MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis.

BACKGROUND: The study of microbiomes using whole-metagenome shotgun sequencing enables the analysis of uncultivated microbial populations that may have important roles in their environments. Extracting individual draft genomes (bins) facilitates metagenomic analysis at the single genome level. Software and pipelines for such analysis have become diverse and sophisticated, resulting in a significant burden for biologists to access and use them. Furthermore, while bin extraction algorithms are rapidly improving, there is still a lack of tools for their evaluation and visualization. RESULTS: To address these challenges, we present metaWRAP, a modular pipeline software for shotgun metagenomic data analysis. MetaWRAP deploys state-of-the-art software to handle metagenomic data processing starting from raw sequencing reads and ending in metagenomic bins and their analysis. MetaWRAP is flexible enough to give investigators control over the analysis, while still being easy-to-install and easy-to-use. It includes hybrid algorithms that leverage the strengths of a variety of software to extract and refine high-quality bins from metagenomic data through bin consolidation and reassembly. MetaWRAP's hybrid bin extraction algorithm outperforms individual binning approaches and other bin consolidation programs in both synthetic and real data sets. Finally, metaWRAP comes with numerous modules for the analysis of metagenomic bins, including taxonomy assignment, abundance estimation, functional annotation, and visualization. CONCLUSIONS: MetaWRAP is an easy-to-use modular pipeline that automates the core tasks in metagenomic analysis, while contributing significant improvements to the extraction and interpretation of high-quality metagenomic bins. The bin refinement and reassembly modules of metaWRAP consistently outperform other binning approaches. Each module of metaWRAP is also a standalone component, making it a flexible and versatile tool for tackling metagenomic shotgun sequencing data. MetaWRAP is open-source software available at https://github.com/bxlab/metaWRAP .

[Research on the occurrence of functional anomalies of the peripheral bronchi (small bronchi disease) in workers in a factory with respiratory noxious substances]. / Cercetari asupra frecventei anomaliilor functionale în bronhiile periferice (boala bronhiilor mici) la muncitorii dintr-o întreprindere cu noxe respiratorii.

A group of 908 subjects has been studied, of which two-thirds were males, classified in 5 categories: unexposed, with light exposure, and severely exposed to inhalation of volatile substances, or various types of dust. A B.M.R.C. file was filled for each of the subjects. This file concerns respiratory symptoms. A forced expirogram was also performed, and FEV 25-75%, FEV 75-85%, and TEM were determined. The two expiratory flows (median and final) are frequently disturbed in subjects without respiratory symptoms, more frequently in smokers with a normal FEV 1. In those exposed to respiratory risk the proportion of alterations increases, but association of smoking with inhalation of noxious chemical substances will determine a modification of FEW 1 and anomalies of the peripheral bronchi occur more frequently in smokers. Between the criteria suggesting the presence of small airways disease, the ratio FEV 25-75% under 60%, with a FEV 1/FVC ratio within normal limits, this being the most sensitive of the criteria, also appears as the most reliable.

[Long-term study of the evolution of chronic bronchitis detected by questionnaire 10 years earlier]. / Studiu longitudinal asupra evolutici bronsitelor cronice, depistate prin chestionar cu 10 ani anterior.

The longitudinal study carried out in a group of inhabitants from Craiova showed that 16,2% of these, classified according to previously filled questionnaires as suffering from chronic bronchitis, and 10,7% of those classified as suffering from minor forms of bronchitis (sporadic symptoms) had died, and one third of them were not found when the investigation was repeated. Re-examination of 106 adults with chronic bronchitis showed that the symptoms had disappeared in two-thirds of them, especially in those who gave up smoking; in 19,8% of them the symptoms had become more severe due to repeated attacks. Bronchial obstruction was present in 36% of the cases, and alterations in the small bronchial ducts were present in two-thirds of the patients. In 18-24% of the patients with minor forms of bronchitis the symptoms were more severe and chronic, and they can be classified as chronically ill patients. Frequently there were altered spirographic values. This study demonstrates that chronic bronchitis may evolve to: a) remission of the symptomatology (especially after suppression of smoking); b) more or less unmodified persistence of symptoms; c) increased severity of the symptoms following repeated acute attacks. Almost 25% of cases with sporadic coughing and expectoration became chronically ill over a period of 10 years. The questionnaire was demonstrated as having retrospective value for making a diagnosis of chronic bronchitis, but cough and expectoration are not sufficient for a differential assessment of the evolution, the spirographic data being of decisive importance.