http://precedings.nature.com/tags/reproducibility Recently posted documents tagged with 'reproducibility' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/3196/version/1 Despite seven hundred thousand new medical references last year, the relationship between a given set of medical features and specific pathophysiology, treatment, and criteria of improvement is often weak. Moreover, the generalization of evidences obtained in specific settings may lead to under-treat or to over-treat a significant proportion of patients. We expose an application of the cybernetic loop, based on traditional medical steps: nosology, semeiology, pathophysiology, therapy and on the four transitions between these steps. This approach leads to formulate eight basic questions evaluating the steps in terms of reproducibility and the transitions in terms of predictivity. We detail two practical applications: 1) the evaluation of a medical decision (implantation of an internal cardioverter-defibrillator) and 2) the evaluation of a specific study (EPHESUS). Using this loop allows to determine clearly when evidence is lacking and/or to which extend an evidence really increases the medical knowledge or just creates a market. http://precedings.nature.com/documents/3196/version/1 Fri, 01 May 2009 19:33:12 UTC Intelligence-based medicine hdl:10101/npre.2009.3196.1 2009-05-01 Pierre Squara Nature Precedings 2009-05-01T19:33:12Z Manuscript Biotechnology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/1720/version/1 This module represents the formalized opinion of the authors and the CARMEN consortium, which identifies the minimum information required to report the use of electrophysiology in a neuroscience study, for submission to the CARMEN system (www.carmen.org.uk). http://precedings.nature.com/documents/1720/version/1 Tue, 25 Mar 2008 18:21:55 UTC Minimum Information about a Neuroscience Investigation (MINI) Electrophysiology hdl:10101/npre.2008.1720.1 2008-03-25 Frank Gibson Nature Precedings 2008-03-25T18:21:55Z Manuscript Neuroscience Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/306/version/2 Reproducibility is a fundamental requirement in scientific experiments and clinical contexts. Recent publications raise concerns about the reliability of microarray technology because of the apparent lack of agreement between lists of differentially expressed genes (DEGs). In this study we demonstrate that (1) such discordance may stem from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion, the lists become much more reproducible, especially when fewer genes are selected; and (3) the instability of short DEG lists based on P cutoffs is an expected mathematical consequence of the high variability of the t-values. We recommend the use of FC ranking plus a non-stringent P cutoff as a baseline practice in order to generate more reproducible DEG lists. The FC criterion enhances reproducibility while the P criterion balances sensitivity and specificity. http://precedings.nature.com/documents/306/version/2 Tue, 03 Jul 2007 12:18:21 UTC The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies hdl:10101/npre.2007.306.2 2007-07-03 Leming D. Shi Nature Precedings 2007-07-03T12:18:21Z Manuscript Biotechnology Bioinformatics http://creativecommons.org/licenses/by/2.5/ http://dx.doi.org/10.1038/npre.2007.306.1 Reproducibility is a fundamental requirement in scientific experiments and clinical contexts. Recent publications raise concerns about the reliability of microarray technology because of the apparent lack of agreement between lists of differentially expressed genes (DEGs). In this study we demonstrate that (1) such discordance may stem from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion, the lists become much more reproducible, especially when fewer genes are selected; and (3) the instability of short DEG lists based on P cutoffs is an expected mathematical consequence of the high variability of the t-values. We recommend the use of FC ranking plus a non-stringent P cutoff as a baseline practice in order to generate more reproducible DEG lists. The FC criterion enhances reproducibility while the P criterion balances sensitivity and specificity. http://dx.doi.org/10.1038/npre.2007.306.1 Mon, 02 Jul 2007 09:20:53 UTC The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies doi:10.1038/npre.2007.306.1 2007-07-02 Leming Shi Nature Precedings 2007-07-02T09:20:53Z Manuscript Biotechnology Bioinformatics http://creativecommons.org/licenses/by/2.5/