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Journal of Biomedical Informatics

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https://www.readbyqxmd.com/read/28214562/leveraging-health-informatics-to-a-foster-smart-systems-response-to-health-disparities-and-health-equity-challenges
#1
Timothy Jay Carney, Amanda Y Kong
Informaticians are challenged to design health IT solutions for complex problems like health disparities but are only achieving mixed results in demonstrating a direct impact on health outcomes. This presentation of collective intelligence and the corresponding terms of smart health, knowledge ecosystem, enhanced health disparities informatics capacities, knowledge exchange, big-data, and situational awareness are means of demonstrating the complex challenges informatics professional face in trying to model, measure, and manage an intelligence and a smart systems response to health disparities...
February 15, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28213145/how-are-you-feeling-a-personalized-methodology-for-predicting-mental-states-from-temporally-observable-physical-and-behavioral-information
#2
Suppawong Tuarob, Conrad S Tucker, Soundar Kumara, C Lee Giles, Aaron L Pincus, David E Conroy, Nilam Ram
It is believed that anomalous mental states such as stress and anxiety not only cause suffering for the individuals, but also lead to tragedies in some extreme cases. The ability to predict the mental state of an individual at both current and future time periods could prove critical to healthcare practitioners. Currently, the practical way to predict an individual's mental state is through mental examinations that involve psychological experts performing the evaluations. However, such methods can be time and resource consuming, mitigating their broad applicability to a wide population...
February 14, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28213144/modeling-and-validating-hl7-fhir-profiles-using-semantic-web-shape-expressions-shex
#3
Harold R Solbrig, Eric Prud'hommeaux, Grahame Grieve, Lloyd McKenzie, Joshua C Mandel, Deepak K Sharma, Guoqian Jiang
BACKGROUND: HL7 Fast Healthcare Interoperability Resources (FHIR) is an emerging open standard for the exchange of electronic healthcare information. FHIR resources are defined in a specialized modeling language. FHIR instances can currently be represented in either XML or JSON. The FHIR and Semantic Web communities are developing a third FHIR instance representation format in Resource Description Framework (RDF). Shape Expressions (ShEx), a formal RDF data constraint language, is a candidate for describing and validating the FHIR RDF representation...
February 14, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28215562/gene-selection-for-tumor-classification-using-neighborhood-rough-sets-and-entropy-measures
#4
Yumin Chen, Zunjun Zhang, Jianzhong Zheng, Ying Ma, Yu Xue
With the development of bioinformatics, tumor classification from gene expression data becomes an important useful technology for cancer diagnosis. Since a gene expression data often contains thousands of genes and a small number of samples, gene selection from gene expression data becomes a key step for tumor classification. Attribute reduction of rough sets has been successfully applied to gene selection field, as it has the characters of data driving and requiring no additional information. However, traditional rough set method deals with discrete data only...
February 12, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28215561/analyzing-structural-changes-in-snomed-ct-s-bacterial-infectious-diseases-using-a-visual-semantic-delta
#5
Christopher Ochs, James T Case, Yehoshua Perl
Thousands of changes are applied to SNOMED CT's concepts during each release cycle. These changes are the result of efforts to improve or expand the coverage of health domains in the terminology. Understanding which concepts changed, how they changed, and the overall impact of a set of changes is important for editors and end users. Each SNOMED CT release comes with delta files, which identify all of the individual additions and removals of concepts and relationships. These files typically contain tens of thousands of individual entries, overwhelming users...
February 12, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28193465/application-of-human-augmentics-a-persuasive-asthma-inhaler
#6
Brent Grossman, Steve Conner, Giselle Mosnaim, Joshua Albers, Jason Leigh, Steve Jones, Robert Kenyon
This article describes a tailored health intervention delivered on a mobile phone platform, integrating low-literacy design strategies and basic principles of behavior change, to promote increased adherence and asthma control among underserved minority adolescents. We based the intervention and design principles on theories of Human Augmentics and the Elaboration Likelihood Model. We tested the efficacy of using electronic monitoring devices that incorporate informative and persuasive elements to improve adherence to a prescribed daily medication regimen intended to reduce use of asthma rescue medications...
February 10, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28193464/igas-a-framework-for-using-electronic-intraoperative-medical-records-for-genomic-discovery
#7
Matthew A Levin, Thomas T Joseph, Janina M Jeff, Rajiv Nadukuru, Stephen B Ellis, Erwin P Bottinger, Eimear E Kenny
OBJECTIVE: Design and implement a HIPAA and Integrating the Healthcare Enterprise (IHE) profile compliant automated pipeline, the integrated Genomics Anesthesia System (iGAS), linking genomic data from the Mount Sinai Health System (MSHS) BioMe biobank to electronic anesthesia records, including physiological data collected during the perioperative period. The resulting repository of multi-dimensional data can be used for precision medicine analysis of physiological readouts, acute medical conditions, and adverse events that can occur during surgery...
