Competências Básicas de Investigação Científica e de Publicação

1. CompetênciasBásicas de InvestigaçãoCientífica e de Publicação Lecture 3: How publishing works and how to become a better author. Phonoaudiology November 2013 Ganesha Associates

2. 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

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

4. 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

5. The importance of rejection rates Ganesha Associates

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. So which journal should I choose?

9. Ganesha Associates 2013

10. Orthopaedic physical therapy BMC Musculoskeletal Disorders Impact Factor : 1.875 J. Orthopaedic and Sports Physical Therapy Impact Factor : 2.538 Physical Therapy Impact Factor : 2.645 Spine Impact Factor : 2.624 Archives of Physical Medicine and Rehabilitation Impact Factor : 2.358 American J. Physical Medicine & Rehabilitation Impact Factor : 1.556 The Journal Of Hand Surgery Impact Factor : 1.572 Knee Surgery, Sports Traumatology, Arthroscopy Impact Factor : 2.676 J. Bone and Joint Surgery Impact Factor : 2.967

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 based on a measure of the average number of citations received by each article. 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.”

15. 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+%]

16. 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

17. 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

18. Journal of Voice: Aims and scope The Journal of Voice includes clinical and research articles that are of interest to all professionals of all backgrounds. Papers are solicited on all aspects of voice, including basic voice science, acoustics, anatomy, synthesis, medical and surgical treatment of voice problems, voice therapy, voice pedagogy, and studies in other areas that increase the knowledge of normal (including performance) and abnormal vocal function in adults and children. Review articles will also be considered.

19. Brazilian Journal of Otorhinolaryngology: Aims and Scope Brazilian Journal of Otorhinolaryngology publishes original contributions in otolaryngology and the associated areas (cranio-maxillo-facial surgery and phoniatrics). The aim of this journal is the national and international divulgation of the scientific production interesting to the otolaryngology, as well as the discussion, in editorials, of subjects of scientific, academic and professional relevance.

20. 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

21. 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

22. 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 • Supply details of possible reviewers

23. 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

24. 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

25. 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

26. 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

28. 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

29. 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!

30. 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!

31. 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

32. Referee’s comments can be confusing

33. 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

34. 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.

35. Break

36. 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?

37. Where does it go wrong? Project proposal Experiment, results, analysis Write article • ? Submit to journal Rejection/ acceptance Re-submit

38. 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

39. 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

40. 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 .

41. 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

42. Finding this information is not difficult

44. Top ten journals in this field 1. Headache Total score: 1.46 2. Pain Total score: 1.24 3. Current pain and headache reports Total score: 0.91 4. Cephalalgia : an international journal of headache Total score: 0.71 5. The journal of pain : official journal of the American Pain Soc Total score: 0.51 6. European journal of neurology : the official journal of the Eur Total score: 0.47 7. Medical hypotheses Total score: 0.41 8. Brain : a journal of neurology Total score: 0.41 9. Chinese medicine Total score: 0.39 10. Neurology Total score: 0.39

48. Conclusions • Make sure your hypothesis is firmly rooted in the current literature • Identify at least one journal that is publishing work based on similar hypotheses • If your reference list does not contain many recently published articles, you have a problem

49. Measuring group performance The h-index is an index that attempts to measure both the productivity and impact of the published work of a scientist or scholar. The index is based on the set of the scientist's most cited papers and the number of citations that they have received in other publications