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Ioannidis, john

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https://www.readbyqxmd.com/read/27896967/methods-to-ensure-the-reproducibility-of-biomedical-research
#1
Konrad J Karczewski, Nicholas P Tatonetti, Arjun K Manrai, Chirag J Patel, C Titus Brown, John P A Ioannidis
Science is not done in a vacuum - across fields of biomedicine, scientists have built on previous research and used data published in previous papers. A mainstay of scientific inquiry is the publication of one's research and recognition for this work is given in the form of citations and notoriety - ideally given in proportion to the quality of the work. Academic incentives, however, may encourage individual researchers to prioritize career ambitions over scientific truth. Recently, the New England Journal of Medicine published a commentary calling scientists who repurpose data "research parasites" who misuse data generated by others to demonstrate alternative hypotheses...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27884869/sex-based-subgroup-differences-in-randomized-controlled-trials-empirical-evidence-from-cochrane-meta-analyses
#2
Joshua D Wallach, Patrick G Sullivan, John F Trepanowski, Ewout W Steyerberg, John P A Ioannidis
OBJECTIVE:  To evaluate the frequency, validity, and relevance of statistically significant (P<0.05) sex-treatment interactions in randomized controlled trials in Cochrane meta-analyses. DESIGN:  Meta-epidemiological study. DATA SOURCES:  Cochrane Database of Systematic Reviews (CDSR) and PubMed. ELIGIBILITY CRITERIA FOR STUDY SELECTION:  Reviews published in the CDSR with sex-treatment subgroup analyses in the forest plots, using data from randomized controlled trials...
November 24, 2016: BMJ: British Medical Journal
https://www.readbyqxmd.com/read/27884175/network-meta-analyses-performed-by-contracting-companies-and-commissioned-by-industry
#3
Ewoud Schuit, John Pa Ioannidis
BACKGROUND: Industry commissions contracting companies to perform network meta-analysis for health technology assessment (HTA) and reimbursement submissions. Our objective was to estimate the number of network meta-analyses performed by consulting companies contracted by industry, to assess whether they were published, and to explore reasons for non-publication. METHODS: We searched MEDLINE for network meta-analyses of randomized trials. Papers were included if they had authors affiliated with any contracting company...
November 25, 2016: Systematic Reviews
https://www.readbyqxmd.com/read/27842706/insomnia-from-drug-treatments-evidence-from-meta-analyses-of-randomized-trials-and-concordance-with-prescribing-information
#4
Anthony G Doufas, Orestis A Panagiotou, Periklis Panousis, Shane Shucheng Wong, John P A Ioannidis
OBJECTIVE: To determine whether drugs used to treat diverse conditions cause insomnia symptoms and whether their prescription information is concordant with this evidence. METHODS: We conducted a survey of meta-analyses (Cochrane Database of Systematic Reviews) and comparisons with package inserts compiled in the Physicians' Desk Reference (PDR). We identified randomized controlled trials (RCTs) in which any drug had been evaluated vs placebo and sleep had been assessed...
