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Journal of Biomedical Informatics

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https://www.readbyqxmd.com/read/28342946/negait-a-new-parser-for-medical-text-simplification-using-morphological-sentential-and-double-negation
#1
Partha Mukherjee, Gondy Leroy, David Kauchak, Srinidhi Rajanarayanan, Damian Y Romero Diaz, Nicole P Yuan, T Gail Pritchard, Sonia Colina
Many different text features influence text readability and content comprehension. Negation is commonly suggested as one such feature, but few general-purpose tools exist to discover negation and studies of the impact of negation on text readability are rare. In this paper, we introduce a new negation parser (NegAIT) for detecting morphological, sentential, and double negation. We evaluated the parser using a human annotated gold standard containing 500 Wikipedia sentences and achieved 95%, 89% and 67% precision with 100%, 80%, and 67% recall, respectively...
March 22, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28336478/an-extended-protocol-for-usability-validation-of-medical-devices-research-design-and-reference-model
#2
Martin Schmettow, Raphaela Schnittker, Jan Maarten Schraagen
This paper proposes and demonstrates an extended protocol for usability validation testing of medical devices. A review of currently used methods for the usability evaluation of medical devices revealed two main shortcomings. Firstly, the lack of methods to closely trace the interaction sequences and derive performance measures. Secondly, a prevailing focus on cross-sectional validation studies, ignoring the issues of learnability and training. The U.S. Federal Drug and Food Administration's recent proposal for a validation testing protocol for medical devices is then extended to address these shortcomings: (1) a novel process measure 'normative path deviations' is introduced that is useful for both quantitative and qualitative usability studies and (2) a longitudinal, completely within-subject study design is presented that assesses learnability, training effects and allows analysis of diversity of users...
March 21, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28336477/a-novel-semantic-representation-for-eligibility-criteria-in-clinical-trials
#3
Efthymios Chondrogiannis, Vassiliki Andronikou, Anastasios Tagaris, Efstathios Karanastasis, Theodora Varvarigou, Masatsugu Tsuji
Eligibility Criteria (EC) comprise an important part of a clinical study, being determinant of its cost, duration and overall success. Their formal, computer-processable description can significantly improve clinical trial design and conduction by enabling their intelligent processing, replicability and linkability with other data. For EC representation purposes, related standards were investigated, along with published literature. Moreover, a considerable number of clinicaltrials.gov studies was analyzed in collaboration with clinical experts for the determination and classification of parameters of clinical research importance...
March 21, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28323113/longitudinal-analysis-of-discussion-topics-in-an-online-breast-cancer-community-using-convolutional-neural-networks
#4
Shaodian Zhang, Edouard Grave, Elizabeth Sklar, Noémie Elhadad
Identifying topics of discussions in online health communities (OHC) is critical to various information extraction applications, but can be difficult because topics of OHC content are usually heterogeneous and domain-dependent. In this paper, we provide a multi-class schema, an annotated dataset, and supervised classifiers based on convolutional neural network (CNN) and other models for the task of classifying discussion topics. We apply the CNN classifier to the most popular breast cancer online community, and carry out cross-sectional and longitudinal analyses to show topic distributions and topic dynamics throughout members' participation...
March 18, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28323114/physician-activity-during-outpatient-visits-and-subjective-workload
#5
Alan Calvitti, Harry Hochheiser, Shazia Ashfaq, Kristin Bell, Yunan Chen, Robert El Kareh, Mark T Gabuzda, Lin Liu, Sara Mortensen, Braj Pandey, Steven Rick, Richard L Street, Nadir Weibel, Charlene Weir, Zia Agha
We describe methods for capturing and analyzing EHR use and clinical workflow of physicians during outpatient encounters and relating activity to physicians' self-reported workload. We collected temporally-resolved activity data including audio, video, EHR activity, and eye-gaze along with post-visit assessments of workload. These data are then analyzed through a combination of manual content analysis and computational techniques to temporally align streams, providing a range of process measures of EHR usage, clinical workflow, and physician-patient communication...
March 17, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28323112/strategies-for-handling-missing-clinical-data-for-automated-surgical-site-infection-detection-from-the-electronic-health-record
#6
Zhen Hu, Genevieve B Melton, Elliot G Arsoniadis, Yan Wang, Mary R Kwaan, Gyorgy J Simon
Proper handling of missing data is important for many secondary uses of electronic health record (EHR) data. Data imputation methods can be used to handle missing data, but their use for analyzing EHR data is limited and specific efficacy for postoperative complication detection is unclear. Several data imputation methods were used to develop data models for automated detection of three types (i.e., superficial, deep, and organ space) of surgical site infection (SSI) and overall SSI using American College of Surgeons National Surgical Quality Improvement Project (NSQIP) Registry 30-day SSI occurrence data as a reference standard...
