GeneTests: an online genetic information resource for health care providers.
(65/351)
OBJECTIVE: This paper describes the GeneTests genetic testing information resource with a focus on the GeneReviews component. METHODS AND FINDINGS: The need for authoritative genetic testing information and issues in the development and maintenance of GeneReviews are discussed: Hampered by lack of currency and content deficits, traditional medical information resources such as textbooks and the published literature are generally inadequate sources of genetic testing information. Problems encountered in developing GeneReviews include the evolution of new authorship models and academic and genetics professionals' skepticism about the quality of Web-based publications. CONCLUSIONS: GeneTests is an authoritative, highly used, and well-regarded resource in the international medical community that is intended for health care providers. Future development issues to address include ways to (1) manage the increasing editing and updating load as content grows and (2) address technical and content issues that need to be considered in displaying GeneReviews as a "just in time" resource in the electronic medical record to achieve the project goal of integrating appropriate use of genetic testing into patient care. (+info)
Automatic document classification of biological literature.
(66/351)
BACKGROUND: Document classification is a wide-spread problem with many applications, from organizing search engine snippets to spam filtering. We previously described Textpresso, a text-mining system for biological literature, which marks up full text according to a shallow ontology that includes terms of biological interest. This project investigates document classification in the context of biological literature, making use of the Textpresso markup of a corpus of Caenorhabditis elegans literature. RESULTS: We present a two-step text categorization algorithm to classify a corpus of C. elegans papers. Our classification method first uses a support vector machine-trained classifier, followed by a novel, phrase-based clustering algorithm. This clustering step autonomously creates cluster labels that are descriptive and understandable by humans. This clustering engine performed better on a standard test-set (Reuters 21578) compared to previously published results (F-value of 0.55 vs. 0.49), while producing cluster descriptions that appear more useful. A web interface allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept. CONCLUSION: We have demonstrated a simple method to classify biological documents that embodies an improvement over current methods. While the classification results are currently optimized for Caenorhabditis elegans papers by human-created rules, the classification engine can be adapted to different types of documents. We have demonstrated this by presenting a web interface that allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept. (+info)
Canadian Association for Immunization Research and Evaluation (CAIRE) guidelines for industry-sponsored clinical trial and epidemiology contract research.
(67/351)
In response to concerns about interactions of academic and public health investigators with industry, the Canadian Association for Immunization Research and Evaluation (CAIRE), in collaboration with six major vaccine manufacturers, developed guidelines for participation in industry-sponsored clinical trial and epidemiology contract research within Canada. Topics addressed include definition of investigators, data ownership, protocol development, data management, data analysis, producing a study report and publication of the results of the study. (+info)
Monte Carlo simulation to reconstruct formaldehyde exposure levels from summary parameters reported in the literature.
(68/351)
OBJECTIVES: This study presents a procedure allowing the numerical synthesis of exposure data reported in different ways in the literature, including summary parameters and single measurements. The procedure was applied to literature regarding formaldehyde exposure in the reconstituted wood panels industry, including oriented-strand board (OSB), medium density fibre board (MDF) and particle board (PB). METHODS: For each publication providing summary parameters we estimated geometric means (GM) and geometric standard deviations (GSD) by assuming lognormality of exposure levels. Monte Carlo simulation was performed to re-create datasets from the sample sizes and estimated GMs and GSDs, allowing their subsequent formatting together with the single measurements. The precision and bias of the methods used to estimate GMs and GSDs were evaluated. RESULTS: Altogether, the 13 articles included in our study yielded a final database of 874 data, of which 732 were simulated. For both area and personal data, exposures corresponding to MDF and PB were similar while OSB levels were lower. The most recent available personal levels (1985-1994) were highest in PB for jobs performed in the vicinity of the press (GM=0.63 mg m-3). Corresponding area levels were highest for PB in the main production zone (GM=0.43 mg m-3). Mixed-effects models fitted to area PB data explained 38% of the total variability. A 6-fold decrease in exposures from 1965 to 1995 was estimated. Replication of the simulation process yielded relative standard deviations of the calculated GMs and GSDs between 10 and 20%. The relative biases of the methods used to estimate GMs and GSDs varied across methods and decreased with higher sample sizes (from approximately 15% for n=5 to less than 5% for n=30, in absolute value). The precision also varied across methods and improved with higher sample sizes (from approximately 30% for n=5 to approximately 10% for n=30). DISCUSSION: This methodology constitutes a new meta-analysis tool that should improve the interpretation of industrial hygiene literature data, but needs to be further validated. (+info)
How to establish a first-class international scientific journal in China?