November 11, 2016: Mayo Clinic Proceedings
https://www.readbyqxmd.com/read/27832824/genome-of-the-asian-longhorned-beetle-anoplophora-glabripennis-a-globally-significant-invasive-species-reveals-key-functional-and-evolutionary-innovations-at-the-beetle-plant-interface
#5
Duane D McKenna, Erin D Scully, Yannick Pauchet, Kelli Hoover, Roy Kirsch, Scott M Geib, Robert F Mitchell, Robert M Waterhouse, Seung-Joon Ahn, Deanna Arsala, Joshua B Benoit, Heath Blackmon, Tiffany Bledsoe, Julia H Bowsher, André Busch, Bernarda Calla, Hsu Chao, Anna K Childers, Christopher Childers, Dave J Clarke, Lorna Cohen, Jeffery P Demuth, Huyen Dinh, HarshaVardhan Doddapaneni, Amanda Dolan, Jian J Duan, Shannon Dugan, Markus Friedrich, Karl M Glastad, Michael A D Goodisman, Stephanie Haddad, Yi Han, Daniel S T Hughes, Panagiotis Ioannidis, J Spencer Johnston, Jeffery W Jones, Leslie A Kuhn, David R Lance, Chien-Yueh Lee, Sandra L Lee, Han Lin, Jeremy A Lynch, Armin P Moczek, Shwetha C Murali, Donna M Muzny, David R Nelson, Subba R Palli, Kristen A Panfilio, Dan Pers, Monica F Poelchau, Honghu Quan, Jiaxin Qu, Ann M Ray, Joseph P Rinehart, Hugh M Robertson, Richard Roehrdanz, Andrew J Rosendale, Seunggwan Shin, Christian Silva, Alex S Torson, Iris M Vargas Jentzsch, John H Werren, Kim C Worley, George Yocum, Evgeny M Zdobnov, Richard A Gibbs, Stephen Richards
BACKGROUND: Relatively little is known about the genomic basis and evolution of wood-feeding in beetles. We undertook genome sequencing and annotation, gene expression assays, studies of plant cell wall degrading enzymes, and other functional and comparative studies of the Asian longhorned beetle, Anoplophora glabripennis, a globally significant invasive species capable of inflicting severe feeding damage on many important tree species. Complementary studies of genes encoding enzymes involved in digestion of woody plant tissues or detoxification of plant allelochemicals were undertaken with the genomes of 14 additional insects, including the newly sequenced emerald ash borer and bull-headed dung beetle...
November 11, 2016: Genome Biology
https://www.readbyqxmd.com/read/27816833/diet-body-size-physical-activity%C3%A2-and-risk-of-prostate-cancer-an-umbrella-review-of-the-evidence
#6
REVIEW
Georgios Markozannes, Ioanna Tzoulaki, Dimitra Karli, Evangelos Evangelou, Evangelia Ntzani, Marc J Gunter, Teresa Norat, John P Ioannidis, Konstantinos K Tsilidis
The existing literature on the relationship between diet, body size, physical activity and prostate cancer risk was summarised by the World Cancer Research Fund Continuous Update Project (CUP). An evaluation of the robustness of this evidence is required to help inform public health policy. The robustness of this evidence was evaluated using several criteria addressing evidence strength and validity, including the statistical significance of the random effects summary estimate and of the largest study in a meta-analysis, number of prostate cancer cases, between-study heterogeneity, 95% prediction intervals, small-study effects bias, excess significance bias and sensitivity analyses with credibility ceilings...
November 3, 2016: European Journal of Cancer
https://www.readbyqxmd.com/read/27789483/very-large-treatment-effects-in-randomised-trials-as-an-empirical-marker-to-indicate-whether-subsequent-trials-are-necessary-meta-epidemiological-assessment
#7
Myura Nagendran, Tiago V Pereira, Grace Kiew, Douglas G Altman, Mahiben Maruthappu, John P A Ioannidis, Peter McCulloch
OBJECTIVE:  To examine whether a very large effect (VLE; defined as a relative risk of ≤0.2 or ≥5) in a randomised trial could be an empirical marker that subsequent trials are unnecessary. DESIGN:  Meta-epidemiological assessment of existing published data on randomised trials. DATA SOURCES:  Cochrane Database of Systematic Reviews (2010, issue 7) with data on subsequent large trials updated to 2015, issue 12. ELIGIBILITY CRITERIA:  All binary outcome forest plots were selected, which contained an index randomised trial with a VLE that was nominally statistically significant (P<0...
October 27, 2016: BMJ: British Medical Journal
https://www.readbyqxmd.com/read/27748217/genetic-etiologies-of-comorbidity-and-stability-for-reading-difficulties-and-adhd-a-replication-study
#8
Sally J Wadsworth, John C DeFries, Erik G Willcutt, Bruce F Pennington, Richard K Olson
Because of recent concerns about the replication of published results in the behavioral and biomedical sciences (Ioannidis, PLoS Medicine, Vol. 2, 2005, p. e124; Open Science Collaboration, Science, Vol. 349, 2015, p. 943; Pashler & Wagenmakers, Perspectives on Psychological Science, Vol. 7, 2012, pp. 528-530), we have conducted a replication of our recently published analyses of longitudinal reading performance and attention deficit-hyperactivity disorder data from twin pairs selected for reading difficulties (Wadsworth et al...