February 10, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28192233/use-of-ontology-structure-and-bayesian-models-to-aid-the-crowdsourcing-of-icd-11-sanctioning-rules
#8
Yun Lou, Samson W Tu, Csongor Nyulas, Tania Tudorache, Robert J G Chalmers, Mark A Musen
The International Classification of Diseases (ICD) is the de facto standard international classification for mortality reporting and for many epidemiological, clinical, and financial use cases. The next version of ICD, ICD-11, will be submitted for approval by the World Health Assembly in 2018. Unlike previous versions of ICD, where coders mostly select single codes from pre-enumerated disease and disorder codes, ICD-11 coding will allow extensive use of multiple codes to give more detailed disease descriptions...
February 10, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28179119/distinguishing-surgical-behavior-by-sequential-pattern-discovery
#9
Arnaud Huaulmé, Sandrine Voros, Laurent Riffaud, Germain Forestier, Alexandre Moreau-Gaudry, Pierre Jannin
OBJECTIVE: Each surgical procedure is unique due to patient's and also surgeon's particularities. In this study, we propose a new approach to distinguish surgical behaviors between surgical sites, levels of expertise and individual surgeons thanks to a pattern discovery method. METHODS: The developed approach aims to distinguish surgical behaviors based on shared longest frequent sequential patterns between surgical process models. To allow clustering, we propose a new metric called SLFSP...
February 4, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28163197/development-of-a-two-stage-gene-selection-method-that-incorporates-a-novel-hybrid-approach-using-the-cuckoo-optimization-algorithm-and-harmony-search-for-cancer-classification
#10
V Elyasigomari, D A Lee, H R C Screen, M H Shaheed
For each cancer type, only a few genes are informative. Due to the so-called 'curse of dimensionality' problem, the gene selection task remains a challenge. To overcome this problem, we propose a two-stage gene selection method called MRMR-COA-HS. In the first stage, the minimum redundancy and maximum relevance (MRMR) feature selection is used to select a subset of relevant genes. The selected genes are then fed into a wrapper setup that combines a new algorithm, COA-HS, using the support vector machine as a classifier...
February 2, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28163196/extraction-of-left-ventricular-ejection-fraction-information-from-various-types-of-clinical-reports
#11
Youngjun Kim, Jennifer H Garvin, Mary K Goldstein, Tammy S Hwang, Andrew Redd, Dan Bolton, Paul A Heidenreich, Stéphane M Meystre
Efforts to improve the treatment of congestive heart failure, a common and serious medical condition, include the use of quality measures to assess guideline-concordant care. The goal of this study is to identify left ventricular ejection fraction (LVEF) information from various types of clinical notes, and to then use this information for heart failure quality measurement. We analyzed the annotation differences between a new corpus of clinical notes from the Echocardiography, Radiology, and Text Integrated Utility package and other corpora annotated for natural language processing (NLP) research in the Department of Veterans Affairs...
February 2, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28159645/driven-to-distraction-the-nature-and-apparent-purpose-of-interruptions-in-critical-care-and-implications-for-hit
#12
Lena Mamykina, Eileen J Carter, Barbara Sheehan, R Stanley Hum, Bridget C Twohig, David R Kaufman
OBJECTIVES: To examine the apparent purpose of interruptions in a Pediatric Intensive Care Unit and opportunities to reduce their burden with informatics solutions. MATERIALS AND METHODS: In this prospective observational study, researchers shadowed clinicians in the unit for one hour at a time, recording all interruptions participating clinicians experienced or initiated, their starting time, duration, and a short description that could help to infer their apparent purpose...
January 31, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28131723/protein-biomarker-druggability-profiling
#13
Subramani Mani, Daniel Cannon, Robin Ohls, Tudor Oprea, Stephen Mathias, Karri Ballard, Oleg Ursu, Cristian Bologa
Developing automated and interactive methods for building a model by incorporating mechanistic and potentially causal annotations of ranked biomarkers of a disease or clinical condition followed by a mapping into a contextual framework in disease-linked biochemical pathways can be used for potential drug-target evaluation and for proposing new drug targets. We demonstrate the potential of this approach using ranked protein biomarkers obtained in neonatal sepsis by enrolling 127 infants (39 infants with late onset neonatal sepsis and 88 control infants) and by performing a focused proteomic profile of the sera and by applying the interactive druggability profiling algorithm (DPA) developed by us...
