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https://www.readbyqxmd.com/read/28444127/hla-class-i-binding-prediction-via-convolutional-neural-networks
#1
Yeeleng S Vang, Xiaohui Xie
Motivation: Many biological processes are governed by protein-ligand interactions. One such example is the recognition of self and nonself cells by the immune system. This immune response process is regulated by the major histocompatibility complex (MHC) protein which is encoded by the human leukocyte antigen (HLA) complex. Understanding the binding potential between MHC and peptides can lead to the design of more potent, peptide-based vaccines and immunotherapies for infectious autoimmune diseases...
April 21, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28438706/towards-generalizable-entity-centric-clinical-coreference-resolution
#2
Timothy Miller, Dmitriy Dligach, Steven Bethard, Chen Lin, Guergana Savova
OBJECTIVE: This work investigates the problem of clinical coreference resolution in a model that explicitly tracks entities, and aims to measure the performance of that model in both traditional in-domain train/test splits and cross-domain experiments that measure the generalizability of learned models. METHODS: The two methods we compare are a baseline mention-pair coreference system that operates over pairs of mentions with best-first conflict resolution and a mention-synchronous system that incrementally builds coreference chains...
April 21, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28428140/automated-annotation-and-classification-of-bi-rads-assessment-from-radiology-reports
#3
Sergio M Castro, Eugene Tseytlin, Olga Medvedeva, Kevin Mitchell, Shyam Visweswaran, Tanja Bekhuis, Rebecca S Jacobson
The Breast Imaging Reporting and Data System (BI-RADS) was developed to reduce variation in the descriptions of findings. Manual analysis of breast radiology report data is challenging but is necessary for clinical and healthcare quality assurance activities. The objective of this study is to develop a natural language processing (NLP) system for automated BI-RADS categories extraction from breast radiology reports. We evaluated an existing rule-based NLP algorithm, and then we developed and evaluated our own method using a supervised machine learning approach...
April 17, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28425575/high-dose-supplementation-of-vitamin-d-affects-measures-of-systemic-inflammation-reductions-in-high-sensitivity-c-reactive-protein-level-and-neutrophil-to-lymphocyte-ratio-nlr-distribution
#4
Seyed-Amir Tabatabaeizadeh, Amir Avan, Afsane Bahrami, Ezzat Khodashenas, Habibollah Esmaeili, Gordon A Ferns, Mojtaba Fattahi Abdizadeh, Majid Ghayour-Mobarhan
BACKGROUND: The prevalence of Vitamin D deficiency is increasing worldwide, which has be shown to be associated with increased risk of cardiovascular disease (CVD), autoimmune disease and metabolic syndrome. These conditions are also associated with a heightened state of inflammation. The aim of the current study was to evaluate the effect of vitamin D supplementation on serum C - reactive protein (CRP) level and Neutrophil-to-lymphocyte ratio (NLR) distribution in a large cohort of adolescent girls...
April 20, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28423797/htp-nlp-a-new-nlp-system-for-high-throughput-phenotyping
#5
Daniel R Schlegel, Chris Crowner, Frank Lehoullier, Peter L Elkin
Secondary use of clinical data for research requires a method to quickly process the data so that researchers can quickly extract cohorts. We present two advances in the High Throughput Phenotyping NLP system which support the aim of truly high throughput processing of clinical data, inspired by a characterization of the linguistic properties of such data. Semantic indexing to store and generalize partially-processed results and the use of compositional expressions for ungrammatical text are discussed, along with a set of initial timing results for the system...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28423792/acronym-disambiguation-in-spanish-electronic-health-narratives-using-machine-learning-techniques
#6
Ignacio Rubio-López, Roberto Costumero, Héctor Ambit, Consuelo Gonzalo-Martín, Ernestina Menasalvas, Alejandro Rodríguez González
Electronic Health Records (EHRs) are now being massively used in hospitals what has motivated current developments of new methods to process clinical narratives (unstructured data) making it possible to perform context-based searches. Current approaches to process the unstructured texts in EHRs are based in applying text mining or natural language processing (NLP) techniques over the data. In particular Named Entity Recognition (NER) is of paramount importance to retrieve specific biomedical concepts from the text providing the semantic type of the concept retrieved...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28419261/challenges-in-adapting-existing-clinical-natural-language-processing-systems-to-multiple-diverse-health-care-settings
#7
David S Carrell, Robert E Schoen, Daniel A Leffler, Michele Morris, Sherri Rose, Andrew Baer, Seth D Crockett, Rebecca A Gourevitch, Katie M Dean, Ateev Mehrotra
Objective: Widespread application of clinical natural language processing (NLP) systems requires taking existing NLP systems and adapting them to diverse and heterogeneous settings. We describe the challenges faced and lessons learned in adapting an existing NLP system for measuring colonoscopy quality. Materials and Methods: Colonoscopy and pathology reports from 4 settings during 2013-2015, varying by geographic location, practice type, compensation structure, and electronic health record...
