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https://www.readbyqxmd.com/read/29335238/automating-quality-measures-for-heart-failure-using-natural-language-processing-a-descriptive-study-in-the-department-of-veterans-affairs
#1
Jennifer Hornung Garvin, Youngjun Kim, Glenn Temple Gobbel, Michael E Matheny, Andrew Redd, Bruce E Bray, Paul Heidenreich, Dan Bolton, Julia Heavirland, Natalie Kelly, Ruth Reeves, Megha Kalsy, Mary Kane Goldstein, Stephane M Meystre
BACKGROUND: We developed an accurate, stakeholder-informed, automated, natural language processing (NLP) system to measure the quality of heart failure (HF) inpatient care, and explored the potential for adoption of this system within an integrated health care system. OBJECTIVE: To accurately automate a United States Department of Veterans Affairs (VA) quality measure for inpatients with HF. METHODS: We automated the HF quality measure Congestive Heart Failure Inpatient Measure 19 (CHI19) that identifies whether a given patient has left ventricular ejection fraction (LVEF) <40%, and if so, whether an angiotensin-converting enzyme inhibitor or angiotensin-receptor blocker was prescribed at discharge if there were no contraindications...
January 15, 2018: JMIR Medical Informatics
https://www.readbyqxmd.com/read/29309523/protein-classification-using-modified-n-grams-and-skip-grams
#2
S M Ashiqul Islam, Benjamin J Heil, Christopher Michel Kearney, Erich J Baker
Motivation: Classification by supervised machine learning greatly facilitates the annotation of protein characteristics from their primary sequence. However, the feature generation step in this process requires detailed knowledge of attributes used to classify the proteins. Lack of this knowledge risks the selection of irrelevant features, resulting in a faulty model. In this study, we introduce a supervised protein classification method with a novel means of automating the work-intensive feature generation step via a Natural Language Processing (NLP)-dependent model, using a modified combination of n-grams and skip-grams (m- NGSG)...
December 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29301098/an-antimicrobial-peptide-and-its-neuronal-receptor-regulate-dendrite-degeneration-in-aging-and-infection
#3
Lezi E, Ting Zhou, Sehwon Koh, Marian Chuang, Ruchira Sharma, Nathalie Pujol, Andrew D Chisholm, Cagla Eroglu, Hiroaki Matsunami, Dong Yan
Infections have been identified as possible risk factors for aging-related neurodegenerative diseases, but it remains unclear whether infection-related immune molecules have a causative role in neurodegeneration during aging. Here, we reveal an unexpected role of an epidermally expressed antimicrobial peptide, NLP-29 (neuropeptide-like protein 29), in triggering aging-associated dendrite degeneration in C. elegans. The age-dependent increase of nlp-29 expression is regulated by the epidermal tir-1/SARM-pmk-1/p38 MAPK innate immunity pathway...
January 3, 2018: Neuron
https://www.readbyqxmd.com/read/29300701/speech2health-a-mobile-framework-for-monitoring-dietary-composition-from-spoken-data
#4
Niloofar Hezarjaribi, Sepideh Mazrouee, Hassan Ghasemzadeh
Diet and physical activity are known as important lifestyle factors in self-management and prevention of many chronic diseases. Mobile sensors such as accelerometers have been used to measure physical activity or detect eating time. In many intervention studies, however, stringent monitoring of overall dietary composition and energy intake is needed. Currently, such a monitoring relies on self-reported data by either entering text or taking an image that represents food intake. These approaches suffer from limitations such as low adherence in technology adoption and time sensitivity to the diet intake context...
January 2018: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/29298665/analysis-of-microarrays-of-mir-34a-and-its-identification-of-prospective-target-gene-signature-in-hepatocellular-carcinoma
#5
Fang-Hui Ren, Hong Yang, Rong-Quan He, Jing-Ning Lu, Xing-Gu Lin, Hai-Wei Liang, Yi-Wu Dang, Zhen-Bo Feng, Gang Chen, Dian-Zhong Luo
BACKGROUND: Currently, some studies have demonstrated that miR-34a could serve as a suppressor of several cancers including hepatocellular carcinoma (HCC). Previously, we discovered that miR-34a was downregulated in HCC and involved in the tumorigenesis and progression of HCC; however, the mechanism remains unclear. The purpose of this study was to estimate the expression of miR-34a in HCC by applying the microarray profiles and analyzing the predicted targets of miR-34a and their related biological pathways of HCC...
