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
Resubmission
Re-review
Acceptance
PUBLICATION!
Adapted from a figure by Dale Benos
Rejection
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:
www.theaps.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
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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
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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 1898 -1998
Online submission
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Manuscript are submitted to APS journals through the
electronic peer review system: www.apscentral.org
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/email 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
www.apscentral.org
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
Examples of images where color is
scientifically necessary
Color photographs/photomicrographs:
Article published 3 ways
• 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). 10.1152/physiolgenomics.00075.2001
• 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: 147-153, 2001. First published April 26, 2001;
10.1152/physiolgenomics.00075.2001
Post-acceptance
publication process
Figures reviewed
for integrity
Author returns
corrected proof
within 48 hrs
Pagination and
final corrections
Accepted,
unedited ms
published in AiPS
Ms copyedited;
figures edited
Page proof
emailed to author
Ms to compositor
Final issue posted
online and print
issue mailed
Online features
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Free access
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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
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
epesanelli@the-aps.org
• Christina Bennett, PhD, Publications Ethics Manager
cbennett@the-aps.org
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
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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)
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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 selfplagiarism
• 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
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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: 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
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