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Texto completo SciELO Brasil
Marie, Suely Kazue Nagahashi
Mendonça, Berenice Bilharinho de
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Id: biblio-1133412
Autor: Lerario, Antonio Marcondes; Mohan, Dipika R; Montenegro, Luciana Ribeiro; Funari, Mariana Ferreira de Assis; Nishi, Mirian Yumie; Narcizo, Amanda de Moraes; Benedetti, Anna Flavia Figueredo; Oba-Shinjo, Sueli Mieko; Vitorino, Aurélio José; Santos, Rogério Alexandre Scripnic Xavier dos; Jorge, Alexander Augusto de Lima; Onuchic, Luiz Fernando; Marie, Suely Kazue Nagahashi; Mendonca, Berenice Bilharinho.
Título: SELAdb: A database of exonic variants in a Brazilian population referred to a quaternary medical center in São Paulo
Fonte: Clinics;75:e1913, 2020. tab, graf.
Idioma: en.
Projeto: FAPESP.
Resumo: OBJECTIVES: High-throughput sequencing of genomes, exomes, and disease-focused gene panels is becoming increasingly common for molecular diagnostics. However, identifying a single clinically relevant pathogenic variant among thousands of genetic polymorphisms is a challenging task. Publicly available genomic databases are useful resources to filter out common genetic variants present in the population and enable the identification of each disease-causing variant. Based on our experience applying these technologies at Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo, Brazil, we recognized that the Brazilian population is not adequately represented in widely available genomic databases. METHODS: Here, we took advantage of our 5-year experience as a high-throughput sequencing core facility focused on individuals with putative genetic disorders to build a genomic database that may serve as a more accurate reference for our patient population: SELAdb. RESULTS/CONCLUSIONS: Currently, our database comprises a final cohort of 523 unrelated individuals, including patients or family members managed by different clinics of HCFMUSP. We compared SELAdb with other publicly available genomic databases and demonstrated that this population is very heterogeneous, largely resembling Latin American individuals of mixed origin, rather than individuals of pure European ancestry. Interestingly, exclusively through SELAdb, we identified a spectrum of known and potentially novel pathogenic variants in genes associated with highly penetrant Mendelian disorders, illustrating that pathogenic variants circulating in the Brazilian population that is treated in our clinics are underrepresented in other population databases. SELAdb is freely available for public consultation at: http://intranet.fm.usp.br/sela
Descritores: Genômica
Bases de Dados Genéticas
-Brasil
Estudos de Coortes
Sequenciamento de Nucleotídeos em Larga Escala
Limites: Humanos
Responsável: BR1.1 - BIREME


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Id: biblio-1247690
Autor: Sánchez Feijóo, Daniela; Andrade Tacuri, Carlos; Cuenca León, Katherine; Orellana Bravo, Paola.
Título: Sensibilidad y especificidad de pruebas moleculares en odontología / Sensitivity and specificity of molecular tests in dentistry
Fonte: Rev. ADM = ADM;78(2):90-94, mar.-abr. 2021.
Idioma: es.
Resumo: La biología molecular tiene mayor afinidad en las áreas de la salud, en odontología su principal aplicación ha sido en la identificación de microorganismos orales patógenos mediante el uso de secuencias genéticas específicas (ácido desoxirribonucleico [DNA], ácido ribonucleico [RNA] y proteínas). Las pruebas a nivel molecular se caracterizan por su rapidez, reproductibilidad, sensibilidad y especificidad de los microorganismos diana. El presente artículo de revisión bibliográfica servirá como herramienta para comprender los principios de las técnicas más destacadas como son: PCR estándar y RT-PCR en tiempo real, PCR con transcriptasa inversa, microarreglos y ensayo por inmunoabsorción ligado a enzimas (ELISA), además de sus ventajas y desventajas respecto a las pruebas convencionales (AU)

