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Jejo D Koola, Sharon E Davis, Omar Al-Nimri, Sharidan K Parr, Daniel Fabbri, Bradley A Malin, Samuel B Ho, Michael E Matheny
OBJECTIVE: Hepatorenal Syndrome (HRS) is a devastating form of acute kidney injury (AKI) in advanced liver disease patients with high morbidity and mortality, but phenotyping algorithms have not yet been developed using large electronic health record (EHR) databases. We evaluated and compared multiple phenotyping methods to achieve an accurate algorithm for HRS identification. MATERIALS AND METHODS: A national retrospective cohort of patients with cirrhosis and AKI admitted to 124 Veterans Affairs hospitals was assembled from electronic health record data collected from 2005 to 2013...
March 9, 2018: Journal of Biomedical Informatics
Mohammed Alsuhaibani, Danushka Bollegala, Takanori Maehara, Ken-Ichi Kawarabayashi
Methods for representing the meaning of words in vector spaces purely using the information distributed in text corpora have proved to be very valuable in various text mining and natural language processing (NLP) tasks. However, these methods still disregard the valuable semantic relational structure between words in co-occurring contexts. These beneficial semantic relational structures are contained in manually-created knowledge bases (KBs) such as ontologies and semantic lexicons, where the meanings of words are represented by defining the various relationships that exist among those words...
2018: PloS One
F Belal, F Ibrahim, Z A Sheribah, H Alaa
In this paper, novel univariate and multivariate regression methods along with model-updating technique were developed and validated for the simultaneous determination of quaternary mixture of imatinib (IMB), gemifloxacin (GMI), nalbuphine (NLP) and naproxen (NAP). The univariate method is extended derivative ratio (EDR) which depends on measuring every drug in the quaternary mixture by using a ternary mixture of the other three drugs as divisor. Peak amplitudes were measured at 294nm, 250nm, 283nm and 239nm within linear concentration ranges of 4...
February 21, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Neacșu Gheorghe Boricean, Oana Roxana Scripcă
We present the case of a 49-year-old patient who was treated with Aripriprazole in context of Paranoid Schizophrenia. The patient had a history of numerous Panuveitis recurrences for the left eye, which led to a marked decrease of the vision VA-NLP and was diagnosed with Multifocal Choroiditis and Panuveitis for the right eye. The examination revealed VA of 20/ 200 for right eye, keratic precipitates, and vitritis. Fundus aspect of the right eye showed multiple discrete, ovoid, yellowish-grey lesions at the posterior pole and periphery, optic disc oedema was present...
October 2017: Romanian Journal of Ophthalmology
Corinna Konieczna, Agnieszka Olejnik-Schmidt, Marcin T Schmidt
BACKGROUND: n. Adhesion of bacteria from the genus Lactobacillus to the gastrointestinal epithelium is, to a considerable degree, dependent on the interactions between adhesins found on the surface of bacterial cells and elements found within the epithelium. A significant role in these interactions is played by bacterial pro teins exposed to the cell wall surface, which are capable of binding to molecules of substances comprising the extracellular matrix of the intestinal epithelium. METHODS: In order to analyze the extracellular proteome of intestinal bacteria in terms of the presence of cell adhesion molecules, a total of twenty strains from the Lactobacillus spp...
January 2018: Acta Scientiarum Polonorum. Technologia Alimentaria
Wenhao Zhu, Tengjun Yao, Jianyue Ni, Baogang Wei, Zhiguo Lu
Textual representations play an important role in the field of natural language processing (NLP). The efficiency of NLP tasks, such as text comprehension and information extraction, can be significantly improved with proper textual representations. As neural networks are gradually applied to learn the representation of words and phrases, fairly efficient models of learning short text representations have been developed, such as the continuous bag of words (CBOW) and skip-gram models, and they have been extensively employed in a variety of NLP tasks...
2018: PloS One
Varsha D Badal, Petras J Kundrotas, Ilya A Vakser
BACKGROUND: Structural modeling of protein-protein interactions produces a large number of putative configurations of the protein complexes. Identification of the near-native models among them is a serious challenge. Publicly available results of biomedical research may provide constraints on the binding mode, which can be essential for the docking. Our text-mining (TM) tool, which extracts binding site residues from the PubMed abstracts, was successfully applied to protein docking (Badal et al...
