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https://www.readbyqxmd.com/read/29145615/iptmnet-an-integrated-resource-for-protein-post-translational-modification-network-discovery
#1
Hongzhan Huang, Cecilia N Arighi, Karen E Ross, Jia Ren, Gang Li, Sheng-Chih Chen, Qinghua Wang, Julie Cowart, K Vijay-Shanker, Cathy H Wu
Protein post-translational modifications (PTMs) play a pivotal role in numerous biological processes by modulating regulation of protein function. We have developed iPTMnet (http://proteininformationresource.org/iPTMnet) for PTM knowledge discovery, employing an integrative bioinformatics approach-combining text mining, data mining, and ontological representation to capture rich PTM information, including PTM enzyme-substrate-site relationships, PTM-specific protein-protein interactions (PPIs) and PTM conservation across species...
November 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29141718/dengue-fever-surveillance-in-india-using-text-mining-in-public-media
#2
Andrea Villanes, Emily Griffiths, Michael Rappa, Christopher G Healey
Despite the improvement in health conditions across the world, communicable diseases remain among the leading mortality causes in many countries. Combating communicable diseases depends on surveillance, preventive measures, outbreak investigation, and the establishment of control mechanisms. Delays in obtaining country-level data of confirmed communicable disease cases, such as dengue fever, are prompting new efforts for short- to medium-term data. News articles highlight dengue infections, and they can reveal how public health messages, expert findings, and uncertainties are communicated to the public...
October 23, 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/29140620/how-agricultural-media-cover-safety-compared-with-periodicals-in-two-other-hazardous-industries
#3
Amanda Marolf, Scott Heiberger, James Evans, Lura Joseph
This analysis featured a uniquely broad look at challenges and potentials for engaging agricultural and other industrial media more effectively in covering safety. It involved a content analysis of selected industry periodicals serving agriculture, mining, and transportation, which are three of the nation's most hazardous industries, in terms of human safety. Use of the social amplification of risk framework (SARF) provided insight on safety coverage. In particular, it tested previous research indicating that media coverage tends to amplify (increase) more than attenuate (decrease) a sense of risk...
January 26, 2017: Journal of Agricultural Safety and Health
https://www.readbyqxmd.com/read/29134146/indicators-for-the-use-of-robotic-labs-in-basic-biomedical-research-a-literature-analysis
#4
Paul Groth, Jessica Cox
Robotic labs, in which experiments are carried out entirely by robots, have the potential to provide a reproducible and transparent foundation for performing basic biomedical laboratory experiments. In this article, we investigate whether these labs could be applicable in current experimental practice. We do this by text mining 1,628 papers for occurrences of methods that are supported by commercial robotic labs. Using two different concept recognition tools, we find that 86%-89% of the papers have at least one of these methods...
2017: PeerJ
https://www.readbyqxmd.com/read/29126123/pedam-a-database-for-pediatric-disease-annotation-and-medicine
#5
Jinmeng Jia, Zhongxin An, Yue Ming, Yongli Guo, Wei Li, Xin Li, Yunxiang Liang, Dongming Guo, Jun Tai, Geng Chen, Yaqiong Jin, Zhimei Liu, Xin Ni, Tieliu Shi
There is a significant number of children around the world suffering from the consequence of the misdiagnosis and ineffective treatment for various diseases. To facilitate the precision medicine in pediatrics, a database namely the Pediatric Disease Annotations & Medicines (PedAM) has been built to standardize and classify pediatric diseases. The PedAM integrates both biomedical resources and clinical data from Electronic Medical Records to support the development of computational tools, by which enables robust data analysis and integration...
November 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29121053/adept-a-semantically-enriched-pipeline-for-extracting-adverse-drug-events-from-free-text-electronic-health-records
#6
Ehtesham Iqbal, Robbie Mallah, Daniel Rhodes, Honghan Wu, Alvin Romero, Nynn Chang, Olubanke Dzahini, Chandra Pandey, Matthew Broadbent, Robert Stewart, Richard J B Dobson, Zina M Ibrahim
Adverse drug events (ADEs) are unintended responses to medical treatment. They can greatly affect a patient's quality of life and present a substantial burden on healthcare. Although Electronic health records (EHRs) document a wealth of information relating to ADEs, they are frequently stored in the unstructured or semi-structured free-text narrative requiring Natural Language Processing (NLP) techniques to mine the relevant information. Here we present a rule-based ADE detection and classification pipeline built and tested on a large Psychiatric corpus comprising 264k patients using the de-identified EHRs of four UK-based psychiatric hospitals...