March 16, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28315408/stemtextsearch-stem-cell-gene-database-with-evidence-from-abstracts
#7
Chou-Cheng Chen, Chung-Liang Ho
BACKGROUND: Previous studies have used many methods to find biomarkers in stem cells, including text mining, experimental data and image storage. However, no text-mining methods have yet been developed which can identify whether a gene plays a positive or negative role in stem cells. DESCRIPTION: StemTextSearch identifies the role of a gene in stem cells by using a text-mining method to find combinations of gene regulation, stem-cell regulation and cell processes in the same sentences of biomedical abstracts...
March 14, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28302519/using-ontology-based-semantic-similarity-to-facilitate-the-article-screening-process-for-systematic-reviews
#8
Xiaonan Ji, Alan Ritter, Po-Yin Yen
OBJECTIVE: Systematic Reviews (SRs) are utilized to summarize evidence from high quality studies and are considered the preferred source of evidence-based practice (EBP). However, conducting SRs can be time and labor intensive due to the high cost of article screening. In previous studies, we demonstrated utilizing established (lexical) article relationships to facilitate the identification of relevant articles in an efficient and effective manner. Here we propose to enhance article relationships with background semantic knowledge derived from Unified Medical Language System (UMLS) concepts and ontologies...
March 13, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28300647/heter-lp-a-heterogeneous-label-propagation-algorithm-and-its-application-in-drug-repositioning
#9
Maryam Lotfi Shahreza, Nasser Ghadiri, Seyed Rasoul Mousavi, Jaleh Varshosaz, James R Green
Drug repositioning offers an effective solution to drug discovery, saving both time and resources by finding new indications for existing drugs. Typically, a drug takes effect via its protein targets in the cell. As a result, it is necessary for drug development studies to conduct an investigation into the interrelationships of drugs, protein targets, and diseases. Although previous studies have made a strong case for the effectiveness of integrative network-based methods for predicting these interrelationships, little progress has been achieved in this regard within drug repositioning research...
March 11, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28288857/a-reductionist-approach-to-extract-robust-molecular-markers-from-microarray-data-series-isolating-markers-to-track-osseointegration
#10
Anwesha Barik, Satarupa Banerjee, Santanu Dhara, Nishant Chakravorty
Complexities in the full genome expression studies hinder the extraction of tracker genes to analyze the course of biological events. In this study, we demonstrate the applications of supervised machine learning methods to reduce the irrelevance in microarray data series and thereby extract robust molecular markers to track biological processes. The methodology has been illustrated by analyzing whole genome expression studies on bone-implant integration (ossointegration). Being a biological process, osseointegration is known to leave a trail of genetic footprint during the course...
March 10, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28284761/embedding-of-semantic-predications
#11
Trevor Cohen, Dominic Widdows
This paper concerns the generation of distributed vector representations of biomedical concepts from structured knowledge, in the form of subject-relation-object triplets known as semantic predications. Specifically, we evaluate the extent to which a representational approach we have developed for this purpose previously, known as Predication-based Semantic Indexing (PSI), might benefit from insights gleaned from neural-probabilistic language models, which have enjoyed a surge in popularity in recent years as a means to generate distributed vector representations of terms from free text...
March 8, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28286031/a-passage-retrieval-method-based-on-probabilistic-information-retrieval-model-and-umls-concepts-in-biomedical-question-answering
#12
Mourad Sarrouti, Said El Alaoui Ouatik
BACKGROUND AND OBJECTIVE: Passage retrieval, the identification of top-ranked passages that may contain the answer for a given biomedical question, is a crucial component for any biomedical question answering (QA) system. Passage retrieval in open-domain QA is a longstanding challenge widely studied over the last decades. However, it still requires further efforts in biomedical QA. In this paper, we present a new biomedical passage retrieval method based on Stanford CoreNLP sentence/passage length, probabilistic information retrieval (IR) model and UMLS concepts...