April 17, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28404537/building-a-comprehensive-syntactic-and-semantic-corpus-of-chinese-clinical-texts
#8
Bin He, Bin Dong, Yi Guan, Jinfeng Yang, Zhipeng Jiang, Qiubin Yu, Jianyi Cheng, Chunyan Qu
OBJECTIVE: To build a comprehensive corpus covering syntactic and semantic annotations of Chinese clinical texts with corresponding annotation guidelines and methods as well as to develop tools trained on the annotated corpus, which supplies baselines for research on Chinese texts in the clinical domain. MATERIALS AND METHODS: An iterative annotation method was proposed to train annotators and to develop annotation guidelines. Then, by using annotation quality assurance measures, a comprehensive corpus was built, containing annotations of part-of-speech (POS) tags, syntactic tags, entities, assertions, and relations...
April 9, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28387421/apn-cd13-is-over-expressed-by-psoriatic-fibroblasts-and-is-modulated-by-cgrp-and-il-4-but-not-by-retinoic-acid-treatment
#9
Pascale Gerbaud, Jean Guibourdenche, Rafika Jarray, Marc Conti, Patricia Palmic, Stéphanie Leclerc-Mercier, Julie Bruneau, Olivier Hermine, Yves Lepelletier, Françoise Raynaud
Psoriasis vulgaris is a common skin inflammatory disease characterized by recurrent flare episodes associated with scaly well-demarcated skin plaques. Skin biopsies from psoriatic patients with high PASI score (22.67 ± 8.67) and from HD were used to study APN/CD13. APN/CD13 is over-expressed in LP and nLP compare to HD skins and fibroblasts. This over-expression is positively correlated with specific enzymatic activity enhancement. However, discrepancies between APN/CD13 expression in LP and nLP prompt us to focus our study on APN/CD13 modulation...
April 7, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/28384151/local-neuropeptide-signaling-modulates-serotonergic-transmission-to-shape-the-temporal-organization-of-c-elegans-egg-laying-behavior
#10
Navonil Banerjee, Raja Bhattacharya, Michael Gorczyca, Kevin M Collins, Michael M Francis
Animal behaviors are often composed of distinct alternating behavioral states. Neuromodulatory signals are thought to be critical for establishing stable behavioral states and for orchestrating transitions between them. However, we have only a limited understanding of how neuromodulatory systems act in vivo to alter circuit performance and shape behavior. To address these questions, we have investigated neuromodulatory signaling in the context of Caenorhabditis elegans egg-laying. Egg-laying activity cycles between discrete states-short bursts of egg deposition (active phases) that alternate with prolonged quiescent periods (inactive phases)...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28380048/a-study-of-the-transferability-of-influenza-case-detection-systems-between-two-large-healthcare-systems
#11
Ye Ye, Michael M Wagner, Gregory F Cooper, Jeffrey P Ferraro, Howard Su, Per H Gesteland, Peter J Haug, Nicholas E Millett, John M Aronis, Andrew J Nowalk, Victor M Ruiz, Arturo López Pineda, Lingyun Shi, Rudy Van Bree, Thomas Ginter, Fuchiang Tsui
OBJECTIVES: This study evaluates the accuracy and transferability of Bayesian case detection systems (BCD) that use clinical notes from emergency department (ED) to detect influenza cases. METHODS: A BCD uses natural language processing (NLP) to infer the presence or absence of clinical findings from ED notes, which are fed into a Bayesain network classifier (BN) to infer patients' diagnoses. We developed BCDs at the University of Pittsburgh Medical Center (BCDUPMC) and Intermountain Healthcare in Utah (BCDIH)...
