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https://www.readbyqxmd.com/read/28602906/counting-trees-in-random-forests-predicting-symptom-severity-in-psychiatric-intake-reports
#1
Elyne Scheurwegs, Madhumita Sushil, Stéphan Tulkens, Walter Daelemans, Kim Luyckx
The CEGS N-GRID 2016 Shared Task (Filannino, Stubbs, Uzuner (2017)) in Clinical Natural Language Processing introduces the assignment of a severity score to a psychiatric symptom, based on a psychiatric intake report. We present a method that employs the inherent interview-like structure of the report to extract relevant information from the report and generate a representation. The representation consists of a restricted set of psychiatric concepts (and the context they occur in), identified using medical concepts defined in UMLS that are directly related to the psychiatric diagnoses present in the Diagnostic and Statistical Manual of Mental Disorders, 4th Edition (DSM-IV) ontology...
June 7, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28598934/feasibility-and-utility-of-lexical-analysis-for-occupational-health-text
#2
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/28508773/word-sense-disambiguation-of-medical-terms-via-recurrent-convolutional-neural-networks
#3
Sven Festag, Cord Spreckelsen
BACKGROUND: Tagging text data with codes representing biomedical concepts plays an important role in medical data management and analysis. A problem occurs if there are ambiguous words linked to several concepts. OBJECTIVES AND METHODS: This study aims at investigating word sense disambiguation based on word embedding and recurrent convolutional neural networks. The study focuses on terms mapped to multiple concepts of the Unified Medical Language System (UMLS)...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28423845/appraising-healthcare-delivery-provision-a-framework-to-model-business-processes
#4
Daniela Luzi, Fabrizio Pecoraro, Oscar Tamburis
Children are dependent on a reliable healthcare system, especially for the delivery of care which crosses the primary/secondary care boundary. A methodology based on UML has been developed to capture and single out meaningful parts of the child healthcare pathways in order to facilitate comparison among 30 EU countries within the MOCHA project. A first application of this methodology has been reported considering asthma management as an example.
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28400312/assigning-clinical-codes-with-data-driven-concept-representation-on-dutch-clinical-free-text
#5
Elyne Scheurwegs, Kim Luyckx, Léon Luyten, Bart Goethals, Walter Daelemans
Clinical codes are used for public reporting purposes, are fundamental to determining public financing for hospitals, and form the basis for reimbursement claims to insurance providers. They are assigned to a patient stay to reflect the diagnosis and performed procedures during that stay. This paper aims to enrich algorithms for automated clinical coding by taking a data-driven approach and by using unsupervised and semi-supervised techniques for the extraction of multi-word expressions that convey a generalisable medical meaning (referred to as concepts)...
April 8, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28340708/phosphoserine-imprinted-nanosensor-for-detection-of-cancer-antigen-125
#6
Sibel Büyüktiryaki, Rıdvan Say, Adil Denizli, Arzu Ersöz
Cancer antigen 125 (CA 125) is widely used as diagnostic biomarker for ovarian cancer. Change in the concentration level of CA 125 is associated with disease progression or regression. CA 125 posseses a phosphorylation site and protein backbone is phosphorylated on serine, before secretion. In this study, we have developed an imprinting method for CA 125 recognition and determination. In this method, methacryloyl antipyrine europium (III) [(MAAP)2-Eu(III)] and methacryloyl antipyrine terbium (III) [(MAAP)2-Tb(III)] have been used as new metal-chelating monomers via metal coordination-chelation interactions...
May 15, 2017: Talanta
https://www.readbyqxmd.com/read/28330106/enhanced-production-of-pectinase-by-aspergillus-terreus-ncft-4269-10-using-banana-peels-as-substrate
#7
Bijay Kumar Sethi, Prativa Kumari Nanda, Santilata Sahoo
Aspergillus terreus NCFT4269.10 was implemented in solid-state (SSF) and liquid static surface fermentation (LSSF) for biosynthesis of pectinase. Amongst various substrates, like, mustard oil cake, neem oil cake, groundnut oil cake, black gram peels, green gram peels, chickling vetch peels/grass pea peels wheat bran, pearl millet residues, finger millet waste, broken rice, banana peels (BP), apple pomace (AP) and orange peels, banana peel (Musa paradisiaca L.; Family: Musaceae) was most suitable for pectinase biosynthesis (LSSF: 400 ± 21...
