RESUMO
TQMD is a tool for high-performance computing clusters which downloads, stores and produces lists of dereplicated prokaryotic genomes. It has been developed to counter the ever-growing number of prokaryotic genomes and their uneven taxonomic distribution. It is based on word-based alignment-free methods (k-mers), an iterative single-linkage approach and a divide-and-conquer strategy to remain both efficient and scalable. We studied the performance of TQMD by verifying the influence of its parameters and heuristics on the clustering outcome. We further compared TQMD to two other dereplication tools (dRep and Assembly-Dereplicator). Our results showed that TQMD is primarily optimized to dereplicate at higher taxonomic levels (phylum/class), as opposed to the other dereplication tools, but also works at lower taxonomic levels (species/strain) like the other dereplication tools. TQMD is available from source and as a Singularity container at [https://bitbucket.org/phylogeno/tqmd ].
RESUMO
Eukaryotes most often synthesize storage polysaccharides in the cytosol or vacuoles in the form of either alpha (glycogen/starch)- or beta-glucosidic (chrysolaminarins and paramylon) linked glucan polymers. In both cases, the glucose can be packed either in water-soluble (glycogen and chrysolaminarins) or solid crystalline (starch and paramylon) forms with different impacts, respectively, on the osmotic pressure, the glucose accessibility, and the amounts stored. Glycogen or starch accumulation appears universal in all free-living unikonts (metazoa, fungi, amoebozoa, etc.), as well as Archaeplastida and alveolata, while other lineages offer a more complex picture featuring both alpha- and beta-glucan accumulators. We now infer the distribution of these polymers in stramenopiles through the bioinformatic detection of their suspected metabolic pathways. Detailed phylogenetic analysis of key enzymes of these pathways correlated to the phylogeny of Stramenopila enables us to retrace the evolution of storage polysaccharide metabolism in this diverse group of organisms. The possible ancestral nature of glycogen metabolism in eukaryotes and the underlying source of its replacement by beta-glucans are discussed.
RESUMO
OBJECTIVES: The aim of this research was to examine the occupational risk factors for Chronic Obstructive Pulmonary Diseases (COPD) in a range of occupations. METHODS: Eleven occupations involving different types of exposure were observed in this multicenter case-control study. Controls and cases were matched for sex, age and smoking. Multiple logistic regression analyses were used to estimate odds ratios (ORs). RESULTS: A total of 1,519 participants were initially recruited between September 2004 and September 2012. After matching, 547 pairs were obtained. The mean age was 56.3 +/- 10.4 years. Smelter workers were the only ones with an increased risk of COPD in this study (OR = 7.6, p < 0.0001, 95% CI [4.5, 12.9]). Physical activity was protective (OR = 0.7), while living in the city was a risk (OR = 1.6). The main used metals were cast iron, aluminum and alloys. Molds and cores were mainly made from sand and synthetic resins. Machine maintenance (65.2%), molding (49.6%), finishing (41.1%) and casting (41.0%) were the most common activities. Almost all workers (95.1%) cleaned the floors and machines with a brush or compressed air. CONCLUSIONS: This study demonstrates the importance of occupational factors in the genesis of COPD, especially among smelter workers. As with the fight against smoking-related disease, the removal or substitution of recognized hazardous agents is the best way of preventing the onset of COPD. This is why it is essential to continue research on its occupational risk factors.
