Cytoscape is one of the most successful network biology analysis and visualization tools, but because of its interactive nature, its role in creating reproducible, scalable, and novel workflows has ...been limited. We describe Cytoscape Automation (CA), which marries Cytoscape to highly productive workflow systems, for example, Python/R in Jupyter/RStudio. We expose over 270 Cytoscape core functions and 34 Cytoscape apps as REST-callable functions with standardized JSON interfaces backed by Swagger documentation. Independent projects to create and publish Python/R native CA interface libraries have reached an advanced stage, and a number of automation workflows are already published.
Vascular atherosclerosis begins in young adulthood and progresses over decades. The condition is associated with considerable morbidity and mortality from coronary, cerebrovascular, and peripheral ...vascular disease. The foundation of contemporary prevention and treatment of atherosclerosis is lowering the serum cholesterol level with 3-hydroxy-3-methylglutaryl–coenzyme A (HMG-CoA) reductase inhibitors (statins). Statins reduce the low-density lipoprotein (LDL) cholesterol level, slow the progression of atherosclerosis, and reduce the morbidity and mortality associated with coronary, cerebrovascular, and peripheral vascular events.
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High-intensity statin therapy is recommended for all patients with established atherosclerotic vascular disease, as well as those at high risk for atherosclerotic vascular disease.
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Isoprene carries approximately half of the flux of non-methane volatile organic carbon emitted to the atmosphere by the biosphere. Accurate representation of its oxidation rate and products is ...essential for quantifying its influence on the abundance of the hydroxyl radical (OH), nitrogen oxide free radicals (NO x ), ozone (O3), and, via the formation of highly oxygenated compounds, aerosol. We present a review of recent laboratory and theoretical studies of the oxidation pathways of isoprene initiated by addition of OH, O3, the nitrate radical (NO3), and the chlorine atom. From this review, a recommendation for a nearly complete gas-phase oxidation mechanism of isoprene and its major products is developed. The mechanism is compiled with the aims of providing an accurate representation of the flow of carbon while allowing quantification of the impact of isoprene emissions on HO x and NO x free radical concentrations and of the yields of products known to be involved in condensed-phase processes. Finally, a simplified (reduced) mechanism is developed for use in chemical transport models that retains the essential chemistry required to accurately simulate isoprene oxidation under conditions where it occurs in the atmosphereabove forested regions remote from large NO x emissions.
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IJS, KILJ, NUK, PNG, UL, UM
Although the cerebral cortex is organized into six excitatory neuronal layers, it is unclear whether glial cells show distinct layering. In the present study, we developed a high-content pipeline, ...the large-area spatial transcriptomic (LaST) map, which can quantify single-cell gene expression in situ. Screening 46 candidate genes for astrocyte diversity across the mouse cortex, we identified superficial, mid and deep astrocyte identities in gradient layer patterns that were distinct from those of neurons. Astrocyte layer features, established in the early postnatal cortex, mostly persisted in adult mouse and human cortex. Single-cell RNA sequencing and spatial reconstruction analysis further confirmed the presence of astrocyte layers in the adult cortex. Satb2 and Reeler mutations that shifted neuronal post-mitotic development were sufficient to alter glial layering, indicating an instructive role for neuronal cues. Finally, astrocyte layer patterns diverged between mouse cortical regions. These findings indicate that excitatory neurons and astrocytes are organized into distinct lineage-associated laminae.
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FZAB, GEOZS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
To the Editor: Nucleic acid aptamers are a novel class of drugs that can be selected to inhibit targets of interest, including protein-protein interactions.1 Pegnivacogin is a ...2'-fluoropyrimidine-modified RNA aptamer that inhibits coagulation factor IXa, coupled to an approximately 40-kDa branched molecule of methoxypolyethylene glycol (mPEG), to increase its concentration and half-life in plasma.2 During the RADAR3 phase 2b clinical trial in patients with acute coronary syndrome, allergic reactions occurred within minutes of a first dose of pegnivacogin in 3 of 640 patients (Table I). Two met criteria for anaphylaxis, and 1 was an isolated dermal reaction; each event was deemed serious, and 1 life-threatening, and together they led to early termination of the trial.3 In a broad investigation into a cause for these 3 events (detailed in Methods in this article's Online Repository at www.jacionline.org), a clinical database review found no other serious allergic reactions (SARs) to pegnivacogin; a quality analysis found no aggregation, degradation, or other deviations of the study product from specifications; and a primate pharmacology study found no evidence that pegnivacogin caused an inflammatory response, histamine release, or complement activation.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
The appropriate selection of lung transplant recipients is an important determinant of outcomes. This consensus document is an update of the recipient selection guidelines published in 2006. The ...Pulmonary Council of the International Society for Heart and Lung Transplantation (ISHLT) organized a Writing Committee of international experts to provide consensus opinion regarding the appropriate timing of referral and listing of candidates for lung transplantation. A comprehensive search of the medical literature was conducted with the assistance of a medical librarian. Writing Committee members were assigned specific topics to research and discuss. The Chairs of the Writing Committee were responsible for evaluating the completeness of the literature search, providing editorial support for the manuscript, and organizing group discussions regarding its content. The consensus document makes specific recommendations regarding the timing of referral and of listing for lung transplantation. These recommendations include discussions not present in previous ISHLT guidelines, including lung allocation scores, bridging to transplant with mechanical circulatory and ventilator support, and expanded indications for lung transplantation. In the absence of high-grade evidence to support decision making, these consensus guidelines remain part of a continuum of expert opinion based on available studies and personal experience. Some positions are immutable. Although transplant is rightly a treatment of last resort for end-stage lung disease, early referral allows proper evaluation and thorough patient education. Subsequent waiting list activation implies a tacit agreement that transplant offers a significant individual survival advantage. It is both the challenge and the responsibility of the transplant community globally to ensure organ allocation maximizes the potential benefits of a scarce resource, thereby achieving that advantage.
Coronary-Artery Bypass Grafting Alexander, John H; Smith, Peter K
The New England journal of medicine,
05/2016, Volume:
374, Issue:
20
Journal Article
Peer reviewed
Coronary-artery bypass grafting (CABG) is very commonly performed. CABG improves survival among patients with multivessel coronary disease; those with more severe coronary disease, diabetes, or left ...ventricular dysfunction are especially likely to benefit.
Coronary-artery bypass grafting (CABG) is a procedure in which autologous arteries or veins are used as grafts to bypass coronary arteries that are partially or completely obstructed by atherosclerotic plaque. CABG is among the most commonly performed major surgical procedures, with approximately 400,000 operations performed annually in the United States. During the past decade, however, there has been nearly a 30% decline in CABG procedures in the United States, despite an aging population and growing evidence to support the effectiveness and safety of the operation.
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This decline has been accompanied by a corresponding increase in percutaneous coronary revascularization procedures. . . .
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