Decreasing the number of false positives in sequence classification

Abstract\ud \ud \ud \ud Background\ud \ud A large number of probabilistic models used in sequence analysis assign non-zero probability values to most input sequences. To decide when a given probability is sufficient the most common way is bayesian binary classification, where the probability of the model characterizing the sequence family of interest is compared to that of an alternative probability model. We can use as alternative model a null model. This is the scoring technique used by sequence analysis tools such as HMMER, SAM and INFERNAL. The most prevalent null models are position-independent residue distributions that include: the uniform distribution, genomic distribution, family-specific distribution and the target sequence distribution. This paper presents a study to evaluate the impact of the choice of a null model in the final result of classifications. In particular, we are interested in minimizing the number of false predictions in a classification. This is a crucial issue to reduce costs of biological validation.\ud \ud \ud \ud Results\ud \ud For all the tests, the target null model presented the lowest number of false positives, when using random sequences as a test. The study was performed in DNA sequences using GC content as the measure of content bias, but the results should be valid also for protein sequences. To broaden the application of the results, the study was performed using randomly generated sequences. Previous studies were performed on aminoacid sequences, using only one probabilistic model (HMM) and on a specific benchmark, and lack more general conclusions about the performance of null models. Finally, a benchmark test with P. falciparum confirmed these results.\ud \ud \ud \ud Conclusions\ud \ud Of the evaluated models the best suited for classification are the uniform model and the target model. However, the use of the uniform model presents a GC bias that can cause more false positives for candidate sequences with extreme compositional bias, a characteristic not described in previous studies. In these cases the target model is more dependable for biological validation due to its higher specificity.We would like to thank Hernando A. del Portillo who proposed the initial biological problem that motivated this study, Sean R. Eddy who helped AML suggesting possible null models for log-odds scoring analysis and for important advice in the final form of the paper, Eric Nawrocki for important insights about Infernal, Alex Coventry for helpful discussion and modification in cmsearch's source code to report negative values, and BIOINFO-Vision Laboratory (University of São Paulo) for computing facilities. During this work, AML was supported by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and Fundação de Amparo a Pesquisa do Estado de São Paulo (FAPESP, 2007/01549-5), AYK was supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and AMD was partially supported by CNPq.We would like to thank Hernando A. del Portillo who proposed the initial biological problem that motivated this study, Sean R. Eddy who helped AML suggesting possible null models for logodds scoring analysis and for important advice in the final form of the paper, Eric Nawrocki for important insights about Infernal, Alex Coventry for helpful discussion and modification in cmsearchs source code to report negative values, and BIOINFOVision Laboratory (University of São Paulo) for computing facilities. During this work, AML was supported by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and Fundação de Amparo a Pesquisa do Estado de São Paulo (FAPESP, 2007/015495), AYK was supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and AMD was partially supported by CNPq.This article has been published as part of BMC Genomics Volume 11 Supplement 5, 2010: Proceedings of the 5th International Conference of the Brazilian Association for Bioinformatics and Computational Biology. The full contents of the supplement are available online at http://www.biomedcentral.com/14712164/11?issue=S5.This article has been published as part of BMC Genomics Volume 11 Supplement 5, 2010: Proceedings of the 5th International Conference of the Brazilian Association for Bioinformatics and Computational Biology. The full contents of the supplement are available online at http://www.biomedcentral.com/1471-2164/11?issue=S5

Flebite associada a cateteres intravenosos periféricos em crianças: estudo de fatores predisponentes

To identify risk factors for phlebitis related to peripheral intravenous catheters (PIC) in children. Methods: A retrospective cohort study conducted in 338 children submitted to intravenous. The variables related to the children and intravenous therapy were investigated, after approval of the ethical merit. Results: From 338 children, nine (2.7%) developed phlebitis. None of the demographic characteristics influenced significantly the development of phlebitis. Regarding to the therapy, there were significant: the use of the PIC for more than five days (p = 0.001), intermittent maintenance (p = 0.001) and greater time permanence of the PIC (p = 0.006). The risk factors were: the presence of predisposing conditions to puncture failure (p = 0.041, OR = 4.645), history of complications (p < 0.001, OR = 40.666); administration of drugs or solutions with extreme pH and osmolarity (p = 0.004, OR = 7.700). Conclusion: The occurrence of the phlebitis did not showed association with demographic characteristics and therapy aspects that represent risk factors, were predisposing conditions for puncture failure, previous complications, drugs administration and solutions with pH extremes and osmolarity182220226Este estudo objetivou identificar fatores de risco para flebite relacionada a cateteres intravenosos periféricos (CIP) em crianças. Métodos: Coorte retrospectiva realizada em 338 crianças submetidas a punção venosa periférica. Foram investigadas variáveis relacionadas à criança e à terapia intravenosa, após aprovação do mérito ético. Resultados: Das 338 crianças, nove (2,7%) desenvolveram flebite. Nenhuma característica demográfica influenciou significativamente o desenvolvimento de flebite. Quanto às características da terapia, foram significantes: utilização do CIP por mais de cinco dias (p = 0,001); manutenção intermitente (p = 0,001) e maior tempo de permanência do CIP (p = 0,006). Representaram fatores de risco: presença de condições predisponentes para insucesso da punção (p = 0,041; OR = 4,645); antecedentes de complicações (p < 0,001, OR = 40,666); administração de drogas ou soluções de elevados pH e osmolaridade (p = 0,004, OR = 7,700). Conclusão: A ocorrência de flebite não apresentou associação com características demográficas, e os aspectos da terapia que representaram fatores de risco foram condições predisponentes para insucesso da punção, antecedentes de complicações, administração de fármacos e soluções com extremos de pH e osmolaridad

