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https://www.readbyqxmd.com/read/28643174/natural-language-processing-for-ehr-based-pharmacovigilance-a-structured-review
#1
REVIEW
Yuan Luo, William K Thompson, Timothy M Herr, Zexian Zeng, Mark A Berendsen, Siddhartha R Jonnalagadda, Matthew B Carson, Justin Starren
The goal of pharmacovigilance is to detect, monitor, characterize and prevent adverse drug events (ADEs) with pharmaceutical products. This article is a comprehensive structured review of recent advances in applying natural language processing (NLP) to electronic health record (EHR) narratives for pharmacovigilance. We review methods of varying complexity and problem focus, summarize the current state-of-the-art in methodology advancement, discuss limitations and point out several promising future directions...
June 22, 2017: Drug Safety: An International Journal of Medical Toxicology and Drug Experience
https://www.readbyqxmd.com/read/28634427/leveraging-food-and-drug-administration-adverse-event-reports-for-the-automated-monitoring-of-electronic-health-records-in-a-pediatric-hospital
#2
Huaxiu Tang, Imre Solti, Eric Kirkendall, Haijun Zhai, Todd Lingren, Jaroslaw Meller, Yizhao Ni
The objective of this study was to determine whether the Food and Drug Administration's Adverse Event Reporting System (FAERS) data set could serve as the basis of automated electronic health record (EHR) monitoring for the adverse drug reaction (ADR) subset of adverse drug events. We retrospectively collected EHR entries for 71 909 pediatric inpatient visits at Cincinnati Children's Hospital Medical Center. Natural language processing (NLP) techniques were used to identify positive diseases/disorders and signs/symptoms (DDSSs) from the patients' clinical narratives...
2017: Biomedical Informatics Insights
https://www.readbyqxmd.com/read/28634104/natural-language-processing-for-asthma-ascertainment-in-different-practice-settings
#3
Chung-Il Wi, Sunghwan Sohn, Mir Ali, Elizabeth Krusemark, Euijung Ryu, Hongfang Liu, Young J Juhn
BACKGROUND: We developed and validated NLP-PAC, a natural language processing (NLP) algorithm based on predetermined asthma criteria (PAC) for asthma ascertainment using electronic health records at Mayo Clinic. OBJECTIVE: To adapt NLP-PAC in a different health care setting, Sanford Children Hospital, by assessing its external validity. METHODS: The study was designed as a retrospective cohort study that used a random sample of 2011-2012 Sanford Birth cohort (n = 595)...
June 17, 2017: Journal of Allergy and Clinical Immunology in Practice
https://www.readbyqxmd.com/read/28616910/-effects-of-limb-ischemic-postconditioning-on-behavioral-improvement-and-proliferation-of-neural-cells-in-rats-with-transient-cerebral-ischemia
#4
Dan Huang, Hong-Hong Liu, Zhen Yang, Yun Qu
OBJECTIVES: To determine the effects of non-invasive limb ischemic postconditioning (NLIP) on the behavioral performance and the expression and distribution of neural cells in rats with ischemic cortex. METHODS: Rats were randomly divided into 3 groups: sham group (n=10), ischemia/reperfusion (I/R) group (n=50), and NLIP group (n=50). Focal cerebral ischemia was induced by intraluminal MCAO in the rats in the I/R and NLIP groups, while no suture was inserted in the sham-operated rats...
May 2017: Sichuan da Xue Xue Bao. Yi Xue Ban, Journal of Sichuan University. Medical Science Edition
https://www.readbyqxmd.com/read/28614702/de-identification-of-psychiatric-intake-records-overview-of-2016-cegs-n-grid-shared-tasks-track-1
#5
Amber Stubbs, Michele Filannino, Özlem Uzuner
The 2016 CEGS N-GRID shared tasks for clinical records contained three tracks. Track 1 focused on de-identification of a new corpus of 1,000 psychiatric intake records. This track tackled de-identification in two sub-tracks: Track 1.A was a "sight unseen" task, where nine teams ran existing de-identification systems, without any modifications or training, on 600 new records in order to gauge how well systems generalize to new data. The best-performing system for this track scored an F1 of 0.799. Track 1.B was a traditional Natural Language Processing (NLP) shared task on de-identification, where 15 teams had two months to train their systems on the new data, then test it on an unannotated test set...
