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https://www.readbyqxmd.com/read/28131722/development-and-empirical-user-centered-evaluation-of-semantically-based-query-recommendation-for-an-electronic-health-record-search-engine
#1
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/28112161/synchronous-deglacial-thermocline-and-deep-water-ventilation-in-the-eastern-equatorial-pacific
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/27605431/purification-characterization-cytotoxicity-and-anticancer-activities-of-l-asparaginase-anti-colon-cancer-protein-from-the-newly-isolated-alkaliphilic-streptomyces-fradiae-neae-82
#11
Noura El-Ahmady El-Naggar, Sahar F Deraz, Hoda M Soliman, Nehal M El-Deeb, Sara M El-Ewasy
L-asparaginase is an important enzyme as therapeutic agents used in combination with other drugs in the treatment of acute lymphoblastic leukemia. A newly isolated actinomycetes strain, Streptomyces sp. NEAE-82, was potentially producing extracellular L-asparaginase, it was identified as Streptomyces fradiae NEAE-82, sequencing product was deposited in the GenBank database under accession number KJ467538. L-asparaginase was purified from the crude enzyme using ammonium sulfate precipitation, dialysis and ion exchange chromatography using DEAE Sepharose CL-6B...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27577424/converting-odm-metadata-to-fhir-questionnaire-resources
#12
Justin Doods, Philipp Neuhaus, Martin Dugas
Interoperability between systems and data sharing between domains is becoming more and more important. The portal medical-data-models.org offers more than 5.300 UMLS annotated forms in CDISC ODM format in order to support interoperability, but several additional export formats are available. CDISC's ODM and HL7's framework FHIR Questionnaire resource were analyzed, a mapping between elements created and a converter implemented. The developed converter was integrated into the portal with FHIR Questionnaire XML or JSON download options...
2016: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/27577422/thesaurus-based-hierarchical-semantic-grouping-of-medical-terms-in-information-extraction
#13
Yassine Lassoued, Léa Deleris
In this paper we describe a semantic approach for grouping medical terms into a hierarchy of concepts based on the UMLS meta-thesaurus. The context of this work is Medical Recap, a Web system that automatically extracts risk information from PubMed abstracts, and then aggregates this knowledge into dependence graphs or Bayesian networks.
2016: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/27577388/key-data-elements-in-myeloid-leukemia
#14
Julian Varghese, Christian Holz, Phillip Neuhaus, Massimo Bernardi, Alexandra Boehm, Arnold Ganser, Steven Gore, Mark Heaney, Andreas Hochhaus, Wolf-Karsten Hofmann, Utz Krug, Carsten Müller-Tidow, Alexandra Smith, Ansgar Weltermann, Theo de Witte, Rüdiger Hehlmann, Martin Dugas
Data standards consisting of key data elements for clinical routine and trial documentation harmonize documentation within and across different health care institutions making documentation more efficient and improving scientific data analysis. This work focusses on the field of myeloid leukemia (ML), where a semantic core of common data elements (CDEs) in routine and trial documentation is established by automatic UMLS-based form analysis of existing documentation models. These CDEs (n = 227) were initially reviewed and commented by leukemia experts before they were systematically surveyed by an international voting process through seven hematologists of four countries...
2016: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/27577352/patient-centered-event-representation-for-the-treatment-of-multifactorial-diseases-current-progress-and-challenges
#15
Yihan Deng, Jan Gaebel, Kerstin Denecke
Events such as clinical interventions, adverse drug events are one of the basic semantic units in the clinical workflow and are the foundation of the pathway representation. Current research has mainly concentrated on event recognition through concept mapping using from medical ontologies (UMLS, SNOMED CT) and gene relation detection in the biological context. However, the analysis of the patient status and the interaction between the patient status and a context event is still at the primary stage. In order to realize an efficient personalized treatment design and pathway planning, the correlation between a patient status and different types of clinical events should be analyzed...