Molecular biology has a greater affinity in the areas of health. In dentistry, its main application has been the identification of pathogenic oral microorganisms, through the use of specific genetic sequences (deoxyribonucleic acid [DNA], ribonucleic acid [RNA] and proteins). Molecular tests are characterized by their rapidity, reproducibility, sensitivity and specificity of target microorganisms. This literature review article will serve as a tool to understand the principles of the most prominent techniques such as: Standard PCR, Real-time RT-PCR, Reverse transcriptase PCR, microarrays and Enzyme-linked immunosorbent assay (ELISA), in addition to their advantages and disadvantages with respect to conventional tests (AU)
Descritores: Sensibilidade e Especificidade
Diagnóstico Bucal/métodos
Biologia Molecular
Doenças da Boca/diagnóstico
-Ensaio de Imunoadsorção Enzimática
Reação em Cadeia da Polimerase
DNA Polimerase Dirigida por RNA
Reação em Cadeia da Polimerase Via Transcriptase Reversa
Bases de Dados Genéticas
Limites: Humanos
Tipo de Publ: Revisão
Responsável: AR29.1 - Biblioteca


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Texto completo SciELO Cuba
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Id: lil-739227
Autor: Martínez Ortiz, Carlos M; Sautié Castellanos, Miguel; Cuza Ferrer, Yordanka; Wisdom Viña, Yinette.
Título: Herramienta web para la clasificación de microsatélites polimórficos en genomas bacterianos / Web Tool for classfication of polymorphic microsatellites in bacteria genomes
Fonte: Rev. cuba. inform. méd;5(1), ene.-jun. 2013.
Idioma: es.
Resumo: Las secuencias repetidas en tándem, específicamente los mini y micro satélites, han demostrado ser muy eficaces en la clasificación de bacterias patogénicas como B. anthracis, M. tuberculosis y P. aeruginosa, entre otras. En humanos es manifiesta su participación estando relacionados con más de ochenta enfermedades, gran parte de ellas de tipo neurodegenerativas, musculares y algunos tipos de cáncer. La herramienta web que presentamos es el resultado de la detección computacional de estas secuencias en genomas bacterianos completos y su correspondiente anotación en la estructura genómica de acuerdo a las diferentes regiones donde estos se localizan. La herramienta tiene como fin primario brindar un sistema relacional que permita al investigador ubicar los microsatélites de diferentes especies bacterianas, con más de un genoma secuenciado para inferir su posible carácter polimórfico, dentro del contexto de la estructura genómica y así proveer un primer acercamiento al rol putativo que los microsatélites desempeñan desde el punto de vista funcional. La herramienta se puede aplicar no solo en estudios taxonómicos y epidemiológicos sino en la detección de posibles relaciones de estas secuencias con las funciones moleculares, procesos biológicos y, en última instancia, las diversas formas de evolución de estas especies. El sitio web brinda el servicio de consultas a la base de datos de microsatélites bacterianos de acuerdo al sistema de tablas relacionales y atributos propios de las mismas. Cuenta además con los servicios típicos de un sitio con estas características como: sistema de autenticación, foro, encuestas, enlaces y documentación sobre la metodología empleada y del tema en cuestión(AU)

The tandem repeat sequences, especially mini and microsatellites, have proven to be very effective in classification of pathogenic bacteria such as B. anthracis, M. tuberculosis and P. aeruginosa, among others. In human beings it is manifest its participation, being related with over eighty diseases, nearly all neurodegenerative and muscular, and some kinds of cancer. The web tool we are offering here is the result of computational detection of these sequences in whole bacteria genomes, and its respective annotation in the genomic structure according to the different regions where they are localized. The primary goal of this tool is to offer a relational system that allows mapping the microsatellites of bacterial species, all of them with more than one genome sequenced to infer their possible polymorphic character, in the context of genomic structure and thus providing a first approach to the putative role they perform from the functional point of view. The tool can be applied not only in taxonomical and epidemiological studies but in the detection of possible relationships of these sequences with the molecular functions, the biological processes and, as a last resort, the different forms of these species evolution. The web site offers the service of queries to the bacterial microsatellites database according to the related tables and its inherent attributes. It also has the typical services of this kind of site like: logging system, forum, polls, links and documentation about the employed methodology and the topic(AU)
Descritores: Bactérias
Repetições de Microssatélites/genética
Sequências de Repetição em Tandem/genética
Bases de Dados Genéticas
Limites: Humanos
Responsável: CU1.1 - Biblioteca Médica Nacional