March 7, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28286030/impact-of-an-electronic-handoff-documentation-tool-on-team-shared-mental-models-in-pediatric-critical-care
#13
Silis Y Jiang, Alexandrea Murphy, Elizabeth M Heitkemper, R Stanley Hum, David R Kaufman, Lena Mamykina
OBJECTIVE: To examine the impact of the implementation of an electronic handoff tool (the Handoff Tool) on shared mental models (SMM) within patient care teams as measured by content overlap and discrepancies in verbal handoff presentations given by different clinicians caring for the same patient. MATERIALS AND METHODS: Researchers observed, recorded, and transcribed verbal handoffs given by different members of patient care teams in a pediatric intensive care unit...
March 7, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28286029/classification-of-toxicity-effects-of-biotransformed-hepatic-drugs-using-whale-optimized-support-vector-machines
#14
Alaa Tharwat, Yasmine S Moemen, Aboul Ella Hassanien
Measuring toxicity is an important step in drug development. Nevertheless, the current experimental methods used to estimate the drug toxicity are expensive and time-consuming, indicating that they are not suitable for large-scale evaluation of drug toxicity in the early stage of drug development. Hence, there is a high demand to develop computational models that can predict the drug toxicity risks. In this study, we used a dataset that consists of 553 drugs that biotransformed in liver. The toxic effects were calculated for the current data, namely, mutagenic, tumorigenic, irritant and reproductive effect...
March 7, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28274758/gfd-net-a-novel-semantic-similarity-methodology-for-the-analysis-of-gene-networks
#15
Juan J Díaz-Montaña, Norberto Díaz-Díaz, Francisco Gómez-Vela
Since the popularization of biological network inference methods, it has become crucial to create methods to validate the resulting models. Here we present GFD-Net, the first methodology that applies the concept of semantic similarity to gene network analysis. GFD-Net combines the concept of semantic similarity with the use of gene network topology to analyze the functional dissimilarity of gene networks based on Gene Ontology (GO). The main innovation of GFD-Net lies in the way that semantic similarity is used to analyze gene networks taking into account the network topology...
March 5, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28267590/unsupervised-ensemble-ranking-of-terms-in-electronic-health-record-notes-based-on-their-importance-to-patients
#16
Jinying Chen, Hong Yu
BACKGROUND: Allowing patients to access their own electronic health record (EHR) notes through online patient portals has the potential to improve patient-centered care. However, EHR notes contain abundant medical jargon that can be difficult for patients to comprehend. One way to help patients is to reduce information overload and help them focus on medical terms that matter most to them. Targeted education can then be developed to improve patient EHR comprehension and the quality of care...
March 3, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28254495/an-artificial-intelligence-framework-for-compensating-transgressions-and-its-application-to-diet-management
#17
Luca Anselma, Alessandro Mazzei, Franco De Michieli
Today, there is considerable interest in personal healthcare. The pervasiveness of technology allows to precisely track human behavior; however, when dealing with the development of an intelligent assistant exploiting data acquired through such technologies, a critical issue has to be taken into account; namely, that of supporting the user in the event of any transgression with respect to the optimal behavior. In this paper we present a reasoning framework based on Simple Temporal Problems that can be applied to a general class of problems,, which we called "cake&carrot problems", to support reasoning in presence of human transgression...
February 27, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28242343/biomedical-applications-of-cell-and-tissue-specific-metabolic-network-models
#18
REVIEW
Hamideh Fouladiha, Sayed-Amir Marashi
The essential goal of biomedical research is to understand the underlying mechanism of disease development. Unfortunately, achieving this goal requires expensive and time-consuming efforts in medical biotechnology. This review focuses on how context-specific genome-scale metabolic network models may facilitate reaching this goal. Such models provide an in silico framework for computational simulation of cellular metabolism, predicting the outcome of experiments. Therefore, by using these models at the initial stages of experimental design, time and cost in biomedical researches may be reduced...
February 24, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28232241/dynamic-strategy-for-personalized-medicine-an-application-to-metastatic-breast-cancer
#19
Xi Chen, Ross Shachter, Allison Kurian, Daniel Rubin
We compare methods to develop an adaptive strategy for therapy choice in a class of breast cancer patients, as an example of approaches to personalize therapies for individual characteristics and each patient's response to therapy. Our model maintains a Markov belief about the effectiveness of the different therapies and updates it as therapies are administered and tumor images are observed, reflecting tumor response. We compare three different approximate methods to solve our analytical model against standard medical practice and show significant potential benefit of the computed dynamic strategies to limit tumor growth and to reduce the number of time periods patients are given chemotherapy, with its attendant side effects...
February 20, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28214562/leveraging-health-informatics-to-a-foster-smart-systems-response-to-health-disparities-and-health-equity-challenges
#20
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
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