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  1. 1. How to Write for and GetPublished in Scientific Journals 論文発表ガイド Hokkaido University Warren Raye, PhD Senior Life Sciences Editor Edanz Group 26 June 2012
  2. 2. A little about me… Author ResearcherVirology, Stem Cell Biology, Arthiritis, Immunology & Molecular Biology Lecturer & teacher Senior Life Sciences Editor Edanz Group | 3
  3. 3. Presentation Section One: Scientific publishing Section Two: Before you start… Section Three: Structuring your manuscript Section Four: Hints and tips Edanz Group | 4
  4. 4. Section One Scientific publishing Why publish? Publishing in English What do journal editors want? Peer review Edanz Group | 5
  5. 5. Why publish? Nature is complex Edanz Group | 6
  6. 6. Why publish? We use complex technologies and methods to understand it… Edanz Group | 7
  7. 7. Why publish? …and the science is often necessarily complex Edanz Group | 8
  8. 8. Why publish? To exchange ideas globally! 国際舞台で意見交換するには明確な文 書表現が重要 研究は世に発表して初めて完 結する Edanz Group | 9
  9. 9. Why publish in English? English is the international language of science 英語は研究の共通語 Other scientists want to hear from Japanese researchers! Become an effective science communicator International reputation enabling collaborations and work opportunities Edanz Group | 10
  10. 10. What do journal editors want? ジャーナル編集長はできるだけ質の高い論文を求めている Will stand up to peer review Original research that advances a field in some way Interesting to the journal’s readership Active research areas Clear and concise English Edanz Group | 11
  11. 11. Peer review improves your manuscript 査読は論文の質を高める Rejection Acceptance Minor revision Major revision Few papers are accepted without revision Rejection and revision are integral to the peer review process Edanz Group | 12
  12. 12. Section Two Before you start … Read Study design Select an appropriate journal Evaluate significance Ethics Edanz Group | 13
  13. 13. Reading helps your writing Both sides of the brain are essential and work in harmony Reading Logic Creativity Reading Writing Similarly, reading and writing are connected Edanz Group | 14
  14. 14. Reading improves your writing Read as often as possible Discuss with your colleagues Assists you with journal selection Provides ideas for your next manuscript 論文の読み方が上達すれば執筆力も向上 Edanz Group | 15
  15. 15. Strategies for reading Read Title and Abstract first Self-assess knowledge of topic Read Results or the relevant parts of the Results (Figures & Tables) Read Discussion for interpretation Refer to Introduction and Methods only if necessary Edanz Group | 16
  16. 16. Experimental design Get it right Critical What is your hypothesis or research question? THE AIM(S) OF YOUR STUDY What methods are appropriate? Do you have the relevant resources? Identify your controls Edanz Group | 17
  17. 17. Experimental design Get it right Sample sizes (n) large enough? Which statistical test(s)? When in doubt – talk to a statistician! Does your study comply with ALL ethics requirements? Edanz Group | 18
  18. 18. Journal Selection Edanz Group | 19
  19. 19. Choosing a target journal: timing The target journal should be chosen: After the results to be published have been obtained (with no new ones coming) After a decision has been made on how high to aim—high, medium or low impact Before writing the manuscript Edanz Group | 20
  20. 20. Choosing a target journal Journal selection should be based on an honest evaluation of the manuscript Compare with the stated aims and scope and impact factor of potential target journals Novelty Aims and Scope Significance Impact Factor Edanz Group | 21
  21. 21. Match your manuscript with the journal What is the message? Who will be interested? How significant are your results? Where have similar articles been published? Edanz Group | 22
  22. 22. Factors to consider Aims and scope Open access or subscriber Publishing frequency Prestige Impact factor Cost Target audience Publication type Which factor is most important to you? Edanz Group | 23
  23. 23. Evaluating significance: importance Specific interest only or of interest to many Affect many (e.g. new tool) Support for (or contradiction of) an existing theory Substantially improve our understanding of a phenomenon or provide a new technology or disease treatment? Edanz Group | 24
