Competências Básicas de Investigação Científica e de Publicação

1. CompetênciasBásicas de InvestigaçãoCientífica e de Publicação Lecture 6: How Publishing works Ganesha Associates

2. Publishing drives the scientific process New consensus view Old consensus view Ganesha Associates

3. For you, getting published is important… • Attribution of priority via peer review • It’s new (probably), you were the first ! • Verification via peer review • Your conclusions are clear and plausible • Your methodology is appropriate • Communication • Integration into the consensus view • Permanent archive • Replication • Professional advancement !! • Broad readership • High rates of citation (= recognition) • CAPES Qualis points • $$$$$ Ganesha Associates

4. So, the Editor has two choices… Ganesha Associates 2013

5. Rejection: Royal Society for Chemistry • “Articles submitted to our journals are pre-screened so the editor that is handling the article decides that the article is either out of the journal scope or that the article is clearly below the quality level of the journal. • The pre-screening rates of our journals varies a lot. Our high quality journals have a pre screen rate of about 80%.” Ganesha Associates 2013

6. Reasons for rejection • Mismatch with journal aims and scope [submit to wrong journal] • Failure to follow journal’s instructions to authors • Badly written, bad English, bad Portuguese • Lack of originality, novelty or significance [weak hypothesis] • Flaws in study design [poor experimental design] • Several of these problems are easily avoidable! Ganesha Associates 2013

7. Lost in translation • “Poor English” often used as a euphemism for “badly written” • Poor Portuguese translates as poor English • If the science is clear (title, abstract, intro, results) the chances of rejection are reduced

8. Which journal should I choose?

9. Selecting the best journal is important

10. The mycology journal ‘ecosystem’ • Important journals - Mycology Dept, UFPE (2006) • Journal of Invertebrate Pathology • Phytopathology • Plant Pathology • Mycological Research • Plant Disease • Applied and Environmental Microbiology • Current Microbiology • Genetics and Molecular Biology • Molecular Plant Pathology • Medical Mycology • Mycopathology • Applied Soil Ecology • ………..and at least 10 more journals! • Note: only three titles contain a reference to mycology ! • Define your journal ecosystem carefully Ganesha Associates

11. Journal selection criteria • Your hypothesis • Aims and scope of journal • Impact Factor • Speed and ease of publication • Publisher’s statistics on circulation, downloads • Colleagues • Qualis ranking

12. What is an Impact factor? • For a given year, the impact factor is the average number of citations per paper published during the two preceding years. • A = number of times articles published in 2006 and 2007 were cited by other indexed journals during 2008. • B = total number of articles published in 2006 and 2007. • 2008 impact factor = A/B. • Used as a proxy for the relative importance of a journal within its field Ganesha Associates

13. Try to publish in international journals with good impact factors Ganesha Associates 2013

14. Journal Selection - Asia Aimed at Reaching Target Audience and Gaining Recognition 69% Convenience 20% n=333

15. A Publisher’s View of the Cell Biology Ecosystem Ganesha Associates

16. Example: Nature press release July 2013 • “The 2012 Journal Citation Report (JCR) places Nature Communications at #3 and Scientific Reports at #8 in the top 10 Multidisciplinary Sciences titles. • Nature remains #1 in the Multidisciplinary Sciences, with an Impact Factor of 38.597, and is the most cited science journal in the world with 554,745 citations in 2012.”

17. Example: RSC press release June 2013 • The Royal Society of Chemistry's publishing portfolio has once again shown outstanding excellence, with the publication of the latest Impact Factors (IF) report from Thomson Reuters. • Six out of the top 20 multidisciplinary chemistry journals are published by the RSC - more than any other publisher.

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22. So getting published isn’t easy… • Journal editors are fiercely competitive • They only want to publish articles that will improve the standing of their journal • So they select only those articles that they think will be highly cited… • And reject the majority of articles sent to them [up to 90+%]

23. Implications for you! • Identify the most important journals in your field • Check their impact factors, Qualis rankings • Read the ‘Aims and Scope’ statements for each journal carefully • Does your hypothesis fit the Aims and Scope? • Can you find similar articles in recently published issues? Ganesha Associates

24. Cell: Aims and Scope • Cell publishes findings of unusual significance in any area of experimental biology, including but not limited to cell biology, molecular biology, neuroscience, immunology, virology and microbiology, cancer, human genetics, systems biology, signaling, and disease. • The basic criterion for considering papers is whether the results provide significant conceptual advances into, or raise provocative questions and hypotheses regarding an interesting biological question. Ganesha Associates