January 25, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28131722/development-and-empirical-user-centered-evaluation-of-semantically-based-query-recommendation-for-an-electronic-health-record-search-engine
#14
David A Hanauer, Danny T Y Wu, Lei Yang, Qiaozhu Mei, Katherine B Murkowski-Steffy, V G Vinod Vydiswaran, Kai Zheng
OBJECTIVE: The utility of biomedical information retrieval environments can be severely limited when users lack expertise in constructing effective search queries. To address this issue, we developed a computer-based query recommendation algorithm that suggests semantically interchangeable terms based on an initial user-entered query. In this study, we assessed the value of this approach, which has broad applicability in biomedical information retrieval, by demonstrating its application as part of a search engine that facilitates retrieval of information from electronic health records (EHRs)...
January 25, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28126605/cognitive-engineering-and-health-informatics-applications-and-intersections
#15
A Zachary Hettinger, Emilie Roth, Ann M Bisantz
Cognitive engineering is an applied field with roots in both cognitive science and engineering that has been used to support design of information displays, decision support, human-automation interaction, and training in numerous high risk domains ranging from nuclear power plant control to transportation and defense systems. Cognitive engineering provides a set of structured, analytic methods for data collection and analysis that intersect with and complement methods of Cognitive Informatics. These methods support discovery of aspects of the work that make performance challenging, as well as the knowledge, skills, and strategies that experts use to meet those challenges...
January 23, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28126604/a-risk-based-framework-for-biomedical-data-sharing
#16
Fida K Dankar, Radja Badji
The problem of biomedical data sharing is a form of gambling; on one hand it incurs the risk of privacy violations and on the other it stands to profit from knowledge discovery. In general, the risk of granting data access to a user depends heavily upon the data requested, the purpose for the access, the user requesting the data (user motives) and the security of the user's environment. While traditional manual biomedical data sharing processes (based on institutional review boards) are lengthy and demanding, the automated ones (known as honest broker systems) disregard the individualities of different requests and offer "one-size-fits-all" solutions to all data requestors...
January 23, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28109951/a-cognitive-approach-for-design-of-a-multimedia-informed-consent-video-and-website-in-pediatric-research
#17
Holly Antal, H Timothy Bunnell, Suzanne M McCahan, Chris Pennington, Tim Wysocki, Kathryn Blake
OBJECTIVE: Poor participant comprehension of research procedures following the conventional face-to-face consent process for biomedical research is common. We describe the development of a multimedia informed consent video and website that incorporates cognitive strategies to enhance comprehension of study related material directed to parents and adolescents. MATERIALS AND METHODS: A multidisciplinary team was assembled for development of the video and website that included human subjects professionals; psychologist researchers; institutional video and web developers; bioinformaticians and programmers; and parent and adolescent stakeholders...
January 18, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28108211/user-centered-design-improves-the-usability-of-drug-drug-interaction-alerts-experimental-comparison-of-interfaces
#18
Daniel R Luna, Daniel A Rizzato Lede, Carlos M Otero, Marcelo R Risk, Fernán González Bernaldo de Quirós
Clinical Decision Support Systems can alert health professionals about drug interactions when they prescribe medications. The Hospital Italiano de Buenos Aires in Argentina developed an electronic health record with drug-drug interaction alerts, using traditional software engineering techniques and requirements. Despite enhancing the drug-drug interaction knowledge database, the alert override rate of this system was very high. We redesigned the alert system using user-centered design (UCD) and participatory design techniques to enhance the drug-drug interaction alert interface...
January 17, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28104458/a-novel-approach-for-predicting-microrna-disease-associations-by-unbalanced-bi-random-walk-on-heterogeneous-network
#19
Jiawei Luo, Qiu Xiao
MicroRNAs (miRNAs) play a critical role by regulating their targets in post-transcriptional level. Identification of potential miRNA-disease associations will aid in deciphering the pathogenesis of human polygenic diseases. Several computational models have been developed to uncover novel miRNA-disease associations based on the predicted target genes. However, due to the insufficient number of experimentally validated miRNA-target interactions as well as the relatively high false-positive and false-negative rates of predicted target genes, it is still challenging for these prediction models to obtain remarkable performances...
January 16, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28089913/physicians-perception-of-alternative-displays-of-clinical-research-evidence-for-clinical-decision-support-a-study-with-case-vignettes
#20
Stacey L Slager, Charlene R Weir, Heejun Kim, Javed Mostafa, Guilherme Del Fiol
OBJECTIVE: To design alternate information displays that present summaries of clinical trial results to clinicians to support decision-making; and to compare the displays according to efficacy and acceptability. METHODS: A 6-between (information display presentation order) by 3-within (display type) factorial design. Two alternate displays were designed based on Information Foraging theory: a narrative summary that reduces the content to a few sentences; and a table format that structures the display according to the PICO (Population, Intervention, Comparison, Outcome) framework...
January 13, 2017: Journal of Biomedical Informatics
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