June 11, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28613206/-evolution-from-percutaneous-nephrolithotomy-to-mini-pcnl-in-supine-position-on-the-treatment-of-complex-renal-calculi-feasibility-study
#6
Fernando Ramón de Fata-Chillón, Helena Gimbernat-Díaz, Cristina Redondo-Redondo, Elisa Meilán-Hernández, Erika Mateo-Martínez
OBJECTIVES: Mini-PCNL is a potentially less invasive technique than standard percutaneous nephrolithotomy (PCNL). We present our experience and results comparing both approaches in large burden complex renal calculi. METHODS: Prospective non randomized study comparing PCNL (24/26F nephroscope; Group A) and Mini-PCNL (15/18F; Group B) perioperative and postoperative results, in 40 (20 each group) consecutive patients between 2013 and 2014. We analyze demographic data, hemoglobin drop, urine culture, stone characteristics, operative time, puncture, number and size of the tract, disintegration energy sources, nephrostomy placement, hospital stay, stone free rate and Clavien-Dindo complications...
June 2017: Archivos Españoles de Urología
https://www.readbyqxmd.com/read/28606869/predicting-mental-conditions-based-on-history-of-present-illness-in-psychiatric-notes-with-deep-neural-networks
#7
Tung Tran, Ramakanth Kavuluru
BACKGROUND: Applications of natural language processing to mental health notes are not common given the sensitive nature of the associated narratives. The CEGS N-GRID 2016 Shared Task in Clinical Natural Language Processing (NLP) changed this scenario by providing the first set of neuropsychiatric notes to participants. This study summarizes our efforts and results in proposing a novel data use case for this dataset as part of the third track in this shared task. OBJECTIVE: We explore the feasibility and effectiveness of predicting a set of common mental conditions a patient has based on the short textual description of patient's history of present illness typically occurring in the beginning of a psychiatric initial evaluation note...
June 9, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28598934/feasibility-and-utility-of-lexical-analysis-for-occupational-health-text
#8
Philip Harber, Gondy Leroy
OBJECTIVE: Assess feasibility and potential utility of natural language processing (NLP) for storing and analyzing occupational health data. METHODS: Basic NLP lexical analysis methods were applied to 89,000 Mine Safety and Health Administration (MSHA) free text records. Steps included tokenization, term and co-occurrence counts, term annotation, and identifying exposure-health effect relationships. Presence of terms in the Unified Medical Language System (UMLS) was assessed...
June 2017: Journal of Occupational and Environmental Medicine
https://www.readbyqxmd.com/read/28579533/de-identification-of-clinical-notes-via-recurrent-neural-network-and-conditional-random-field
#9
Zengjian Liu, Buzhou Tang, Xiaolong Wang, Qingcai Chen
De-identification, identifying information from data, such as protected health information (PHI) present in clinical data, is a critical step to enable data to be shared or published. The 2016 Centers of Excellence in Genomic Science (CEGS) Neuropsychiatric Genome-scale and RDOC Individualized Domains (N-GRID) clinical natural language processing (NLP) challenge contains a de-identification track in de-identifying electronic medical records (EMRs) (i.e., track 1). The challenge organizers provide 1000 annotated mental health records for this track, 600 out of which are used as a training set and 400 as a test set...
June 1, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28578250/increased-in-synthetic-cannabinoids-related-harms-results-from-a-longitudinal-web-based-content-analysis
#10
Francois R Lamy, Raminta Daniulaityte, Ramzi W Nahhas, Monica J Barratt, Alan G Smith, Amit Sheth, Silvia S Martins, Edward W Boyer, Robert G Carlson
BACKGROUND: Synthetic Cannabinoid Receptor Agonists (SCRA), also known as "K2" or "Spice," have drawn considerable attention due to their potential of abuse and harmful consequences. More research is needed to understand user experiences of SCRA-related effects. We use semi-automated information processing techniques through eDrugTrends platform to examine SCRA-related effects and their variations through a longitudinal content analysis of web-forum data. METHOD: English language posts from three drug-focused web-forums were extracted and analyzed between January 1st 2008 and September 30th 2015...