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Texto completo SciELO Chile
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Id: biblio-950852
Autor: Wang, Min; Yan, Jingjun; He, Xingxing; Zhong, Qiang; Zhan, Chengye; Li, Shusheng.
Título: Candidate genes and pathogenesis investigation for sepsis-related acute respiratory distress syndrome based on gene expression profile
Fonte: Biol. Res;49:1-9, 2016. ilus, graf, tab.
Idioma: en.
Resumo: BACKGROUND: Acute respiratory distress syndrome (ARDS) is a potentially devastating form of acute inflammatory lung injury as well as a major cause of acute respiratory failure. Although researchers have made significant progresses in elucidating the pathophysiology of this complex syndrome over the years, the absence of a universal detail disease mechanism up until now has led to a series of practical problems for a definitive treatment. This study aimed to predict some genes or pathways associated with sepsis-related ARDS based on a public microarray dataset and to further explore the molecular mechanism of ARDS. RESULTS: A total of 122 up-regulated DEGs and 91 down-regulated differentially expressed genes (DEGs) were obtained. The up- and down-regulated DEGs were mainly involved in functions like mitotic cell cycle and pathway like cell cycle. Protein-protein interaction network of ARDS analysis revealed 20 hub genes including cyclin B1 (CCNB1), cyclin B2 (CCNB2) and topoisomerase II alpha (TOP2A). A total of seven transcription factors including forkhead box protein M1 (FOXM1) and 30 target genes were revealed in the transcription factor-target gene regulation network. Furthermore, co-cited genes including CCNB2-CCNB1 were revealed in literature mining for the relations ARDS related genes. CONCLUSIONS: Pathways like mitotic cell cycle were closed related with the development of ARDS. Genes including CCNB1, CCNB2 and TOP2A, as well as transcription factors like FOXM1 might be used as the novel gene therapy targets for sepsis related ARDS
Descritores: Transtornos Respiratórios/genética
Sepse/complicações
Sepse/genética
Estudos de Associação Genética
Transcriptoma
-Fatores de Transcrição
Regulação para Baixo
Ciclo Celular/genética
Regulação para Cima
Marcação de Genes
Perfilação da Expressão Gênica
Bases de Dados Genéticas
Mapas de Interação de Proteínas
Limites: Humanos
Responsável: CL1.1 - Biblioteca Central


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Texto completo SciELO Brasil
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Id: biblio-889318
Autor: Jiang, Xue; Feng, Lichun; Dai, Baoqiang; Li, Liping; Lu, Weiwei.
Título: Identification of key genes involved in nasopharyngeal carcinoma / Identificação dos principais genes envolvidos no carcinoma nasofaríngeo
Fonte: Braz. j. otorhinolaryngol. (Impr.);83(6):670-676, Nov.-Dec. 2017. tab, graf.
Idioma: en.
Resumo: Abstract Introduction: Nasopharyngeal carcinoma is the most common cancer originating from the nasopharynx. Objective: To study the mechanisms of nasopharyngeal carcinoma, we analyzed GSE12452 microarray data. Methods: GSE12452 was downloaded from the Gene Expression Omnibus database and included 31 nasopharyngeal carcinoma samples and 10 normal nasopharyngeal tissue samples. The differentially expressed genes were screened by ANOVA in the PGS package. Using the BiNGO plugin in Cytoscape and pathway enrichment analysis in the PGS package, functional and pathway enrichment analyses were performed separately to predict potential functions of the differentially expressed genes. Furthermore, Transcription factor-differentially expressed gene pairs were searched, and then the transcription factor-differentially expressed gene regulatory network was visualized using Cytoscape software. Results: A total of 487 genes were screened as differentially expressed genes between the nasopharyngeal carcinoma samples and the normal nasopharyngeal tissue samples. Enrichment analysis indicated that PTGS2 was involved in the regulation of biological process and small cell lung cancer. ZIC2 and OVOL1 may function in nasopharyngeal carcinoma through targeting significantly up-regulated genes (such as PTGS2, FN1, CXCL9 and CXCL10) in the Transcription factor-differentially expressed gene regulatory network (e.g., ZIC2→PTGS2 and OVOL1→CXCL10). Conclusion: PTGS2, FN1, CXCL9, CXCL10, ZIC2 and OVOL1 might play roles in nasopharyngeal carcinoma.