  24. 24. Evaluating significance: novelty How new are my results compared with those already published? New findings Incremental Conceptual advances advances Low to medium Medium to high impact factor impact factor Edanz Group | 25
  25. 25. Evaluating significance: relevance Are my findings of relevance only to a specific geographical region or ethnic population or do they have implications for other regions and populations? High impact factor journals may consider specific findings if they are the first of their kind or of international significance. Edanz Group | 26
  26. 26. Evaluating significance: appeal Is my work in an area of ‘popular appeal’? E.g. is it likely to be reported in mainstream or lay scientific media Examples: Optogenetics Higgs boson Epigenetics Global warming Stem cells Clean tech Edanz Group | 27
  27. 27. Publication ethicsDo not … Multiple submissions Plagiarism Improper author contribution Data fabrication and falsification Improper use of human subjects and animals Conflicts of interest 非倫理的行為は不正行為 Edanz Group | 28
  28. 28. Section Three Structuring your manuscript You are telling a story Beginning → Middle → End Must be easy to read and easy to understand 読者にとって理解しやすくする Edanz Group | 29
  29. 29. ‘Tell them three times’ Introduction = Beginning Assertion ‘tell them what you are going to tell them,’ Body = Middle Evidence ‘tell them,’ Conclusion = End Affirmation ‘tell them again what you told them’. Edanz Group | 30
  30. 30. Basic manuscript structure Expanded IMRaD model Abstract Introduction Assertion Methods Results Evidence and Discussion Affirmation References Edanz Group | 31
  31. 31. The ‘write’ order 論文に記載される順番と同じ順序で執筆しないこと For maximum clarity and consistency: Methods Write during your research Results Introduction Write after selecting your Discussion target journal Title Write last Abstract Edanz Group | 32
  32. 32. Abstract Summarizes your work アブストラクトは論文の中で最も重要なセクション Concise (100–300 words) 1–4 sentences – describe problem(s) addressed 1–4 sentences –objectives/hypotheses 1–2 sentences – techniques; avoid details 1–3 sentences – most important results Final sentence – concluding statement アブストラクトは独立したものとして読めること Edanz Group | 33
  33. 33. Introduction Why? What question (problem) was studied? どのような問題を研究したのか? The answer to this question is contained within your Introduction Beginning → Middle → End Edanz Group | 34
  34. 34. Introduction Beginning Sufficient background information Puts your work into context Start with a broad background General Specific Comprehensive literature review Cite reviews Edanz Group | 35
  35. 35. Introduction Middle Rationale The reason(s) for doing this work? Why is it important? Justify your work Explain how you tried to address the problem (1–2 sentences) Do not state results from your study Edanz Group | 36
  36. 36. Introduction End State the methods you plan to use Clearly and explicitly state 1–3 specific hypotheses or objectives of your study Edanz Group | 37
  37. 37. Methods How did you carry out your work? 問題をどのように研究したのか? Subheadings Easier to read Past tense New methods must be described in sufficient detail that they can be reproduced Established methods can be referenced Save time and effort Edanz Group | 38
  38. 38. Results What did you find? 何を発見したのか? Accurate, brief, clear Use subheadings Use past tense to describe your results When referring to figures and tables, use present tense Do not explain your results Do not duplicate data among figures, tables and text Edanz Group | 39
  39. 39. Display items Tables and figures Present a large amount of data quickly and efficiently Present most significant result as a figure or table Keep it simple — use separate panels if necessary Avoid duplication with the text Label all parts of your figures Legends must be able to ‘stand alone’ 図表は効果的なコミュニケーション方法 Edanz Group | 40
  40. 40. Display items Tables Clear concise legend/caption Data divided ) intocategoriesfor clarity Abbreviations defined Edanz Group | 41
  41. 41. Display items FiguresAxes clearly labeled Stained mouse tumor sections. Scale bar is provided in both images. Clear, ‘stand J Mol Med alone’ legend DOI 10.1007/s00109-012-0863-6 Edanz Group | 42
  42. 42. Discussion So what? What do these findings mean? 発見が意味するものは? The answer to this question is in the Discussion Beginning → Middle → End Edanz Group | 43
