1. Publishing 101 Dos and donts of publishing in APS journals Kim E. Barrett, Chair, APS Publications Committee Margaret Reich, APS Director of Publications and Executive Editor Editor Panel: Dennis Brown, AJP-Cell; Alberto Nasjletti, AJP-Heart

2. Outline of presentation Preparing your work for publication in APS journals – K. Barrett Practical tips for MS submission and review; Current developments in scientific publishing – M. Reich Ethical pitfalls in scientific publishing – K. Barrett, M. Reich, A. Nasjletti, D. Brown Audience participation requested! Editor Q&A A. Nasjletti and D. Brown

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 dont exist No publication, no promotion Yardstick of productivity No publication, no funding What have you done for me lately? Publishing your work is vital for success

6. Completion of research Preparation of manuscript Submission of manuscript Assignment and review Decision Rejection Revision Acceptance Resubmission Re-review PUBLICATION! Rejection Adapted from a figure by Dale Benos

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 All three criteria should be satisfied

9. Whos 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 the journal, its editor, and why you submitted your paper there Read the instructions Avoid careless 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: www.the-aps.org/publications/ i4a/i4a/prep_manuscript.htm

14. The revision process If your paper is returned for revision, you are in good company Its OK to get mad, but dont act on it! Try to understand what the reviewers are really saying If the reviewers did not understand your work, is it because you didnt 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 LPUs 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 MS submission and review; Current developments in scientific publishing Margaret Reich APS Director of Publications

19. Online Submission and Peer Review APS Central, www.apscentral.orgwww.apscentral.org Have a credit card ready to pay the $50 mss submission fee via e-commerce Sign and fax the mandatory submission form Acceptable file types Text: Word doc or rtf Figs: PDF (much preferred), EPS, ppt, or TIFF APS research journals times to first decision range from 22 to 30 days

20. AiPS--Articles in PresS Manuscript published automatically and immediately upon acceptance You will not have an option to opt out or fix anything! PDF form of accepted manuscript Published, not a preprint Citable, using a DOI Indexed in PubMed, Medline

21. Publication Process, cont. If you have sent preferred file types during peer review, you will speed your time to publication Important to follow Instructions to avoid delays Check before submitting; instructions are improved all the time CopyeditingEfficient and quite automated Art EditingHelp for Authors

22. Art Editing Challenges of working with digital art Simplified instructions online: PDF! Submit color images only if you intend for them to be published in color APS members who are first or last authors get free color! Color figures are allowed only if scientifically necessary

23. Examples of color images that are not scientifically necessary: that are not scientifically necessary:

24. Examples of scientifically necessary color images Color photographs/photomicrographs:

25. To Composition Copyedited ms and edited figures go to compositor Page proof (rapid-proof) is created E-mail is sent to author and copy editor for proofreading, so both can download pdf Author should print out proof, mark it up, and mail it back within 48 hrs Order reprints and/or toll-free link

26. Proof Approved Article is paginated in an issue Final corrections are made Files go to printer Files go to HighWire for publishing online

27. Publication Online publication in journal issue on the HW site Print publication mails ~ 2 weeks later Reprints mail ~ 4 weeks after issue mails

28. Same Article Published 3 Ways Articles in PresS Final Journal issue published online (HW) Journal issue printed and mailed

29. Referencing the Versions Article in PresS DOIDigital Object Identifier Scarafia LE, Winter A, and 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, and 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

30. Online Features As part of the HW Library of the Sciences and Medicine, search across over 900 of the worlds leading journals PLUS incorporate a Medline search RSS feeds available Auto e-toc Have tables of contents of journals youre interested in automatically e-mailed to you CiteTrack Alerts you when content is published that matches criteria that you choose

31. APS Legacy Content Scanned articles going back to first publication in 1898 Collection includes all APS Journals together, 1898-1996 One-time payment of $2000 for the entire collection, perpetual access Tell your librarian!

32. Free Access All 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 Author pays choice for free access

33. OA Choice, Author Pays Author pays choice for immediate Open Access for Physiological Genomics since 2003 Author pays OA choice for ALL research journals, July 2007 Fee is $2000

34. NIH Policy Grant authors permission to post article in PMC with free release 12 months after publication

35. Wellcome Trust, other Funding Agency Policies Mandate funded authors post article to PMC, made free in 6 months This is before APSs free access period Paying OA choice fee allows aus to comply, makes article free immediately WT and other funding agencies have said they will support these fees

36. Contact Information Margaret Reich, Director of Publications, mreich@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

37. Ethical pitfalls in scientific publishing Kim E. Barrett Margaret Reich Alberto Nasjletti (Editor, AJP-Heart) Dennis Brown (Editor, AJP-Cell)

38. 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

39. 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

40. 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)

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

42. 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

43. 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

44. 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

45. 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

46. 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 dont fit your hypothesis Dont try to beautify images with Photoshop – any manipulations must apply to the whole image

47. 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.

48. Improper editing

49. Improper grouping Authors should not generate composite images, even if obtained in a single capture, unless dividing lines are inserted to make clear that the resulting image was not visible in the actual experiment

50. Improper adjustment Authors should not adjust contrast, color balance or brightness unless applied to the entire figures and the adjustment does not obscure, eliminate or misrepresent the originally-captured information. Adjustments should be disclosed in the figure legend.

51. 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

52. 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

53. 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

54. CASE SCENARIOS

55. 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 students progress towards completion of his thesis. Is the PIs 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?

56. 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?

57. Editor Q&A Alberto Nasjletti Dennis Brown