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Text mining

Deyse Almeida Dos Reis, Aníbal da Fonseca Santiago, Laura Pereira Nascimento, Hubert Mathias Peter Roeser
In developing countries, it is uncommon to find watersheds that have been the object of detailed environmental studies. It makes the assessment of the magnitude of environmental impacts and pollution of these sites difficult. This research demonstrated ways to understand the dynamics of river bottom sediments contamination, even for watersheds with a lack of environmental data. Based on geochemical affinity, we conducted a comprehensive study on the concentration of metals and metalloids. Then, we discussed the probable origin of the concentration of these elements at the bottom sediment along the Matipó River...
January 22, 2017: Environmental Science and Pollution Research International
Cheng Zhen, Caizhong Zhu, Haoyang Chen, Yiru Xiong, Junyuan Tan, Dong Chen, Jin Li
OBJECTIVE: To systematically explore the molecular mechanism for hepatocellular carcinoma (HCC) metastasis and identify regulatory genes with text mining methods. RESULTS: Genes with highest frequencies and significant pathways related to HCC metastasis were listed. A handful of proteins such as EGFR, MDM2, TP53 and APP, were identified as hub nodes in PPI (protein-protein interaction) network. Compared with unique genes for HBV-HCCs, genes particular to HCV-HCCs were less, but may participate in more extensive signaling processes...
January 17, 2017: Oncotarget
Robin Paynter, Lionel L Bañez, Eileen Erinoff, Jennifer Matsuura, Shannon Potter
No abstract text is available yet for this article.
January 17, 2017: Journal of Clinical Epidemiology
Stephen L Luther, Susan S Thomason, Sunil Sabharwal, Dezon K Finch, James McCart, Peter Toyinbo, Lina Bouayad, Michael E Matheny, Glenn T Gobbel, Gail Powell-Cope
BACKGROUND: Pressure ulcers (PrUs) are a frequent, serious, and costly complication for veterans with spinal cord injury (SCI). The health care team should periodically identify PrU risk, although there is no tool in the literature that has been found to be reliable, valid, and sensitive enough to assess risk in this vulnerable population. OBJECTIVE: The immediate goal is to develop a risk assessment model that validly estimates the probability of developing a PrU...
January 19, 2017: JMIR Research Protocols
Rezarta Islamaj Doğan, Sun Kim, Andrew Chatr-Aryamontri, Christie S Chang, Rose Oughtred, Jennifer Rust, W John Wilbur, Donald C Comeau, Kara Dolinski, Mike Tyers
A great deal of information on the molecular genetics and biochemistry of model organisms has been reported in the scientific literature. However, this data is typically described in free text form and is not readily amenable to computational analyses. To this end, the BioGRID database systematically curates the biomedical literature for genetic and protein interaction data. This data is provided in a standardized computationally tractable format and includes structured annotation of experimental evidence. BioGRID curation necessarily involves substantial human effort by expert curators who must read each publication to extract the relevant information...
2017: Database: the Journal of Biological Databases and Curation
Anatoly Mayburd, Ancha Baranova
PURPOSE: Novel, "outside of the box" approaches are needed for evaluating candidate molecules, especially in oncology. Throughout the years of 2000-2010, the efficiency of drug development fell to barely acceptable levels, and in the second decade of this century, levels have improved only marginally. This dismal condition continues despite unprecedented progress in the development of a variety of high-throughput tools, computational methods, aggregated databases, drug repurposing programs and innovative chemistries...
October 2016: Journal of Pharmacy & Pharmaceutical Sciences: a Publication of the Canadian Society for Pharmaceutical Sciences
Jeongkyun Kim, Jung-Jae Kim, Hyunju Lee
Diseases are developed by abnormal behavior of genes in biological events such as gene regulation, mutation, phosphorylation, and epigenetics and post-translational modification. Many studies of text mining attempted to identify the relationship between gene and disease by mining the literature, but they did not consider the biological events in which genes show abnormal behaviour in response to diseases. In this study, we propose to identify disease-related genes that are involved in the development of disease through biological events from Medline abstracts...
January 5, 2017: Scientific Reports
Lucas Sinclair, Umer Z Ijaz, Lars Juhl Jensen, Marco J L Coolen, Cecile Gubry-Rangin, Alica Chroňáková, Anastasis Oulas, Christina Pavloudi, Julia Schnetzer, Aaron Weimann, Ali Ijaz, Alexander Eiler, Christopher Quince, Evangelos Pafilis
Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context...
2016: PeerJ
Ayush Singhal, Robert Leaman, Natalie Catlett, Thomas Lemberger, Johanna McEntyre, Shawn Polson, Ioannis Xenarios, Cecilia Arighi, Zhiyong Lu
Text mining in the biomedical sciences is rapidly transitioning from small-scale evaluation to large-scale application. In this article, we argue that text-mining technologies have become essential tools in real-world biomedical research. We describe four large scale applications of text mining, as showcased during a recent panel discussion at the BioCreative V Challenge Workshop. We draw on these applications as case studies to characterize common requirements for successfully applying text-mining techniques to practical biocuration needs...
2016: Database: the Journal of Biological Databases and Curation
Jiewen Du, Xin Yan, Zhihong Liu, Lu Cui, Peng Ding, Xiaoqing Tan, Xiuming Li, Huihao Zhou, Qiong Gu, Jun Xu
MOTIVATION: Small molecule drug candidates with attractive toxicity profiles that modulate target proteins through non-covalent interactions are usually favored by scientists and pharmaceutical industry. In the past decades, many non-covalent binding agents have been developed for different diseases. However, an increasing attention has been paid to covalent binding agents in pharmaceutical fields during recent years. Many covalent binding agents entered clinical trials and exerted significant advantages for diseases such as infection, cancers, gastrointestinal disorders, central nervous system or cardiovascular diseases...