25. Genomics: Aims and Scope • The goal of Genomics is to promote the understanding of the structure, function, and evolution of genomes in all kingdoms of life and the application of genome sciences and technologies to challenging problems in biology and medicine. The scope of the journal is broad and we welcome original, full-length, and timely papers in all of the following areas: • Comparative genomics analysis that yields valuable insights into conserved and divergent aspects of function, regulation, and evolution • Bioinformatics and computational biology with particular emphasis on data mining and improvements in data annotation and integration • Functional genomics approaches involving the use of large-scale and/or high-throughput methods to understand genome-scale function and regulation of transcriptomes and proteomes • Identification of genes involved in disease and complex traits, including responses to drugs and other xenobiotics • Significant advances in genetic and genomics technologies and their applications, including chemical genomics Ganesha Associates

26. Gastroenterology: Aims and Scope • Gastroenterology publishes novel clinical and basic studies on all aspects of the digestive system, including the liver and pancreas, as well as nutrition. • The types of articles Gastroenterology publishes include original papers, review articles, case reports, and special category manuscripts. Ganesha Associates

27. Agricultural and Forest Meteorology • Agricultural and Forest Meteorology is an international journal for the publication of original articles and reviews on the inter-relationship between meteorology and the fields of plant, animal and soil sciences, ecology, and biogeochemistry. Emphasis is on basic and applied scientific research relevant to practical problems in agriculture, forestry, and natural ecosystems. Articles must appeal to an international audience. Theoretical models should be tested against experimental data. Special issues devoted to single topics are also published. Ganesha Associates

28. Inside a primary journal: Cell • Cell was launched in 1974 as the journal of exciting biology.  • Now a part of Elsevier’s Cell Press, a family of 15 journals, • Cell’s Ph.D.-trained scientific editors work with authors, reviewers, and editorial board members with the goal of publishing 26 issues of the most interesting discoveries in biology every year Ganesha Associates

29. Cell’s editorial structure • In-house Editors • Employed by the journal’s publisher to carry out administrative and copy-editing roles • Editor-in-Chief • Major figure in the field • Editorial Board • Represent all of the major sub-fields, act as advisors to the Editor-in-Chief. Usually recognised experts in their respective fields • Referees • Selected by the Editorial Board, usually an expert in the specific area covered by the manuscript Ganesha Associates

30. Editorial evaluation process - Cell • All submissions are initially evaluated in depth by the Editor-in-Chief or sent to an appropriate member of the Editorial Board. • Papers that do not conform to the general criteria for publication will be returned to the authors without detailed review, typically within 3-5 days. • Otherwise, manuscripts will be sent to reviewers who have agreed in advance to assess the paper rapidly. • The editors will make every effort to reach decisions on these papers within 3 weeks of the submission date.  • Accepted papers will be published within 3 months of acceptance. Ganesha Associates

31. What is the Editor looking for ? • Plausibility • Is the experimental design robust ? • How effectively have the alternative hypotheses been excluded ? • Topicality • Is the work original • Is it interesting ? • Is it relevant ? • Is it useful ? Ganesha Associates

32. Covering letter format • Address to the editor personally • State your manuscript title and publication type • Give a brief background, rationale and description of your results • Explain the importance of your findings and why they would be of interest to the journal’s target audience • Provide corresponding author details

33. The role of peer review • History • Anonymous • Multiple, to avoid bias • Validation/accreditation • Selecting the best • Or avoiding the worse ? • Alternatives • Neuroscience • PLosOne • Elsevier Ganesha Associates

34. Peer review – the pros • The process forces authors to meet the standards of their discipline and achieve scientific objectivity. • Publications that do not involve peer review are likely to be regarded with suspicion by scholars and professionals in many fields. • Peer review is important to achieve clear, precise writing. Ganesha Associates

35. Peer review – the cons • A peer is likely to be a competitor. How objective are they going to be ? • Most articles get published and the quality of articles published in high impact titles such as Nature is highly variable. • Authors are encouraged by the publishing process to exaggerate their claims and even be selective of the data being published, leading to bias • Negative findings are rarely published, leading to further bias when judging the effectiveness say of new medical technologies Ganesha Associates

36. Alternatives: PLOS ONE • PLOS ONEis a journal that publishes reports of original research from all disciplines within science and medicine. • PLOS ONE will rigorously peer-review manuscripts and will publish all papers that are technically sound. • Judgments about the importance of any particular paper are made after publication by the readership, I,e, citations, article downloads. Ganesha Associates

37. Alternatives: Neuroscience Peer-Review Consortium • The NPRC was created to reduce the inefficiency that arises when an author submits a manuscript to a journal after the same manuscript has been reviewed and rejected by another journal. • In many cases, publication of good manuscripts is delayed as editors from each journal attempt to find reviewers, send the reviews, and wait for the reviews to be returned. • Often the same reviewer is asked to review the same manuscript multiple times. • The NPRC streamlines this process by allowing reviews solicited by one journal to be forwarded and re-used by other member journals. • However, ultimate control of manuscript submission remains in the hands of authors as reviews are forwarded only when the author requests this service. Ganesha Associates

38. A letter of rejection Dear Author, We have received the reports from our advisors on your manuscript XYZ-D-13-00220 “Title********************************". With regret, I must inform you that, based on the advice received, I have decided that your manuscript cannot be accepted for publication in the Journal of Imaginary Microbiology. Below, please find the comments for your perusal. You are kindly requested to also check the website for possible reviewer attachment(s). I would like to thank you very much for forwarding your manuscript to us for consideration and wish you every success in finding an alternative place of publication. With kind regards, Editor

39. What to do next • Unconditional rejection • Editor offers no opportunity for appeal • Show comments to colleagues • Revise as though the rejection was conditional • Submit to a different journal • Conditional rejection • Regard this as an opportunity to improve your paper • Show comments to colleagues • Respond to all comments and record your actions in a covering letter • Consider submitting to a better journal!

