How to write a paper 3 20120121


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  • Dear Colleagues.
    Since January 29, I publish a video blog with graphic tutorials to
    scientific publishing, called KEEP CALM and PUBLISH PAPERS. I hope,
    you may find this interesting when writing your thesis, paper or
    making a presentation.

    Best regards
    Pawel Jerzy Wojcik, Ph.D.
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How to write a paper 3 20120121

  1. 1. How to write a paper (3): Publication Kyushu University Warren Raye, PhD Senior Life Sciences Editor Edanz Group Japan 21 January 2012
  2. 2. Submitting your manuscript  Most journals use online submission systems  Editorial Manager  ScholarOne  BioMed Central  Bench>Press  JournalSoft  Editorial Express  Can take several hours – prepare yourself! Edanz Group Japan | 2
  3. 3. Online submission systems  Journals manage large volumes of manuscripts  For editors, authors AND reviewers  Often contains useful ‘hidden’ information  Register your details beforehand! Edanz Group Japan | 3
  4. 4. More than the manuscript …  Journal instructions are not always clear  With your manuscript: Cover letter Declaration of perceived competing interests Potential peer reviewers Potential editors Figure and table files in correct format and resolution Copyright forms Payment forms  Save yourself time and effort Edanz Group Japan | 4
  5. 5. Presubmission enquiries  Unsure of manuscript suitability  Original research articles and review articles  Enquire before your manuscript is finished  DOES NOT guarantee acceptance  Your query should be short, polite and professional Edanz Group Japan | 5
  6. 6. Recommending reviewers “… the contact details (including email addresses) of at least four potential peer reviewers for your paper. These should be experts in your field of study, who will be able to provide an objective assessment of the manuscript's quality. Any peer reviewers you suggest should not have recently published with any of the authors of your manuscript and should not be members of the same research institution.”  Who ARE these experts?  Read as much as possible!  Know your competitors  Provide a reason for recommending/excluding a reviewer  Editors have the final decision on reviewer choice Edanz Group Japan | 6
  7. 7. Potential reviewers  From your reading and references  Groups doing similar work, producing similar results  Possible collaborators  Networking  Meetings, conferences and congresses  People that comment positively  Aim for younger and mid-level scientists  Scientists new to a field Edanz Group Japan | 7
  8. 8. 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 Japanese bird species” by Raye et al. We would like to have the manuscript considered for publication in Archives of Virology. Please let me know of your decision at your earliest convenience. Sincerely yours, Warren Raye, PhD Edanz Group Japan | 8
  9. 9. Your cover letter General rules  Address to the editor personally  Provide manuscript title and publication type  Background, rationale, description of results  Explain importance of your findings  Why would they be of interest to the journal’s target audience?  Provide corresponding author details Edanz Group Japan | 9
  10. 10. Cover letter Example Dear Dr Lisberger, Please find enclosed our manuscript entitled “Amyloid-like inclusions in the brains of Huntington’s disease patients”, by McGowan et al., which we would like to submit for publication as a Research Paper in Neuroscience. Recent immunohistochemical studies have revealed the presence of neuronal inclusions containing an N-terminal portion of the mutant huntingtin protein and ubiquitin in the brain tissues of Huntington’s disease (HD) patients; however, the role of these inclusions in the disease process has remained unclear. One suspected disease-causing mechanism in Huntington’s disease and other polyglutamine disorders is the potential for the mutant protein to undergo a conformational change to a more stable anti-parallel β-sheet structure… Give the background to the research To confirm if the immunohistochemically observed huntingtin- and ubiquitin-containing inclusions display amyloid features, we performed Congo red staining and both polarizing and confocal microscopy on post-mortem human brain tissues obtained from five HD patients, two AD patients, and two normal controls. Congo red staining revealed a small number of amyloid-like inclusions showing green birefringence by polarized microscopy, in a variety of cortical regions.... ….detected inclusions observed in parallel sections, suggesting that only a relatively small proportion of inclusions in HD adopt an amyloid-like structure. What was done and what was found Interest to readers We believe our findings would appeal to a broad audience, such as the readership of Neuroscience. As a wide-reaching journal journal’s publishing original research on all aspects of neuroscience… We confirm that this manuscript has not been published elsewhere and is not under consideration by another journal. All authors have approved the manuscript and agree with submission to Neuroscience. We have read and have abided by the statement of ethical standards for manuscripts submitted to Neuroscience. The authors have no conflicts of interest to declare. Conforms to journal requirements Please address all correspondence to…. Edanz Group Japan | 10
