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2014 36th Annual international Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014

作者： Vieira, Gilson Amaro, Edson Baccala, Luiz A. Inter-institutional Grad Program on Bioinformatics Universidade de São Paulo São Paulo Brazil

ISBN: (纸本)9781424479290

We propose a new Blind Source Separation technique for whole-brain activity estimation that best profits from FMRI's intrinsic spatial sparsity. The Local Sparse Component Analysis (LSCA) combines wavelet analysis, group-separable regularizers, contiguity-constrained clusterization and principal components analysis (PCA) into a unique spatial sparse representation of FMRI images towards efficient dimensionality reduction without sacrificing physiological characteristics by avoiding artificial stochastic model constraints. The LSCA outperforms classical PCA source reconstruction for artificial data sets over many noise levels. A real FMRI data illustration reveals resting-state activities in regions hard to observe, such as thalamus and basal ganglia, because of their small spatial scale. © 2014 IEEE.

关键词： Blind source separation Correlation Principal component analysis Signal to noise ratio Sparse matrices Vectors Wavelet packets

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YBYRÁ facilitates comparison of large phylogenetic trees

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BMC bioinformatics 2015年第1期16卷 1-4页

作者： Machado, Denis Jacob Inter-institutional Grad Program on Bioinformatics University of São Paulo Rua do Matão tv. 14 no. 101 sala 137 São Paulo05508-090 Brazil

Background: The number and size of tree topologies that are being compared by phylogenetic systematists is increasing due to technological advancements in high-throughput DNA sequencing. However, we still lack tools to facilitate comparison among phylogenetic trees with a large number of terminals. Results: The "YBYRÁ" project integrates software solutions for data analysis in phylogenetics. It comprises tools for (1) topological distance calculation based on the number of shared splits or clades, (2) sensitivity analysis and automatic generation of sensitivity plots and (3) clade diagnoses based on different categories of synapomorphies. YBYRÁ also provides (4) an original framework to facilitate the search for potential rogue taxa based on how much they affect average matching split distances (using MSdist). Conclusions: YBYRÁ facilitates comparison of large phylogenetic trees and outperforms competing software in terms of usability and time efficiency, specially for large data sets. The programs that comprises this toolkit are written in Python, hence they do not require installation and have minimum dependencies. © 2015 Machado.

关键词： Phylogenetic

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Local dimension-reduced dynamical spatio-temporal models for resting state network estimation

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Brain Informatics 2015年第2期2卷 53-63页

作者： Vieira, Gilson Amaro, Edson Baccalá, Luiz A. Inter-institutional Grad Program on Bioinformatics University of São Paulo São Paulo Brazil LIM-44 Department of Radiology University of São Paulo São Paulo Brazil Escola Politécnica University of São Paulo São Paulo Brazil

To overcome the limitations of independent component analysis (ICA), today’s most popular analysis tool for investigating whole-brain spatial activation in resting state functional magnetic resonance imaging (fMRI), we present a new class of local dimension-reduced dynamical spatio-temporal model which dispenses the independence assumptions that severely limit deeper connectivity descriptions between spatial components. The new method combines novel concepts of group sparsity with contiguity-constrained clusterization to produce physiologically consistent regions of interest in illustrative fMRI data whose causal interactions may then be easily estimated, something impossible under the usual ICA assumptions. © 2015, The Author(s).

关键词： Activation analysis

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Local Sparse Component Analysis for Blind Source Separation: An application to resting state FMRI

Local Sparse Component Analysis for Blind Source Separation:...

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Annual international Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： Gilson Vieira Edson Amaro Luiz A. Baccala Inter-institutional Grad Program on Bioinformatics Universidade de Sao Paulo Sao Paulo Brazil

关键词： Principal component analysis Correlation Sparse matrices Vectors Signal to noise ratio Wavelet packets Blind source separation

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Local dimension-reduced dynamical spatio-temporal models for resting state network estimation

Local dimension-reduced dynamical spatio-temporal models for...

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2014 international Conference on Brain Informatics and Health, BIH 2014

作者： Vieira, Gilson Amaro Jr., Edson Baccalá, Luiz A. Inter-institutional Grad Program on Bioinformatics University of São Paulo São Paulo SP 05508-050 Brazil Escola Politécnica University of São Paulo São Paulo SP 05508-900 Brazil

ISBN: (纸本)9783319098906

Resting-state Functional Magnetic Resonance Imaging (FMRI) analysis has consistently shown the presence of specific spatial activation patterns. Independent component analysis (ICA) has been the analysis algorithm of choice even though its underlying assumptions preclude deeper connectivity analysis. By combining novel concepts of group sparsity with contiguity-constrained clusterization, we developed a new class of Local dimension-reduced Dynamical Spatio-Temporal Models (LDSTM) for estimating whole-brain dynamical models whereby the causal relationships between well localized spatial components can be identified. Experimental results of LDSTM on group resting-state FMRI data reveal physiologically plausible spatio-temporal brain connectivity patterns among participants. © 2014 Springer international Publishing.