(69/351)
Hundreds of scientific journals are published in China. However, only scores of them are included in Science Citation Index by the Institute for Scientific Information, with impact factors of only 1 or less. Thus, how to establish a first-class international scientific journal in China is an important but difficult topic that deserves extensive exploration. World Journal of Gastroenterology (WJG) sets a good example although it has experienced setbacks on the road towards success. Concepts and pursuits that affirm the overall development direction, innovation and dreams that provide impetus and aspiration for higher objectives, team work and unique pattern that assure excellent quality and service, and culture and environment that also determine the speed and direction of the development, are believed to be the major factors contributing to the success of WJG. It is recommended that the effective resolution to the above issue is to learn from Chinese examples such as WJG rather than from "how foreign journals do". (+info)
Effect of the Women's Health Initiative study publication on hormone replacement therapy use among women who have undergone BRCA1/2 testing.
(70/351)
BACKGROUND: Since the publication, in July 2002, of the Women's Health Initiative (WHI) study, use of hormone replacement therapy (HRT) has decreased substantially in the general population. However, little is known about the effect of WHI study results on HRT use among women at high risk of breast cancer. The purpose of this study is to compare HRT use, prepublication versus postpublication of the WHI study, among women tested for BRCA1/2 mutations. METHODS: Participants were >35 years of age and had received their result of genetic testing (delivered within the interdisciplinary research program Interdisciplinary Health Research International Team on Breast Cancer Susceptibility), no later than February 28, 2005. HRT use was reported in self-administered questionnaires, 1 year after result disclosure. Women returning their questionnaire before July 17, 2002 were classified as pre-WHI, whereas those returning it after October 15, 2002 comprised the post-WHI group. RESULTS: Four hundred fifty-seven women (199 and 258 in the pre-WIH and post-WHI groups, respectively) were included in this analysis. Globally, there was no difference in HRT use between prepublication and postpublication of the WHI study (8% and 11%, respectively; prevalence ratio, 0.74; 95% confidence interval, 0.43-1.28). However, noncarriers of the familial mutation were less likely to use HRT after publication of the WHI study results (9%) than before (21%; P = 0.03). CONCLUSIONS: Overall, HRT use among women tested for BRCA1/2 mutations is relatively low and apparently uninfluenced by the WHI study findings. However, the HRT use reduction among noncarriers is similar to that of women in the general population and consistent with the Canadian Cancer Society's recent HRT use recommendations. (+info)
Comprehending technical texts: predicting and defining unfamiliar terms.
(71/351)
We investigate how to improve access to medical literature for health consumers. Our focus is on medical terminology. We present a method to predict automatically in a given text which medical terms are unlikely to be understood by a lay reader. Our method, which is linguistically motivated and fully unsupervised, relies on how common a specific term is in texts that we already know are familiar to a lay reader. Once a term is identified as unfamiliar, an appropriate definition is mined from the Web to be provided to the reader. Our experiments show that the prediction and the addition of definitions significantly improve lay readers' comprehension of sentences containing technical medical terms. (+info)
Exploiting semantic relations for literature-based discovery.
(72/351)
We propose using semantic predications to enhance literature-based discovery (LBD) systems, which currently depend exclusively on co-occurrence of words or concepts in target documents. In this paper, the predications, which are produced by the combined application of two natural language processing systems, BioMedLEE and SemRep, are coupled with an LBD system BITOLA. Initial experiments suggest this approach can uncover new associations that were not possible using previous methods. (+info)