publishing 101 dos and don

1. Publishing 101Dos and don�ts of publishing in APS journals

3. Preparing your work for publication in APS journals Kim E. Barrett Chair, Publications Committee

4. Preparing your work for publication The overall process Issues to consider before you start to write Authorship Journal Elements of a journal article The review/revision process Tips to enhance your chances of acceptance

5. Why is publication so important? No publication, no project Your results must be available for others, or it is as if they don�t exist No publication, no promotion Yardstick of productivity No publication, no funding What have you done for me lately?

7. Authorship Decide on authors, and their order, as early as possible Preferably before even starting the project Authors should include only those who have made a substantive intellectual contribution to the project reported, and can defend the data and conclusions publicly

8. Criteria for authorship Generate at least part of the intellectual content Conception or design of the work Data analysis and interpretation Draft, critically review, or revise the intellectual content Approve the final version to be submitted

9. Who�s an author? The student who did the experiments and wrote the first draft of the manuscript? The technician who measured cytokine levels in 150 samples? The PI who had the idea in the first place, guided the student, and reviewed the manuscript? The department chair who provided space and resources for the study, dropped by the lab occasionally to chat, but knew little or nothing about the experiments?

10. Choosing the right journal Target audience �Who would be interested in reading this paper?� Import and significance of the findings Seek input from colleagues Decide on the journal before beginning to write

11. Essential elements of a manuscript Based on what was known and unknown, why did you do the study? Introduction How did you do the study? Methods What did you find? Results What does it mean in the context of the existing body of knowledge? Discussion

12. Tips for success Know about the journal, its editor, and why you submitted your paper there Read the instructions Avoid carelessness - spelling, grammar, formatting mistakes Make sure references are appropriate and accurate Remember who your reviewers might be! Ensure appropriate file format, including figures Is the on-line version the one you want the reviewers to see? Confirm receipt

13. APS instructions for manuscript preparation A wealth of information can be found at the following website:

14. The revision process If your paper is returned for revision, you are in good company It�s OK to get mad, but don�t act on it! Try to understand what the reviewers are really saying If the reviewers did not understand your work, is it because you didn�t present it clearly in the first place? Look for clues from the editor (the final arbiter) as to the extent of revision needed Re-writes only More experiments

15. Responding to reviewers Complete additional experiments if needed Address all comments in a point-by-point fashion Resist the temptation to prepare an impassioned response to points with which you disagree Stand firm (diplomatically) if that is truly the right thing to do Sincerely thank the editor and reviewers for helping you to improve your work They have invested a lot of time, mostly on a voluntary basis Ask a neutral colleague to review your response

16. Major reasons for rejection Inappropriate for the journal Do your homework Merely confirmatory/incremental Avoid LPU�s Describes poorly-designed or inconclusive studies Focus on your hypothesis Poorly written Great science in an ugly package can still be rejected

17. Summary Do the study with the paper in mind Assign authorship appropriately Chose the right journal Seek input from colleagues See the wood as well as the trees Remember who the reviewers might be If unsure about ethics, ask!

18. Practical tips for submission and review Rita Scheman APS Director of Publications

19. Publishing with the APS � who? Scientific Editors and Editorial Assistants Peer Review Department Permissions Editorial Department Copyeditors Journal Supervisors Compositor/Printer (Cadmus) Online host (HighWire) The APS Chair of Publications, Kim Barrett, will be involved in the publications process if ethical issues ariseThe APS Chair of Publications, Kim Barrett, will be involved in the publications process if ethical issues arise

20. APS has migrated to eJournal Press peer review web-based software for all manuscript submissions APS membership not prerequisite for publication APS journals average acceptance rate: 47% Submission site is at: www.apscentral.org Our online submission system is called APS Central. It is web-based, and to be prepared to upload a manuscript, you need to have the following things ready.Our online submission system is called APS Central. It is web-based, and to be prepared to upload a manuscript, you need to have the following things ready.

21. www.apscentral.org

22. Online submission and peer review cont�d. Have a credit card ready to pay the $50 mss submission fee via e-commerce system Sign and fax the mandatory submission form Acceptable file types Text: Word doc or rtf Figs: PDF (much preferred), EPS, PPT, or TIFF If you have sent preferred file types, you will speed your time to publication APS research journal time to first decision ranges from 22 to 33 days You need to have the following things readyYou need to have the following things ready

