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Trends in Scientific, Technical and Medical Publishing

Trends in Scientific, Technical and Medical Publishing. Associação Brasileira de Editores Científicos VIII Workshop de Editoração Científica 10 a 13 N ovembro 2014 Campos do Jordão /SP. CV. BSc Physics 1971, PhD Neuroscience 1976, post doc Epidemiology 1975-1979

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Trends in Scientific, Technical and Medical Publishing

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  1. Trends in Scientific, Technical and Medical Publishing AssociaçãoBrasileira de EditoresCientíficos VIII Workshop de EditoraçãoCientífica10 a 13 Novembro 2014Campos do Jordão/SP Ganesha Associates CC BY 3.0

  2. CV • BSc Physics 1971, PhD Neuroscience 1976, post doc Epidemiology 1975-1979 • Visiting Researcher, UFPe 1978-79, 1984 • Editor, Publisher, Director at Elsevier Science, 1979 – 2005 • Pubmed systems expert, NCBI, NIH 2006-2007 • STM business analyst, Outsell Inc, 2009-2011 • Visiting Professor UFPe, 2006-2008, 2012-2014 • Independent consultant Ganesha Associates 2006-2014 • Consultant, European Bioinformatics Institute ELIXIR impact project 2015 Ganesha Associates CC BY 3.0

  3. Trends in STM publishing • Globalisation will trump nationalism • Traditional publishing morphs into informatics • Publishing 2.0 is broken • What can we do to fix it? Ganesha Associates CC BY 3.0

  4. The growing importance of metrics Ganesha Associates CC BY 3.0

  5. Brasil: Ganesha Associates CC BY 3.0

  6. BRIC output: documents Ganesha Associates CC BY 3.0 Source: International Comparative Activity Performance – Elsevier 2011

  7. Ganesha Associates CC BY 3.0

  8. Citation quality is a problem Ganesha Associates CC BY 3.0

  9. EPI : English Proficiency Index by age Ganesha Associates CC BY 3.0

  10. Ganesha Associates CC BY 3.0

  11. Summary • As the markets of emerging countries mature, focus will move from commodity-based economies to knowledge-based economies. • Basic research funding will increasingly be directed towards areas that can demonstrate high impact on subsequent levels of technological innovation. • Science and economics know no borders, global collaborations will be the norm. • National governments will actively manage the intellectual property that they create with the objective of attracting global companies to invest with them. Ganesha Associates CC BY 3.0

  12. A brief history of scientific publishing • According to Bishop Sprat's History of the Royal Society (1667), society members sought to reject "amplifications, digressions, and swellings of style...bringing all things as near the Mathematical plainness, as they can: and preferring the language of Artizans, Countrymen, and Merchants, before that, of Wits and Scholars." Ganesha Associates CC BY 3.0

  13. A brief history of scientific publishing Ganesha Associates CC BY 3.0

  14. Scientific publishing is a very profitable Ganesha Associates CC BY 3.0

  15. Open access mandates • National Institute of Health (NIH) Public Access Policy – 2008 • Hargreaves Review of Intellectual Property and Growth – 2011 • EC says that it is aiming for 60% of all European publicly funded research articles to be open access by 2016 - 2012 • Finch Group Report – June 2012 • RCUK Policy on Open Access – July 2012, amended March 2013 • Fair Access to Science and Technology Research Act (FASTR) – February 2013 • White House Office of Science and Technology Policy (OSTP) – February 2013 • Green almost unanimously favoured over Gold (Exception UK) Ganesha Associates CC BY 3.0

  16. The emergence of Open Access Clockwise: Harold Varmus, Michael Eisen, Pat Brown and David Lipman Ganesha Associates CC BY 3.0

  17. History of sequence info => open access Ganesha Associates CC BY 3.0

  18. Data growth curves of 5 major EMBL-EBI resources (European Genome-phenome Archive (EGA); European Nucleotide Archive (ENA); Proteomics data repository (PRIDE); Metabolomics resource (MetaboLights); and Functional genomics database (ArrayExpress) over the years 2005-2013. Source: EMBL-EBI. Ganesha Associates CC BY 3.0

  19. Ganesha Associates CC BY 3.0

  20. ELIXIR: the European Research Infrastructure for biological data • ELIXIR connects national infrastructures and EMBL-EBI • Launched in 2014 • 11 Member states + EMBL signed agreement • Czech Republic, Estonia, Denmark, Finland,Israel, Netherlands, Norway,Portugal, Switzerland, Sweden, UK • 6 countries have signed MoU and prepare national signature • Belgium, Greece, France, Italy, Slovenia, Spain Ganesha Associates CC BY 3.0

  21. ELIXIR connects national centres and EMBL-EBI to build a sustainable European infrastructure for biological research data. medicine agriculture bioindustries ELIXIR underpins life science research – across academia and industry. environment www.elixir-europe.org Ganesha Associates CC BY 3.0