January 3, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29261751/egard-extracting-associations-between-genomic-anomalies-and-drug-responses-from-text
#6
A S M Ashique Mahmood, Shruti Rao, Peter McGarvey, Cathy Wu, Subha Madhavan, K Vijay-Shanker
Tumor molecular profiling plays an integral role in identifying genomic anomalies which may help in personalizing cancer treatments, improving patient outcomes and minimizing risks associated with different therapies. However, critical information regarding the evidence of clinical utility of such anomalies is largely buried in biomedical literature. It is becoming prohibitive for biocurators, clinical researchers and oncologists to keep up with the rapidly growing volume and breadth of information, especially those that describe therapeutic implications of biomarkers and therefore relevant for treatment selection...
2017: PloS One
https://www.readbyqxmd.com/read/29242345/eudicot-plant-specific-sphingolipids-determine-host-selectivity-of-microbial-nlp-cytolysins
#7
Tea Lenarčič, Isabell Albert, Hannah Böhm, Vesna Hodnik, Katja Pirc, Apolonija B Zavec, Marjetka Podobnik, David Pahovnik, Ema Žagar, Rory Pruitt, Peter Greimel, Akiko Yamaji-Hasegawa, Toshihide Kobayashi, Agnieszka Zienkiewicz, Jasmin Gömann, Jenny C Mortimer, Lin Fang, Adiilah Mamode-Cassim, Magali Deleu, Laurence Lins, Claudia Oecking, Ivo Feussner, Sébastien Mongrand, Gregor Anderluh, Thorsten Nürnberger
Necrosis and ethylene-inducing peptide 1-like (NLP) proteins constitute a superfamily of proteins produced by plant pathogenic bacteria, fungi, and oomycetes. Many NLPs are cytotoxins that facilitate microbial infection of eudicot, but not of monocot plants. Here, we report glycosylinositol phosphorylceramide (GIPC) sphingolipids as NLP toxin receptors. Plant mutants with altered GIPC composition were more resistant to NLP toxins. Binding studies and x-ray crystallography showed that NLPs form complexes with terminal monomeric hexose moieties of GIPCs that result in conformational changes within the toxin...
December 15, 2017: Science
https://www.readbyqxmd.com/read/29221286/automatic-lung-rads%C3%A2-classification-with-a-natural-language-processing-system
#8
Sebastian E Beyer, Brady J McKee, Shawn M Regis, Andrea B McKee, Sebastian Flacke, Gilan El Saadawi, Christoph Wald
Background: Our aim was to train a natural language processing (NLP) algorithm to capture imaging characteristics of lung nodules reported in a structured CT report and suggest the applicable Lung-RADS™ (LR) category. Methods: Our study included structured, clinical reports of consecutive CT lung screening (CTLS) exams performed from 08/2014 to 08/2015 at an ACR accredited Lung Cancer Screening Center. All patients screened were at high-risk for lung cancer according to the NCCN Guidelines®...
September 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/29218888/identifying-natural-health-product-and-dietary-supplement-information-within-adverse-event-reporting-systems
#9
Vivekanand Sharma, Indra Neil Sarkar
Data on safety and efficacy issues associated with natural health products and dietary supplements (NHP&S) remains largely cloistered within domain specific databases or embedded within general biomedical data sources. A major challenge in leveraging analytic approaches on such data is due to the inefficient ability to retrieve relevant data, which includes a general lack of interoperability among related sources. This study developed a thesaurus of NHP&S ingredient terms that can be used by existing biomedical natural language processing (NLP) tools for extracting information of interest...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218408/transcription-profiling-and-identification-of-infection-related-genes-in-phytophthora-cactorum
#10
Xiao-Ren Chen, Shen-Xin Huang, Ye Zhang, Gui-Lin Sheng, Bo-Yue Zhang, Qi-Yuan Li, Feng Zhu, Jing-You Xu
Phytophthora cactorum, an oomycete pathogen, infects more than 200 plant species within several plant families. To gain insight into the repertoire of the infection-related genes of P. cactorum, Illumina RNA-Seq was used to perform a global transcriptome analysis of three life cycle stages of the pathogen, mycelia (MY), zoospores (ZO) and germinating cysts with germ tubes (GC). From over 9.8 million Illumina reads for each library, 18,402, 18,569 and 19,443 distinct genes were identified for MY, ZO and GC libraries, respectively...