23. Online submission, peer review, copyediting Important to follow instructions to avoid delays Check before submitting APS Instructions to Authors are updated and refined regularly Copyediting�efficient and standardized Time to final issue publication now 2.3 months You will also be asked to send the files used for traditional publishing, a Word file for text and .eps or .tif files for figures. This is where the two technologies clash�unfortunately, the files that are best for viewing on the internet are not always the best for print production. Until the technology improves, we need to ask you to do this step. Copyediting and art editing are part of the �traditional� publishing model, but there is little that is traditional about them anymore. APS has used technology to streamline the copy editing and the art editing processes.You will also be asked to send the files used for traditional publishing, a Word file for text and .eps or .tif files for figures. This is where the two technologies clash�unfortunately, the files that are best for viewing on the internet are not always the best for print production. Until the technology improves, we need to ask you to do this step. Copyediting and art editing are part of the �traditional� publishing model, but there is little that is traditional about them anymore. APS has used technology to streamline the copy editing and the art editing processes.

24. AiPS - Articles in PresS Manuscript published automatically and immediately upon acceptance You will not have the option to opt out or fix anything! PDF format of accepted manuscript Published, not a �preprint� Citable, using a DOI Indexed in PubMed, Medline In order to decrease time from acceptance to publication, APS developed a way to publish the accepted manuscript within one week of acceptance. We call these published articles �Articles in presS.�In order to decrease time from acceptance to publication, APS developed a way to publish the accepted manuscript within one week of acceptance. We call these published articles �Articles in presS.�

25. Working with digital art Simplified instructions online: PDF! Submit color images only if you intend for them to be published in color Figures will be published in color only if scientifically necessary APS members who are first or last authors get free (scientifically necessary) color Avoid manipulating figures and subsequent potential ethical problems Art reviewed by APS Art Department FOR AUTHORS NOT CREATING FIGURES IN ILLUSTRATOR, PHOTOSHOP OR PPT, PREFERRED FORMAT IS PDF. Adobe PDF is a universal file format that preserves all the fonts, formatting, graphics, and color of any source document, regardless of the application and platform used to create it. -������������ Adobe PDF files are compact and can be shared, viewed, navigated, and printed exactly as intended by anyone with the Adobe Acrobat software. You can convert any document to Adobe PDF using the full version of Adobe Acrobat 3.0 � 7.0 software. The free Acrobat Reader does not have this ability. Eliminates software and hardware incompatibility issues between Authors and APS ��������� Maintains design integrity to ensure what you send is what is received ��������� Image-quality is resolution-independent ��������� Better results in both print and online publication when created properly Note: These benefits may not hold true for authors creating PDFs with a non-Adobe product such as Ghostwriter FOR AUTHORS NOT CREATING FIGURES IN ILLUSTRATOR, PHOTOSHOP OR PPT, PREFERRED FORMAT IS PDF. Adobe PDF is a universal file format that preserves all the fonts, formatting, graphics, and color of any source document, regardless of the application and platform used to create it. -������������ Adobe PDF files are compact and can be shared, viewed, navigated, and printed exactly as intended by anyone with the Adobe Acrobat software. You can convert any document to Adobe PDF using the full version of Adobe Acrobat 3.0 � 7.0 software. The free Acrobat Reader does not have this ability. Eliminates software and hardware incompatibility issues between Authors and APS ��������� Maintains design integrity to ensure what you send is what is received ��������� Image-quality is resolution-independent ��������� Better results in both print and online publication when created properly Note: These benefits may not hold true for authors creating PDFs with a non-Adobe product such as Ghostwriter

28. Copyedited ms and edited figures go to compositor (external vendor, Cadmus) Page proof (Cadmus Rapid-Proof) is created PDF of proof e-mailed to author and to the copyeditor for proofreading Author dowloads, prints out proof, marks it up, and mails/faxes back within 48 hrs Author orders reprints and/or toll-free link So now the text and art editing are done, and the edited files go to our Compositor for page layout. Page proof is electronic now. I�d like to tell you more about these toll free links. Toll free links can be purchased on reprint order form � A link can be created from a URL of choice to your article online, unlimited use $150 Offer to all editorial articles (reviews; editorials, commmentaries) 50 free reprints or a toll free link -So now the text and art editing are done, and the edited files go to our Compositor for page layout. Page proof is electronic now. I�d like to tell you more about these toll free links. Toll free links can be purchased on reprint order form � A link can be created from a URL of choice to your article online, unlimited use $150 Offer to all editorial articles (reviews; editorials, commmentaries) 50 free reprints or a toll free link -

29. Proof approved Article is paginated into an issue Final corrections are made Files go to printer Files to HighWire for publishing online

31. Article published 3 ways Articles in PresS (accepted, pre-copyedited version) In final journal issue online In final print journal issue So, in one sense, you could say that the same article is published 3 times. Once as an AiPS, once online in its completed form with the journal issue, and once in print. And each of these versions is slightly different: the APS is not edited, and the copyedited online article may contain electronic supplemental material that cannot appear in the print version. How do you, we, and others keep these versions straight?So, in one sense, you could say that the same article is published 3 times. Once as an AiPS, once online in its completed form with the journal issue, and once in print. And each of these versions is slightly different: the APS is not edited, and the copyedited online article may contain electronic supplemental material that cannot appear in the print version. How do you, we, and others keep these versions straight?

