Dataset Information

HubViz: A Novel Tool for Hub-centric Visualization.

ABSTRACT: Visualization algorithms have been widely used for intuitive interrogation of genomic data and popularly used tools include MDS, t-SNE, and UMAP. However, these algorithms are not tuned for the visualization of binary data and none of them consider the hubness of observations for the visualization. In order to address these limitations, here we propose hubViz, a novel tool for hub-centric visualization of binary data. We evaluated the performance of hubViz with its application to the gene expression data measured in multiple brain regions of rats exposed to cocaine, the single-cell RNA-seq data of peripheral blood mononuclear cells treated with interferon beta, and the literature mining data to investigate relationships among diseases. We further evaluated the performance of hubViz using simulation studies. We showed that hubViz provides effective visual inspection by locating the hub in the center and the contrasting elements in the opposite sides around the center. We believe that hubViz and its software can be powerful tools that can improve visualizations of various genomic data. The hubViz is implemented as an R package hubviz, which is publicly available at https://dongjunchung.github.io/hubviz/.

SUBMITTER: Nam JH

PROVIDER: S-EPMC7402588 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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hubViz: A Novel Tool for Hub-centric Visualization.

Nam Jin Hyun JH Yun Jonghyun J Jin Ick Hoon IH Chung Dongjun D

Chemometrics and intelligent laboratory systems : an international journal sponsored by the Chemometrics Society 20200607

Visualization algorithms have been widely used for intuitive interrogation of genomic data and popularly used tools include MDS, t-SNE, and UMAP. However, these algorithms are not tuned for the visualization of binary data and none of them consider the hubness of observations for the visualization. In order to address these limitations, here we propose hubViz, a novel tool for hub-centric visualization of binary data. We evaluated the performance of hubViz with its application to the gene expres ...[more]

PMID: 32753773

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Project description:BackgroundPericardial access is necessary for the application of epicardial cardiac therapies including ablation catheters, pacing and defibrillation leads, and left atrial appendage closure systems. Pericardial access under fluoroscopic guidance is difficult in patients without pericardial effusions and may result in coronary artery damage, ventricular injury, or perforation with potentially life-threatening pericardial bleeding in up to 10% of cases. There is a clinical need for a pericardial access technique to safely deliver epicardial cardiac therapies.MethodsIn this paper, we describe the design and evaluation of a novel videoscope and tool kit to percutaneously access the pericardial space under direct visualization. Imaging is performed by a micro-CMOS camera with an automatic gain adjustment software to prevent image saturation. Imaging quality is quantified using known optical targets, while tool performance is evaluated in pediatric insufflation and pericardial access simulators. Device safety and efficacy is demonstrated by infant porcine preclinical studies (N = 6).ResultsThe videoscope has a resolution of 400 × 400 pixels, imaging rate of 30 frames per second, and fits within the lumen of a 14G needle. The tool can resolve features smaller than 39.4 µm, achieves a magnification of 24x, and has a maximum of 3.5% distortion within the field of view. Successful pericardial access was achieved in pediatric simulators and acute in vivo animal studies. During in vivo testing, it took the electrophysiologist an average of 66.83 ± 32.86 s to insert the pericardial access tool into the thoracic space and visualize the heart. After visualizing the heart, it took an average of 136.67 ± 80.63 s to access the pericardial space under direct visualization. The total time to pericardial access measured from needle insertion was 6.7 × quicker than pericardial access using alternative direct visualization techniques. There was no incidence of ventricular perforation.ConclusionsPercutaneous pericardial access under direct visualization is a promising technique to access the pericardial space without complications in simulated and in vivo animal models.

Dataset Information

HubViz: A Novel Tool for Hub-centric Visualization.

Publications

hubViz: A Novel Tool for Hub-centric Visualization.

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