December 7, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29212484/clinical-features-of-visual-disturbances-secondary-to-isolated-sphenoid-sinus-inflammatory-diseases
#11
Lanlan Chen, Libin Jiang, Bentao Yang, Prem S Subramanian
BACKGROUND: Visual disturbances associated with isolated sphenoid sinus inflammatory diseases (ISSIDs) are easily misdiagnosed due to the nonspecific symptoms and undetectable anatomical location. The main objective of this retrospective case series is to investigate the clinical features of visual disturbances secondary to ISSIDs. METHODS: Clinical data of 23 patients with unilateral or bilateral visual disturbances secondary to ISSIDs from 2004 to 2014 with new symptoms were collected...
December 6, 2017: BMC Ophthalmology
https://www.readbyqxmd.com/read/29202185/clinical-documentation-variations-and-nlp-system-portability-a-case-study-in-asthma-birth-cohorts-across-institutions
#12
Sunghwan Sohn, Yanshan Wang, Chung-Il Wi, Elizabeth A Krusemark, Euijung Ryu, Mir H Ali, Young J Juhn, Hongfang Liu
Objective: To assess clinical documentation variations across health care institutions using different electronic medical record systems and investigate how they affect natural language processing (NLP) system portability. Materials and Methods: Birth cohorts from Mayo Clinic and Sanford Children's Hospital (SCH) were used in this study (n = 298 for each). Documentation variations regarding asthma between the 2 cohorts were examined in various aspects: (1) overall corpus at the word level (ie, lexical variation), (2) topics and asthma-related concepts (ie, semantic variation), and (3) clinical note types (ie, process variation)...
November 30, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29201171/an-integrated-bioinformatical-analysis-of-mir-19a-target-genes-in-multiple-myeloma
#13
Hongyan Lv, Xianda Wu, Guiru Ma, Lixia Sun, Jianbo Meng, Xiaoning Song, Jinqiao Zhang
MicroRNA (miR)-19a, as an oncomiR, has been studied in several types of cancer; however, its role in the development and progression of multiple myeloma (MM) remains unclear. The present study used a bioinformatics approach to investigate the involvement of miR-19a in MM. miR-19a targets were predicted using target prediction programs, followed by screening for differentially expressed genes in MM. The function of these genes was then annotated using gene ontology term enrichment, signaling pathway enrichment and protein-protein interaction (PPI) analysis...
November 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/29191207/medical-subdomain-classification-of-clinical-notes-using-a-machine-learning-based-natural-language-processing-approach
#14
Wei-Hung Weng, Kavishwar B Wagholikar, Alexa T McCray, Peter Szolovits, Henry C Chueh
BACKGROUND: The medical subdomain of a clinical note, such as cardiology or neurology, is useful content-derived metadata for developing machine learning downstream applications. To classify the medical subdomain of a note accurately, we have constructed a machine learning-based natural language processing (NLP) pipeline and developed medical subdomain classifiers based on the content of the note. METHODS: We constructed the pipeline using the clinical NLP system, clinical Text Analysis and Knowledge Extraction System (cTAKES), the Unified Medical Language System (UMLS) Metathesaurus, Semantic Network, and learning algorithms to extract features from two datasets - clinical notes from Integrating Data for Analysis, Anonymization, and Sharing (iDASH) data repository (n = 431) and Massachusetts General Hospital (MGH) (n = 91,237), and built medical subdomain classifiers with different combinations of data representation methods and supervised learning algorithms...
December 1, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/29186491/clamp-a-toolkit-for-efficiently-building-customized-clinical-natural-language-processing-pipelines
#15
Ergin Soysal, Jingqi Wang, Min Jiang, Yonghui Wu, Serguei Pakhomov, Hongfang Liu, Hua Xu
Existing general clinical natural language processing (NLP) systems such as MetaMap and Clinical Text Analysis and Knowledge Extraction System have been successfully applied to information extraction from clinical text. However, end users often have to customize existing systems for their individual tasks, which can require substantial NLP skills. Here we present CLAMP (Clinical Language Annotation, Modeling, and Processing), a newly developed clinical NLP toolkit that provides not only state-of-the-art NLP components, but also a user-friendly graphic user interface that can help users quickly build customized NLP pipelines for their individual applications...
