Group B Streptococcus rectovaginal colonization screening on term pregnancies: culture or polymerase chain reaction?

Objectives The aim of this study was to evaluate if screening Group B Streptococcus colonization by intrapartum polymerase chain reaction could improve intrapartum administration of antibiotic prophylaxis, compared with antepartum culture screening and analyze the sensitivity and specificity of polymerase chain reaction test. Methods 198 pregnant women with Group B Streptococcus colonization antepartum culture screening were included. When they arrived at hospital for delivery, two rectovaginal swabs were collected: for culture and polymerase chain reaction method. Results The rate of Group B Streptococcus colonization antepartum detected by culture was 16.7%; at delivery was 17.2% when detected by culture and 19.7% using polymerase chain reaction method. The rate of inconclusive polymerase chain reaction tests was 0.5%. Considering intrapartum culture screening as gold standard, sensitivity and specificity of polymerase chain reaction test for intrapartum Group B Streptococcus colonization was 97.1% and 95.7%, respectively. The global rate of discordance between antepartum and intrapartum Group B Streptococcus colonization was 6.6%. The rate of women not treated with intrapartum antibiotic prophylaxis in the setting of positive intrapartum culture was significantly lower using intrapartum polymerase chain reaction test (0.5%) than with antepartum culture method (3.5%, p = 0.035). Conclusion The use of intrapartum antibiotic prophylaxis can be more efficient when screening Group B Streptococcus colonization intrapartum by polymerase chain reaction test. Polymerase chain reaction method had a good performance in our study, with high sensitivity and specificity

Brazilian flora extracts as source of novel antileishmanial and antifungal compounds

Natural products have long been providing important drug leads for infectious diseases. Leishmaniasis is a protozoan parasitic disease found mainly in developing countries, and it has toxic therapies with few alternatives. Fungal infections have been the main cause of death in immunocompromised patients and new drugs are urgently needed. In this work, a total of 16 plant species belonging to 11 families, selected on an ethnopharmacological basis, were analyzed in vitro against Leishmania (L.) chagasi, Leishmania (L.) amazonensis, Candida krusei, and C. parapsilosis. Of these plant species, seven showed antifungal activity against C. krusei, five showed antileishmanial activity against L. chagasi and four against L. amazonensis, among them species of genus Plectranthus. Our findings confirm the traditional therapeutic use of these plants in the treatment of infectious and inflammatory disorders and also offer insights into the isolation of active and novel drug prototypes, especially those used against neglected diseases as Leishmaniasis.Instituto Adolfo Lutz Serviço de Parasitologia Laboratório de Toxinologia AplicadaUniversidade Federal de São Paulo (UNIFESP) Departamento de Ciências Exatas e da TerraInstituto Plantarum de Estudos da FloraUNIFESP, Depto. de Ciências Exatas e da TerraSciEL

A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series

<p>Abstract</p> <p>Background</p> <p>The ability to monitor the change in expression patterns over time, and to observe the emergence of coherent temporal responses using gene expression time series, obtained from microarray experiments, is critical to advance our understanding of complex biological processes. In this context, biclustering algorithms have been recognized as an important tool for the discovery of local expression patterns, which are crucial to unravel potential regulatory mechanisms. Although most formulations of the biclustering problem are NP-hard, when working with time series expression data the interesting biclusters can be restricted to those with contiguous columns. This restriction leads to a tractable problem and enables the design of efficient biclustering algorithms able to identify all maximal contiguous column coherent biclusters.</p> <p>Methods</p> <p>In this work, we propose <it>e</it>-CCC-Biclustering, a biclustering algorithm that finds and reports all maximal contiguous column coherent biclusters with approximate expression patterns in time polynomial in the size of the time series gene expression matrix. This polynomial time complexity is achieved by manipulating a discretized version of the original matrix using efficient string processing techniques. We also propose extensions to deal with missing values, discover anticorrelated and scaled expression patterns, and different ways to compute the errors allowed in the expression patterns. We propose a scoring criterion combining the statistical significance of expression patterns with a similarity measure between overlapping biclusters.</p> <p>Results</p> <p>We present results in real data showing the effectiveness of <it>e</it>-CCC-Biclustering and its relevance in the discovery of regulatory modules describing the transcriptomic expression patterns occurring in <it>Saccharomyces cerevisiae </it>in response to heat stress. In particular, the results show the advantage of considering approximate patterns when compared to state of the art methods that require exact matching of gene expression time series.</p> <p>Discussion</p> <p>The identification of co-regulated genes, involved in specific biological processes, remains one of the main avenues open to researchers studying gene regulatory networks. The ability of the proposed methodology to efficiently identify sets of genes with similar expression patterns is shown to be instrumental in the discovery of relevant biological phenomena, leading to more convincing evidence of specific regulatory mechanisms.</p> <p>Availability</p> <p>A prototype implementation of the algorithm coded in Java together with the dataset and examples used in the paper is available in <url>http://kdbio.inesc-id.pt/software/e-ccc-biclustering</url>.</p

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PanGEA: Identification of allele specific gene expression using the 454 technology

<p>Abstract</p> <p>Background</p> <p>Next generation sequencing technologies hold great potential for many biological questions. While mainly used for genomic sequencing, they are also very promising for gene expression profiling. Sequencing of cDNA does not only provide an estimate of the absolute expression level, it can also be used for the identification of allele specific gene expression.</p> <p>Results</p> <p>We developed PanGEA, a tool which enables a fast and user-friendly analysis of allele specific gene expression using the 454 technology. PanGEA allows mapping of 454-ESTs to genes or whole genomes, displaying gene expression profiles, identification of SNPs and the quantification of allele specific gene expression. The intuitive GUI of PanGEA facilitates a flexible and interactive analysis of the data. PanGEA additionally implements a modification of the Smith-Waterman algorithm which deals with incorrect estimates of homopolymer length as occuring in the 454 technology</p> <p>Conclusion</p> <p>To our knowledge, PanGEA is the first tool which facilitates the identification of allele specific gene expression. PanGEA is distributed under the Mozilla Public License and available at: <url>http://www.kofler.or.at/bioinformatics/PanGEA</url></p

Vibrational analysis of d-PCL(530)/siloxane based hybrids doped with two lithium salts

Published online: 22 May 2013The present study has been focused on environmentally friendly sol-gel derived electrolytes based on a di-urethane cross-linked d-PCL(530)/siloxane network (where d represents di, PCL identifies the poly(ε–caprolactone) biopolymer and 530 is the average molecular weight in g.mol-1) doped with a wide range of concentration of lithium perchlorate (LiClO4) and lithium bis(trifluoromethanesulfonyl)imide (LiTFSI). Fourier Transform Infrared and Raman (FT-IR and FT-Raman, respectively) spectroscopies have been applied to evaluate the extent of ionic association. Characteristic bands of the PCL(530) segments, of the urethane cross-links and of the anions have been examined to gain insight into the cation/biopolymer, cation/anion and cation/cross-link interactions. In both electrolyte systems “free” ions and contact ions have been identified. The addition of salt modifies the hydrogen-bonded array of the host matrix, causing the destruction/formation of the urethane/urethane aggregates.Fundação para a Ciência e a Tecnologia (FCT