  22. The future • Publicly funded and large biomedical research funders are committed to open access publishing. • Smaller charitable funders are supportive of the aims of open access, but are concerned about the practical implications for their budgets and their funded researchers. • Biomedical research funders are now turning their attention to other priorities for sharing research outputs, including data, protocols and negative results. • Publishing priorities of biomedical research funders [BMJ Open 17 Sept 2014] Ganesha Associates CC BY 3.0

  23. Summary • To be of use information resources need to be interconnected and freely accessible • This is not a job that can be undertaken by publishers alone • Funders and end-users will drive the changes Ganesha Associates CC BY 3.0

  24. The Publishing 2.0 business model is broken… • Open access alone is not yet the answer. • PLoS 2013 income tax return: • Turnover $33.43m • Profit margin 17%. • CEO salary $479k. • “Bad open-access publishers are still growing like crazy.” [Nature, 7 August 2014] Ganesha Associates CC BY 3.0

  25. Scientific assessment Ganesha Associates CC BY 3.0

  26. Scientific assessment - 1 • “Subjective assessments of the merit and likely impact of scientific publications are routinely made by scientists during their own research, and as part of promotion, appointment, and government committees.” • The San Francisco Declaration on Research Assessment (DORA, 2012) intends to halt the practice of correlating the journal impact factor with the merits of a specific scientist's contributions. • But then what…? Ganesha Associates CC BY 3.0

  27. Scientific assessment - 2 • “In a large cohort of NHLBI-funded cardiovascular R01 grants, we were unable to find an association between better percentile ranking and higher scientific impact as assessed by citation metrics.” [Circulation Research 9 January 2014] • “Peer review should be able to tell us what research projects will have the biggest impacts,” Lauer contends. In fact, we explicitly tell scientists it’s one of the main criteria for review. But what we found is that peer review is not predicting outcomes at all. And that’s quite disconcerting.” Michael Lauer, NHLBI, NIH, Science August 2014 Ganesha Associates CC BY 3.0

  28. Scientific assessment - 3 • “Using two large datasets (F1000 and Wellcome Trust) in which scientists have made qualitative assessments of scientific merit, we show that scientists are poor at judging scientific merit and the likely impact of a paper, and that their judgment is strongly influenced by the journal in which the paper is published. • We also demonstrate that the number of citations a paper accumulates is a poor measure of merit and we argue that although it is likely to be poor, the impact factor, of the journal in which a paper is published, may be the best measure of scientific merit currently available.” [PLoS Biology 2013] Ganesha Associates CC BY 3.0

  29. Scientific assessment - 4 • “Most journals exchange some manuscripts with at least one other journal. • Resubmission flows occurred preferentially within subgroups of journals. • Partitioning of the network … revealed seven principal journal clusters. • These were strongly consistent with subject categories as defined by the Institute for Scientific Information” [Science 23 November 2012] Ganesha Associates CC BY 3.0

  30. Irreproducibility - 1 • Drug development: The biotechnology company Amgen was unable to replicate the vast majority of published pre-clinical research studies - only 6 out of 53 landmark cancer studies could be replicated, a success rate of 11%. [Nature 28 March 2012] • Cancer research: There are many technical reasons why experimental results, particularly in cancer research, cannot be reproduced, including unrecognized variables in the complex experimental model, poor documentation of procedures, selective reporting of the most-positive findings, misinterpretation of technical noise as biological signal and, in the most extreme cases, fabrication of data. [Nature Reviews Clinical Oncology, 1 October 2013] Ganesha Associates CC BY 3.0

  31. Irreproducibility - 2 • The Consort Statement is an evidence-based, minimum set of recommendations for reporting randomized trials. It offers a standard way for authors to prepare reports of trial findings, facilitating their complete and transparent reporting, and aiding their critical appraisal and interpretation [2010, BMJ, NEJM, Lancet, JAMA] • Nature research journals introduce editorial measures to address the problem by improving the consistency and quality of reporting in life-sciences articles. See [Nature 24 April 2013] • NIH plans to enhance reproducibility [Nature 24 January 2014] Ganesha Associates CC BY 3.0

  32. Bias • “Positive results have a better chance of being published, are published earlier, and are published in journals with higher impact factors. Conclusions exclusively based on published studies, therefore, can be misleading”. [BMJ 2005] • Misuse of citations: “A complete citation network was constructed from all PubMed indexed English literature papers addressing the belief that β amyloid, a protein accumulated in the brain in Alzheimer’s disease, is produced by and injures skeletal muscle of patients with inclusion body myositis. • We found that citation was often used to generate inappropriate information cascades resulting in unfounded authority of claims.” [BMJ 2009] Ganesha Associates CC BY 3.0

  33. Conflicts of interest • Publication of industry-supported trials was associated with an increase in journal impact factors. Sales of reprints may provide a substantial income. We suggest that journals disclose financial information in the same way that they require them from their authors, so that readers can assess the potential effect of different types of papers on journals’ revenue and impact. [PLoS Medicine October 2010] • Statins. The BMJ and authors withdraw statements suggesting that adverse events occur in 18-20% of patients due to misunderstanding of statistical results. [BMJ 2014] Ganesha Associates CC BY 3.0