  43. 43. Discussion Beginning Avoid repeating the results section Answer the research question(s) posed Emphasize the major finding(s) first What is your major conclusion, based on the results you have presented? Edanz Group | 44
  44. 44. Discussion Middle Interpret your results … Compare with other studies Same or different? Possible reasons why? Unexpected results Briefly describe any limitations Sample sizes Complementary tests How could experiments be improved? Edanz Group | 45
  45. 45. Discussion End Restate major conclusion(s) In summary … OR In conclusion … Possible real world applications and implications Suggest future work“Clinical and research priorities include furthering our understanding of thepathogenesis of M. pneumoniae-associated CNS disease, development ofmore reliable serologic assays, and defining the role of quantitative PCR indistinguishing acute infection from asymptomatic carriage and prolongedpost-infection shedding” – Bitun & Richardson Curr Infect Dis Rep 2010, 12:282-290 Edanz Group | 46
  46. 46. Section Four Hints and tips Clear communication Language Cover letters Responding to reviewer comments Edanz Group | 47
  47. 47. ExpectationsInformation is easier tointerpret and more uniformwhen placed where mostreaders expect to find itGood writers are aware ofthese expectationsReadability Edanz Group | 48
  48. 48. Verb placement Readers expect verbs to closely follow subjects 読者は主語の後ろに動詞が続くと考えている Subject Sentence Verb Verb . Subject and verb far apart = poor readability Edanz Group | 49
  49. 49. Avoid reader confusion Readers can be confused if subject and verb are separated by too much contentThe smallest of the URFs (URFA6L), a 207-nucleotide (nt) reading frame overlapping out ofphase the [NH2]-terminal portion of theadenosinetriphosphatase (ATPase) subunit 6 gene,has been identified as the animal equivalent of therecently discovered yeast H-ATPase subunit 8 gene. 読者にとって理解しやすくする Edanz Group | 50
  50. 50. Avoid reader confusionThe smallest of the URFs is URFA6L, a 207-nucleotide (nt) reading frameoverlapping out of phase the [NH2]-terminal portion of theadenosinetriphosphatase (ATPase) subunit 6 gene; it has been identified as theanimal equivalent of the recently discovered yeast H-ATPase subunit 8 gene.The smallest of the URFs (URFA6L) has been identifiedas the animal equivalent of the recently discovered yeastH-ATPase subunit 8 gene; URFA6L is a 207-nucleotide (nt)reading frame overlapping out of phase the [NH2]-terminal portion of the adenosinetriphosphatase (ATPase)subunit 6 gene.We identified the smallest of the URFs (URFA6L) as theanimal equivalent of the recently discovered yeast H-ATPase subunit 8 gene. URFA6L is a … . Edanz Group | 51
  51. 51. Which voice? Active vs. passive Use the active voice unless your target journal states otherwise 可能な限り能動態を使うBlood samples were collected from 256 patients.We collected blood from 256 patients. Edanz Group | 52
  52. 52. Active voice Subject Verb Active Sentences written in the active voice are: SIMPLE DIRECT CLEAR EASY TO READ Edanz Group | 53
  53. 53. Stress position Readers focus on information at the end of a sentence. Subject Verb take-home information . Edanz Group | 54
  54. 54. Stress positionThe dog sat when her mistress offered a treat.The dog sat when a treat was offered by her mistress.When the mistress offered her a treat, the dog sat. Readers, without thinking, concentrate on the end of a sentence. 無意識に、文書の末尾にある情報に重点を置く Edanz Group | 55
  55. 55. Topic position Readers expect a sentence/phrase to be a story about whoever shows up first Subject Topic position Verb Stress position . Edanz Group | 56
  56. 56. Topic position sentence idea idea idea idea Topic link Linkage and context The family went into the courtyard to see the new puppy. The dog sat when her owner offered a treat. Everyone was so excited they broke into applause. However, as the courtyard was situated right next to my bedroom, the sound woke me from my sleep. Edanz Group | 57
  57. 57. Topic sentences Easier to read Indicates to the reader the main idea of a paragraph Provides the writer with a focus Should be the first sentence of a paragraph Then discuss/explain the topic Summarize with a concluding sentence Beginning → Middle → End Edanz Group | 58