March 5, 2018: BMC Bioinformatics
Joy T Wu, Franck Dernoncourt, Sebastian Gehrmann, Patrick D Tyler, Edward T Moseley, Eric T Carlson, David W Grant, Yeran Li, Jonathan Welt, Leo Anthony Celi
Advancement of Artificial Intelligence (AI) capabilities in medicine can help address many pressing problems in healthcare. However, AI research endeavors in healthcare may not be clinically relevant, may have unrealistic expectations, or may not be explicit enough about their limitations. A diverse and well-functioning multidisciplinary team (MDT) can help identify appropriate and achievable AI research agendas in healthcare, and advance medical AI technologies by developing AI algorithms as well as addressing the shortage of appropriately labeled datasets for machine learning...
April 2018: International Journal of Medical Informatics
Sheng-Feng Sung, Kuanchin Chen, Darren Philbert Wu, Ling-Chien Hung, Yu-Hsiang Su, Ya-Han Hu
OBJECTIVE: To reduce errors in determining eligibility for intravenous thrombolytic therapy (IVT) in stroke patients through use of an enhanced task-specific electronic medical record (EMR) interface powered by natural language processing (NLP) techniques. MATERIALS AND METHODS: The information processing algorithm utilized MetaMap to extract medical concepts from IVT eligibility criteria and expanded the concepts using the Unified Medical Language System Metathesaurus...
April 2018: International Journal of Medical Informatics
Ashkan Zehfroosh, Elena Kokkoni, Herbert G Tanner, Jeffrey Heinz
This paper offers a new approach to learning discrete models for human-robot interaction (HRI) from small data. In the motivating application, HRI is an integral part of a pediatric rehabilitation paradigm that involves a play-based, social environment aiming at improving mobility for infants with mobility impairments. Designing interfaces in this setting is challenging, because in order to harness, and eventually automate, the social interaction between children and robots, a behavioral model capturing the causality between robot actions and child reactions is needed...
July 2017: Mediterranean Conference on Control & Automation: [proceedings]
Danielle R McClanahan, Joseph C English
Nail psoriasis (NP) and nail lichen planus (NLP) can be limiting, stigmatizing and difficult to treat. Dermatologists commonly treat psoriasis and lichen planus but when associated onychodystrophy is present or is an isolated finding, some develop apprehension. The goal of this review is to develop therapeutic ladders to be used as a guide for the management of NP and NLP in everyday clinical practice. Evidence-based therapies for NP are robust and range from topical treatments to conventional systemic therapies (i...
February 27, 2018: American Journal of Clinical Dermatology
Sourav Das Chowdhury, Atasi Pal, Sayan Chatterjee, Ranjan Sen, Mrinmay Pal
In this paper, we propose an all-normal-dispersion ytterbium-fiber laser with a novel ring cavity architecture having two nonlinear amplifying loop mirrors (NALM) as saturable absorbers, capable of delivering distinctly different pulses with adjustable features. By optimizing the loop lengths of the individual NALMs, the cavity can be operated to deliver Q-switched mode-locked (Q-ML) pulse bunches with adjustable repetition rates, mode-locked pulses in dissipative soliton resonance (DSR) regime or noise-like pulse (NLP) regime with tunable pulse width...
February 10, 2018: Applied Optics
B E Jones, B R South, Y Shao, C C Lu, J Leng, B C Sauer, A V Gundlapalli, M H Samore, Q Zeng
BACKGROUND:  Identifying pneumonia using diagnosis codes alone may be insufficient for research on clinical decision making. Natural language processing (NLP) may enable the inclusion of cases missed by diagnosis codes. OBJECTIVES:  This article (1) develops a NLP tool that identifies the clinical assertion of pneumonia from physician emergency department (ED) notes, and (2) compares classification methods using diagnosis codes versus NLP against a gold standard of manual chart review to identify patients initially treated for pneumonia...
January 2018: Applied Clinical Informatics
Sebastian Gehrmann, Franck Dernoncourt, Yeran Li, Eric T Carlson, Joy T Wu, Jonathan Welt, John Foote, Edward T Moseley, David W Grant, Patrick D Tyler, Leo A Celi
In secondary analysis of electronic health records, a crucial task consists in correctly identifying the patient cohort under investigation. In many cases, the most valuable and relevant information for an accurate classification of medical conditions exist only in clinical narratives. Therefore, it is necessary to use natural language processing (NLP) techniques to extract and evaluate these narratives. The most commonly used approach to this problem relies on extracting a number of clinician-defined medical concepts from text and using machine learning techniques to identify whether a particular patient has a certain condition...
