Publishing 101

Dos and don’ts of publishing

Martin Frank, Ph.D.

Executive Director, American Physiological Society

Panel

: Irving Zucker, Ph.D.

Shu Chien, M.D., Ph.D.

FAOPS Meeting,

Taipei, Taiwan September 12, 2011

Outline of Presentation

• • • Preparing your work for publication Ethical pitfalls in scientific publishing – Audience participation requested!

Panel Q&A – Irving Zucker, Shu Chien

About the American Physiological Society

• • • • • • • • APS founded in 1887 Currently has approximately 11,000 member Holds a large annual meeting and several small conferences APS publishes 14 journals – AJP started in 1898 All journals online in 1996-1998 (HighWire) Content free 12 months after publication Legacy content scanned and online (1898-1996) Offers an extensive list of K-12 and minority programs

APS Journal Collection ( www.physiology.org

)

Preparing your Work for Publication in a Scientific Journal

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

Rejection Completion of research Preparation of manuscript Submission of manuscript Assignment and review Decision Acceptance

PUBLICATION!

Revision Resubmission Re-review 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

Introduction

• • • • Two main purposes – Get reader interested in the topic – Prepare reader to understand the paper What is the question being asked?

Where did the question come from?

Why are you asking that question?

Introduction - continued

• • • • • Keep it short Brief review of pertinent literature – Place your study in historical context – Provide a general description of field Statement of the hypothesis and/or research question(s) State animal or material used in study No data summary

Methods

• Purpose – Foundation for results analysis – Builds the readers’ confidence in your results • Before you write the draft… – Review the journal requirements – Develop an outline and review with co-authors

•

Methods Section Components

Major Components – Study design – Rationale – Experiments completed • How much detail?

– Don’t replicate the lab notebook – Review the journal space limitations – Detail should allow replication of your work – Cite previously published methods – Describe modifications of published methods – For new methods, provide additional detail • Can others repeat your work based on this description?

Results Section Tells a Story!

• • • • • Results are presented in a logical order – May not be the chronological order Only the relevant results are presented – Do not replicate lab notebook Include a brief rationale for the experiments Include transitions between experiments or results Distinguish between results and analysis

Discussion

• • • • • Write after Results Section Synthesize your results Describe their relevance Look at the literature critically Use an outline for structure

Discussion - continued

• • • • • State the answer to the question you asked at the beginning of the discussion Follow up with supporting evidence Explain your answer Discuss the most important conclusions first Write in present tense

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: www.the-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 Choose 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!

Ethical Pitfalls in Scientific Publishing

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

The Magnitude of the Problem

140 120 100 80 60 40 20 0

APS Ethical Cases

(total number per year)

APS Ethical Cases in 2010

by Category Plagiarism Miscellaneous Human/Animal Protocols Figure Manipulation Falsification of Data Duplication of Data Duplicate Publication/ Submission Conflict of Interest Authorship 0 5 10 15 20 25 30 35 40 45 50 75 80 85 90 Number of cases

Common Ethical Issues

• • • • • • • • • • Inappropriate manipulation of figures Duplication of data Duplicate publication Animal welfare concerns Data fabrication/falsification Authorship disputes Human welfare concerns Plagiarism Conflicts of interest Others (e.g., reviewer bias, submission irregularities)

Prior Publication

• • • Submitted material is already published articles published in any publication, even online-only, non peer-reviewed publications, such as Nature Precedings or the physics arXiv articles, book chapters, and long abstracts containing original data in figures and tables, especially in proceedings publications posters containing original data disseminated beyond meeting attendees, e.g., displayed in websites such as that maintained by F1000

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

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

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 – Do not alter the background of blots such that information is lost Improper grouping – Do not splice and reassemble noncontiguous lanes of gels Improper adjustment – Do not move, remove, introduce, obscure, or enhance any specific feature within an 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: 11-15 (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: 11-15 (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

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

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?

Q&A

Irving Zucker Shu Chien Martin Frank

Thank You!

• Martin Frank – [email protected]

– 1-301-634-7118