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https://www.readbyqxmd.com/read/28919106/selecting-relevant-features-from-the-electronic-health-record-for-clinical-code-prediction
#1
Elyne Scheurwegs, Boris Cule, Kim Luyckx, Léon Luyten, Walter Daelemans
A multitude of information sources is present in the electronic health record (EHR), each of which can contain clues to automatically assign diagnosis and procedure codes. These sources however show information overlap and quality differences, which complicates the retrieval of these clues. Through feature selection, a denser representation with a consistent quality and less information overlap can be obtained. We introduce and compare coverage-based feature selection methods, based on confidence and information gain...
September 14, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28883198/analysis-of-annotated-data-models-for-improving-data-quality
#2
Hannes Ulrich, Ann-Kristin Kock-Schoppenhauer, Björn Andersen, Josef Ingenerf
The public Medical Data Models (MDM) portal with more than 9.000 annotated forms from clinical trials and other sources provides many research opportunities for the medical informatics community. It is mainly used to address the problem of heterogeneity by searching, mediating, reusing, and assessing data models, e. g. the semi-interactive curation of core data records in a special domain. Furthermore, it can be used as a benchmark for evaluating algorithms that create, transform, annotate, and analyse structured patient data...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28882809/the-user-knows-what-to-call-it-incorporating-patient-voice-through-user-contributed-tags-on-a-participatory-platform-about-health-management
#3
Annie T Chen, Rachel M Carriere, Samantha Jan Kaplan
BACKGROUND: Body listening, described as the act of paying attention to the body's signals and cues, can be an important component of long-term health management. OBJECTIVE: The aim of this study was to introduce and evaluate the Body Listening Project, an innovative effort to engage the public in the creation of a public resource-to leverage collective wisdom in the health domain. This project involved a website where people could contribute their experiences of and dialogue with others concerning body listening and self-management...
September 7, 2017: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/28830409/word2vec-inversion-and-traditional-text-classifiers-for-phenotyping-lupus
#4
Clayton A Turner, Alexander D Jacobs, Cassios K Marques, James C Oates, Diane L Kamen, Paul E Anderson, Jihad S Obeid
BACKGROUND: Identifying patients with certain clinical criteria based on manual chart review of doctors' notes is a daunting task given the massive amounts of text notes in the electronic health records (EHR). This task can be automated using text classifiers based on Natural Language Processing (NLP) techniques along with pattern recognition machine learning (ML) algorithms. The aim of this research is to evaluate the performance of traditional classifiers for identifying patients with Systemic Lupus Erythematosus (SLE) in comparison with a newer Bayesian word vector method...
August 22, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/28815139/semanticfind-locating-what-you-want-in-a-patient-record-not-just-what-you-ask-for
#5
John M Prager, Jennifer J Liang, Murthy V Devarakonda
We present a new model of patient record search, called SemanticFind, which goes beyond traditional textual and medical synonym matches by locating patient data that a clinician would want to see rather than just what they ask for. The new model is implemented by making extensive use of the UMLS semantic network, distributional semantics, and NLP, to match query terms along several dimensions in a patient record with the returned matches organized accordingly. The new approach finds all clinically related concepts without the user having to ask for them...
2017: AMIA Summits on Translational Science Proceedings
https://www.readbyqxmd.com/read/28797709/word-embeddings-and-recurrent-neural-networks-based-on-long-short-term-memory-nodes-in-supervised-biomedical-word-sense-disambiguation
#6
Antonio Jimeno Yepes
Word sense disambiguation helps identifying the proper sense of ambiguous words in text. With large terminologies such as the UMLS Metathesaurus ambiguities appear and highly effective disambiguation methods are required. Supervised learning algorithm methods are used as one of the approaches to perform disambiguation. Features extracted from the context of an ambiguous word are used to identify the proper sense of such a word. The type of features have an impact on machine learning methods, thus affect disambiguation performance...
August 7, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28733236/novel-tryptophan-metabolic-pathways-in-auxin-biosynthesis-in-silkworm
#7
Chiaki Yokoyama, Mami Takei, Yoshiaki Kouzuma, Shinji Nagata, Yoshihito Suzuki
In the course of our study of the biosynthetic pathway of auxin, a class of phytohormones, in insects, we proposed the biosynthetic pathway tryptophan (Trp)→indole-3-acetaldoxime (IAOx)→indole-3-acetadehyde (IAAld)→indole-3-acetic acid (IAA). In this study, we identified two branches in the metabolic pathways in the silkworm, possibly affecting the efficiency of IAA production: Trp→indole-3-pyruvic acid→indole-3-lactic acid and IAAld→indole-3-ethanol. We also determined the apparent conversion activities (2...
August 2017: Journal of Insect Physiology
https://www.readbyqxmd.com/read/28732500/linking-clinical-quality-indicators-to-research-evidence-a-case-study-in-asthma-management-for-children
#8
Miew Keen Choong, Guy Tsafnat, Peter Hibbert, William B Runciman, Enrico Coiera
BACKGROUND: Clinical quality indicators are used to monitor the performance of healthcare services and should wherever possible be based on research evidence. Little is known however about the extent to which indicators in common use are based on research. The objective of this study is to measure the extent to which clinical quality indicators used in asthma management in children with outcome measurements can be linked to results in randomised controlled clinical trial (RCT) reports...
July 21, 2017: BMC Health Services Research
https://www.readbyqxmd.com/read/28732343/an-ultrasensitive-electrochemical-biosensor-for-polynucleotide-kinase-assay-based-on-gold-nanoparticle-mediated-lambda-exonuclease-cleavage-induced-signal-amplification
#9
Lin Cui, Yueying Li, Mengfei Lu, Bo Tang, Chun-Yang Zhang
Polynucleotide kinase (PNK) plays an essential role in cellular nucleic acid metabolism and the cellular response to DNA damage. However, conventional methods for PNK assay suffer from low sensitivity and involve multiple steps. Herein, we develop a simply electrochemical method for sensitive detection of PNK activity on the basis of Au nanoparticle (AuNP)-mediated lambda exonuclease cleavage-induced signal amplification. We use [Ru(NH3)6](3+) as the electrochemically active indicator and design two DNA strands (i...
July 13, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28688492/quantifying-the-informativeness-for-biomedical-literature-summarization-an-itemset-mining-method
#10
Milad Moradi, Nasser Ghadiri
OBJECTIVE: Automatic text summarization tools can help users in the biomedical domain to access information efficiently from a large volume of scientific literature and other sources of text documents. In this paper, we propose a summarization method that combines itemset mining and domain knowledge to construct a concept-based model and to extract the main subtopics from an input document. Our summarizer quantifies the informativeness of each sentence using the support values of itemsets appearing in the sentence...
July 2017: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/28602906/counting-trees-in-random-forests-predicting-symptom-severity-in-psychiatric-intake-reports
#11
Elyne Scheurwegs, Madhumita Sushil, Stéphan Tulkens, Walter Daelemans, Kim Luyckx
The CEGS N-GRID 2016 Shared Task (Filannino et al., 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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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