关键词： Independent component analysis

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Poster: Chronic disease prevention: A Translational bioinformatics approach

Poster: Chronic disease prevention: A Translational Bioinfor...

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IEEE international Conference on Computational Advances in Bio and Medical Sciences (ICCABS)

作者： Juliana Tarossi Pollettini Alessandra Alaniz Macedo Inter-Institutional Grad Program on Bioinformatics University of São Paulo Sao Paulo Brazil Department of Physics and Mathematics FFCLRP University of São Paulo Sao Paulo Brazil

The socioeconomic transformations in the last decades and its consequent changes to societies lifestyle have increased the incidence of chronic diseases. Genomic medicine has suggested that the exposure to risk factors since conception may influence gene expression and consequently induce the development of chronic diseases in adulthood . Scientific papers bringing up these discoveries indicate that epigenetics must be exploited in order to prevent diseases of high prevalence, such as cardiovascular diseases, diabetes and obesity. According to Butte, the effective transformation of results from biomedical research into knowledge that actually improves public health has been considered an important domain of informatics and has been called Translational bioinformatics. This paper proposes the ChronDiseaSSys surveillance system aiming to alert health professionals about human development problems. This system automatically discovers scientific papers relating chronic diseases to risk factors after analyzing patient's clinical records. As a result, the healthcare professional will be able to create a routine setting up the best growing conditions. Since chronic diseases are a serious health problem world wide and lead the causes of mortality with 60% of all deaths, the results suggest that bioinformatics researches are able to directly benefit public health.

关键词： Diseases bioinformatics Unified modeling language Abstracts Public healthcare Electronic mail

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Independent component versus Local Sparse Component Analysis in resting state fMRI

Independent component versus Local Sparse Component Analysis...

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Annual international Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： Gilson Vieira Edson Amaro João R. Sato Luiz A. Baccalá Inter-institutional Grad Program on Bioinformatics Universidade de São Paulo São Paulo Brazil Center of Mathematics Computation and Cognition Universidade Federal do ABC Santo Andre Brazil

Independent Component Analysis (ICA) algorithms are potentially powerful ways of localizing sources of cerebral activity in resting state functional Magnetic Resonance Imaging (fMRI). But the assumptions underling the nature of identified sources limits this tool. By creating local one-dimensional approximations, Local Sparse Component Analysis (LSCA) can separate contiguous sources on the basis of their sparse representation into smoothness spaces via the 3D wavelet transformation. In this paper we systematically compare Probabilistic ICA (PICA) and LSCA for analyzing resting state fMRI across healthy participants. We show that the PICA sources usually representing biologically plausible components can in fact be decomposed into several LSCA sources that are not necessarily independent from each other. In addition, we show that LSCA identifies sources that approximate much better the local variations of the blood oxygenation level-dependent (BOLD) signal than PICA sources.

关键词： Correlation Time series analysis Wavelet transforms Independent component analysis Magnetic resonance imaging Standards Visualization

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Typical Aspects of the Granular Cell Tumor of the Oral Cavity

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international Journal of Otolaryngology and Head & Neck Surgery 2014年第6期3卷 318-322页

作者： Paula Prieto-Oliveira Sergio Vitorino Cardoso Florence Zumbaio Mistro Sergio Kignel Suzana Cantanhede Orsini Machado de Sousa Marco Tullio Brazao-Silva Inter-Institutional Grad Program on Bioinformatics University of Sao PauloSao PauloBrazil Department of Oral Pathology School of DentistryFederal University of UberlandiaUberlandiaBrazil Department of Semiology School of DentistryFundacao Herminio OmettoArarasBrazil Department of Oral Pathology School of DentistryUniversity of Sao PauloSao PauloBrazil Department of Oral Diagnosis School of DentistrySchool of Health SciencesUniversity of the State of AmazonasManausBrazil

Granular cell tumor (GCT) is a rare neoplasm that can occur in any part of the body, but mostly they are located intraorally. Its histogenetic origin remains controversial, but it probably arises from Schwann cells and is generally benign. The tumor is typically asymptomatic and appears as a nodule, with a relatively high predilection for the tongue. This article reports a case of a 72-year-old woman treated at the Center of Oral Diagnosis of the Fundação Hermínio Ometto Dental School. The patient presented with an asymptomatic nodule in the dorsal surface of the tongue for approximately 4 months. The patient was submitted to an excisional biopsy and histopatological examination revealed polyhedral cells with granular aspect. The immunohistochemical staining for S-100 presented strong reactivity, confirming the diagnosis of GCT. Finally, we made a concise discussion about the pathogenesis and fundamental clinico-pathological aspects of GCT making the differential diagnosis.

