SummaryFQC is software that facilitates quality control of FASTQ files by carrying out a QC protocol using FastQC, parsing results, and aggregating quality metrics into an interactive dashboard designed to richly summarize individual sequencing runs. The dashboard groups samples in dropdowns for navigation among the data sets, utilizes human-readable configuration files to manipulate the pages and tabs, and is extensible with CSV data.Availability and implementationFQC is implemented in Python 3 and Javascript, and is maintained under an MIT license. Documentation and source code is available at: https://github.com/pnnl/fqc.
Between April and November 1982, 27 of 140 patients in a hemodialysis center in Louisiana were infected with rapidly growing mycobacteria; 14 had bacteremia alone, 3 had soft-tissue infections, 1 had an access-graft infection, and 9 had widely disseminated disease. Of 26 identified isolates, 25 were Mycobacterium chelonei ssp. abscessus, and one was an M. chelonei-like organism. One factor common to all patients was exposure to processed hemodialyzers (artificial kidneys). Environmental sampling of the water-treatment system showed widespread contamination with nontuberculous mycobacteria, which were also recovered from the patient's side (blood compartment) of five of 31 hemodialyzers that had been processed and were ready for use. The formaldehyde concentration was less than 2% in two of three such contaminated dialyzers tested. We hypothesize that patients became infected when their blood circulated through processed dialyzers that contained viable rapidly growing mycobacteria. This outbreak demonstrates that hemodialysis patients may be at risk for developing infections with rapidly growing mycobacteria and that such infections may go unrecognized when routine culture methods are used. It also emphasizes the importance of using effective procedures to disinfect dialyzers in hemodialysis centers.
Poor health does trigger changes in living arrangement. Both physical (i.e., chronic conditions and functional status) and mental (i.e., depressed affect) health conditions play a role in such transitions. Because health conditions are correlated with competing risks of mortality, attrition, and proxy interview, health effects on changes in living arrangement are likely underestimated.
Abstract.-1. While phylogenies have been getting easier to build, it has been difficult to re-use, combine, and synthesize the information they provide because published trees are often only available as image files, and taxonomic information is not standardized across studies.2. The Open Tree of Life (OTL) project addresses these issues by providing a digital tree that 15 encompasses all organisms, built by combining taxonomic information and published phylogenies. The project also provides tools and services to query and download parts of this synthetic tree, as well as the source data used to build it. Here, we present rotl, an R package
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