Publishing 101 Dos and don’ts of publishing in APS journals Hershel Raff, Chair, APS Publications Committee Kim Barrett, Vice-Chair, APS Publications Committee Rita Scheman, APS Director of Publications, Executive Editor Panel: P. Kay Lund, AJP GI Charles H. Lang, AJP-Endo

Outline of presentation Preparing your work for publication in APS journals – H. Raff Practical tips for MS submission and review; recent developments in scientific publishing – R. Scheman Ethical pitfalls in scientific publishing – K. Barrett, R. Scheman, PK Lund, CH Lang – Audience participation requested! Editor Q&A – PK Lund, CH Lang

Preparing your work for publication in APS journals Hershel Raff Chair, Publications Committee

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

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? Publishing your work is vital for success

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

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

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

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?

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

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

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

APS instructions for manuscript preparation A wealth of information can be found at the following website: aps.org/publications/authorinfo/index.htm

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

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

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

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!

- PRACTICAL TIPS FOR SUBMISSION AND REVIEW - RECENT DEVELOPMENTS IN SCIENTIFIC PUBLISHING Rit a Scheman

APS journals Original research journals: AJP - Cell Physiology AJP - Endocrinology and Metabolism AJP - Gastrointestinal and Liver Physiology AJP - Heart and Circulatory Physiology AJP - Lung Cellular and Molecular Physiology AJP - Regulatory, Integrative and Comparative Physiology AJP - Renal Physiology Physiological Genomics Journal of Applied Physiology Journal of Neurophysiology Advances in Physiology Education Review journals: Physiology Physiological Reviews APS newsletter: The Physiologist Legacy content collection – all APS journals

Online submission Manuscript are submitted to APS journals through the electronic peer review system: APS membership not prerequisite for publication Have a credit card ready to pay the $50 mss submission fee via e-commerce Sign and fax/mail/ mandatory submission form Corresponding author completes electronic conflict of interest disclosure form Corresponding author may sign manuscript transmittal form on behalf and with the agreement of all authors

Online submission cont’d. Acceptable file types – Text: Word doc or rtf – Figs: PDF (much preferred), EPS, PPT, or TIFF Rigorous peer review APS research journals time to first decision averages 25 days APS journals average acceptance rate: 45% APS journals average time from acceptance to final issue publication is 2.2 months

AiPS - Articles in PresS Manuscript published immediately upon acceptance in PDF format – You will not have the option for any changes – Last opportunity for changes is final revision Published, not a “preprint” Citable, using a DOI Indexed in PubMed, Medline

Submitting artwork Simplified instructions APS website: PDF! Submit color images only if you intend for them to be published in color Figures are published in color only if scientifically necessary APS members who are first or last authors are granted free (scientifically necessary) color Physiological Genomics online only as of January 2011 – no color restrictions Avoid figure manipulation and subsequent potential ethical problems - more on this next

Examples of images where color is not scientifically necessary not scientifically necessary

Examples of images where color is scientifically necessary Color photographs/photomicrographs:

Article published 3 ways Articles in PresS Articles in PresS (accepted, pre-copyedited version) In final journal issue online In final print journal issue (most titles)

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) /physiolgenomics Print issue of journal – Includes DOI reference Scarafia LE, Winter A, Swinney DC. Quantitative expression analysis of the cellular specificity of HECT-domain ubiquitin E3 ligases. Physiol Genomics 4: , First published April 26, 2001; /physiolgenomics

Post-acceptance publication process Figures reviewed for integrity Accepted, unedited ms published in AiPS Ms copyedited; figures edited Ms to compositor Page proof ed to author Author returns corrected proof within 48 hrs Pagination and final corrections Final issue posted online and print issue mailed

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Free access All APS journals are free online to all Members All articles free to all 12 months after publication Free links to APS journals from reference lists Free online access to developing countries Patient Link – free access for the public on request AuthorChoice program for public access upon publication

AuthorChoice: author pays option AuthorChoice for immediate open access AuthorChoice e-option for ALL research journals Fee is $2000 for research articles, $3000 for review articles

NIH mandatory 12-month Public Access Policy The NIH Public Access Policy requires scientists to submit final peer-reviewed journal manuscripts that arise from NIH funds to PubMedCentral upon acceptance for publication As of July 2008 journal issues, APS delivers the final published article to PMC on behalf of NIH-funded authors Authors need do nothing but tell us about funding source PMC will make the PMCID number available in PubMed, which is attached to the abstract PMC will make the full text of the article freely available 12 months after final publication, in compliance with NIH policy

Wellcome Trust, Howard Hughes Institute, other funding agency policies These agencies mandate that funded authors post article to PMC, to be made freely available in 6 months This is a shorter than APS’ free access period Paying AuthorChoice fee allows authors to comply, makes article free immediately Wellcome Trust-funded authors must sign an addendum to the mandatory submission form The Wellcome Trust and other funding agencies support these fees APS uploads manuscripts on publication on behalf of authors funded by agencies with earlier than 12-month mandates

Contact information Rita Scheman, Director of Publications Gil Ebner, Peer Review Manager Mark Goodwin, Editorial Manager Eric Pesanelli, Editorial Art Manager Christina Bennett, PhD, Publications Ethics Manager

Ethical pitfalls in scientific publishing K. Barrett H. Raff P. Kay Lund, EIC - AJP GI Charles H. Lang, EIC - AJP-Endo

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

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

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

Prior publication APS defines this as – Data – Extended verbatim text passages – Tables or illustrations

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

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

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

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

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

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

Improper editing Boxes revealed during processing for publication; removal reveals debris Bottom image from Rossner and Yamada, J. Cell Biol. 166: (2004)

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

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. Images from Rossner and Yamada, J. Cell Biol. 166: (2004)

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

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

Pick up the FREE Ethical Poster at the APS Booth! (Booth 138)

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

CASE SCENARIOS Led by H. Raff

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? Adapted from a scenario authored by Dale Benos, UAB

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?

Editor Q&A P. Kay Lund, AJP GI Charles H. Lang, AJP-Endo