2017: PloS One
https://www.readbyqxmd.com/read/29106666/tadb-2-0-an-updated-database-of-bacterial-type-ii-toxin-antitoxin-loci
#7
Yingzhou Xie, Yiqing Wei, Yue Shen, Xiaobin Li, Hao Zhou, Cui Tai, Zixin Deng, Hong-Yu Ou
TADB2.0 (http://bioinfo-mml.sjtu.edu.cn/TADB2/) is an updated database that provides comprehensive information about bacterial type II toxin-antitoxin (TA) loci. Compared with the previous version, the database refined and the new data schema is employed. With the aid of text mining and manual curation, it recorded 6193 type II TA loci in 870 replicons of bacteria and archaea, including 105 experimentally validated TA loci. In addition, the newly developed tool TAfinder combines the homolog searches and the operon structure detection, allowing the prediction for type II TA pairs in bacterial genome sequences...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29106618/eram-encyclopedia-of-rare-disease-annotations-for-precision-medicine
#8
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/29106580/physical-activity-phenotyping-with-activity-bigrams-and-their-association-with-bmi
#9
Louise A C Millard, Kate Tilling, Debbie A Lawlor, Peter A Flach, Tom R Gaunt
Background: Analysis of physical activity usually focuses on a small number of summary statistics derived from accelerometer recordings: average counts per minute and the proportion of time spent in moderate-vigorous physical activity or in sedentary behaviour. We show how bigrams, a concept from the field of text mining, can be used to describe how a person's activity levels change across (brief) time points. These variables can, for instance, differentiate between two people spending the same time in moderate activity, where one person often stays in moderate activity from one moment to the next and the other does not...
June 29, 2017: International Journal of Epidemiology
https://www.readbyqxmd.com/read/29091328/educational-effects-using-a-robot-patient-simulation-system-for-development-of-clinical-attitude
#10
S Abe, N Noguchi, Y Matsuka, C Shinohara, T Kimura, K Oka, K Okura, O M M Rodis, F Kawano
INTRODUCTION: The aim of this study was to assess the effectiveness of improving the attitude of dental students towards the use of a full-body patient simulation system (SIMROID) compared to the traditional mannequin (CLINSIM) for dental clinical education. MATERIALS AND METHODS: The participants were 10 male undergraduate dental students who had finished clinical training in the university hospital 1 year before this study started. They performed a crown preparation on an upper pre-molar tooth using SIMROID and CLINSIM as the practical clinical trials...
November 1, 2017: European Journal of Dental Education: Official Journal of the Association for Dental Education in Europe
https://www.readbyqxmd.com/read/29071308/a-text-mining-framework-for-supporting-systematic-reviews
#11
Dingcheng Li, Zhen Wang, Liwei Wang, Sunghwan Sohn, Feichen Shen, Mohammad Hassan Murad, Hongfang Liu
Systematic reviews (SRs) involve the identification, appraisal, and synthesis of all relevant studies for focused questions in a structured reproducible manner. High-quality SRs follow strict procedures and require significant resources and time. We investigated advanced text-mining approaches to reduce the burden associated with abstract screening in SRs and provide high-level information summary. A text-mining SR supporting framework consisting of three self-defined semantics-based ranking metrics was proposed, including keyword relevance, indexed-term relevance and topic relevance...
November 2016: Am J Inf Manag
https://www.readbyqxmd.com/read/29066897/an-annotated-corpus-with-nanomedicine-and-pharmacokinetic-parameters
#12
Nastassja A Lewinski, Ivan Jimenez, Bridget T McInnes
A vast amount of data on nanomedicines is being generated and published, and natural language processing (NLP) approaches can automate the extraction of unstructured text-based data. Annotated corpora are a key resource for NLP and information extraction methods which employ machine learning. Although corpora are available for pharmaceuticals, resources for nanomedicines and nanotechnology are still limited. To foster nanotechnology text mining (NanoNLP) efforts, we have constructed a corpus of annotated drug product inserts taken from the US Food and Drug Administration's Drugs@FDA online database...
2017: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/29063568/capturing-the-patient-s-perspective-a-review-of-advances-in-natural-language-processing-of-health-related-text
#13
G Gonzalez-Hernandez, A Sarker, K O'Connor, G Savova
Background: Natural Language Processing (NLP) methods are increasingly being utilized to mine knowledge from unstructured health-related texts. Recent advances in noisy text processing techniques are enabling researchers and medical domain experts to go beyond the information encapsulated in published texts (e.g., clinical trials and systematic reviews) and structured questionnaires, and obtain perspectives from other unstructured sources such as Electronic Health Records (EHRs) and social media posts. Objectives: To review the recently published literature discussing the application of NLP techniques for mining health-related information from EHRs and social media posts...
