Tissue Specificity in AS

<p>The figure shows the body system distribution of differential/specific splicing. The instances were obtained from literature mining (left panel) and analysis of EST data ([<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010010#pcbi-0010010-b33" target="_blank">33</a>]; right panel). Each square is colored according to the ratio between the corresponding count and the highest count within the panel. Letter codes for anatomical systems are as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010010#pcbi-0010010-g002" target="_blank">Figure 2</a>. P represents a unique transcript.</p

Creating Specialized Databases for Events of Interest

<p>A database of physiologically occurring AS events can be generated in two steps. Each step may involve machine learning or rule-based methods. The first step involves the identification of sentences from scientific text. These sentences can be parsed in a second step to extract frequently occurring semantic patterns.</p

Toxicity of aerosols of nicotine and pyruvic acid (separate and combined) in Sprague–Dawley rats in a 28-day OECD 412 inhalation study and assessment of systems toxicology

<div><p></p><p>Toxicity of nebulized nicotine (Nic) and nicotine/pyruvic acid mixtures (Nic/Pyr) was characterized in a 28-day Organization for Economic Co-operation and Development 412 inhalation study with additional transcriptomic and lipidomic analyses. Sprague–Dawley rats were nose-only exposed, 6 h/day, 5 days/week to filtered air, saline, nicotine (50 µg/l), sodium pyruvate (NaPyr, 33.9 µg/l) or equimolar Nic/Pyr mixtures (18, 25 and 50 µg nicotine/l). Saline and NaPyr caused no health effects, but rats exposed to nicotine-containing aerosols had decreased body weight gains and concentration-dependent increases in liver weight. Blood neutrophil counts were increased and lymphocyte counts decreased in rats exposed to nicotine; activities of alkaline phosphatase and alanine aminotransferase were increased, and levels of cholesterol and glucose decreased. The only histopathologic finding in non-respiratory tract organs was increased liver vacuolation and glycogen content. Respiratory tract findings upon nicotine exposure (but also some phosphate-buffered saline aerosol effects) were observed only in the larynx and were limited to adaptive changes. Gene expression changes in the lung and liver were very weak. Nic and Nic/Pyr caused few significant changes (including Cyp1a1 gene upregulation). Changes were predominantly related to energy metabolism and fatty acid metabolism but did not indicate an obvious toxicity-related response. Nicotine exposure lowered plasma lipids, including cholesteryl ester (CE) and free cholesterol and, in the liver, phospholipids and sphingolipids. Nic, NaPyr and Nic/Pyr decreased hepatic triacylglycerol and CE. In the lung, Nic and Nic/Pyr increased CE levels. These data suggest that only minor biologic effects related to inhalation of Nic or Nic/Pyr aerosols were observed in this 28-day study.</p></div

Additional file 2 of Crowdsourced benchmarking of taxonomic metagenome profilers: lessons learned from the sbv IMPROVER Microbiomics challenge

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Additional file 10 of Crowdsourced benchmarking of taxonomic metagenome profilers: lessons learned from the sbv IMPROVER Microbiomics challenge

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Additional file 4 of Crowdsourced benchmarking of taxonomic metagenome profilers: lessons learned from the sbv IMPROVER Microbiomics challenge

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