  58. 58. Readability“only 4% of readers understand a 27-word sentence the first time” Reader objectives Only need to read once Do not have to read slowly Can understand author logic immediately Edanz Group | 59
  59. 59. Sentence length Keep it short & simple We examined numerous peer-reviewed journals Easy to read articles had an average sentence length of around 17 words Sentences that are 15–20 words Long sentences and repetition One sentence: one idea 1文につき1つのアイデア Edanz Group | 60
  60. 60. Simple is best 簡潔な表現が理解しやすい Simple language is best Makes your science more relevant Minimizes confusion – maximizes understanding Science is often complex Use simple language to help more people understand your work Edanz Group | 61
  61. 61. Cover letters Competition for publication space and for editors’ attention is very high It may not be enough to send a cover letter to a journal editor like this:Dear Editor-in-Chief,I am sending you our manuscript entitled “Techniques to detect circoviruses in Japanesebird species” by Raye et al. We would like to have the manuscript considered forpublication in Virology Methods Online.Please let me know of your decision at your earliest convenience.Sincerely yours,Warren Raye, PhD Edanz Group | 62
  62. 62. Your cover letter General rules 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 Edanz Group | 63
  63. 63. Cover letters ExampleDear Dr Graeber,Please find enclosed our manuscript entitled “Amyloid-like inclusions in the brains of Huntington’s disease patients”, byMcGowan et al., which we would like to submit for publication as a Research Paper in Neurogenetics.Recent immunohistochemical studies have revealed the presence of neuronal inclusions containing an N-terminal portion ofthe mutant huntingtin protein and ubiquitin in the brain tissues of Huntington’s disease (HD) patients; however, the role of Give thethese inclusions in the disease process has remained unclear. One suspected disease-causing mechanism in Huntington’s background todisease and other polyglutamine disorders is the potential for the mutant protein to undergo a conformational change to a the researchmore stable anti-parallel β-sheet structure…To confirm if the immunohistochemically observed huntingtin- and ubiquitin-containing inclusions display amyloid features, weperformed Congo red staining and both polarizing and confocal microscopy on post-mortem human brain tissues obtained What was donefrom five HD patients, two AD patients, and two normal controls. Congo red staining revealed a small number of amyloid-like and what wasinclusions showing green birefringence by polarized microscopy, in a variety of cortical regions.... ….detected inclusions foundobserved in parallel sections, suggesting that only a relatively small proportion of inclusions in HD adopt an amyloid-likestructure.We believe our findings would appeal to a broad audience, such as the readership of Neurogenetics. As a wide-reaching journal Interest topublishing original research on all aspects of neuroscience… journal’s readersWe confirm that this manuscript has not been published elsewhere and is not under consideration by another journal. Allauthors have approved the manuscript and agree with submission to Neurogenetics. We have read and have abided by the Conforms tostatement of ethical standards for manuscripts submitted to Neurogenetics. The authors have no conflicts of interest to journaldeclare. requirementsPlease address all correspondence to…. Edanz Group | 64
  64. 64. Peer review Very few papers are Rejection Acceptance Minor immediately accepted Major revision without need for any revision revisions Complete rejection Journal editor Major revisions decision Minor revisions Acceptance Edanz Group | 65
  65. 65. Reasons for rejection: the science Methods Validations Research question Data versus Statistics conclusions Edanz Group | 66
  66. 66. Reasons for rejection: the manuscript Methods detail Citations Rationale and aims Results format Limitations Edanz Group | 67
  67. 67. Reasons for rejection: otherInappropriate journal Inappropriate selected: scope, timing: too early impact, audience or late Edanz Group | 68
  68. 68. Revision How to respond 査読者はボランティアゆえ、礼儀正しく接しま しょう! Politely respond to all the reviewers’ comments in a response letter Make it easy to see the changes Refer to line and page numbers Different color font Highlight the text Edanz Group | 69