June 2016: 3 Biotech
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/28286031/a-passage-retrieval-method-based-on-probabilistic-information-retrieval-model-and-umls-concepts-in-biomedical-question-answering
#9
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/28241760/early-recognition-of-multiple-sclerosis-using-natural-language-processing-of-the-electronic-health-record
#10
Herbert S Chase, Lindsey R Mitrani, Gabriel G Lu, Dominick J Fulgieri
BACKGROUND: Diagnostic accuracy might be improved by algorithms that searched patients' clinical notes in the electronic health record (EHR) for signs and symptoms of diseases such as multiple sclerosis (MS). The focus this study was to determine if patients with MS could be identified from their clinical notes prior to the initial recognition by their healthcare providers. METHODS: An MS-enriched cohort of patients with well-established MS (n = 165) and controls (n = 545), was generated from the adult outpatient clinic...
February 28, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/28131722/development-and-empirical-user-centered-evaluation-of-semantically-based-query-recommendation-for-an-electronic-health-record-search-engine
#11
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)...
March 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28112161/synchronous-deglacial-thermocline-and-deep-water-ventilation-in-the-eastern-equatorial-pacific
#12
Natalie E Umling, Robert C Thunell
The deep ocean is most likely the primary source of the radiocarbon-depleted CO2 released to the atmosphere during the last deglaciation. While there are well-documented millennial scale Δ(14)C changes during the most recent deglaciation, most marine records lack the resolution needed to identify more rapid ventilation events. Furthermore, potential age model problems with marine Δ(14)C records may obscure our understanding of the phase relationship between inter-ocean ventilation changes. Here we reconstruct changes in deep water and thermocline radiocarbon content over the last deglaciation in the eastern equatorial Pacific (EEP) using benthic and planktonic foraminiferal (14)C...
January 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28092493/enhancing-collaborative-case-diagnoses-through-unified-medical-language-system-based-disambiguation-a-case-study-of-the-zika-virus
#13
Albert Moreira, Raúl Alonso-Calvo, Alberto Muñoz, José Crespo
BACKGROUND: During clinical case diagnoses, especially in low-resourced areas, the use of vocabularies within Unified Medical Language System (UMLS) can strengthen discussions between health professionals and, in certain cases, eliminate the need, enabling faster treatment. INTRODUCTION: This article presents the benefits of using UMLS as a collaborative discussion tool and verifies its impact. MATERIALS AND METHODS: The Sanar system has been improved by UMLS when using text retrieval to extract relevant medical concepts from cases investigated by the user and to provide contextualized searches of related articles...
January 16, 2017: Telemedicine Journal and E-health: the Official Journal of the American Telemedicine Association
https://www.readbyqxmd.com/read/28077885/designing-and-implementation-of-retina-image-drawing-system-and-automatic-report-generation-from-retina-examinations
#14
Reza Safdari, Mehrshad Mokhtaran, Shahram Tahmasebian
INTRODUCTION: Electronic medical records as one of major parts of electronic health records is an important application of Medical Informatics. EMR includes different types of data, Graphical items being one of these data types. To this end, a standard structure for storing and recovering and finally exchanging this data type is required. In order to standardize information items in this research, UMLS standard is used. In this research, graphical information from fondues designing in retina surgery forms is used for the task of implementation...