  34. Summary • Bibliometrics, citation network analysis and informatics can provide insight into how the publishing process is working and can be improved. • Publishers can add more value by getting the basics right, rather than obsessing about “quality” Ganesha Associates CC BY 3.0

  35. Publishing 3.0 • The growth of information (articles, data, etc) is effectively exponential – discovery, curationand analysis are now bigger problems than creation of new content. • Funders need to drive the reconstruction of the process – NCBI/EBI as models of information use rather launching eLife • Impact of mega-journals such as PLoS ONE, Brain Research, BBA. Ganesha Associates CC BY 3.0

  36. Publishing 3.0 • Publishing cycle: Funder[Strategy]> Proposal> Funder[Peer Review: Likely outcome]> Researcher> Manuscript> Editor[Peer Review: Methodology+?]> Publisher[Standards]> User[Usefulness] • What defines good science, and what in general defines "Quality”? • The funder and the reader who determine “purpose” and “usefulness”. • The editor checks that basic methodology is appropriate, argumentation clear, rules of scientific writing met, etc. • The publisher creates the XML, links, applies data standards Ganesha Associates CC BY 3.0

  37. Publishing 3.0 • Each field supports a hierarchy of journals but only journals at the top and bottom will be strong brands. • And the one at the bottom will probably be PLoS ONE! • National journals will only flourish if the can establish themselves as a global brand • Adoption of international open access business models Ganesha Associates CC BY 3.0

  38. Publishing 3.0 • Not all journals will thrive • Need more ambition in the aims and scope, instructions to authors • Objective, transparent editorial selection process and clearer feedback to authors. • English! Ganesha Associates CC BY 3.0

  39. Publishing 3.0 • Reasons for rejection. Hypothesis unclearand/or unoriginal, submitted to the wrong journal, badly written (Portuguese/English). • The metaphor of “dwarfs standing on the shoulders of giants” expresses the meaning of "discovering truth by building on previous discoveries". • But where are the giants and how do you climb on their shoulders? • The virtual library, science without borders: reading English, collaboration Ganesha Associates CC BY 3.0

  40. Publishing 3.0 • The role of national journals, The Brazilian Journal of… vs. The Journal of the Brazilian… • A stepping stone on the path to excellence or permanent gateway to mediocrity? Aim high(er)! • Examples: The Caatinga, the malnourished Nordestino rat, nursing care pathways for catheterisation in a hospital in Sao Paulo. • The role of SciELO as a publishing platform: Professionalization, internationalization, financial sustainability. Meeting 2 December Ganesha Associates CC BY 3.0

  41. Advantages to being a Canadian national publisher? • “Canadian voice” • Research community support • University support • Community knowledge • Language • Trusted brand

  42. Areas for improvement • Aims and scope: Our mission is to promote scientific knowledge generated in the rigor of the research methodology and ethics. The purpose of *** is to publish the outcomes of original research to advance the practice of *** in the medical, surgical management, education, research and information technology and communication. • Abstracts: The summary should be structured into five sections (Background, Objectives, Methods, Results, Conclusions) when it is an Original Article, avoiding abbreviations and considering the maximum number of words. • Figures: Figure legends should be double-spaced, and be numbered and placed before the References. Ganesha Associates CC BY 3.0

  43. Conclusions • The STM publishing environment is changing rapidly. • Brazilian STM publishers have an opportunity to reinvent themselves in a form that can be globally competitive. • In order to achieve this goal they must professionalise their services and partner with key funders and user groups Ganesha Associates CC BY 3.0

  44. Referee’s comments 1.The statistical analysis is incomplete. It is not clear why a chi-square association test was performed in Table 3, instead of the multivariable logistic regression. In addition, age, sex, and SES should be adjusted. 
2.The literature discussion is incomplete and biased. There should be a fair assessment and discussion since not all studies reported an inverse association between atopic diseases and childhood leukemia.
3.The discussion about the paper by Chang et al regarding potential biases seems unfair, and the author failed to mention another medical record-based paper by Logan Spector (EJC 2004) that also reported a positive association between atopic diseases and childhood ALL.
4.Overall, I do not see any substantial improvement over the current literature regarding the association between atopic diseases and childhood leukemia. The study design of this paper still suffers from the possibility of reverse causality and does not contribute anything novel to the literature. 5. A key strength of this study is that it examines these associations in a different population with a different immune profile than has previously been examined - a population that per the authors in lines 166-167 has a high incidence of parasite infection. Important limitations include the sample size and the methods of exposure assessment. Ganesha Associates CC BY 3.0

  45. Journals unit for reproducibility A group of editors representing more than 30 major journals; representatives from funding agencies; and scientific leaders assembled at the American Association for the Advancement of Science’s headquarters in June 2014 to discuss principles and guidelines for preclinical biomedical research. The gathering was convened by the US National Institutes of Health, Nature and Science (see Science346, 679; 2014). The attendees agreed on a common set of Principles and Guidelines in Reporting Preclinical Research (see go.nature.com/ezjl1p) that list proposed journal policies and author reporting requirements in order to promote transparency and reproducibility. Ganesha Associates CC BY 3.0

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