Flebitis asociada con catéteres venosos periféricos en niños: estudio de factores predisponentes

Objective: To identify risk factors for phlebitis related to peripheral intravenous catheters (PIC) in children. Methods: A retrospective cohort study conducted in 338 children submitted to intravenous. The variables related to the children and intravenous therapy were investigated, after approval of the ethical merit. Results: From 338 children, nine (2.7%) developed phlebitis. None of the demographic characteristics influenced significantly the development of phlebitis. Regarding to the therapy, there were significant: the use of the PIC for more than five days (p = 0.001), intermittent maintenance (p = 0.001) and greater time permanence of the PIC (p = 0.006). The risk factors were: the presence of predisposing conditions to puncture failure (p = 0.041, OR = 4.645), history of complications (p < 0.001, OR = 40.666); administration of drugs or solutions with extreme pH and osmolarity (p = 0.004, OR = 7.700). Conclusion: The occurrence of the phlebitis did not showed association with demographic characteristics and therapy aspects that represent risk factors, were predisposing conditions for puncture failure, previous complications, drugs administration and solutions with pH extremes and osmolarity.Objetivo: Identificar los factores de riesgo para flebitis relacionada con catéteres venosos periféricos (CVP) en niños. Métodos: Estudio de cohorte, retrospectivo, realizado en 338 niños sometidos a punción venosa. Fueron investigadas variables relacionadas con los niños y con la terapia intravenosa, después de aprobación ética. Resultados: De los 338 niños, nueve (2,7%) tuvieron flebitis. Ninguna característica demográfica influenció significantemente el desarrollo de flebitis. Cuanto a la terapia, fueron significativas: uso de CVP por más de cinco días (p = 0,001); mantenimiento intermitente (p = 0,001); y permanencia más larga (p = 0,006). Representaron factores de riesgo: condiciones que predisponen el fracaso de la punción (p = 0,041, OR = 4,645); e histórico de complicaciones (p < 0,001, OR = 40,666); administración de fármacos o soluciones de pH y la osmolaridad altos (p = 0,004, OR = 7,700). Conclusión: Las características demográficas no influenciaron la ocurrencia de flebitis y los factores de riesgo fueron la presencia de condiciones predisponentes para el fracaso de la punción, complicaciones anteriores, la administración de medicamentos y soluciones con pH extremos y osmolaridad.Este estudo objetivou identificar fatores de risco para flebite relacionada a cateteres intravenosos periféricos (CIP) em crianças.Métodos: Coorte retrospectiva realizada em 338 crianças submetidas a punção venosa periférica. Foram investigadas variáveis relacionadas à criança e à terapia intravenosa, após aprovação do mérito ético. Resultados: Das 338 crianças, nove (2,7%) desenvolveram flebite. Nenhuma característica demográfica influenciou significativamente o desenvolvimento de flebite. Quanto às características da terapia, foram significantes: utilização do CIP por mais de cinco dias (p = 0,001); manutenção intermitente (p = 0,001) e maior tempo de permanência do CIP (p = 0,006). Representaram fatores de risco: presença de condições predisponentes para insucesso da punção (p = 0,041; OR = 4,645); antecedentes de complicações (p < 0,001, OR = 40,666); administração de drogas ou soluções de elevados pH e osmolaridade (p = 0,004, OR = 7,700). Conclusão: A ocorrência de flebite não apresentou associação com características demográficas, e os aspectos da terapia que representaram fatores de risco foram condições predisponentes para insucesso da punção, antecedentes de complicações, administração de fármacos e soluções com extremos de pH e osmolaridade.Universidade Estadual de CampinasUniversidade Federal de São Paulo (UNIFESP)UNIFESP, EPMSciEL

