Competências Básicas de Investigação Científica e de Publicação

1. CompetênciasBásicas de InvestigaçãoCientífica e de Publicação Lecture 3: Publishing, avoiding rejection and low citation rates 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. 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.”

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19. 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+%]

20. 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

21. 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

22. 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

23. 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

24. 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

25. 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

26. Cell’s editorial structure • In-house Editor • 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

27. 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

28. 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

29. 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

30. 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

31. Peer review – the pros • A peer is someone who is of the same or equal standing as another. Thus peer review is review performed by individuals considered to be professional equals. • The process forces authors to meet the standards of their discipline and achieve scientific objectivity. • Publications and awards that have not undergone 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. This is just as true for professional scientists as it is for students. • The outcomes of peer review are acceptance, conditional acceptance or rejection Ganesha Associates

32. 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

33. Alternatives: PLOS ONE • PLOS ONE will rigorously peer-review your submissions and publish all papers that are judged to be technically sound. • Judgments about the importance of any particular paper are made after publication by the readership. • PLOS ONE features reports of original research from all disciplines within science and medicine. Ganesha Associates

35. 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

36. 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!

37. 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!

38. 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

39. 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

40. 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

41. 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

42. 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.

43. Break

44. You… • How can we improve our research outputs? • Quantity • Quality • How can we avoid rejection? • How can we increase citation rates? • How can we publish in quality journals?

45. Main opportunities for success - 2013 • Start with a well-defined hypothesis that has its foundations firmly rooted in the international literature. • Have a clear message • Develop a well-structured writing style • Understand the publishing process • Choose the right journal at the beginning of the project Ganesha Associates 2013

46. The research process Project proposal Experiment, results, analysis Write article • ? Submit to journal Rejection/ acceptance Re-submit

47. Project titles – the problem starts here • Análise dos limiares de sensibilidade à pressão e à corrente elétrica em acupontos em indivíduos com e sem migrânea • Frequência, localização anatômica e limiar de percepção dolorosa em pontos gatilhos miofasciais na cabeça e pescoço em mulheres com migrânea. • Ultrassonografia e eletromiografia de superfície dos músculos flexores cervicais em mulheres com migrânea e cefaleia do tipo tensional

48. Titles are easily improved – focus on outcomes rather than methods • DIAPHRAGM RELEASE MANUAL TECHNIQUE EFFECTS ON DIAPHRAGMATIC MOBILITY, RESPIRATORY MUSCLE STRENGTH AND EXERCISE PERFORMANCE IN COPD PATIENTS: A RANDOMIZED CONTROLLED TRIAL. • MANUAL DIAPHRAGM RELEASE TECHNIQUE INCREASES TIDAL VOLUME IN ELDERLY COPD PATIENTS

49. Frequência, localização anatômica e limiar de percepção dolorosa em pontos gatilhos miofasciais na cabeça e pescoço em mulheres com migrânea. Context: Migraine is a very common pain syndrome and the mechanisms that can cause or aggravate the pain and the consequences of its chronicity are still not completely understood. Studies have shown that migraine is associated with a central sensitization phenomena in which noxious stimuli cause changes in the central nervous system , sensitizing cranial nociceptors and reducing their activation threshold . In this context , the constant peripheral nociceptive input due to myofascial trigger points in the muscles of the head and neck may be associated with the onset of the migraine attack . The elucidation of the role of trigger points in migraine is essential in order to establish and direct physical therapy through tools useful for patients with myofascial disorders associated with migrainous framework . Objective: To evaluate and compare differences in the frequency , anatomical location and sensory threshold pressure of the trigger points of the trapezius ( descending fibers ) , masseter , sternocleidomastoid , in women with and without migraine .

50. Hypotheses – mechanism not measurement • Patients with migraine have a higher amount of myofascial trigger points in the temporalis, masseter, sternocleidomastoid and descending trapezius muscles. • Patients with migraine have a low threshold for pain sensation in these points. • Cutaneous mechanical cephalic and extra-cephalic allodynia vary within one month