关键词： Granular Cell Tumor Mouth Diagnosis

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Brazilian version of the multifactorial memory questionnaire for older adults: Preliminary results

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Alzheimer's & Dementia 2015年第7期11卷 P712-P712页

作者： Sharon Sanz Simon Renata Avila Gilson Vieira Cassio M. Campos Bottino University of São Paulo/School of Medicine São Paulo Brazil University of Sao Paulo/School of Medicine Sao Paulo Brazil University of São Paulo/Inter-institutional Grad Program on Bioinformatics São Paulo Brazil

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An integrative approach to investigate the respective roles of single-nucleotide variants and copy-number variants in Attention-Deficit/Hyperactivity Disorder (vol 6, 22851, 2016)

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SCIENTIFIC REPORTS 2016年第1期6卷 22851-22851页

作者： Lima, Leandro de Araujo Feio-dos-Santos, Ana Cecilia Belangero, Sintia Iole Gadelha, Ary Bressan, Rodrigo Affonseca Salum, Giovanni Abrahao Pan, Pedro Mario Moriyama, Tais Silveira Graeff-Martins, Ana Soledade Tamanaha, Ana Carina Alvarenga, Pedro Krieger, Fernanda Valle Fleitlich-Bilyk, Bacy Jackowski, Andrea Parolin Brietzke, Elisa Sato, Joao Ricardo Polanczyk, Guilherme Vanoni Mari, Jair de Jesus Manfro, Gisele Gus do Rosario, Maria Conceiao Miguel, Euripedes Constantino Puga, Renato David Tahira, Ana Carolina Souza, Viviane Neri Chile, Thais Gouveia, Gisele Rodrigues Simoes, Sergio Nery Chang, Xiao Pellegrino, Renata Tian, Lifeng Glessner, Joseph T. Hashimoto, Ronaldo Fumio Rohde, Luis Augusto Sleiman, Patrick M. A. Hakonarson, Hakon Brentani, Helena Inter-institutional Grad Program on Bioinformatics University of São Paulo São Paulo SP Brazil Center for Applied Genomics The Children’s Hospital of Philadelphia Philadelphia PA USA Department & Institute of Psychiatry University of São Paulo Medical School São Paulo SP Brazil National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq) São Paulo SP Brazil Department of Psychiatry Federal University of São Paulo São Paulo SP Brazil National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq) São Paulo SP Brazil Department of Psychiatry Federal University of São Paulo São Paulo SP Brazil National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq) São Paulo SP Brazil Department of Psychiatry Federal University of São Paulo São Paulo SP Brazil National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq) São Paulo SP Brazil Department of Psychiatry Hospital de Clínicas de Porto Alegre Federal University of Rio Grande do Sul Porto Alegre RS Brazil National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq) São Paulo SP Brazil Department of Psychiatry Federal University of São Paulo São Paulo SP Brazil Department & Institute of Psychiatry University of São Paulo Medical School São Paulo SP Brazil National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq) São Paulo SP Brazil Department of Psychiatry Federal University of São Paulo São Paulo SP Brazil Department & Institute of Psychiatry University of São Paulo Medical School São Paulo SP Brazil National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq) São Paulo SP Brazil National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq) São Paulo SP Brazil Department of Psychiatry Federal University of São Paulo São Paulo SP Brazil Department & Institute of Psychiatry University of S

Many studies have attempted to investigate the genetic susceptibility of Attention-Deficit/Hyperactivity Disorder (ADHD), but without much success. The present study aimed to analyze both single-nucleotide and copy-number variants contributing to the genetic architecture of ADHD. We generated exome data from 30 Brazilian trios with sporadic ADHD. We also analyzed a Brazilian sample of 503 children/adolescent controls from a High Risk Cohort Study for the Development of Childhood Psychiatric Disorders, and also previously published results of five CNV studies and one GWAS meta-analysis of ADHD involving children/adolescents. The results from the Brazilian trios showed that cases with de novo SNVs tend not to have de novo CNVs and vice-versa. Although the sample size is small, we could also see that various comorbidities are more frequent in cases with only inherited variants. Moreover, using only genes expressed in brain, we constructed two “in silico” protein-protein interaction networks, one with genes from any analysis, and other with genes with hits in two analyses. Topological and functional analyses of genes in this network uncovered genes related to synapse, cell adhesion, glutamatergic and serotoninergic pathways, both confirming findings of previous studies and capturing new genes and genetic variants in these pathways.

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