32. Citing the versions Article in PresS DOI�Digital Object Identifier Scarafia LE, Winter A, Swinney DC. Quantitative expression analysis of the cellular specificity of HECT-domain ubiquitin E3 ligases. Physiol Genomics (April 26, 2001). 10.1152/physiolgenomics.00075.2001 Print issue of journal Scarafia LE, Winter A, Swinney DC. Quantitative expression analysis of the cellular specificity of HECT-domain ubiquitin E3 ligases. Physiol Genomics 4: 147-153, 2001. First published April 26, 2001; 10.1152/physiolgenomics.00075.2001 The AiPS and final online version of an article will always be linked (describe how that works). In print, we will include the AiPS DOI reference, and hope that other publishers will do so, so that this becomes the standard. This way it is always clear what version you are looking at and what versions of the article exist. The AiPS and final online version of an article will always be linked (describe how that works). In print, we will include the AiPS DOI reference, and hope that other publishers will do so, so that this becomes the standard. This way it is always clear what version you are looking at and what versions of the article exist.

33. Online features As part of the HighWire Library of the Sciences and Medicine, search across over 1000 of the world�s leading journals while incorporating a PubMed search Etocs Have tables of contents of journals of interest automatically e-mailed to you RSS feed Get Etocs and other journal content via RSS CiteTrack Alerts you when content is published that matches criteria that you choose Nearly 2 million articles on the HighWire site are available for free!

34. APS Legacy content Scanned articles dating from first issues of publication in 1898 Collection includes all APS Journals, 1898-1998 One-time payment of $2000 for the entire collection, perpetual access Tell your librarian

35. All APS journals free online to all Members All articles free to all 12 months after publication Free links to HW journals from reference lists Free online access to developing countries Patient Link, Podcasts AuthorChoice program for free access Add logoAdd logo

36. AuthorChoice for immediate open access Physiological Genomics since 2003 AuthorChoice option for ALL research journals since July 2007 Fee is $2000 for research articles, $3000 for review articles

37. NIH mandatory 12-monthPublic Access Policy The NIH Public Access Policy requires scientists to submit final peer-reviewed journal manuscripts accepted for publication after April 7, 2008 that arise from NIH funds to PubMedCentral (PMC) As of July 2008 journal issues, APS uploads the final published article to PMC for NIH-funded authors and authors funded by other agencies, e.g., Wellcome Trust and HHMI Authors need do nothing but tell us about funding source APS has PMC make the article free 12 months after final publication in compliance with NIH policy Under the NIH Public Access Policy, NIH is requiring that its funded investigators submit to PubMed Central (PMC) all manuscripts accepted after April 7, 2008, resulting from research supported in whole or in part with direct costs from NIH. � As of the July 2008 Journal issues, if you are NIH funded, APS will upload the final published article to PMC for you; you do not need to do anything more to meet this requirement. APS will have PMC make the article free 12 months after final publication. This period of time is consistent with our existing policy to make all content publicly available through HighWire Press 12 months after print publication, and keeps you in compliance with your Under the NIH Public Access Policy, NIH is requiring that its funded investigators submit to PubMed Central (PMC) all manuscripts accepted after April 7, 2008, resulting from research supported in whole or in part with direct costs from NIH. � As of the July 2008 Journal issues, if you are NIH funded, APS will upload the final published article to PMC for you; you do not need to do anything more to meet this requirement. APS will have PMC make the article free 12 months after final publication. This period of time is consistent with our existing policy to make all content publicly available through HighWire Press 12 months after print publication, and keeps you in compliance with your

38. Wellcome Trust, Howard Hughes Medical Institute, other funding agency policies Mandate funded authors post article to PMC, made free in 6 months This is a shorter than APS� free access period Paying AuthorChoice fee allows authors to comply, makes article free immediately WT-funded authors must sign an addendum to the mandatory submission form WT and other funding agencies have said they will support these fees

39. Contact information Rita Scheman, Director of Publications rscheman@the-aps.org Gil Ebner, Peer Review Manager gebner@the-aps.org Mark Goodwin, Editorial Manager mgoodwin@the-aps.org Eric Pesanelli, Editorial Art Manager epesanel@the-aps.org

