Genoviz Software Development Kit: Java tool kit for building genomics visualization applications

<p>Abstract</p> <p>Background</p> <p>Visualization software can expose previously undiscovered patterns in genomic data and advance biological science.</p> <p>Results</p> <p>The Genoviz Software Development Kit (SDK) is an open source, Java-based framework designed for rapid assembly of visualization software applications for genomics. The Genoviz SDK framework provides a mechanism for incorporating adaptive, dynamic zooming into applications, a desirable feature of genome viewers. Visualization capabilities of the Genoviz SDK include automated layout of features along genetic or genomic axes; support for user interactions with graphical elements (Glyphs) in a map; a variety of Glyph sub-classes that promote experimentation with new ways of representing data in graphical formats; and support for adaptive, semantic zooming, whereby objects change their appearance depending on zoom level and zooming rate adapts to the current scale. Freely available demonstration and production quality applications, including the Integrated Genome Browser, illustrate Genoviz SDK capabilities.</p> <p>Conclusion</p> <p>Separation between graphics components and genomic data models makes it easy for developers to add visualization capability to pre-existing applications or build new applications using third-party data models. Source code, documentation, sample applications, and tutorials are available at <url>http://genoviz.sourceforge.net/</url>.</p

Comparative Analysis of Spatial Patterns of Gene Expression in Drosophila melanogaster Imaginal Discs

Abstract. Determining the precise spatial extent of expression of genes across different tissues, along with knowledge of the biochemical function of the genes is critical for understanding the roles of various genes in the development of metazoan organisms. To address this problem, we have developed high-throughput methods for generating images of gene expression in Drosophila melanogaster imaginal discs and for the automated analysis of these images. Our method automatically learns tissue shapes from a small number of manually segmented training examples and automatically aligns, extracts and scores new images, which are analyzed to generate gene expression maps for each gene. We have developed a reverse lookup procedure that enables us to identify genes that have spatial expression patterns most similar to a given gene of interest. Our methods enable us to cluster both the genes and the pixels that of the maps, thereby identifying sets of genes that have similar patterns, and regions of the tissues of interest that have similar gene expression profiles across a large number of genes. Primary keyphrases: Genomic imaging, Gene expression analysis, Clustering

Killian Jamieson Diverticulum, the Great Mimicker: A Case Series and Contemporary Review

OBJECTIVE: To assess barium esophagram (BAS) as a diagnostic marker for patients with Killian Jamieson diverticula (KJD). METHODS: Prospective, multicenter cohort study of individuals enrolled in the Prospective OUtcomes of Cricopharyngeus Hypertonicity (POUCH) Collaborative. Patient demographics, comorbidities, radiographic imaging reports, laryngoscopy findings, patient-reported outcome measures (PROM), and operative reporting were abstracted from a REDCap database and summarized using means, medians, percentages, frequencies. Paired t-tests and Wilcoxon Signed Rank test were used to test pre- to post-operative differences in RSI, EAT-10, and VHI-10 scores. Diagnostic test evaluation including sensitivity, specificity, positive, and negative predictive value with 95% confidence intervals were calculated comparing BAS findings to operative report. RESULTS: A total of 287 persons were enrolled; 13 (4%) patients were identified with confirmed KJD on operative reports. 100% underwent open transcervical excision. BAS has a 46.2% (95% confidence interval [CI]: 23.2, 70.9) sensitivity and 97.8% (95% CI: 95.3, 99.0) specificity in detecting a KJD and 50% (95% CI: 25.4, 74.6) positive predictive value but 97.4% (95%CI: 94.8, 98.7) negative predictive value. Preoperatively, patients reported mean (SD) RSI and EAT-10 of 19.4 (9) and 8.3 (7.5) accordingly. Postoperatively, patients reported mean (SD) RSI and EAT-10 as 5.4 (6.2) and 2.3 (3.3). Both changes in RSI and EAT-10 were statistically significant (p = 0.008, p = 0.03). CONCLUSION: KJD are rare and represent LEVEL OF EVIDENCE: Level 4 Laryngoscope, 2022

Initial sequencing and analysis of the human genome

International audienc