Resumo Introdução: O carcinoma nasofaríngeo é o câncer mais comum originário da nasofaringe. Objetivo: Estudar os mecanismos do câncer de nasofaringe; dados do microarray GSE12452 foram analisados. Método: GSE12452 foi obtido da base de dados Gene Expression Omnibus e inclui 31 amostras de carcinoma nasofaríngeo e 10 amostras de tecido nasofaríngeo normal. Os genes diferencialmente expressos foram analisados por ANOVA no kit PGS. Usando o plugin BiNGO no Cytoscape e análise de enriquecimento da via no kit PGS, análises de enriquecimento funcional e da via foram realizadas separadamente para prever as potenciais funções dos genes diferencialmente expressos. Além disso, os pares Fator de Transcrição - genes diferencialmente expressos foram pesquisados e em seguida a sua rede reguladora foi visualizada usando o programa Cytoscape. Resultados: Um total de 487 genes foram analisados como genes diferencialmente expressos entre as amostras de carcinoma nasofaríngeo e amostras de tecido nasofaríngeo normal. A análise de enriquecimento indicou que PTGS2 estava envolvido na regulação do processo biológico e câncer pulmonar de pequenas células. ZIC2 e OVOL1 podem funcionar no carcinoma nasofaríngeo almejando-se de maneira significativa os genes suprarregulados (como o PTGS2, FN1, CXCL9 e CXCL10) na rede reguladora de fator de transcrição - genes diferencialmente expressos (p.ex., ZIC2→PTGS2 e OVOL1→CXCL10). Conclusão: PTGS2, FN1, CXCL9, CXCL10, ZIC2 e OVOL1 podem desempenhar alguns papéis no carcinoma de nasofaringe.
Descritores: Carcinoma/genética
Expressão Gênica
Neoplasias Nasofaríngeas/genética
-Fatores de Transcrição/genética
Proteínas Nucleares/genética
Carcinoma/patologia
Análise por Conglomerados
Regulação para Baixo
Regulação para Cima
Neoplasias Nasofaríngeas/patologia
Análise de Variância
Perfilação da Expressão Gênica
Bases de Dados Genéticas
Análise em Microsséries
Redes Reguladoras de Genes
Quimiocina CXCL9/genética
Quimiocina CXCL10/genética
Carcinoma Nasofaríngeo
Limites: Humanos
Responsável: BR1.1 - BIREME


