41,005 papers found

OBJECTIVE: Quantify tradeoffs in performance, reproducibility, and resource demands across several strategies for developing clinically relevant word embeddings. MATERIALS AND METHODS: We trained separate embeddings on all full-text manuscripts in the Pubmed Central (PMC) Open Access subset, case reports therein, the…

Since it is becoming increasingly laborious to manually extract useful information embedded in the ever-growing volumes of literature, automated intelligent text analysis tools are becoming more and more essential to assist in this task. PubFinder (www.glycosciences.de/tools/PubFinder) is a publicly available web tool…

OBJECTIVE: Network meta-analyses (NMAs) aim to rank the benefits (or harms) of interventions, based on all available randomized controlled trials. Thus, the identification of relevant data is critical. We assessed the conduct of the literature searches in NMAs. STUDY DESIGN: Published NMAs were retrieved by searching…

UNLABELLED: Leishmaniasis is a highly relevant neglected tropical disease. It has important consequences in affected populations, including a high fatality rate in its visceral form. It is present in Latin America, then it is necessary to promote more research on it. A bibliometric assessment of the Latin American scie…

MOTIVATION: Medical Subject Headings (MeSHs) are used by National Library of Medicine (NLM) to index almost all citations in MEDLINE, which greatly facilitates the applications of biomedical information retrieval and text mining. To reduce the time and financial cost of manual annotation, NLM has developed a software p…

OBJECTIVE: The Cochrane Handbook of Systematic Reviews contains search filters to find randomized controlled trials (RCTs) in Ovid MEDLINE: one maximizing sensitivity and another balancing sensitivity and precision. These filters were originally published in 1994 and were adapted and updated in 2008. To determine the p…

Citations are used ubiquitously in biomedical full-text articles and play an important role for representing both the rhetorical structure and the semantic content of the articles. As a result, text mining systems will significantly benefit from a tool that automatically extracts the content of a citation. In this stud…

BACKGROUND: Systematic reviews involve searching multiple bibliographic databases to identify eligible studies. As this type of evidence synthesis is increasingly pursued, the use of various electronic platforms can help researchers improve the efficiency and quality of their research. We examined the accuracy and effi…

AIMS: Serotonin transporter (5-HTT) plays a central role in the regulation of serotonin (5-hydroxytryptamine [5-HT]) synaptic function. Disturbances in 5-HT transmission are the most frequently reported neurobiological substrates of suicidal behavior. Emerging evidence has shown that the common polymorphisms in the 5-H…

Biomedical literature contains unstructured, rich information regarding proteins, ligands, diseases as well as biological pathways in which they are involved. Systematically analyzing such textual corpus has the potential for biomedical discovery of new protein-protein interactions and hidden drug indications. For this…

MOTIVATION: Automatically quantifying semantic similarity and relatedness between clinical terms is an important aspect of text mining from electronic health records, which are increasingly recognized as valuable sources of phenotypic information for clinical genomics and bioinformatics research. A key obstacle to deve…

BACKGROUND: The task of recognizing and identifying species names in biomedical literature has recently been regarded as critical for a number of applications in text and data mining, including gene name recognition, species-specific document retrieval, and semantic enrichment of biomedical articles. RESULTS: In this…

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to identify the exact resources that are reported or to a…

BACKGROUND: Many authors are concerned which types of peer-review articles can be cited most in academics and who were the highest-cited authors in a scientific discipline. The prerequisites are determined by: (1) classifying article types; and (2) quantifying co-author contributions. We aimed to apply Medical Subject…

OBJECTIVES: Laryngeal rhabdomyomas are extremely rare, benign striated muscle tumors that have been documented only ∼50 times in the literature. They can be subdivided into two types: fetal and adult types, with the adult type being more common. Common presenting symptoms include hoarseness or progressive dyspha…

BACKGROUND: Figures are ubiquitous in biomedical full-text articles, and they represent important biomedical knowledge. However, the sheer volume of biomedical publications has made it necessary to develop computational approaches for accessing figures. Therefore, we are developing the Biomedical Figure Search engine (…