40. Ethical pitfalls in scientific publishing Kim E. Barrett Rita Scheman Curt Sigmund (Editor, AJP-Regu) Michael Matthay (Editor, AJP-Lung)

41. Ethical responsibilities of a scientist Intellectual honesty Accurate assignment of credit Fairness in peer review Collegiality in scientific interactions Transparency in conflicts of interest Protection of human and animal subjects

42. Ethical issues at APS Ethical cases are increasing among submissions to APS journals, and in the scientific literature overall Ignorance of appropriate standards Funding, promotions pressures? APS takes ethical matters very seriously, and has developed clearly-stated policies Authors found to have violated these policies are subject to a variety of actions, up to and including notification of their institution and/or sanctions for the most serious offenses The Publications Committee recommends on the disposition of ethical issues to the Executive Cabinet of APS, with the APS Council serving as an appeals body if necessary Our goal in this session is to provide you with information that should allow you to avoid ethical pitfalls

43. Common ethical issues (in order of prevalence at APS) Redundant publication Animal welfare concerns Authorship disputes Duplicate publication Human welfare concerns Data fabrication/falsification Increasingly, includes inappropriate manipulation of figures Plagiarism Conflicts of interest Others (e.g., reviewer bias, submission irregularities)

44. Prior publication APS defines this as: Data Extended verbatim text passages Tables or illustrations

45. Redundant publication Definition Using text or data from another paper/prior publication (usually your own) in a new paper Also called auto- or self-plagiarism How to avoid Do not include material from a previous study in a new one, even for statistical analysis Repeat control groups as needed

46. Human and animal welfare issues Definition Treatment of experimental subjects that does not conform with accepted standards and journal policy How to avoid Obtain prospective IRB/IACUC approval for the study protocol Do not deviate from the protocol Obtain approval for amendments as needed before altering the protocol

47. Authorship disputes Definition Disputes arising from the addition, deletion, or change in the order of authors How to avoid Agree on authors and their order before starting the study Ensure all authors meet criteria for authorship Sign publishers� authorship forms

48. Duplicate publication Definition Submission of or publication of the same paper or substantial parts of a paper in more than one place How to avoid Do not submit a paper to more than one journal at a time Wait until your paper is rejected before submitting elsewhere Withdraw a paper if you decide not to re-submit after being invited to do so

49. Data fabrication/falsification Definition Changing or making up data in a manuscript Intended to �improve� the results Includes digital manipulation of images (blots, micrographs, etc.) How to avoid Present the exact results obtained Do not withhold data that don�t fit your hypothesis Don�t try to beautify images with Photoshop � any manipulations must apply to the whole image

50. Unacceptable figure manipulation Improper editing Improper grouping Improper adjustment Authors should not: Move Remove Introduce Obscure Enhance any specific feature within a image. Images should appear as captured in the lab.

51. Improper editing

52. Improper grouping

53. Improper adjustment

54. Plagiarism Definition Taking the work of another Copying a figure, table, or even wording from a published or unpublished paper without attribution How to avoid Provide citation to the work of others Obtain copyright permission if needed Do not copy exact wording from another source, even if referenced, unless in quotes

55. Conflicts of interest Definition Real or perceived conflict due to employment, consulting, or investment in entities with an interest in the outcome of the research How to avoid Disclose all potential conflicts to the Editor and within the manuscript, and on Disclosure form

56. Pick up the FREE Ethical Poster at the APS booth! (Booth 108)

57. Reviewer issues Reviewers can also engage in unethical behavior Bias Conflict of interest Misappropriation of privileged information Reviewers are obligated to: Maintain confidentiality Inform the editor if circumstances preclude a unbiased review or could represent even a perceived conflict Provide fair and collegial assessments

59. Scenario 1 A PI asks a graduate student working in her group to assist in the peer-review of a manuscript from a competing group of investigators. The manuscript contains details of a method that would greatly accelerate the student�s progress towards completion of his thesis. Is the PI�s action acceptable? What are the obligations of the PI in this scenario? What are the obligations of the student? Can the student adopt the new method for his own work? If so, when?

60. Scenario 2 You are completing a post-doctoral fellowship and submit your last paper with your PI as senior author and two graduate students as co-authors. After you have left the lab, the paper is returned with a request for additional experiments. Your former PI asks another post-doc to complete these, and adds her name to the paper as middle author. You object to this addition and refuse to sign the change of authorship form. Is your decision the right one? Who else has rights that must be respected in this scenario? How might the PI have handled the situation differently?

61. Editor Q&A Michael Matthay Curt Sigmund