  69. 69. Revision How to respond Conduct the additional experiments suggested If this is impossible, you MUST explain why You can disagree with reviewers BUT provide evidence (cite references) Comply with deadlines Edanz Group | 70
  70. 70. Post-referee revisions The responseDear Dr. _____________: [address the editor byname]Thank you for your consideration of our manuscriptentitled _____________ [insert manuscript titlehere]. We have reviewed the comments of thereviewers and have thoroughly revised themanuscript. We found the comments helpful, andbelieve our revised manuscript represents asignificant improvement over our initial submission.In response to the reviewers’ suggestions we have[summarize the key changes here] Edanz Group | 71
  71. 71. Post-referee revisions Point-by-point[After the introduction to the response, address allreviewer points individually]Reviewer Comment: In your analysis of the data you have chosen touse a somewhat obscure fitting function (regression). In my opinion,a simple Gaussian function would have sufficed. Moreover, theresults would be more instructive and easier to compare to previousresults.Response: We agree with the reviewer’s assessment of the analysis.Our tailored function makes it impossible to fully interpret the datain terms of the prevailing theories. In addition, in its current form itwould be difficult to tell that this measurement constitutes asignificant improvement over previously reported values. We haveredone the analysis using a Gaussian fitting function. Edanz Group | 72
  72. 72. Post-referee revisions Disagreement[Sometimes you will disagree with the reviewer. Keepyour response polite and professional]Reviewer Comment: In your analysis of the data you have chosento use a somewhat obscure fitting function (regression). In myopinion, a simple Gaussian function would have sufficed. Moreover,the results would be more instructive and easier to compare toprevious results.Response: We agree with the reviewer that a simple Gaussian fitwould facilitate comparison with the results of other studies.However, our tailored function allows for the analysis of the data interms of the Smith model [Smith et al, 1998]. We have added twosentences to the paper (page 3 paragraph 2) to explain the use ofthis function and Smith’s model. Edanz Group | 73
  73. 73. Understanding reviewer comments “The English needs to be improved” “Your writing is difficult to understand” Grammar Long, complex sentences and paragraphs Non-native expressions Gaps in the logic Poor organization of the manuscript Flow Too much information Edanz Group | 74
  74. 74. Understanding reviewer comments“The authors hypothesized to look for the pharmacokinetics ofthe insulin using this 4 mm needle; However they didnt dobioequivalence analyses for glucose pharmacodynamics. That isone of my concerns about this methodology.” Questions from reviewers may not always be apparent Cosmetic changes Edanz Group | 75
  75. 75. Help your readers understand“If you can’t explain something simply,you don’t understand it well.” – Albert Einstein Write to express not impress Consider your audience – their native language may not be English 読者に研究を理解してもらう Edanz Group | 76
  76. 76. Online resources Edanzedanzediting.co.jp/hoku2012 Springer Exemplarwww.springerexemplar.com/ Google Scholarscholar.google.com/ Purdue Online Writing Labowl.english.purdue.edu/owl/ Edanz Group | 77
  77. 77. Free resource Edanz Group | 78
  78. 78. Free resource – Journal Advisor Edanz Group | 79
  79. 79. Edanz Journal Selectorsimplifying publication success Edanz Group | 80
  80. 80. 1. Insert English sample text Author’s abstract, short description, key phrases or abstract from a similar paper Edanz Group | 81
  81. 81. 2. Filter and refine Revise your sample textImpact FactorFrequencyPublishingmodel Edanz Group | 82
  82. 82. 3. Narrow your optionsMatch AnalysisBasic journalinformation Matched previous publications Edanz Group | 83
  83. 83. 4. Visit journal websites Edanz Group | 84
  84. 84. edanzediting.com/journal_advisor follow us on twitter: @JournalAdvisor Edanz Group | 85
  85. 85. Thank youGood luck! Edanz Group | 86
  86. 86. Any questions?edanzediting.co.jp/hoku2012 Edanz Group | 87