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Id: biblio-1017082
Autor: Mei, Lanju; Dong, Na; Li, Fosheng; Li, Na; Yao, Min; Chen, Fang; Tang, Lin.
Título: Transcriptome analysis of female and male flower buds of Idesia polycarpa Maxim. var. vestita Diels
Fonte: Electron. j. biotechnol;29:39-46, sept. 2017. ilus, tab, graf.
Idioma: en.
Projeto: Science and Technology support projects of Sichuan Province.
Resumo: Background: Idesia polycarpa Maxim. var. vestita Diels, a dioecious plant, is widely used for biodiesel due to the high oil content of its fruits. However, it is hard to distinguish its sex in the seedling stage, which makes breeding and production problematic as only the female tree can produce fruits, and the mechanisms underlying sex determination and differentiation remain unknown due to the lack of available genomic and transcriptomic information. To begin addressing this issue, we performed the transcriptome analysis of its female and male flower. Results: 28,668,977 and 22,227,992 clean reads were obtained from the female and male cDNA libraries, respectively. After quality checks and de novo assembly, a total of 84,213 unigenes with an average length of 1179 bp were generated and 65,972 unigenes (78.34%) could be matched in at least one of the NR, NT, Swiss-Prot, COG, KEGG and GO databases. Functional annotation of the unigenes uncovered diverse biological functions and processes, including reproduction and developmental process, which may play roles in sex determination and differentiation. The Kyoto Encyclopedia of Genes and Genomes pathway analysis showed many unigenes annotated as metabolic pathways, biosynthesis of secondary metabolites pathways, plant­ pathogen interaction, and plant hormone signal transduction. Moreover, 29,953 simple sequence repeats were identified using the microsatellite software. Conclusion: This work provides the first detailed transcriptome analysis of female and male flower of I. polycarpa and lays foundations for future studies on the molecular mechanisms underlying flower bud development of I. polycarpa.
Descritores: Reprodução/genética
Salicaceae/genética
Transcriptoma
-Análise de Sequência de RNA
Genes de Plantas
Repetições de Microssatélites
Salicaceae/crescimento & desenvolvimento
Bases de Dados Genéticas
Sequenciamento de Nucleotídeos em Larga Escala
Anotação de Sequência Molecular
Responsável: CL1.1 - Biblioteca Central


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Id: biblio-906287
Autor: Bonini, Jéssica Augusti; Stringhini, Rômulo M; Facalde, Laís; Librelotto, Giovani R.
Título: Estendendo o domínio da Ontocancro 3. 0 para abordar o Inflammaging / Extending the field of Ontocancro 3. 0 to approach the Inflammaging
Fonte: J. health inform;8(supl.I):341-351, 2016. ilus, graf.
Idioma: pt.
Conferência: Apresentado em: Congresso Brasileiro de Informática em Saúde, 15, Goiânia, 27-30 nov. 2016.
Resumo: Esse trabalho tem o objetivo de integrar os dados das versões anteriores da Ontocancro, projeto que visa o desenvolvimento de estudos na área da genética, e as especificações do termo Inflammaging, o qual é definido pelo estado inflamatório crônico devido ao envelhecimento. A Ontocancro 3.0 possibilitou a disponibilização de uma maior quantidade de dados, importantes para a compreensão do processo celular do Câncer, Alzheimer e Diabetes tipo 2, doenças com possível origem no estado inflamatório.

That work aims to integrate data from previous versions of Ontocancro, a project that aims to develop studiesin genetics, and the specifications of Inflammaging term, which is defined by chronic inflammatory condition due toaging. The 3.0 Ontocancro allowed the provision of a larger amount of data, important for understanding the cellular process of cancer, Alzheimer's disease and type 2 diabetes, diseases with a possible rise in the inflammatory state.
Descritores: Biologia Computacional
Bases de Dados Genéticas
Ontologia Genética
-Congressos como Assunto
Limites: Humanos
Responsável: BR21.1 - Biblioteca J Baeta Vianna- Campus Saúde UFMG