November 24, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29176335/acute-angle-closure-glaucoma-as-a-first-presentation-of-coats-disease-a-case-report
#16
Mazen Amro, Ali A Haydar, Sylvain El-Khoury, Karim F Tomey, George Cherfan, Ziad Khoueir
PURPOSE: To report an unusual first manifestation of Coats' disease presenting as an acute angle closure glaucoma attack in an adult patient. PATIENTS AND METHODS: A 37-year-old African woman presented to the emergency department with severe headache, ocular pain, and no light perception (NLP) in the left eye. The left pupil was mid-dilated and nonreactive, and the intraocular pressure by applanation tonometry was 47▒mm Hg. Slit-lamp examination revealed anterior subcapsular opacification (glaukomflecken), posterior synechiae, and total angle closure with iris-bombé...
November 23, 2017: Journal of Glaucoma
https://www.readbyqxmd.com/read/29170941/a-sibling-mediated-intervention-for-children-with-autism-spectrum-disorder-using-the-natural-language-paradigm-nlp
#17
Vicki Spector, Marjorie H Charlop
We taught three typically developing siblings to occasion speech by implementing the Natural Language Paradigm (NLP) with their brothers with autism spectrum disorder (ASD). A non-concurrent multiple baseline design across children with ASD and sibling dyads was used. Ancillary behaviors of happiness, play, and joint attention for the children with ASD were recorded. Generalization of speech for the children with ASD across setting and peers was also measured. During baseline, the children with ASD displayed few target speech behaviors and the siblings inconsistently occasioned speech from their brothers...
November 23, 2017: Journal of Autism and Developmental Disorders
https://www.readbyqxmd.com/read/29149763/formulation-and-anti-neurotoxic-activity-of-baicalein-incorporating-neutral-nanoliposome
#18
Farhang Aliakbari, Ali Akbar Shabani, Hassan Bardania, Hossein Mohammad-Beigi, Amir Tayaranian Marvian, Faezeh Dehghani Esmatabad, Abbas Ali Vafaei, Seyed Abbas Shojaosadati, Ali Akbar Saboury, Gunna Christiansen, Daniel E Otzen, Dina Morshedi
Despite extensive studies of the effects of herbal-derived small molecules in the biopharmaceutical and biomedical sciences, their low solubility and stability remain a challenge. Here we focus on baicalein, a small molecule showing potential against neurodegenerative diseases such as Parkinson's and Alzheimer's. However, therapeutic usage in vivo is challenged by low solubility and stability. To address this we have applied neutrally-charged nanoliposome (NLP) as carrier for baicalein. Baicalein was incorporated into NLP to form NLP-Ba at molar baicalain:lipid ratios of up to 1:3, giving a drug entrapment efficiency of 96...
November 11, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/29141128/immune-enhancing-effect-of-nanometric-lactobacillus-plantarum-nf1-nlp-nf1-in-a-mouse-model-of-cyclophosphamide-induced-immunosuppression
#19
Dae-Woon Choi, Sun Young Jung, Jisu Kang, Young-Do Nam, Seong-Il Lim, Ki Tae Kim, Hee Soon Shin
Nanometric Lactobacillus plantarum nF1 (nLp-nF1) is a biogenics consisting of dead L. plantarum pre-treated with heat and a nanodispersion process. In this study, we investigated the immune-enhancing effects of nLp-nF1 in vivo and in vitro. To evaluate the immunostimulatory effects of nLp-nF1, mice immunosuppressed by cyclophosphamide (CPP) treatment were administered with nLp-nF1. As expected, CPP restricted the immune response of mice, whereas oral administration of nLp-nF1 significantly increased total IgG in serum, and cytokine production [interleukin-12 (IL-12) and tumor necrosis factor alpha (TNF-α)] in bone marrow cells...
November 15, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29135365/deep-learning-to-classify-radiology-free-text-reports
#20
Matthew C Chen, Robyn L Ball, Lingyao Yang, Nathaniel Moradzadeh, Brian E Chapman, David B Larson, Curtis P Langlotz, Timothy J Amrhein, Matthew P Lungren
Purpose To evaluate the performance of a deep learning convolutional neural network (CNN) model compared with a traditional natural language processing (NLP) model in extracting pulmonary embolism (PE) findings from thoracic computed tomography (CT) reports from two institutions. Materials and Methods Contrast material-enhanced CT examinations of the chest performed between January 1, 1998, and January 1, 2016, were selected. Annotations by two human radiologists were made for three categories: the presence, chronicity, and location of PE...
November 13, 2017: Radiology
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