Jigsaw: investigative analysis on text document collections through visualization

This article describes the Jigsaw system for helping investigative analysis across collections of text documents. Jigsaw provides multiple visualizations of the documents and the entities within them to help investigators discern embedded stories and plots. Our early focus within Jigsaw has not been on legal documents and E-discovery, but we feel that the system may have potential in these areas as well. This article illustrates Jigsaw’s views and operations using Enron email archives as example documents

Characterization of the 2016-2017 dermatology standardized letter of recommendation

© 2018 Matrix Medical Communications. All rights reserved. Objective: We aimed to analyze the reformatted standard letter of recommendation (SLOR) for dermatology residents to examine trends in grading and content based on the positions of the letter writers, their backgrounds, and their relationship with the applicant, as well as to evaluate the SLOR\u27s ability to discriminate applicants. Design: This was a retrospective characterization study of dermatology SLORs from the 2016-17 application cycle. Setting: We examined SLORs received by The Ohio State University, the University of Oklahoma, and Hofstra University Northwell Health dermatology residency programs. Participants: We included dermatology residency applicants and their letter writers from the 2016-17 application cycle. Results: A total of 141 SLORs were analyzed from 115 applicants. SLORs demonstrated grade inflation from letter writers of all backgrounds. Ratings for research potential and inquisitive nature were significantly lower than ratings for other categories. Letter writers with limited clinical and research contact graded applicants significantly lower than did writers who had more extensive contact. Word boxes were underutilized. Conclusion: The dermatology SLOR is useful in differentiating applicants, and ratings correlate with the relationships that letter writers have with their applicants. Residency programs should be aware of these findings when evaluating letters of recommendation for applicants

Mechanistic insights into the acetate-accelerated synthesis of crystalline ceria nanoparticles

Recent increasing uses of ceria in research and industrial applications have fostered continuing developments of efficient routes to synthesize the material. Here we report our investigation of the effects and the mechanistic roles of lithium acetate to accelerate the growth of crystalline ceria nanoparticles in ozone-mediated synthesis. By increasing the mole ratio of the acetate to cerium nitrate in the reactions, the reaction yields of ceria nanoparticles were observed to increase from ca. 10% to up to over 90% by cerium content in 30 min reactions. Microscopy images and Raman spectra of the assynthesized nanoparticles revealed that increasing the acetate additions led to a decrease in average particle size and size range but an increase in crystallinity. Through analyzing the organic by-products in the reaction mixtures, the acetate was inferred to base-catalyze the formation of acetals and cerium complexes and accelerate the formation of Ce–O–Ce bonds and hence the growth of ceria nanoparticles through alcohol-like condensation reactions

Generation and evaluation of a Glaesserella (Haemophilus) parasuis capsular mutant

Glaesserella (Haemophilus) parasuis is a commensal of the upper respiratory tract in pigs and also the causative agent of Glässer's disease, which causes significant morbidity and mortality in pigs worldwide. Isolates are characterized into 15 serovars by their capsular polysaccharide, which has shown a correlation to isolate pathogenicity. To investigate the role capsule plays in G. parasuis virulence and host interaction, a capsule mutant of the serovar 5 strain HS069 was generated (HS069Δcap) through allelic exchange following natural transformation. HS069Δcap was unable to cause signs of systemic disease during a pig challenge study and had increased sensitivity to complement killing and phagocytosis by alveolar macrophages. When compared to the parent strain, HS069Δcap produced more robust biofilm and adhered equivalently to 3D4/31 cells; however, it was unable to persistently colonize the nasal cavity of inoculated pigs, with all pigs clearing HS069Δcap by 5 days post-challenge. Our results indicate the importance of capsular polysaccharide to G. parasuis virulence as well as nasal colonization in pigs

Updated resonance photo-decay amplitudes to 2 GeV

We present the results of an energy-dependent and set of single-energy partial-wave analyses of single-pion photoproduction data. These analyses extend from threshold to 2 GeV in the laboratory photon energy, and update our previous analyses to 1.8 GeV. Photo-decay amplitudes are extracted for the baryon resonances within this energy range. We consider two photoproduction sum rules and the contributions of two additional resonance candidates found in our most recent analysis of $\pi N$ elastic scattering data. Comparisons are made with previous analyses.Comment: Revtex, 26 pages, 3 figures. Postscript figures available from ftp://clsaid.phys.vt.edu/pub/pr or indirectly from http://clsaid.phys.vt.edu/~CAPS

Interactive metagenomic visualization in a Web browser

<p>Abstract</p> <p>Background</p> <p>A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their hierarchical contexts and their prediction confidence. The current tools for visualizing metagenomic data, however, omit or distort quantitative hierarchical relationships and lack the facility for displaying secondary variables.</p> <p>Results</p> <p>Here we present Krona, a new visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. Krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming. The HTML5 and JavaScript implementation enables fully interactive charts that can be explored with any modern Web browser, without the need for installed software or plug-ins. This Web-based architecture also allows each chart to be an independent document, making them easy to share via e-mail or post to a standard Web server. To illustrate Krona's utility, we describe its application to various metagenomic data sets and its compatibility with popular metagenomic analysis tools.</p> <p>Conclusions</p> <p>Krona is both a powerful metagenomic visualization tool and a demonstration of the potential of HTML5 for highly accessible bioinformatic visualizations. Its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. Both the Krona rendering code and conversion tools are freely available under a BSD open-source license, and available from: <url>http://krona.sourceforge.net</url>.</p