PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model.

MotivationElectronic health records (EHRs) are quickly becoming omnipresent in healthcare, but interoperability issues and technical demands limit their use for biomedical and clinical research. Interactive and flexible software that interfaces directly with EHR data structured around a common data model (CDM) could accelerate more EHR-based research by making the data more accessible to researchers who lack computational expertise and/or domain knowledge.ResultsWe present PatientExploreR, an extensible application built on the R/Shiny framework that interfaces with a relational database of EHR data in the Observational Medical Outcomes Partnership CDM format. PatientExploreR produces patient-level interactive and dynamic reports and facilitates visualization of clinical data without any programming required. It allows researchers to easily construct and export patient cohorts from the EHR for analysis with other software. This application could enable easier exploration of patient-level data for physicians and researchers. PatientExploreR can incorporate EHR data from any institution that employs the CDM for users with approved access. The software code is free and open source under the MIT license, enabling institutions to install and users to expand and modify the application for their own purposes.Availability and implementationPatientExploreR can be freely obtained from GitHub: https://github.com/BenGlicksberg/PatientExploreR. We provide instructions for how researchers with approved access to their institutional EHR can use this package. We also release an open sandbox server of synthesized patient data for users without EHR access to explore: http://patientexplorer.ucsf.edu.Supplementary informationSupplementary data are available at Bioinformatics online

Clinical approach to the diagnosis of autoimmune encephalitis in the pediatric patient

Autoimmune encephalitis (AE) is an important and treatable cause of acute encephalitis. Diagnosis of AE in a developing child is challenging because of overlap in clinical presentations with other diseases and complexity of normal behavior changes. Existing diagnostic criteria for adult AE require modification to be applied to children, who differ from adults in their clinical presentations, paraclinical findings, autoantibody profiles, treatment response, and long-term outcomes.A subcommittee of the Autoimmune Encephalitis International Working Group collaborated through conference calls and email correspondence to consider the pediatric-specific approach to AE. The subcommittee reviewed the literature of relevant AE studies and sought additional input from other expert clinicians and researchers.Existing consensus criteria for adult AE were refined for use in children. Provisional pediatric AE classification criteria and an algorithm to facilitate early diagnosis are proposed. There is also discussion about how to distinguish pediatric AE from conditions within the differential diagnosis.Diagnosing AE is based on the combination of a clinical history consistent with pediatric AE and supportive diagnostic testing, which includes but is not dependent on antibody testing. The proposed criteria and algorithm require validation in prospective pediatric cohorts.Copyright © 2020 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology

Infant Botulism

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66984/2/10.1177_000992289303201105.pd

Integrated Carbon Budget Models for the Everglades Terrestrial-Coastal-Oceanic Gradient: Current Status and Needs for Inter-Site Comparisons

Recent studies suggest that coastal ecosystems can bury significantly more C than tropical forests, indicating that continued coastal development and exposure to sea level rise and storms will have global biogeochemical consequences. The Florida Coastal Everglades Long Term Ecological Research (FCE LTER) site provides an excellent subtropical system for examining carbon (C) balance because of its exposure to historical changes in freshwater distribution and sea level rise and its history of significant long-term carbon-cycling studies. FCE LTER scientists used net ecosystem C balance and net ecosystem exchange data to estimate C budgets for riverine mangrove, freshwater marsh, and seagrass meadows, providing insights into the magnitude of C accumulation and lateral aquatic C transport. Rates of net C production in the riverine mangrove forest exceeded those reported for many tropical systems, including terrestrial forests, but there are considerable uncertainties around those estimates due to the high potential for gain and loss of C through aquatic fluxes. C production was approximately balanced between gain and loss in Everglades marshes; however, the contribution of periphyton increases uncertainty in these estimates. Moreover, while the approaches used for these initial estimates were informative, a resolved approach for addressing areas of uncertainty is critically needed for coastal wetland ecosystems. Once resolved, these C balance estimates, in conjunction with an understanding of drivers and key ecosystem feedbacks, can inform cross-system studies of ecosystem response to long-term changes in climate, hydrologic management, and other land use along coastlines

Microspatial variability in community structure and photophysiology of calcified macroalgal microbiomes revealed by coupling of hyperspectral and high-resolution fluorescence imaging

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. The attached file is the published version of the article

Sensor networks and personal health data management: software engineering challenges

The advances of 5G, sensors, and information technologies enabled proliferation of smart pervasive sensor networks. 5G mobile networks provide low-power, high-availability, high density, and high-throughput data capturing by sensor networks and continuous streaming of multiple measured variables. Rapid progress in sensors that can measure vital signs, advances in the management of medical knowledge, and improvement of algorithms for decision support, are fueling a technological disruption to health monitoring. The increase in size and complexity of wireless sensor networks and expansion into multiple areas of health monitoring creates challenges for system design and software engineering practices. In this paper, we highlight some of the key software engineering and data-processing issues, along with addressing emerging ethical issues of data management. The challenges associated with ensuring high dependability of sensor network systems can be addressed by metamorphic testing. The proposed conceptual solution combines data streaming, filtering, cross-calibration, use of medical knowledge for system operation and data interpretation, and IoT-based calibration using certified linked diagnostic devices. Integration of blockchain technologies and artificial intelligence offers a solution to the increasing needs for higher accuracy of measurements of vital signs, high-quality decision-making, and dependability, including key medical and ethical requirements of safety and security of the data