2018: PloS One
Harsheen Kaur, Sunghwan Sohn, Chung-Il Wi, Euijung Ryu, Miguel A Park, Kay Bachman, Hirohito Kita, Ivana Croghan, Jose A Castro-Rodriguez, Gretchen A Voge, Hongfang Liu, Young J Juhn
BACKGROUND: Thus far, no algorithms have been developed to automatically extract patients who meet Asthma Predictive Index (API) criteria from the Electronic health records (EHR) yet. Our objective is to develop and validate a natural language processing (NLP) algorithm to identify patients that meet API criteria. METHODS: This is a cross-sectional study nested in a birth cohort study in Olmsted County, MN. Asthma status ascertained by manual chart review based on API criteria served as gold standard...
February 13, 2018: BMC Pulmonary Medicine
Sunghwan Sohn, Chung-Il Wi, Stephen T Wu, Hongfang Liu, Euijung Ryu, Elizabeth Krusemark, Alicia Seabright, Gretchen A Voge, Young J Juhn
NLP algorithm successfully determined asthma prognosis (i.e., no remission, long-term remission, and intermittent remission) by taking into account asthma symptoms documented in EMR, and addressed the limitations of billing code-based asthma outcome assessment.
February 10, 2018: Journal of Allergy and Clinical Immunology
Naveed Afzal, Vishnu Priya Mallipeddi, Sunghwan Sohn, Hongfang Liu, Rajeev Chaudhry, Christopher G Scott, Iftikhar J Kullo, Adelaide M Arruda-Olson
BACKGROUND: Critical limb ischemia (CLI) is a complication of advanced peripheral artery disease (PAD) with diagnosis based on the presence of clinical signs and symptoms. However, automated identification of cases from electronic health records (EHRs) is challenging due to absence of a single definitive International Classification of Diseases (ICD-9 or ICD-10) code for CLI. METHODS AND RESULTS: In this study, we extend a previously validated natural language processing (NLP) algorithm for PAD identification to develop and validate a subphenotyping NLP algorithm (CLI-NLP) for identification of CLI cases from clinical notes...
March 2018: International Journal of Medical Informatics
Stuart McTaggart, Clifford Nangle, Jacqueline Caldwell, Samantha Alvarez-Madrazo, Helen Colhoun, Marion Bennie
Background: Efficient generation of structured dose instructions that enable researchers to calculate drug exposure is central to pharmacoepidemiology studies. Our aim was to design and test an algorithm to codify dose instructions, applied to the NHS Scotland Prescribing Information System (PIS) that records about 100 million prescriptions per annum. Methods: A natural language processing (NLP) algorithm was developed that enabled free-text dose instructions to be represented by three attributes - quantity, frequency and qualifier - specified by three, three and two variables, respectively...
February 6, 2018: International Journal of Epidemiology
Billy Chiu, Sampo Pyysalo, Ivan Vulić, Anna Korhonen
BACKGROUND: Word representations support a variety of Natural Language Processing (NLP) tasks. The quality of these representations is typically assessed by comparing the distances in the induced vector spaces against human similarity judgements. Whereas comprehensive evaluation resources have recently been developed for the general domain, similar resources for biomedicine currently suffer from the lack of coverage, both in terms of word types included and with respect to the semantic distinctions...
February 5, 2018: BMC Bioinformatics
Jennifer J Knickelbine, Christopher J Konop, India R Viola, Colette B Rogers, Lynn A Messinger, Martha M Vestling, Antony O W Stretton
Neuropeptides can have significant effects on neurons and synapses, but among the ~250 predicted peptides in nematodes, few have been functionally characterized. Here, we report new neuropeptides in the 4 RME nerve ring motorneurons of the nematode Ascaris suum. These GABAergic neurons are involved in three-dimensional head movement. Mass spectrometry (MS) of single dissected RMEs detected a total of 12 neuropeptides (encoded by 5 genes), 9 of which are novel. None of these are expressed in the DI/VI inhibitory GABAergic motorneurons that synapse onto body wall muscle...
February 5, 2018: ACS Chemical Neuroscience
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