Client Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite

The GPRO suite is an in-progress bioinformatic project for -omics data analysis. As part of the continued growth of this project, we introduce a client- and server-side solution for comparative transcriptomics and analysis of variants. The client-side consists of two Java applications called 'RNASeq' and 'VariantSeq' to manage pipelines and workflows based on the most common command line interface tools for RNA-seq and Variant-seq analysis, respectively. As such, 'RNASeq' and 'VariantSeq' are coupled with a Linux server infrastructure (named GPRO Server-Side) that hosts all dependencies of each application (scripts, databases, and command line interface software). Implementation of the Server-Side requires a Linux operating system, PHP, SQL, Python, bash scripting, and third-party software. The GPRO Server-Side can be installed, via a Docker container, in the user's PC under any operating system or on remote servers, as a cloud solution. 'RNASeq' and 'VariantSeq' are both available as desktop (RCP compilation) and web (RAP compilation) applications. Each application has two execution modes: a step-by-step mode enables each step of the workflow to be executed independently, and a pipeline mode allows all steps to be run sequentially. 'RNASeq' and 'VariantSeq' also feature an experimental, online support system called GENIE that consists of a virtual (chatbot) assistant and a pipeline jobs panel coupled with an expert system. The chatbot can troubleshoot issues with the usage of each tool, the pipeline jobs panel provides information about the status of each computational job executed in the GPRO Server-Side, while the expert system provides the user with a potential recommendation to identify or fix failed analyses. Our solution is a ready-to-use topic specific platform that combines the user-friendliness, robustness, and security of desktop software, with the efficiency of cloud/web applications to manage pipelines and workflows based on command line interface software

Association Between Preexisting Versus Newly Identified Atrial Fibrillation and Outcomes of Patients With Acute Pulmonary Embolism

Background Atrial fibrillation (AF) may exist before or occur early in the course of pulmonary embolism (PE). We determined the PE outcomes based on the presence and timing of AF. Methods and Results Using the data from a multicenter PE registry, we identified 3 groups: (1) those with preexisting AF, (2) patients with new AF within 2 days from acute PE (incident AF), and (3) patients without AF. We assessed the 90-day and 1-year risk of mortality and stroke in patients with AF, compared with those without AF (reference group). Among 16 497 patients with PE, 792 had preexisting AF. These patients had increased odds of 90-day all-cause (odds ratio [OR], 2.81; 95% CI, 2.33-3.38) and PE-related mortality (OR, 2.38; 95% CI, 1.37-4.14) and increased 1-year hazard for ischemic stroke (hazard ratio, 5.48; 95% CI, 3.10-9.69) compared with those without AF. After multivariable adjustment, preexisting AF was associated with significantly increased odds of all-cause mortality (OR, 1.91; 95% CI, 1.57-2.32) but not PE-related mortality (OR, 1.50; 95% CI, 0.85-2.66). Among 16 497 patients with PE, 445 developed new incident AF within 2 days of acute PE. Incident AF was associated with increased odds of 90-day all-cause (OR, 2.28; 95% CI, 1.75-2.97) and PE-related (OR, 3.64; 95% CI, 2.01-6.59) mortality but not stroke. Findings were similar in multivariable analyses. Conclusions In patients with acute symptomatic PE, both preexisting AF and incident AF predict adverse clinical outcomes. The type of adverse outcomes may differ depending on the timing of AF onset.info:eu-repo/semantics/publishedVersio

Characterization of hybrid cobalt-porous silicon systems: protective effect of the Matrix in the metal oxidation

This is an Open Access article distributed under the terms of the Creative Commons Attribution License.-- et al.Abstract In the present work, the characterization of cobalt-porous silicon (Co-PSi) hybrid systems is performed by a combination of magnetic, spectroscopic, and structural techniques. The Co-PSi structures are composed by a columnar matrix of PSi with Co nanoparticles embedded inside, as determined by Transmission Electron Microscopy (TEM). The oxidation state, crystalline structure, and magnetic behavior are determined by X-Ray Absorption Spectroscopy (XAS) and Alternating Gradient Field Magnetometry (AGFM). Additionally, the Co concentration profile inside the matrix has been studied by Rutherford Backscattering Spectroscopy (RBS). It is concluded that the PSi matrix can be tailored to provide the Co nanoparticles with extra protection against oxidation.We acknowledge the MEC and Consejo Superior de Investigaciones Científicas for financial support (PE-2010 6 0E 013). We would like to thank the BM25-SpLine staff for the technical support. This work has been supported by MICINN through projects FIS-2008-06249, MAT2009-14578-C03-02, MAT2008-06858-C02-01, and MAT2008-06858-C02-02, as well as Comunidad de Madrid, project NANOBIOMAGNET (S2009/MAT-1726) and European project MAGNIFYCO (Contract NMP4-SL-2009-228622).Acknowledgements We acknowledge the European Synchrotron Radiation Facility for provision of synchrotron radiation facilities and the MEC and Consejo Superior de Investigaciones Científicas for financial support (PE-2010 6 0E 013). We would like to thank the BM25-SpLine staff for the technical support. This work has been supported by MICINN through projects FIS-2008-06249, MAT2009-14578-C03-02, MAT2008-06858-C02-01, and MAT2008-06858-C02-02, as well as Comunidad de Madrid, project NANOBIOMAGNET (S2009/MAT-1726) and European project MAGNIFYCO (Contract NMP4-SL-2009-228622). Technical support from ICTS Centro Nacional de Microscopia Electrónica (UCM, Madrid) is gratefully acknowleged.Peer Reviewe