October 2016: Acta Informatica Medica: AIM
https://www.readbyqxmd.com/read/28069052/toward-a-comprehensive-drug-ontology-extraction-of-drug-indication-relations-from-diverse-information-sources
#15
Mark E Sharp
BACKGROUND: Drug ontologies could help pharmaceutical researchers overcome information overload and speed the pace of drug discovery, thus benefiting the industry and patients alike. Drug-disease relations, specifically drug-indication relations, are a prime candidate for representation in ontologies. There is a wealth of available drug-indication information, but structuring and integrating it is challenging. RESULTS: We created a drug-indication database (DID) of data from 12 openly available, commercially available, and proprietary information sources, integrated by terminological normalization to UMLS and other authorities...
January 10, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27884812/consumers-use-of-umls-concepts-on-social-media-diabetes-related-textual-data-analysis-in-blog-and-social-q-a-sites
#16
Min Sook Park, Zhe He, Zhiwei Chen, Sanghee Oh, Jiang Bian
BACKGROUND: The widely known terminology gap between health professionals and health consumers hinders effective information seeking for consumers. OBJECTIVE: The aim of this study was to better understand consumers' usage of medical concepts by evaluating the coverage of concepts and semantic types of the Unified Medical Language System (UMLS) on diabetes-related postings in 2 types of social media: blogs and social question and answer (Q&A). METHODS: We collected 2 types of social media data: (1) a total of 3711 blogs tagged with "diabetes" on Tumblr posted between February and October 2015; and (2) a total of 58,422 questions and associated answers posted between 2009 and 2014 in the diabetes category of Yahoo! Answers...
November 24, 2016: JMIR Medical Informatics
https://www.readbyqxmd.com/read/27810481/evaluating-semantic-similarity-between-chinese-biomedical-terms-through-multiple-ontologies-with-score-normalization-an-initial-study
#17
Wenxin Ning, Ming Yu, Dehua Kong
BACKGROUND: Semantic similarity estimation significantly promotes the understanding of natural language resources and supports medical decision making. Previous studies have investigated semantic similarity and relatedness estimation between biomedical terms through resources in English, such as SNOMED-CT or UMLS. However, very limited studies focused on the Chinese language, and technology on natural language processing and text mining of medical documents in China is urgently needed...
December 2016: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/27777627/fedrr-fast-exhaustive-detection-of-redundant-hierarchical-relations-for-quality-improvement-of-large-biomedical-ontologies
#18
Guangming Xing, Guo-Qiang Zhang, Licong Cui
BACKGROUND: Redundant hierarchical relations refer to such patterns as two paths from one concept to another, one with length one (direct) and the other with length greater than one (indirect). Each redundant relation represents a possibly unintended defect that needs to be corrected in the ontology quality assurance process. Detecting and eliminating redundant relations would help improve the results of all methods relying on the relevant ontological systems as knowledge source, such as the computation of semantic distance between concepts and for ontology matching and alignment...
2016: BioData Mining
https://www.readbyqxmd.com/read/27659604/automatic-classification-of-registered-clinical-trials-towards-the-global-burden-of-diseases-taxonomy-of-diseases-and-injuries
#19
Ignacio Atal, Jean-David Zeitoun, Aurélie Névéol, Philippe Ravaud, Raphaël Porcher, Ludovic Trinquart
BACKGROUND: Clinical trial registries may allow for producing a global mapping of health research. However, health conditions are not described with standardized taxonomies in registries. Previous work analyzed clinical trial registries to improve the retrieval of relevant clinical trials for patients. However, no previous work has classified clinical trials across diseases using a standardized taxonomy allowing a comparison between global health research and global burden across diseases...
2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27643689/mapping-phenotypic-information-in-heterogeneous-textual-sources-to-a-domain-specific-terminological-resource
#20
Noha Alnazzawi, Paul Thompson, Sophia Ananiadou
Biomedical literature articles and narrative content from Electronic Health Records (EHRs) both constitute rich sources of disease-phenotype information. Phenotype concepts may be mentioned in text in multiple ways, using phrases with a variety of structures. This variability stems partly from the different backgrounds of the authors, but also from the different writing styles typically used in each text type. Since EHR narrative reports and literature articles contain different but complementary types of valuable information, combining details from each text type can help to uncover new disease-phenotype associations...
2016: PloS One
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