  11. 11. Communication Journals  Polite and professional  Query manuscript status  Address to the appropriate person  Quote the manuscript ID number  Officially withdraw your manuscript if response is inadequate – VERY IMPORTANT  Submit elsewhere  AVOID harassing journal editors Edanz Group Japan | 11
  12. 12. Peer review  Very few papers are immediately accepted without need for any revisions  Free, expert advice Rejection Acceptance Minor revision Major revision Complete rejection Journal editor decision Major revisions Minor revisions Acceptance Edanz Group Japan | 12
  13. 13. Revision How to respond  Politely respond to ALL the reviewers’ comments in a response letter  Make it easy to see changes  Use specific line, page and/or paragraph numbers  Different color font  Highlight the text Edanz Group Japan | 13
  14. 14. 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 Japan | 14
  15. 15. Your response letter The preamble Dear Dr. _____________: [address the editor by name] Thank you for your consideration of our manuscript entitled _____________ [insert manuscript title here]. We have reviewed the comments of the reviewers and have thoroughly revised the manuscript. We found the comments helpful, and believe our revised manuscript represents a significant improvement over our initial submission. In response to the reviewers’ suggestions we have … [summarize the key changes here] Edanz Group Japan | 15
  16. 16. Point-by-point response Agreeing After the preamble, address every reviewer point individually 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. Response: We agree with the reviewer’s assessment of the analysis. Our tailored function makes it impossible to fully interpret the data in terms of the prevailing theories. In addition, in its current form it would be difficult to tell that this measurement constitutes a significant improvement over previously reported values. We have reanalyzed our data using a Gaussian fitting function. Edanz Group Japan | 16
  17. 17. Point-by-point response Disagreement Sometimes you will disagree with the reviewer. Keep your response polite and professional 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. 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 manuscript (page 3, line 4) to justify the use of this function and Smith’s model. Edanz Group Japan | 17
  18. 18. Post-referee revisions Often, a reviewer comment that you think is incorrect will identify a part of the manuscript that requires further explanation. Original: We then fit the data to a super-Gaussian. From this, we extracted the reaction time [Smith et al. 1998]. Revised: We then fit the data to a super-Gaussian. We elected to use this function to facilitate analysis using the Smith model [Smith et al. 1998]. According to the Smith model, the reaction time is dependent on the intensity and width of the fitted peak. Using this model, we extracted the reaction time. Edanz Group Japan | 18
  19. 19. 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 Japan | 19
  20. 20. Understanding reviewer comments “The authors hypothesized to look for the pharmacokinetics of the insulin using this 4 mm needle; However they didn't do bioequivalence analyses for glucose pharmacodynamics. That is one of my concerns about this methodology.”  Questions from reviewers may not always be apparent  Cosmetic changes Edanz Group Japan | 20
  21. 21. Why are journal guidelines important? ジャーナルガイドラインはなぜ重要 か?  A major difference between acceptance and rejection  Saves your time  Time to publication is quicker  Demonstrates respect for the journal and editors Edanz Group Japan | 21
  22. 22. Journal guidelines ジャーナルガイドラ イン Edanz Group Japan | 22
  23. 23. What to look for? 注視する点は?  Check journal website and sample papers  Types of papers published  Word counts  Total  Each section  Order of sections  IMRaD  Variation of IMRaD Edanz Group Japan | 23
  24. 24. Increase manuscript appeal  Research highlights  What’s new?  Highlights novelty  Lay summaries  Reach a wider audience  Graphical abstracts Edanz Group Japan | 24
  25. 25. Graphical abstract  Usually a single-panel image  Conveys the ‘take-home’ message or main findings of an article Edanz Group Japan | 25
  26. 26. Resources and links 参考資料 This presentation Templates Guidelines Edanz Group Japan | 26
  27. 27. Thank you Good luck! ご清聴ありがとうございました 。 Edanz Group Japan | 27