2016: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/27577335/attempting-to-use-metamap-in-clinical-practice-a-feasibility-study-on-the-identification-of-medical-concepts-from-italian-clinical-notes
#16
Emma Chiaramello, Alessia Paglialonga, Francesco Pinciroli, Gabriella Tognola
This study assessed the feasibility of using MetaMap to identify medical concepts from clinical notes written in Italian. We performed two experiments: in "EXP 1", we used MetaMap to annotate Italian texts using a knowledge source consisting of Italian UMLS sources only; in "EXP 2", we used MetaMap to analyze an English unsupervised translated version of the original Italian texts. We considered medical concepts related to three semantic categories: "Disorders", "Findings" and "Symptoms". Average recall, precision and F-measure were equal to 0...
2016: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/27571414/statistical-techniques-complement-uml-when-developing-domain-models-of-complex-dynamical-biosystems
#17
Richard A Williams, Jon Timmis, Eva E Qwarnstrom
Computational modelling and simulation is increasingly being used to complement traditional wet-lab techniques when investigating the mechanistic behaviours of complex biological systems. In order to ensure computational models are fit for purpose, it is essential that the abstracted view of biology captured in the computational model, is clearly and unambiguously defined within a conceptual model of the biological domain (a domain model), that acts to accurately represent the biological system and to document the functional requirements for the resultant computational model...
2016: PloS One
https://www.readbyqxmd.com/read/27570647/learning-low-dimensional-representations-of-medical-concepts
#18
Youngduck Choi, Chill Yi-I Chiu, David Sontag
We show how to learn low-dimensional representations (embeddings) of a wide range of concepts in medicine, including diseases (e.g., ICD9 codes), medications, procedures, and laboratory tests. We expect that these embeddings will be useful across medical informatics for tasks such as cohort selection and patient summarization. These embeddings are learned using a technique called neural language modeling from the natural language processing community. However, rather than learning the embeddings solely from text, we show how to learn the embeddings from claims data, which is widely available both to providers and to payers...
2016: AMIA Summits on Translational Science Proceedings
https://www.readbyqxmd.com/read/27566685/respiratory-gated-time-of-flight-pet-ct-during-whole-body-scan-for-lung-lesions-feasibility-in-a-routine-clinical-setting-and-quantitative-analysis
#19
Naohisa Suzawa, Yasutaka Ichikawa, Masaki Ishida, Yoya Tomita, Ryohei Nakayama, Hajime Sakuma
PURPOSE: To demonstrate the feasibility of respiratory gating during whole-body scan for lung lesions in routine (18)F-FDG PET/CT examinations using a time-of-flight (TOF)-capable scanner to determine the effect of respiratory gating on reduction of both misregistration (between CT and PET) and image blurring, and on improvement of the maximum standardized uptake value (SUVmax). MATERIALS AND METHODS: Patients with lung lesions who received FDG PET/CT were prospectively studied...
December 2016: Annals of Nuclear Medicine
https://www.readbyqxmd.com/read/27497800/evaluating-electronic-health-record-data-sources-and-algorithmic-approaches-to-identify-hypertensive-individuals
#20
Pedro L Teixeira, Wei-Qi Wei, Robert M Cronin, Huan Mo, Jacob P VanHouten, Robert J Carroll, Eric LaRose, Lisa A Bastarache, S Trent Rosenbloom, Todd L Edwards, Dan M Roden, Thomas A Lasko, Richard A Dart, Anne M Nikolai, Peggy L Peissig, Joshua C Denny
OBJECTIVE: Phenotyping algorithms applied to electronic health record (EHR) data enable investigators to identify large cohorts for clinical and genomic research. Algorithm development is often iterative, depends on fallible investigator intuition, and is time- and labor-intensive. We developed and evaluated 4 types of phenotyping algorithms and categories of EHR information to identify hypertensive individuals and controls and provide a portable module for implementation at other sites...
January 2017: Journal of the American Medical Informatics Association: JAMIA
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