December 23, 2016: Bioinformatics
Claire E Welsh, Marco Duz, Timothy D H Parkin, John F Marshall
Electronic medical records from first opinion equine veterinary practice may represent a unique resource for epidemiologic research. The appropriateness of this resource for risk factor analyses was explored as part of an investigation into clinical and pharmacologic risk factors for laminitis. Amalgamated medical records from seven UK practices were subjected to text mining to identify laminitis episodes, systemic or intra-synovial corticosteroid prescription, diseases known to affect laminitis risk and clinical signs or syndromes likely to lead to corticosteroid use...
January 1, 2017: Preventive Veterinary Medicine
Emma Terämä, Melanie Smallman, Simon J Lock, Charlotte Johnson, Martin Zaltz Austwick
Big changes to the way in which research funding is allocated to UK universities were brought about in the Research Excellence Framework (REF), overseen by the Higher Education Funding Council, England. Replacing the earlier Research Assessment Exercise, the purpose of the REF was to assess the quality and reach of research in UK universities-and allocate funding accordingly. For the first time, this included an assessment of research 'impact', accounting for 20% of the funding allocation. In this article we use a text mining technique to investigate the interpretations of impact put forward via impact case studies in the REF process...
2016: PloS One
Yan Huang, Li Wang, Lin-Sen Zan
Adipogenesis is the process of cell differentiation through which preadipocytes become adipocytes. Lots of research is currently ongoing to identify genes, including their gene products and microRNAs, that correlate with fat cell development. However, information fragmentation hampers the identification of key regulatory genes and pathways. Here, we present a database of literature-curated adipogenesis-related regulatory interactions, designated the Adipogenesis Regulation Network (ARN,, which currently contains 3101 nodes (genes and microRNAs), 1863 regulatory interactions, and 33,969 expression records associated with adipogenesis, based on 1619 papers...
December 16, 2016: Scientific Reports
Abeed Sarker, Graciela Gonzalez
In this data article, we present to the data science, natural language processing and public heath communities an unlabeled corpus and a set of language models. We collected the data from Twitter using drug names as keywords, including their common misspelled forms. Using this data, which is rich in drug-related chatter, we developed language models to aid the development of data mining tools and methods in this domain. We generated several models that capture (i) distributed word representations and (ii) probabilities of n-gram sequences...
February 2017: Data in Brief
S Paisley, J Seva, M Stevenson, R Archer, L Preston, J Chilcott, M Thornhill
No abstract text is available yet for this article.
November 2016: Value in Health: the Journal of the International Society for Pharmacoeconomics and Outcomes Research
Allison J Lazard, Adam J Saffer, Gary B Wilcox, Arnold DongWoo Chung, Michael S Mackert, Jay M Bernhardt
BACKGROUND: As the use of electronic cigarettes (e-cigarettes) rises, social media likely influences public awareness and perception of this emerging tobacco product. OBJECTIVE: This study examined the public conversation on Twitter to determine overarching themes and insights for trending topics from commercial and consumer users. METHODS: Text mining uncovered key patterns and important topics for e-cigarettes on Twitter. SAS Text Miner 12...
December 12, 2016: JMIR Public Health and Surveillance
Karin Verspoor, Anika Oellrich, Nigel Collier, Tudor Groza, Philippe Rocca-Serra, Larisa Soldatova, Michel Dumontier, Nigam Shah
This special issue covers selected papers from the 18th Bio-Ontologies Special Interest Group meeting and Phenotype Day, which took place at the Intelligent Systems for Molecular Biology (ISMB) conference in Dublin in 2015. The papers presented in this collection range from descriptions of software tools supporting ontology development and annotation of objects with ontology terms, to applications of text mining for structured relation extraction involving diseases and phenotypes, to detailed proposals for new ontologies and mapping of existing ontologies...
December 12, 2016: Journal of Biomedical Semantics
Matt Winkler, Alan S Abrahams, Richard Gruss, Johnathan P Ehsani
Toy-related injuries account for a significant number of childhood injuries and the prevention of these injuries remains a goal for regulatory agencies and manufacturers. Text-mining is an increasingly prevalent method for uncovering the significance of words using big data. This research sets out to determine the effectiveness of text-mining in uncovering potentially dangerous children's toys. We develop a danger word list, also known as a 'smoke word' list, from injury and recall text narratives. We then use the smoke word lists to score over one million Amazon reviews, with the top scores denoting potential safety concerns...
October 2016: Decision Support Systems
Miki Tagawa, Yoshio Matsuda, Tomoko Manaka, Makiko Kobayashi, Michitaka Ohwada, Shigeki Matsubara
AIM: The aim of the study was to examine the possibility of converting subjective textual data written in the free column space of the Mother and Child Handbook (MCH) into objective information using text mining and to compare any monthly changes in the words written by the mothers. METHODS: Pregnant women without complications (n = 60) were divided into two groups according to State-Trait Anxiety Inventory grade: low trait anxiety (group I, n = 39) and high trait anxiety (group II, n = 21)...
December 9, 2016: Journal of Obstetrics and Gynaecology Research
Guangyu Shan, Yiming Lu, Bo Min, Wubin Qu, Chenggang Zhang
Prebiotics contribute to the well-being of their host by altering the composition of the gut microbiota. Discovering new prebiotics is a challenging and arduous task due to strict inclusion criteria; thus, highly limited numbers of prebiotic candidates have been identified. Notably, the large numbers of published studies may contain substantial information attached to various features of known prebiotics that can be used to predict new candidates. In this paper, we propose a medical subject headings (MeSH)-based text mining method for identifying new prebiotics with structured texts obtained from PubMed...
December 2016: Medicine (Baltimore)
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