2017: PloS One
https://www.readbyqxmd.com/read/28375665/application-of-a-natural-language-processing-algorithm-to-asthma-ascertainment-an-automated-chart-review
#12
Chung-Il Wi, Sunghwan Sohn, Mary C Rolfes, Alicia Seabright, Euijung Ryu, Gretchen Voge, Kay A Bachman, Miguel A Park, Hirohito Kita, Ivana T Croghan, Hongfang Liu, Young J Juhn
RATIONALE: Difficulty of asthma ascertainment and its associated methodological heterogeneity have created significant barriers to asthma care and research. OBJECTIVES: We evaluated the validity of an existing natural language processing (NLP) algorithm for asthma criteria to enable an automated chart review utilizing electronic medical records (EMRs). METHODS: The study was designed as a retrospective birth cohort study utilizing a random sample of 500 subjects from the 1997-2007 Mayo Birth Cohort who were born at Mayo Clinic and enrolled in primary pediatric care at Mayo Clinic Rochester...
April 4, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28358859/vocalizations-of-female-frogs-contain-nonlinear-characteristics-and-individual-signatures
#13
Fang Zhang, Juan Zhao, Albert S Feng
Anuran vocalization is sexually dimorphic, with males doing the bulk of vocalizing. Female vocalization is rare and has been observed in a handful of species, including the concave-eared torrent frog (Odorrana tormota). Females O. tormota have been reported to emit moderate-level calls to attract males. In contrast to males, female's vocal signals show no evidence of nonlinear phenomena (NLP). However, with females emitting calls so infrequently that this conclusion must be considered tentative in light of the limited supporting data...
2017: PloS One
https://www.readbyqxmd.com/read/28348631/optic-neuropathy-as-the-initial-presenting-sign-of-n-methyl-d-aspartate-nmda-encephalitis
#14
Mark Mugavin, Brett H Mueller, Masoom Desai, Karl C Golnik
A 52-year-old woman presented with painless vision loss for 3 months. She was in custody for allegedly robbing a bank and had recently been diagnosed with paranoid schizophrenia. She had 20/100 VA OD, a 2+RAPD, and optic atrophy. Extensive diagnostic workup including MRI, Fluorescein Angiography, Infectious Disease Panel, lumbar puncture, and leptomeningeal biopsy were unrevealing. Vision in her right eye declined to NLP and her left eye declined to 20/200 VA. Anti N-methyl-D-aspartate (NMDA) Autoimmune Encephalitis was diagnosed based on CSF serology and clinical suspicion...
April 2017: Neuro-ophthalmology
https://www.readbyqxmd.com/read/28347963/comparison-of-batch-cultivation-strategies-for-cost-effective-biomass-production-of-micractinium-inermum-nlp-f014-using-a-blended-wastewater-medium
#15
Seonghwan Park, Jeongmi Kim, Younghyun Park, Suyoung Son, Sunja Cho, Changwon Kim, Taeho Lee
Two competitive strategies, fed-batch and sequencing-batch cultivation, were compared in cost-effective biomass production of a high lipid microalgae, Micractinium inermum NLP-F014 using a blended wastewater medium. For fed-batch cultivations, additional nutrient was supplemented at day 2 (FB1) or consecutively added at day 2 and 4 (FB2). Through inoculum size test, 1.0g-DCWL(-1) was selected for the sequencing-batch cultivation (SB) where about 65% of culture was replaced with fresh medium every 2days. Both fed-batch cultivations showed the maximum biomass productivity of 0...
March 14, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28347453/creation-of-a-simple-natural-language-processing-tool-to-support-an-imaging-utilization-quality-dashboard
#16
Jordan Swartz, Christian Koziatek, Jason Theobald, Silas Smith, Eduardo Iturrate
BACKGROUND: Testing for venous thromboembolism (VTE) is associated with cost and risk to patients (e.g. radiation). To assess the appropriateness of imaging utilization at the provider level, it is important to know that provider's diagnostic yield (percentage of tests positive for the diagnostic entity of interest). However, determining diagnostic yield typically requires either time-consuming, manual review of radiology reports or the use of complex and/or proprietary natural language processing software...
