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https://www.readbyqxmd.com/read/29107882/improved-screen-printed-carbon-electrode-for-multiplexed-label-free-amperometric-immuniosensor-addressing-its-conductivity-and-reproducibility-challenges
#1
Lihua Zhao, Hongliang Han, Zhanfang Ma
A new screen-printed carbon electrode (SPCE) with multiple working electrodes and one signal output channel without counter and reference electrodes was designed. The multiple working electrodes can be individually modified for each target of interest. The SPCE contained one signal output channel, making the immuniosensor be realized by common single-channel electrochemical workstation. The counter and reference electrodes were independent of disposable SPCE, reducing costs and eliminating precious metal pollution...
October 19, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29106618/eram-encyclopedia-of-rare-disease-annotations-for-precision-medicine
#2
Jinmeng Jia, Zhongxin An, Yue Ming, Yongli Guo, Wei Li, Yunxiang Liang, Dongming Guo, Xin Li, Jun Tai, Geng Chen, Yaqiong Jin, Zhimei Liu, Xin Ni, Tieliu Shi
Rare diseases affect over a hundred million people worldwide, most of these patients are not accurately diagnosed and effectively treated. The limited knowledge of rare diseases forms the biggest obstacle for improving their treatment. Detailed clinical phenotyping is considered as a keystone of deciphering genes and realizing the precision medicine for rare diseases. Here, we preset a standardized system for various types of rare diseases, called encyclopedia of Rare disease Annotations for Precision Medicine (eRAM)...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29072893/an-interpretable-classification-framework-for-information-extraction-from-online-healthcare-forums
#3
Jun Gao, Ninghao Liu, Mark Lawley, Xia Hu
Online healthcare forums (OHFs) have become increasingly popular for patients to share their health-related experiences. The healthcare-related texts posted in OHFs could help doctors and patients better understand specific diseases and the situations of other patients. To extract the meaning of a post, a commonly used way is to classify the sentences into several predefined categories of different semantics. However, the unstructured form of online posts brings challenges to existing classification algorithms...
2017: Journal of Healthcare Engineering
https://www.readbyqxmd.com/read/29065591/semantic-modeling-for-exposomics-with-exploratory-evaluation-in-clinical-context
#4
Jung-Wei Fan, Jianrong Li, Yves A Lussier
Exposome is a critical dimension in the precision medicine paradigm. Effective representation of exposomics knowledge is instrumental to melding nongenetic factors into data analytics for clinical research. There is still limited work in (1) modeling exposome entities and relations with proper integration to mainstream ontologies and (2) systematically studying their presence in clinical context. Through selected ontological relations, we developed a template-driven approach to identifying exposome concepts from the Unified Medical Language System (UMLS)...
2017: Journal of Healthcare Engineering
https://www.readbyqxmd.com/read/29065580/an-interpretable-classification-framework-for-information-extraction-from-online-healthcare-forums
#5
Jun Gao, Ninghao Liu, Mark Lawley, Xia Hu
Online healthcare forums (OHFs) have become increasingly popular for patients to share their health-related experiences. The healthcare-related texts posted in OHFs could help doctors and patients better understand specific diseases and the situations of other patients. To extract the meaning of a post, a commonly used way is to classify the sentences into several predefined categories of different semantics. However, the unstructured form of online posts brings challenges to existing classification algorithms...
2017: Journal of Healthcare Engineering
https://www.readbyqxmd.com/read/29038097/recommending-education-materials-for-diabetic-questions-using-information-retrieval-approaches
#6
Yuqun Zeng, Xusheng Liu, Yanshan Wang, Feichen Shen, Sijia Liu, Majid Rastegar-Mojarad, Liwei Wang, Hongfang Liu
BACKGROUND: Self-management is crucial to diabetes care and providing expert-vetted content for answering patients' questions is crucial in facilitating patient self-management. OBJECTIVE: The aim is to investigate the use of information retrieval techniques in recommending patient education materials for diabetic questions of patients. METHODS: We compared two retrieval algorithms, one based on Latent Dirichlet Allocation topic modeling (topic modeling-based model) and one based on semantic group (semantic group-based model), with the baseline retrieval models, vector space model (VSM), in recommending diabetic patient education materials to diabetic questions posted on the TuDiabetes forum...
October 16, 2017: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/28978337/towards-refactoring-the-molecular-function-ontology-with-a-uml-profile-for-function-modeling
#7
Patryk Burek, Frank Loebe, Heinrich Herre
BACKGROUND: Gene Ontology (GO) is the largest resource for cataloging gene products. This resource grows steadily and, naturally, this growth raises issues regarding the structure of the ontology. Moreover, modeling and refactoring large ontologies such as GO is generally far from being simple, as a whole as well as when focusing on certain aspects or fragments. It seems that human-friendly graphical modeling languages such as the Unified Modeling Language (UML) could be helpful in connection with these tasks...
October 4, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28962565/a-novel-data-driven-workflow-combining-literature-and-electronic-health-records-to-estimate-comorbidities-burden-for-a-specific-disease-a-case-study-on-autoimmune-comorbidities-in-patients-with-celiac-disease
#8
Jean-Baptiste Escudié, Bastien Rance, Georgia Malamut, Sherine Khater, Anita Burgun, Christophe Cellier, Anne-Sophie Jannot
BACKGROUND: Data collected in EHRs have been widely used to identifying specific conditions; however there is still a need for methods to define comorbidities and sources to identify comorbidities burden. We propose an approach to assess comorbidities burden for a specific disease using the literature and EHR data sources in the case of autoimmune diseases in celiac disease (CD). METHODS: We generated a restricted set of comorbidities using the literature (via the MeSH® co-occurrence file)...
September 29, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/28938912/semantic-annotation-in-biomedicine-the-current-landscape
#9
REVIEW
Jelena Jovanović, Ebrahim Bagheri
The abundance and unstructured nature of biomedical texts, be it clinical or research content, impose significant challenges for the effective and efficient use of information and knowledge stored in such texts. Annotation of biomedical documents with machine intelligible semantics facilitates advanced, semantics-based text management, curation, indexing, and search. This paper focuses on annotation of biomedical entity mentions with concepts from relevant biomedical knowledge bases such as UMLS. As a result, the meaning of those mentions is unambiguously and explicitly defined, and thus made readily available for automated processing...
September 22, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28919106/selecting-relevant-features-from-the-electronic-health-record-for-clinical-code-prediction
#10
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...
October 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28883198/analysis-of-annotated-data-models-for-improving-data-quality
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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