June 1, 2017: International Journal on Drug Policy
https://www.readbyqxmd.com/read/28571784/predictive-modeling-for-classification-of-positive-valence-system-symptom-severity-from-initial-psychiatric-evaluation-records
#11
Jose D Posada, Amie J Barda, Lingyun Shi, Diyang Xue, Victor Ruiz, Pei-Han Kuan, Neal D Ryan, Fuchiang Rich Tsui
In response to the challenges set forth by the CEGS N-GRID 2016 Shared Task in Clinical Natural Language Processing, we describe a framework to automatically classify initial psychiatric evaluation records to one of four positive valence system severities: absent, mild, moderate, or severe. We used a dataset provided by the event organizers to develop a framework comprised of natural language processing (NLP) modules and 3 predictive models (two decision tree models and one Bayesian network model) used in the competition...
May 29, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28561130/the-effects-of-natural-language-processing-on-cross-institutional-portability-of-influenza-case-detection-for-disease-surveillance
#12
Jeffrey P Ferraro, Ye Ye, Per H Gesteland, Peter J Haug, Fuchiang Rich Tsui, Gregory F Cooper, Rudy Van Bree, Thomas Ginter, Andrew J Nowalk, Michael Wagner
OBJECTIVES: This study evaluates the accuracy and portability of a natural language processing (NLP) tool for extracting clinical findings of influenza from clinical notes across two large healthcare systems. Effectiveness is evaluated on how well NLP supports downstream influenza case-detection for disease surveillance. METHODS: We independently developed two NLP parsers, one at Intermountain Healthcare (IH) in Utah and the other at University of Pittsburgh Medical Center (UPMC) using local clinical notes from emergency department (ED) encounters of influenza...
May 31, 2017: Applied Clinical Informatics
https://www.readbyqxmd.com/read/28542568/nesfatin-1-like-peptide-is-a-novel-metabolic-factor-that-suppresses-feeding-and-regulates-whole-body-energy-homeostasis-in-male-wistar-rats
#13
Kavishankar Gawli, Naresh Ramesh, Suraj Unniappan
Nucleobindin-1 has high sequence similarity to nucleobindin-2, which encodes the anorectic and metabolic peptide, nesfatin-1. We previously reported a nesfatin-1-like peptide (NLP), anorectic in fish and insulinotropic in mice islet beta-like cells. The main objective of this research was to determine whether NLP is a metabolic regulator in male Wistar rats. A single intraperitoneal (IP) injection of NLP (100 μg/kg BW) decreased food intake and increased ambulatory movement, without causing any change in total activity or energy expenditure when compared to saline-treated rats...
2017: PloS One
https://www.readbyqxmd.com/read/28529113/integrating-natural-language-processing-expertise-with-patient-safety-event-review-committees-to-improve-the-analysis-of-medication-events
#14
Allan Fong, Nicole Harriott, Donna M Walters, Hanan Foley, Richard Morrissey, Raj R Ratwani
OBJECTIVES: Many healthcare providers have implemented patient safety event reporting systems to better understand and improve patient safety. Reviewing and analyzing these reports is often time consuming and resource intensive because of both the quantity of reports and length of free-text descriptions in the reports. METHODS: Natural language processing (NLP) experts collaborated with clinical experts on a patient safety committee to assist in the identification and analysis of medication related patient safety events...
May 11, 2017: International Journal of Medical Informatics
https://www.readbyqxmd.com/read/28508772/concept-based-retrieval-from-critical-incident-reports
#15
Kerstin Denecke
BACKGROUND: Critical incident reporting systems (CIRS) are used as a means to collect anonymously entered information of incidents that occurred for example in a hospital. Analyzing this information helps to identify among others problems in the workflow, in the infrastructure or in processes. OBJECTIVES: The entire potential of these sources of experiential knowledge remains often unconsidered since retrieval of relevant reports and their analysis is difficult and time-consuming, and the reporting systems often do not provide support for these tasks...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28506958/enhancing-comparative-effectiveness-research-with-automated-pediatric-pneumonia-detection-in-a-multi-institutional-clinical-repository-a-phis-pilot-study
#16
Stephane Meystre, Ramkiran Gouripeddi, Joel Tieder, Jeffrey Simmons, Rajendu Srivastava, Samir Shah
BACKGROUND: Community-acquired pneumonia is a leading cause of pediatric morbidity. Administrative data are often used to conduct comparative effectiveness research (CER) with sufficient sample sizes to enhance detection of important outcomes. However, such studies are prone to misclassification errors because of the variable accuracy of discharge diagnosis codes. OBJECTIVE: The aim of this study was to develop an automated, scalable, and accurate method to determine the presence or absence of pneumonia in children using chest imaging reports...