August 2017: Yearbook of Medical Informatics
https://www.readbyqxmd.com/read/29063565/clinical-research-informatics-supporting-the-research-study-lifecycle
#14
S B Johnson
Objectives: The primary goal of this review is to summarize significant developments in the field of Clinical Research Informatics (CRI) over the years 2015-2016. The secondary goal is to contribute to a deeper understanding of CRI as a field, through the development of a strategy for searching and classifying CRI publications. Methods: A search strategy was developed to query the PubMed database, using medical subject headings to both select and exclude articles, and filtering publications by date and other characteristics...
August 2017: Yearbook of Medical Informatics
https://www.readbyqxmd.com/read/29063547/clinical-information-systems-as-the-backbone-of-a-complex-information-logistics-process-findings-from-the-clinical-information-systems-perspective-for-2016
#15
W O Hackl, T Ganslandt
Objective: To summarize recent research and to propose a selection of best papers published in 2016 in the field of Clinical Information Systems (CIS). Method: The query used to retrieve the articles for the CIS section of the 2016 edition of the IMIA Yearbook of Medical Informatics was reused. It again aimed at identifying relevant publications in the field of CIS from PubMed and Web of Science and comprised search terms from the Medical Subject Headings (MeSH) catalog as well as additional free text search terms...
August 2017: Yearbook of Medical Informatics
https://www.readbyqxmd.com/read/29063546/clinical-information-systems-as-the-backbone-of-a-complex-information-logistics-process-findings-from-the-clinical-information-systems-perspective-for-2016
#16
W O Hackl, T Ganslandt
Objective: To summarize recent research and to propose a selection of best papers published in 2016 in the field of Clinical Information Systems (CIS). Method: The query used to retrieve the articles for the CIS section of the 2016 edition of the IMIA Yearbook of Medical Informatics was reused. It again aimed at identifying relevant publications in the field of CIS from PubMed and Web of Science and comprised search terms from the Medical Subject Headings (MeSH) catalog as well as additional free text search terms...
August 2017: Yearbook of Medical Informatics
https://www.readbyqxmd.com/read/29061554/stopping-antidepressants-and-anxiolytics-as-major-concerns-reported-in-online-health-communities-a-text-mining-approach
#17
Adeline Abbe, Bruno Falissard
BACKGROUND: Internet is a particularly dynamic way to quickly capture the perceptions of a population in real time. Complementary to traditional face-to-face communication, online social networks help patients to improve self-esteem and self-help. OBJECTIVE: The aim of this study was to use text mining on material from an online forum exploring patients' concerns about treatment (antidepressants and anxiolytics). METHODS: Concerns about treatment were collected from discussion titles in patients' online community related to antidepressants and anxiolytics...
October 23, 2017: JMIR Mental Health
https://www.readbyqxmd.com/read/29061162/whole-transcriptome-analysis-of-human-erythropoietic-cells-during-ontogenesis-suggests-a-role-of-vegfa-gene-as-modulator-of-fetal-hemoglobin-and-pharmacogenomic-biomarker-of-treatment-response-to-hydroxyurea-in-%C3%AE-type-hemoglobinopathy-patients
#18
Vasiliki Chondrou, Petros Kolovos, Argyro Sgourou, Alexandra Kourakli, Alexia Pavlidaki, Vlasia Kastrinou, Anne John, Argiris Symeonidis, Bassam R Ali, Adamantia Papachatzopoulou, Theodora Katsila, George P Patrinos
BACKGROUND: Human erythropoiesis is characterized by distinct gene expression profiles at various developmental stages. Previous studies suggest that fetal-to-adult hemoglobin switch is regulated by a complex mechanism, in which many key players still remain unknown. Here, we report our findings from whole transcriptome analysis of erythroid cells, isolated from erythroid tissues at various developmental stages in an effort to identify distinct molecular signatures of each erythroid tissue...
October 23, 2017: Human Genomics
https://www.readbyqxmd.com/read/29039392/development-and-validation-of-a-novel-rapid-clinical-text-mining-approach-based-on-word-embeddings-nimbleminer
#19
Maxim Topaz, Katherine Gaddes, Margret McDonald, Kathryn Bowles
No abstract text is available yet for this article.
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/29038733/mining-comorbidity-patterns-using-retrospective-analysis-of-big-collection-of-outpatient-records
#20
Svetla Boytcheva, Galia Angelova, Zhivko Angelov, Dimitar Tcharaktchiev
BACKGROUND: Studying comorbidities of disorders is important for detection and prevention. For discovering frequent patterns of diseases we can use retrospective analysis of population data, by filtering events with common properties and similar significance. Most frequent pattern mining methods do not consider contextual information about extracted patterns. Further data mining developments might enable more efficient applications in specific tasks like comorbidities identification. METHODS: We propose a cascade data mining approach for frequent pattern mining enriched with context information, including a new algorithm MIxCO for maximal frequent patterns mining...
December 2017: Health Information Science and Systems
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