40. Reviewer comments - example • The paper needs to be formatted properly for the journal. • This reviewer was only able to find information for papers submitted with Introduction, materials and methods, results and discussion sections while much of this is in the paper the format appears to be incorrect even for a short communication. • Itwas difficult to find the number of samples taken or to understand the experimental set-up as written; changing the style to a more traditional journal format as suggested above would help with this. • In addition the most important reference Brown et al 2013 is missing!

41. Reviewer comments - example • This paper describes clinical and cytogenetic finding in a child with retinoblastoma who had an aggressive fatal course. The authors postulate that this may be related to changes in chromosome 6. However, it is difficult to see how the findings here either promote or negate that hypothesis. In addition several other problems should be addressed: • Abstract, line 9: could (not should) • Abstract: define IO • Staging details at the time of initial diagnosis are inadequate. Were scans done of the head? chest? abdomen? pelvis? bone? • One assumes that the right eye was normal at initial diagnosis but this is not stated. Ganesha Associates

42. Reviewer comments – example, cont’d e. Staging details at the time of initial relapse are inadequate. Were scans done of the head? chest? abdomen? pelvis? bones? f. What was the csf cytology at the time of initial relapse? g. What cytologic studies were performed on the ocular, marrow and other tumors at the initial relapse to prove that this was retinoblastoma? h. What is MADIT? i. If the authors are going to postulate that chromosome 6 abnormalities are important then other publications require more careful review and more detailed presentation of findings. How does one more case advancethehypothesis? Ganesha Associates

43. Reviewer Comments – main problems Author’s Hypothesis: This case represents a particularly aggressive form of retinoblastoma which can be diagnosed by the observation of a rare chromosomal abnormality Referees Hypotheses: The initial treatment of the retinoblastoma was ineffective But assuming it wasn’t: Several chromosomal abnormalities described – no evidence that specific chromosomal defect chosen was connected with the disease severity Ganesha Associates

44. Why were the referee’s comments confusing?

45. Referee response letter • Respond to all of the reviewers’ comments • Describe all of the changes you have made in the letter • Also describe the reasons why you have not made suggested changes • Make it easy to see the changes have made in the manuscript itself • Refer to line and page numbers • Different color font • Highlight the text

46. Referee response letter • If you disagree with the reviewer with the reviewerbe clear why: • Reviewer Comment: In your analysis of the data you have chosen to use a somewhat obscure fitting function (regression). In my opinion, a simple Gaussian function would have sufficed. Moreover, the results would be more instructive and easier to compare to previous results. • Author response: We agree with the reviewer that a simple Gaussian fit would facilitate comparison with the results of other studies. However, our tailored function allows for the analysis of the data in terms of the Smith model [Smith et al, 1998]. We have added two sentences to the paper (page 3 paragraph 2) to explain the use of this function and Smith’s model.

47. Ten simple rules to help you get published • Read many papers, and learn from both the good and the bad work of others. It is never too early to become a critic • The more objective you can be about your work, the better that work will ultimately become. • Good editors and reviewers will be objective about your work. • If you do not write well in the English language, take lessons early; it will be invaluable later. • Learn to live with rejection. • Philip E. Bourne, PLoS • http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0010057 Ganesha Associates

48. Ten simple rules to help you get published • The ingredients of good science are obvious - novelty of research topic, comprehensive coverage of the relevant literature, good data, good analysis including strong statistical support, and a thought-provoking discussion • Start writing the paper the day you have the idea of what questions to pursue • Become a reviewer early in your career. • Decide early on where to try to publish your paper. • Quality is everything • Philip E. Bourne, PLoS • http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0010057 Ganesha Associates

49. Some more suggestions to help you get published • Choosing a problem • Something that you have a personal interest in • Based on a current experimental paradigm recognized by the international scientific community • And for which you have intellectual support, e.g. experimental design, data interpretation, etc • For which experimental resources are available, affordable • Mestrado/Doutorado projects • Choose a supervisor with a good research record • Specify the research problem early during the first year • Try to shape first year course work around these specific needs • Pay more attention to experimental design, not just statistics • Don’t attempt one big experiment, but plan several • Seek progress reviews at regular intervals Ganesha Associates