December 2016: Twin Research and Human Genetics: the Official Journal of the International Society for Twin Studies
https://www.readbyqxmd.com/read/27687052/meta-analysis-comparing-established-risk-prediction-models-euroscore-ii-sts-score-and-acef-score-for-perioperative-mortality-during-cardiac-surgery
#9
Patrick G Sullivan, Joshua D Wallach, John P A Ioannidis
A wide variety of multivariable risk models have been developed to predict mortality in the setting of cardiac surgery; however, the relative utility of these models is unknown. This study investigated the literature related to comparisons made between established risk prediction models for perioperative mortality used in the setting of cardiac surgery. A systematic review was conducted to capture studies in cardiac surgery comparing the relative performance of at least 2 prediction models cited in recent guidelines (European System for Cardiac Operative Risk Evaluation [EuroSCORE II], Society for Thoracic Surgeons 2008 Cardiac Surgery Risk Models [STS] score, and Age, Creatinine, Ejection Fraction [ACEF] score) for the outcomes of 1-month or inhospital mortality...
August 23, 2016: American Journal of Cardiology
https://www.readbyqxmd.com/read/27682343/five-minutes-with-john-ioannidis
#10
Susan Mayor
No abstract text is available yet for this article.
2016: BMJ: British Medical Journal
https://www.readbyqxmd.com/read/27666373/revel-an-ensemble-method-for-predicting-the-pathogenicity-of-rare-missense-variants
#11
Nilah M Ioannidis, Joseph H Rothstein, Vikas Pejaver, Sumit Middha, Shannon K McDonnell, Saurabh Baheti, Anthony Musolf, Qing Li, Emily Holzinger, Danielle Karyadi, Lisa A Cannon-Albright, Craig C Teerlink, Janet L Stanford, William B Isaacs, Jianfeng Xu, Kathleen A Cooney, Ethan M Lange, Johanna Schleutker, John D Carpten, Isaac J Powell, Olivier Cussenot, Geraldine Cancel-Tassin, Graham G Giles, Robert J MacInnis, Christiane Maier, Chih-Lin Hsieh, Fredrik Wiklund, William J Catalona, William D Foulkes, Diptasri Mandal, Rosalind A Eeles, Zsofia Kote-Jarai, Carlos D Bustamante, Daniel J Schaid, Trevor Hastie, Elaine A Ostrander, Joan E Bailey-Wilson, Predrag Radivojac, Stephen N Thibodeau, Alice S Whittemore, Weiva Sieh
The vast majority of coding variants are rare, and assessment of the contribution of rare variants to complex traits is hampered by low statistical power and limited functional data. Improved methods for predicting the pathogenicity of rare coding variants are needed to facilitate the discovery of disease variants from exome sequencing studies. We developed REVEL (rare exome variant ensemble learner), an ensemble method for predicting the pathogenicity of missense variants on the basis of individual tools: MutPred, FATHMM, VEST, PolyPhen, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP, SiPhy, phyloP, and phastCons...
October 6, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/27634930/methods-to-increase-reproducibility-in-differential-gene-expression-via-meta-analysis
#12
Timothy E Sweeney, Winston A Haynes, Francesco Vallania, John P Ioannidis, Purvesh Khatri
Findings from clinical and biological studies are often not reproducible when tested in independent cohorts. Due to the testing of a large number of hypotheses and relatively small sample sizes, results from whole-genome expression studies in particular are often not reproducible. Compared to single-study analysis, gene expression meta-analysis can improve reproducibility by integrating data from multiple studies. However, there are multiple choices in designing and carrying out a meta-analysis. Yet, clear guidelines on best practices are scarce...
September 14, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27620683/the-mass-production-of-redundant-misleading-and-conflicted-systematic-reviews-and-meta-analyses
#13
John P A Ioannidis
POLICY POINTS: Currently, there is massive production of unnecessary, misleading, and conflicted systematic reviews and meta-analyses. Instead of promoting evidence-based medicine and health care, these instruments often serve mostly as easily produced publishable units or marketing tools. Suboptimal systematic reviews and meta-analyses can be harmful given the major prestige and influence these types of studies have acquired. The publication of systematic reviews and meta-analyses should be realigned to remove biases and vested interests and to integrate them better with the primary production of evidence...
