80.9%), followed by cellular process (73.7%). We tested twenty genes that encode proteins with potential role in biological control. RT-qPCR analysis showed that none of these genes were expressed when T. harzianum was challenged with itself. These genes showed different patterns of expression during in vitro interaction between T. harzianum and F. solani. (C) 2012 Elsevier Inc. All rights reserved.