shinyGEO: a web-based application for analyzing gene expression omnibus datasets.

The Gene Expression Omnibus (GEO) is a public repository of gene expression data. Although GEO has its own tool, GEO2R, for data analysis, evaluation of single genes is not straightforward and survival analysis in specific GEO datasets is not possible without bioinformatics expertise. We describe a web application, shinyGEO, that allows a user to download gene expression data sets directly from GEO in order to perform differential expression and survival analysis for a gene of interest. In addition, shinyGEO supports customized graphics, sample selection, data export and R code generation so that all analyses are reproducible. The availability of shinyGEO makes GEO datasets more accessible to non-bioinformaticians, promising to lead to better understanding of biological processes and genetic diseases such as cancer. AVAILABILITY AND IMPLEMENTATION: Web application and source code are available from http://gdancik.github.io/shinyGEO/ CONTACT: dancikg@easternct.eduSupplementary information: Supplementary data are available at Bioinformatics online.

Feasibility of an electronic stethoscope system for monitoring neonatal bowel sounds.

OBJECTIVE: Bowel dysfunction remains a major problem in neonates. Traditional auscultation of bowel sounds as a diagnostic aid in neonatal gastrointestinal complications is limited by skill and inability to document and reassess. Consequently, we built a unique prototype to investigate the feasibility of an electronic monitoring system for continuous assessment of bowel sounds. METHOD: We attained approval by the Institutional Review Boards for the investigational study to test our system. The system incorporated a prototype stethoscope head with a built-in microphone connected to a digital recorder. Recordings made over extended periods were evaluated for quality. We also considered the acoustic environment of the hospital, where the stethoscope was used. The stethoscope head was attached to the abdomen with a hydrogel patch designed especially for this purpose. We used the system to obtain recordings from eight healthy, full-term babies. A scoring system was used to determine loudness, clarity, and ease of recognition comparing it to the traditional stethoscope. The recording duration was initially two hours and was increased to a maximum of eight hours. RESULTS: Median duration of attachment was three hours (3.75, 2.68). Based on the scoring, the bowel sound recording was perceived to be as loud and clear in sound reproduction as a traditional stethoscope. We determined that room noise and other noises were significant forms of interference in the recordings, which at times prevented analysis. However, no sound quality drift was noted in the recordings and no patient discomfort was noted. Minimal erythema was observed over the fixation site which subsided within one hour. CONCLUSION: We demonstrated the long-term recording of infant bowel sounds. Our contributions included a prototype stethoscope head, which was affixed using a specially designed hydrogel adhesive patch. Such a recording can be reviewed and reassessed, which is new technology and an improvement over current practice. The use of this system should also, theoretically, reduce risk of infection. Based on our research we concluded that while automatic assessment of bowel sounds is feasible over an extended period, there will be times when analysis is not possible. One limitation is noise interference. Our larger goals include producing a meaningful vital sign to characterize bowel sounds that can be produced in real-time, as well as providing automatic control for patient feeding pumps.