September 2016: Milbank Quarterly
https://www.readbyqxmd.com/read/27601477/health-outcomes-during-the-2008-financial-crisis-in-europe-systematic-literature-review
#14
Divya Parmar, Charitini Stavropoulou, John P A Ioannidis
OBJECTIVE:  To systematically identify, critically appraise, and synthesise empirical studies about the impact of the 2008 financial crisis in Europe on health outcomes. DESIGN:  Systematic literature review. DATA SOURCES:  Structural searches of key databases, healthcare journals, and organisation based websites. REVIEW METHODS:  Empirical studies reporting on the impact of the financial crisis on health outcomes in Europe, published from January 2008 to December 2015, were included...
2016: BMJ: British Medical Journal
https://www.readbyqxmd.com/read/27599208/systematic-evaluation-of-the-associations-between-environmental-risk-factors-and-dementia-an-umbrella-review-of-systematic-reviews-and-meta-analyses
#15
Vanesa Bellou, Lazaros Belbasis, Ioanna Tzoulaki, Lefkos T Middleton, John P A Ioannidis, Evangelos Evangelou
INTRODUCTION: Dementia is a heterogeneous neurodegenerative disease, whose etiology results from a complex interplay between environmental and genetic factors. METHODS: We searched PubMed to identify meta-analyses of observational studies that examined associations between nongenetic factors and dementia. We estimated the summary effect size using random-effects and fixed-effects model, the 95% CI, and the 95% prediction interval. We assessed the between-study heterogeneity (I-square), evidence of small-study effects, and excess significance...
September 4, 2016: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/27599158/citation-metrics-a-primer-on-how-not-to-normalize
#16
John P A Ioannidis, Kevin Boyack, Paul F Wouters
Citation metrics are increasingly used to appraise published research. One challenge is whether and how to normalize these metrics to account for differences across scientific fields, age (year of publication), type of document, database coverage, and other factors. We discuss the pros and cons for normalizations using different approaches. Additional challenges emerge when citation metrics need to be combined across multiple papers to appraise the corpus of scientists, institutions, journals, or countries, as well as when trying to attribute credit in multiauthored papers...
September 2016: PLoS Biology
https://www.readbyqxmd.com/read/27548059/correction-multiple-citation-indicators-and-their-composite-across-scientific-disciplines
#17
John P A Ioannidis, Richard Klavans, Kevin W Boyack
[This corrects the article DOI: 10.1371/journal.pbio.1002501.].
August 2016: PLoS Biology
https://www.readbyqxmd.com/read/27507038/systematic-assessment-of-pharmaceutical-prescriptions-in-association-with-cancer-risk-a-method-to-conduct-a-population-wide-medication-wide-longitudinal-study
#18
Chirag J Patel, Jianguang Ji, Jan Sundquist, John P A Ioannidis, Kristina Sundquist
It is a public health priority to identify the adverse and non-adverse associations between pharmaceutical medications and cancer. We search for and evaluate associations between all prescribed medications and longitudinal cancer risk in participants of the Swedish Cancer Register (N = 9,014,975). We associated 552 different medications with incident cancer risk (any, breast, colon, and prostate) during 5.5 years of follow-up (7/1/2005-12/31/2010) in two types of statistical models, time-to-event and case-crossover...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27487843/an-overview-of-methods-for-network-meta-analysis-using-individual-participant-data-when-do-benefits-arise
#19
Thomas Pa Debray, Ewoud Schuit, Orestis Efthimiou, Johannes B Reitsma, John Pa Ioannidis, Georgia Salanti, Karel Gm Moons
Network meta-analysis (NMA) is a common approach to summarizing relative treatment effects from randomized trials with different treatment comparisons. Most NMAs are based on published aggregate data (AD) and have limited possibilities for investigating the extent of network consistency and between-study heterogeneity. Given that individual participant data (IPD) are considered the gold standard in evidence synthesis, we explored statistical methods for IPD-NMA and investigated their potential advantages and limitations, compared with AD-NMA...
August 2, 2016: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/27467098/what-happens-when-underperforming-big-ideas-in-research-become-entrenched
#20
Michael J Joyner, Nigel Paneth, John P A Ioannidis
No abstract text is available yet for this article.
October 4, 2016: JAMA: the Journal of the American Medical Association
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