May 15, 2017: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/28506904/ordinal-convolutional-neural-networks-for-predicting-rdoc-positive-valence-psychiatric-symptom-severity-scores
#17
Anthony Rios, Ramakanth Kavuluru
BACKGROUND: The CEGS N-GRID 2016 Shared Task in Clinical Natural Language Processing (NLP) provided a set of 1000 neuropsychiatric notes to participants as part of a competition to predict psychiatric symptom severity scores. This paper summarizes our methods, results, and experiences based on our participation in the second track of the shared task. OBJECTIVE: Classical methods of text classification usually fall into one of three problem types: binary, multi-class, and multi-label classification...
May 12, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28502651/rack-1-a-multifaceted-regulator-is-required-for-c-%C3%A2-elegans-innate-immunity-against-s-%C3%A2-flexneri-m9ot-infection
#18
Shanmugam Marudhupandiyan, Udayakumar Prithika, Boopathi Balasubramaniam, Krishnaswamy Balamurugan
The nematode C. elegans has the ability to clear off bacterial colonization in the intestine using pathogen specific innate immune response. Here, we show that C. elegans RACK-1 has been vital in determining the survival of worms under specific pathogenic infection. Among various pathogens tested, S. flexneri M9OT (SF) exhibited highest pathogenicity by killing rack-1 mutant worm-VC3013 earlier when compared to WT. The expression level of rack-1 mRNA was found to be decreased and it further indicated that the host translational event appeared to be affected during SF infection...
May 11, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28499156/treatment-of-chemical-cleaning-wastewater-and-cost-optimization-by-response-surface-methodology-coupled-nonlinear-programming
#19
Yang Yang, Zhen Zhou, Chenjie Lu, Yunke Chen, Honghua Ge, Libing Wang, Cheng Cheng
The real alkaline cleaning wastewater (ACW) was treated by a process consisting of neutralization, NaClO oxidation and aluminum sulfate (AS) coagulation, and a novel response surface methodology coupled nonlinear programming (RSM-NLP) approach was developed and used to optimize the oxidation-coagulation process under constraints of relevant discharge standards. Sulfuric acid neutralization effectively removed chemical oxygen demand (COD), surfactant alkylphenol ethoxylates (OP-10) and silicate at the optimum pH of 7...
May 9, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28489820/discovery-of-nitrate-cpk-nlp-signalling-in-central-nutrient-growth-networks
#20
Kun-Hsiang Liu, Yajie Niu, Mineko Konishi, Yue Wu, Hao Du, Hoo Sun Chung, Lei Li, Marie Boudsocq, Matthew McCormack, Shugo Maekawa, Tetsuya Ishida, Chao Zhang, Kevan Shokat, Shuichi Yanagisawa, Jen Sheen
Nutrient signalling integrates and coordinates gene expression, metabolism and growth. However, its primary molecular mechanisms remain incompletely understood in plants and animals. Here we report unique Ca(2+) signalling triggered by nitrate with live imaging of an ultrasensitive biosensor in Arabidopsis leaves and roots. A nitrate-sensitized and targeted functional genomic screen identifies subgroup III Ca(2+)-sensor protein kinases (CPKs) as master regulators that orchestrate primary nitrate responses. A chemical switch with the engineered mutant CPK10(M141G) circumvents embryo lethality and enables conditional analyses of cpk10 cpk30 cpk32 triple mutants to define comprehensive nitrate-associated regulatory and developmental programs...
May 10, 2017: Nature
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