No-match ORESTES explored as tumor markers

Sequencing technologies and new bioinformatics tools have led to the complete sequencing of various genomes. However, information regarding the human transcriptome and its annotation is yet to be completed. The Human Cancer Genome Project, using ORESTES (open reading frame EST sequences) methodology, contributed to this objective by generating data from about 1.2 million expressed sequence tags. Approximately 30% of these sequences did not align to ESTs in the public databases and were considered no-match ORESTES. On the basis that a set of these ESTs could represent new transcripts, we constructed a cDNA microarray. This platform was used to hybridize against 12 different normal or tumor tissues. We identified 3421 transcribed regions not associated with annotated transcripts, representing 83.3% of the platform. The total number of differentially expressed sequences was 1007. Also, 28% of analyzed sequences could represent noncoding RNAs. Our data reinforces the knowledge of the human genome being pervasively transcribed, and point out molecular marker candidates for different cancers. To reinforce our data, we confirmed, by real-time PCR, the differential expression of three out of eight potentially tumor markers in prostate tissues. Lists of 1007 differentially expressed sequences, and the 291 potentially noncoding tumor markers were provided

No-match ORESTES explored as tumor markers

Sequencing technologies and new bioinformatics tools have led to the complete sequencing of various genomes. However, information regarding the human transcriptome and its annotation is yet to be completed. The Human Cancer Genome Project, using ORESTES (open reading frame EST sequences) methodology, contributed to this objective by generating data from about 1.2 million expressed sequence tags. Approximately 30% of these sequences did not align to ESTs in the public databases and were considered no-match ORESTES. On the basis that a set of these ESTs could represent new transcripts, we constructed a cDNA microarray. This platform was used to hybridize against 12 different normal or tumor tissues. We identified 3421 transcribed regions not associated with annotated transcripts, representing 83.3% of the platform. The total number of differentially expressed sequences was 1007. Also, 28% of analyzed sequences could represent noncoding RNAs. Our data reinforces the knowledge of the human genome being pervasively transcribed, and point out molecular marker candidates for different cancers. To reinforce our data, we confirmed, by real-time PCR, the differential expression of three out of eight potentially tumor markers in prostate tissues. Lists of 1007 differentially expressed sequences, and the 291 potentially noncoding tumor markers were provided

Quality of work life: repercussions for the health of nursing worker in intensive care

RESUMO: Objetivos: caracterizar as situa&ccedil;&otilde;es que favorecem ou interferem na Qualidade de Vida no Trabalho de enfermagem em terapia intensiva e analisar as repercuss&otilde;es da Qualidade de Vida no Trabalho na sa&uacute;de do trabalhador de enfermagem da terapia intensiva. M&eacute;todos: Pesquisa qualitativa, descritiva, desenvolvida em um hospital da rede privada do Munic&iacute;pio do Rio de Janeiro. Sujeitos 15 profissionais de enfermagem, o per&iacute;odo de coleta de dados foi julho de 2008. O instrumento utilizado foi &agrave; entrevista semiestruturada. A an&aacute;lise dos dados deu-se atrav&eacute;s da an&aacute;lise tem&aacute;tica de conte&uacute;do. Resultados: Os resultados demonstraram que, dentro da institui&ccedil;&atilde;o, existem cargas de trabalho que provocam o desgaste f&iacute;sico e mental. Conclui-se que esta situa&ccedil;&atilde;o acaba gerando conflitos de sentimentos e repercuss&otilde;es na sa&uacute;de do trabalhador sob forma de estresse e dores no corpo. &nbsp

Quality of work life: repercussions for the health of nursing worker in intensive care

RESUMO: Objetivos: caracterizar as situações que favorecem ou interferem na Qualidade de Vida no Trabalho de enfermagem em terapia intensiva e analisar as repercussões da Qualidade de Vida no Trabalho na saúde do trabalhador de enfermagem da terapia intensiva. Métodos: Pesquisa qualitativa, descritiva, desenvolvida em um hospital da rede privada do Município do Rio de Janeiro. Sujeitos 15 profissionais de enfermagem, o período de coleta de dados foi julho de 2008. O instrumento utilizado foi à entrevista semiestruturada. A análise dos dados deu-se através da análise temática de conteúdo. Resultados: Os resultados demonstraram que, dentro da instituição, existem cargas de trabalho que provocam o desgaste físico e mental. Conclui-se que esta situação acaba gerando conflitos de sentimentos e repercussões na saúde do trabalhador sob forma de estresse e dores no corpo.