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Texto completo SciELO Brasil
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Id: biblio-890679
Autor: Yang, Guodong; Chen, Shuping; Ma, Aiqun; Lu, Jun; Wang, Tingzhong.
Título: Identification of the difference in the pathogenesis in heart failure arising from different etiologies using a microarray dataset
Fonte: Clinics;72(10):600-608, Oct. 2017. tab, graf.
Idioma: en.
Projeto: Science and Technology Program.
Resumo: OBJECTIVES: Clinically, patients with chronic heart failure arising from different etiologies receive the same treatment. However, the prognoses of these patients differ. The purpose of this study was to elucidate whether the pathogenesis of heart failure arising from different etiologies differs. METHODS: Heart failure-related dataset GSE1145 was obtained from the Gene Expression Omnibus database. Differentially expressed genes were identified using R. A protein-protein interaction network of the differentially expressed genes was constructed using Search Tool for the Retrieval of Interacting Genes. The modules in each network were analyzed by Molecular Complex Detection of Cytoscape. The Database for Annotation, Visualization and Integrated Discovery was used to obtain the functions of the modules. RESULTS: Samples contained in GSE1145 were myocardial tissues from patients with dilated cardiomyopathy, familial cardiomyopathy, hypertrophic cardiomyopathy, ischemic cardiomyopathy, and post-partum cardiomyopathy. The differentially expressed genes, modules, and functions of the modules associated with different etiologies varied. Abnormal formation of extracellular matrix was overlapping among five etiologies. The change in cytoskeleton organization was specifically detected in dilated cardiomyopathy. The activation of the Wnt receptor signaling pathway was limited to hypertrophic cardiomyopathy. The change in nucleosome and chromatin assembly was associated with only familial cardiomyopathy. Germ cell migration and disrupted cellular calcium ion homeostasis were solely detected in ischemic cardiomyopathy. The change in the metabolic process of glucose and triglyceride was detected in only post-partum cardiomyopathy. CONCLUSION: These results indicate that the pathogenesis of heart failure arising from different etiologies varies, which may provide molecular evidence supporting etiology-based treatment for heart failure patients.
Descritores: Expressão Gênica
Insuficiência Cardíaca/genética
Cardiomiopatias/genética
-Valores de Referência
Estudos de Casos e Controles
Regulação da Expressão Gênica
Perfilação da Expressão Gênica
Bases de Dados Genéticas
Análise em Microsséries
Mapas de Interação de Proteínas
Insuficiência Cardíaca/terapia
Cardiomiopatias/complicações
Limites: Humanos
Responsável: BR1.1 - BIREME


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Id: biblio-848121
Autor: Souza, Paulo Vinicius Sporleder de.
Título: Biobancos, dados genéticos e proteção jurídico-penal da intimidade / Biobanks, genetic data and legal and criminal protection of privacy
Fonte: Rev. AMRIGS;56(3):68-73, jul.-set. 2012.
Idioma: pt.
Resumo: O artigo trata da questão dos biobancos para pesquisa e dos aspectos jurídicos relacionados à proteção de dados genéticos dos sujeitos de pesquisa. Mais especificamente, além da definição de biobancos e dados genéticos, analisa-se os dados genéticos e testes genéticos e a relação médico-sujeito de pesquisa, bem como a proteção criminal da intimidade genética, sugerindo-se a criação de uma lei que regulamente a coleta, o acesso, a utilização e o armazenamento dos dados genéticos a fim de prevenir testes genéticos para fins médicos arbitrários (AU)

The article deals with the issue of biobanks for research and legal aspects related to the protection of genetic data of study subjects. More specifically, besides the definition of biobanks and genetic data, we analyze genetic data and genetic testing and the physician-subject relationship in research, as well as criminal protection of genetic privacy, suggesting the creation of a law that regulates the collection, access, use and storage of genetic data to prevent genetic testing for arbitrary medical purposes (AU)
Descritores: Bases de Dados Genéticas/legislação & jurisprudência
Privacidade Genética/legislação & jurisprudência
Testes Genéticos/legislação & jurisprudência
Limites: Humanos
Responsável: BR18.1 - Biblioteca FAMED/HCPA


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Id: biblio-843501
Autor: Barajas-Martinez, Hector; Hu, Dan; Baranchuk, Adrian.
Título: Genetics bases of cardiac sodium channel mutations linked to inherited cardiac arrhythmias / Bases genéticas de mutações de canal de sódio cardíaco ligadas a arritmias cardíacas herdadas / Bases genéticas de las mutaciones del canal de sodio cardíaco relacionadas con arritmias cardiacas hereditarias
Fonte: Rev. bras. crescimento desenvolv. hum;26(3):277-279, 2016.
Idioma: en.
Descritores: Arritmias Cardíacas/congênito
Arritmias Cardíacas/diagnóstico
Canalopatias
Bases de Dados Genéticas
Canais de Sódio/genética
-Hereditariedade
Fenótipo
Limites: Humanos
Masculino
Feminino
Responsável: BR85.1 - Biblioteca Dante Moreira Leite



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