1,721,256 research outputs found
Summarizing post-processed data of exon targets in pediatric cancer
No full text<h2>Supplementary docker image from the manuscript titled "Discovery of immunotherapy targets for pediatric solid and brain tumors by exon-level expression."</h2>
<p>After downloading the file.</p>
<p>User can run the following command to load the docker image</p>
<p><code>docker load < CSEminer_3_figure_data_generation.tar</code></p>
<p><code>docker ps -l</code></p>
<p><code>docker run -it cseminer_example:version1 sh</code></p>
<h2>This should prompt the user to be inside the docker environment</h2>
<h2>Next, run the following command</h2>
<p><code>sh step2_run_code_v2.sh</code></p>
<p><code>exit</code></p>
<p># Several output file will be generated</p>
<h2>Next, run the following command to get a list of docker images and copy the output folder to your local system.</h2>
<p><code>docker ps -l</code></p>
<p><code># Look for container id</code></p>
<p><code>docker cp [CONTAINER ID]:/app/OutputFolder/ .</code></p>
<h3><br>For example </h3>
<p>CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES</p>
<p>43e92d65f679 cseminer_example:version1 "sh" 9 minutes ago Exited (0) 9 minutes ago kind_wilson</p>
<p><code>docker cp 43e92d65f679:/app/OutputFolder/ .</code></p>
<p>--------------------------------------------</p>
<p>Additional source code can be found <a href="https://github.com/shawlab-moffitt/CSEminer-manuscript/tree/main/3_figure_data_generation">here.</a></p>
<p>Instructions on how the image was generated can be found <a href="https://github.com/shawlab-moffitt/CSEminer-manuscript/tree/main/3_figure_data_generation_docker">here</a>.</p>
Interactive Shiny App of Heatmap of Exons
No full text<h2>Shiny app that generates heatmaps from the manuscript "Discovery of immunotherapy targets for pediatric solid and brain tumors by exon-level expression."</h2>
<p> </p>
Replication Data for: Deglacial perspectives of future sea level for Singapore
No full textThis dataset contains the relative sea-level data from the geological reconstructions and instrumental records used to quantify magnitudes and rates of relative sea-level change since the last glacial maximum for the Sunda Shelf and Singapore. Also included are the Error-in-Variables Integrated Gaussian Process model files
Endobronchial ultrasound and the assessment of airway wall thickness in asthma
No full textWhilst high resolution computer tomography (HRCT) scanning lends support to the notion that the airways are thickened in asthma, this technique is limited by its sensitivity of measurement, inter-observer variability and necessity for radiation exposure. This is the first work to describe endobronchial ultrasound (EBUS) using a radial probe instead under direct vision into the airways during fibre-optic bronchoscopy to measure total airway wall thickness (AWT) in vivo. The technique was validated in an in vitro model (sheep airway) and in vivo by comparison with HRCT measurements in mild/moderate asthmatic and healthy volunteer subjects. In the asthmatic group these findings were related to PC20 histamine, as a measure of BHR, post-bronchodilator FEV, reversibility to β2 agonists, and duration of asthma. Endobronchial biopsies were assessed for histological markers of airway remodelling – reticular basement membrane thickness (RbMt), submucosal collagen and proteoglycan deposition. Inter and intraobserver variability using EBUS to measure AWT were good and were in agreement with those by HRCT. Increased AWT was found in asthmatics but contrary to that predicted by mathematical models it was inversely correlated with BHR and reversibility to β2 agonists. Although RbMt, submucosal collagens I, III, V and proteoglycans perlican, biglycan, decorin, fibronectin were increased in asthmatic subjects over controls, no correlations were found with AWT. I suggest that increased AWT in asthmatics leads to ‘stiffening’ of the airways which opposes excessive bronchoconstriction and is therefore beneficial in protecting the airways from closure.</p
Holocene Relative Sea-Level Changes from Near-, Intermediate-, and Far-Field Locations
No full textHolocene relative sea-level (RSL) records exhibit spatial and temporal variability that arises mainly from the interaction of eustatic (land ice volume and thermal expansion) and isostatic (glacio- and hydro-) factors. We fit RSL histories from near-, intermediate-, and far-field locations with noisy-input Gaussian process models to assess rates of RSL change. Records from near-field regions (e.g., Antarctica, Greenland, Canada, Sweden, and Scotland) reveal a complex pattern of RSL fall from a maximum marine limit due to the net effect of eustatic sea-level rise and glacio-isostatic uplift with rates of RSL fall as great as -69 ± 9 m/ka. Intermediate-field regions (e.g., mid-Atlantic and Pacific coasts of the United States, Netherlands, Southern France, St. Croix) display variable rates of RSL rise from the cumulative effect of isostatic and eustatic factors. Fast rates of RSL rise (up to 10 ± 1 m/ka) are found in the early Holocene in regions near the center of forebulge collapse. Far-field RSL records exhibit a mid-Holocene highstand, the timing (between 8 and 4 ka) and magnitude (between <1 and 6 m) of which varies among South America, Africa, Asia and Oceania regions.Peer reviewe
Estimating global mean sea-level rise and its uncertainties by 2100 and 2300 from expert assessment
No full textRaw data used in compilation of the estimating global mean sea-level rise and its uncertainties by 2100 and 2300 from expert assessmen
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
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