May 2017: International Journal of Medical Informatics
https://www.readbyqxmd.com/read/28346138/dilation-of-fusion-pores-by-crowding-of-snare-proteins
#17
Zhenyong Wu, Oscar D Bello, Sathish Thiyagarajan, Sarah Marie Auclair, Wensi Vennekate, Shyam S Krishnakumar, Ben O'Shaughnessy, Erdem Karatekin
Hormones and neurotransmitters are released through fluctuating exocytotic fusion pores that can flicker open and shut multiple times. Cargo release and vesicle recycling depend on the fate of the pore, which may reseal or dilate irreversibly. Pore nucleation requires zippering between vesicle-associated v-SNAREs and target membrane t-SNAREs, but the mechanisms governing the subsequent pore dilation are not understood. Here, we probed the dilation of single fusion pores using v-SNARE-reconstituted ~23-nm-diameter discoidal nanolipoprotein particles (vNLPs) as fusion partners with cells ectopically expressing cognate, 'flipped' t-SNAREs...
March 27, 2017: ELife
https://www.readbyqxmd.com/read/28300378/comparison-of-linear-and-nonlinear-programming-approaches-for-worst-case-dose-and-minmax-robust-optimization-of-intensity-modulated-proton-therapy-dose-distributions
#18
Maryam Zaghian, Wenhua Cao, Wei Liu, Laleh Kardar, Sharmalee Randeniya, Radhe Mohan, Gino Lim
Robust optimization of intensity-modulated proton therapy (IMPT) takes uncertainties into account during spot weight optimization and leads to dose distributions that are resilient to uncertainties. Previous studies demonstrated benefits of linear programming (LP) for IMPT in terms of delivery efficiency by considerably reducing the number of spots required for the same quality of plans. However, a reduction in the number of spots may lead to loss of robustness. The purpose of this study was to evaluate and compare the performance in terms of plan quality and robustness of two robust optimization approaches using LP and nonlinear programming (NLP) models...
March 2017: Journal of Applied Clinical Medical Physics
https://www.readbyqxmd.com/read/28293873/the-association-between-nd-yag-laser-and-desensitizing-dentifrices-for-the-treatment-of-dentin-hypersensitivity
#19
Sandra Ribeiro Cunha, Stephanie Assimakopoulos Garófalo, Taís Scaramucci, Denise Maria Zezell, Ana Cecilia Corrêa Aranha
This study aims to evaluate the association between Nd:YAG laser (with and without a photoabsorber) and two desensitizing dentifrices containing 15% NovaMin or 8% arginine, as potential treatments for dentin hypersensitivity (DH). DH was simulated by EDTA application for 2 min. Specimens were then analyzed with an environmental scanning electron microscope (ESEM) to ensure open dentin tubules (ODT), counted by using ImageJ software. Specimens were randomized into eight groups (n = 10): Laser (L), Laser+Photoabsorber (LP), Arginine (A), Arginine+Laser (AL), Arginine+Laser+Photoabsorber (ALP), NovaMin (N), NovaMin+Laser (NL), and NovaMin+Laser+Photoabsorber (NLP)...
May 2017: Lasers in Medical Science
https://www.readbyqxmd.com/read/28270190/social-media-for-arthritis-related-comparative-effectiveness-and-safety-research-and-the-impact-of-direct-to-consumer-advertising
#20
Jeffrey R Curtis, Lang Chen, Phillip Higginbotham, W Benjamin Nowell, Ronit Gal-Levy, James Willig, Monika Safford, Joseph Coe, Kaitlin O'Hara, Roee Sa'adon
BACKGROUND: Social media may complement traditional data sources to answer comparative effectiveness/safety questions after medication licensure. METHODS: The Treato platform was used to analyze all publicly available social media data including Facebook, blogs, and discussion boards for posts mentioning inflammatory arthritis (e.g. rheumatoid, psoriatic). Safety events were self-reported by patients and mapped to medical ontologies, resolving synonyms. Disease and symptom-related treatment indications were manually redacted...
March 7, 2017: Arthritis Research & Therapy
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