Competências Básicas de Investigação Científica e de Publicação

1. CompetênciasBásicas de InvestigaçãoCientífica e de Publicação Lecture 1: How publishing works August 2014 Ganesha Associates

2. Publishing is an essential research skill determining likelihood of acceptance navigating a submission system in a second language assessing relevance to research topic comparing journals Peer Review Journal Selection Publication Success Writing Submission Preparation decision to re-submit, or try a different journal writing an outline understanding comments writing in English formatting to guidelines citation management long decision timelines Publication ethics

3. www.ganesha-associates.com Ganesha Associates

4. Me… • BSc Physics 1971, PhD Neuroscience 1976, post doc 1975-1979 • Visiting Professor, UFPe 1978-79 • 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, 2007, 2008, 2012, 2013 Ganesha Associates

5. Getting published in a good journal is important because… • 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 • Contribute to building the story • Permanent archive • Replication • Professional advancement !! • Broad readership • High rates of citation (= recognition) • CAPES Qualis points • $$$$$ Ganesha Associates

6. Assessment of departmental performance

7. Your goals as researchers • Get your paper published • At first/second attempt • In a Qualis A journal • And receive lots of citations…

8. But, the Editor has other ideas… Ganesha Associates 2013

9. Editorial review process Submit article Screening Rejection Peer review Rejection Revision Acceptance

10. Screening: Royal Society for Chemistry • “Articles submitted to our journals are 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 screening rates of our journals varies a lot. Our high quality journals have a pre screen rate of about 80%.” • So only 20% of articles ever get to the peer review stage (and 80% of them are rejected!) Ganesha Associates 2013

11. So overall rejection rates are high Ganesha Associates

12. Some comments on 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 helps authors to develop clear, precise writing styles. Ganesha Associates

13. Peer review – the cons • A peer is likely to be a competitor. So how objective are they going to be ? • 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 • Citation rates of individual articles published in high impact titles such as Nature is highly variable. Ganesha Associates

14. What is the Editor looking for ? • Will the article get cited (and boost the IF?)? • Is the subject of the article relevant to any of the main stories currently being published in the journal? • Are the findings novel, interesting to the readership? • Is the purpose of the research clearly stated in the title, abstract? • Is the experimental design appropriate? Ganesha Associates

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

16. 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+%] • But ultimately, most manuscripts are published, somewhere… • So learn how to climb the quality ladder

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

18. What can authors do to avoid rejection? Project proposal Experiment, results, analysis Write article • ? Submit to journal Rejection/ acceptance Re-submit

19. What can authors do to avoid rejection? Project proposal Experiment, results, analysis Write article Make sure your problem is well-defined right from the start and is derived directly from the current literature! • ? Submit to journal Rejection/ acceptance Re-submit

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

21. Journal selection criteria • Your hypothesis – where have other recent papers on this subject been published? • Are the aims and scope of journal appropriate? • The Impact Factor and Qualis ranking • Speed and ease of publication • Publisher’s statistics on circulation, downloads

22. Submission to wrong journal • Dear Profa, • The manuscript that you submitted to JOURNALNAME falls outside the scope of the journal and cannot be considered for publication. Although in the past the journal has published research in this field, with the change of editorship a few years ago it was decided that this type of research reported does not contribute to our basic understanding of the auditory system. Please do not consider this as a judgment on the value of your research. Because your research may have a clinical application, you could consider sending this manuscript to a more clinically oriented journal. • Editor in Chief

23. So which journal should I choose?

24. Example: Communities of arbuscularmycorrhizal fungi in dry tropical forests of Northeast Brazil The arbuscularmycorrhizal association is one of the important strategies used by plants in arid and semiarid regions to support water scarcity and soil nutrient deficiency. In this study the diversity and activity of arbuscularmycorrhizal fungi (AMF) were investigated in two types of dry tropical forest. Soil and roots samples were collected in areas of thorny dry woody savanna (TDWS) and in areas of mixed savanna and montane deciduous shrub (SMDS) in Pernambuco State, Brazil. Twenty seven species from 10 genera of Glomeromycota were identified, and Acaulospora was the most representative. An average of 50 spores per 100 g of soil was recovered from the two areas. The infection potential of the AMF was determined using colonized root fragments and extraradical mycelium and demonstrated the importance of these propagules for the colonization of roots. Under the same semiarid conditions, the two tropical dry forests studied harbored distinct AMF communities indicating that the soil and vegetation type are the key influencers of the composition and activity of these fungi in the studied areas. Ganesha Associates 2013

25. Use eTBLAST to find similar articles Ganesha Associates 2013

26. Use eTBLAST to find similar articles Ganesha Associates 2013

27. Top 10 Journals in this area of research 1. Mycorrhiza    Total score: 8.23 2. Oecologia    Total score: 1.40 3. The New phytologist    Total score: 1.31 4. Mycologia    Total score: 0.81 5. Molecular ecology    Total score: 0.75 6. Ying yong sheng tai xuebao = The journal of applied ecology     Total score: 0.67 7. Applied and environmental microbiology    Total score: 0.65 8. Environmental microbiology    Total score: 0.62 9. Revista de biología tropical    Total score: 0.46 10. Journal of plant physiology    Total score: 0.44 Ganesha Associates 2013

28. EDANZ Journal Selector Ganesha Associates 2013

29. Ganesha Associates 2013

30. Oecologia: Aims and scope Oecologia publishes innovative ecological research of international interest. We seek reviews, advances in methodology, and original contributions, emphasizing the following areas: - Population ecology- Plant-microbe-animal interactions- Ecosystem ecology- Community ecology- Global change ecology- Conservation ecology- Behavioral ecology- Physiological Ecology In general, studies that are purely descriptive, mathematical, documentary, and/or natural history will not be considered.

31. Ganesha Associates 2013

32. Mycorrhiza: Aims and scope Mycorrhiza is an international journal devoted to research into mycorrhizas - the widest symbioses in nature, involving plants and a range of soil fungi world-wide. The scope of Mycorrhizacovers all aspects of research into mycorrhizas, including molecular biology of the plants and fungi, fungal systematics, development and structure of mycorrhizas, and effects on plant physiology, productivity, reproduction and disease resistance. The scope also includes interactions between mycorrhizal fungi and other soil organisms and effects of mycorrhizas on plant biodiversity and ecosystem structure. Mycorrhiza contains original papers, short notes and review articles, along with commentaries and news items. It forms a platform for new concepts and discussions, and is a basis for a truly international forum of mycorrhizologists from all over the world.

33. Ganesha Associates 2013

34. Impact factors and Qualis ? Ganesha Associates 2013

35. What is an Impact factor? • For a given year (2013), the impact factor is the average number of citations per paper published during the two preceding years. • A = number of times articles published in 2011 and 2012 were cited by other indexed journals during 2013. • B = total number of articles published in 2011 and 2012. • 2013 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

36. Orthopaedic physical therapy BMC Musculoskeletal Disorders Impact Factor/Qualis: 1.875/C J. Orthopaedic and Sports Physical TherapyImpact Factor/Qualis: 2.538/A1 Physical Therapy in Sport Impact Factor/Qualis: 2.645/A2 Spine Impact Factor/Qualis: 2.624/C Archives of Physical Medicine and Rehabilitation Impact Factor/Qualis: 2.358/A1 American J. Physical Medicine & Rehabilitation Impact Factor/Qualis: 1.556/A1 The Journal Of Hand Surgery Impact Factor/Qualis: 1.572/C Knee Surgery, Sports Traumatology, Arthroscopy Impact Factor/Qualis: 2.676/B1 J. Bone and Joint Surgery Impact Factor : 2.967/C

37. Try to publish in mainstream, international journals…

38. …where the citation levels are higher

39. Impact factors and research assessment – the future • Publishers LOVE impact factors! • “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.” • Researchers and funding agencies HATE them! • But citations do prove that your work is being integrated into the consensus view for your discipline Source: Nature press release July 2013

40. Break

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

42. What can authors do to improve? Project proposal Experiment, results, analysis Write article Make sure your problem is well-defined right from the start and is derived directly from the current literature! • ? Submit to journal Rejection/ acceptance Re-submit

43. Project titles – what is your problem? • 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

44. 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 COPD - Chronic obstructive pulmonary disorder

45. Hypotheses – should be about mechanism not measurement • Patients with migraine will have a higher number of myofascial trigger points in the temporalis, masseter, sternocleidomastoid and descending trapezius muscles. • Patients with migraine will have a low threshold for pain sensation in these points. • Cutaneous mechanical cephalic and extra-cephalic allodyniawill vary during the month Allodynia is pain due to a stimulus which does not normally provoke pain

46. Hypotheses negated – do we learn anything new? • Patients with migraine will have a lower number of myofascial trigger points in the temporalis, masseter, sternocleidomastoid and descending trapezius muscles. • Patients with migraine will have a higher threshold for pain sensation in these points. • Cutaneous mechanical cephalic and extra-cephalic allodyniawill not vary during the month Allodynia is pain due to a stimulus which does not normally provoke pain

47. Abstracts – what is your problem? 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 myofascialtrigger 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 measure differences in the frequency , anatomical location and sensory threshold pressure of the trigger points of the trapezius (descending fibers), masseter and sternocleidomastoid muscles in women with and without migraine .

48. Reduction in perceived stress as a migraine trigger: the "let-down headache" hypothesis. • OBJECTIVE: To test whether level of perceived stress and reductions in levels of perceived stress (i.e., "let-down") are associated with the onset of migraine attacks in persons with migraine. • METHODS: Patients with migraine from a tertiary headache center were invited to participate in a 3-month electronic diary study. Participants entered data daily regarding migraine attack experience, subjective stress ratings, and other data. Stress was assessed using 2 measures: the Perceived Stress Scale and the Self-Reported Stress Scale. Logit-normal, random-effects models were used to estimate the odds ratio for migraine occurrence as a function of level of stress over several time frames. • RESULTS: Of 22 enrolled participants, 17 (median age 43.8 years) completed >30 days of diaries, yielding 2,011 diary entries including 110 eligible migraine attacks (median 5 attacks per person). Level of stress was not generally associated with migraine occurrence. However, decline in stress from one evening diary to the next was associated with increased migraine onset over the subsequent 6, 12, and 18 hours, with odds ratios ranging from 1.5 to 1.9 (all p values < 0.05) for the Perceived Stress Scale. Decline in stress was associated with migraine onset after controlling for level of stress for all time points. Findings were similar using the Self-Reported Stress Scale. • CONCLUSIONS: Reduction in stress from one day to the next is associated with migraine onset the next day. Decline in stress may be a marker for an impending migraine attack and may create opportunities for preemptive pharmacologic or behavioral interventions. Neurology. 2014 Apr 22;82(16):1395-401. Impact Factor 8.25

49. Developing better hypotheses is not difficult