Transcript Interacting with Professional Editors

Interacting with Professional
Biomedical Journal Editors
Vivian Siegel, Ph.D.
Director, Center for Science
Communication, Dept of Medicine, VUMC
1
The Plan
• Describe who professional editors are and
what they do, and offer advice on
presenting your research that helps them
become your advocates rather than your
administrators
• How many of you have published papers?
Interacted in the past with professional
journal editors?
2
Who are professional editors?
• Editors are
– Trained in Research (most have PhDs or MDs
and postdoctoral experience)
– Oriented towards the research community,
rather than the publishing community
– Generalists (like to think broadly, and don’t
know your work as well as you do)
– Try to make each decision consistent with
journal policy and with other decisions being
made by the journal
3
What does this mean for you?
• You can treat professional editors as your
colleagues
• You need to help editors appreciate the
significance of your work
• You need to appreciate that sometimes
“larger forces” are at play than
confidentiality allows an editor to explain
4
The Job of an Editor
• Determine whether a paper might “in principle” be
appropriate for a journal (evaluate)
• Identify appropriate reviewers to help then decide
whether to publish a paper (oversee peer review)
• Explain that decision to you in as constructive and
transparent a manner possible (communicate with
authors)
• Respond to comments from you that might lead them to
reconsider that decision (re-evaluate)
• Identify important new areas of research (imagine the
future)
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The Evaluation Stage
• Assume that all the data are correct, and the
interpretations are valid – is this paper
appropriate for the journal? (scope, significance)
– Placing the paper in the context of what is already known, how
significant is the advance?
• could the result have been predicted based on what was already
known?
• does the result change the way you think? answer a longstanding
question? open a new line of research?
• does the result belong in a textbook? Should the speaker be invited
to give a seminar?
• If yes, is the paper logically sound?
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What Do Editors Need to Know to
Evaluate a Paper?
What’s New and Why Should I Care?
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What’s New and Why Should I
Care?
•
•
•
•
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Abstract
Introduction
Discussion
Cover Letter
Own Knowledge/Literature Search
The editor will read your Introduction and Cover
Letter but will also do a literature search. Don’t
avoid relevant related information that impacts
(negatively) on the significance and novelty of
your work.
8
Don’t hide what’s important
about your work
• First and last paragraphs
• Overstating or understating what’s already
known
• Presubmission Inquiries/Cover Letters
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Presubmission Inquiries
• Enable you to get an editorial perspective
on your work prior to submission
• Are the only time you can query several
journals at the same time
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What Should a Presubmission
Inquiry Contain?
All the information needed to make an editorial
judgment on the paper (1-2 pages).
– The important question being answered by your
paper, and why it’s important
– The significance of your results to and beyond your
field
– Why you think the scope and significance might make
the paper appropriate for the journal
– A structured abstract
– Any special needs, such as quick review, if you have
them
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The Tone of a Presubmission
Inquiry
• Pretend you’re writing to a senior
colleague (perhaps a mentor),
experienced but not necessarily
knowledgeable about your particular
research project
• Respectful to the editor, enthusiastic about
your work; may (with appropriate
qualifications) claim novelty even if you
won’t do it in the text
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Example of a presubmission inquiry
“I would like to submit a presubmission inquiry regarding
suitability of our manuscript, "Subversion of cellular autophagy
pathway by RNA viruses" by William T. Jackson, Thomas H.
Giddings Jr., Sara Mulinyawe, Ron Kopito and Karla Kirkegaard
for publication in PLoS Biology. Cellular autophagy is a field
that is just entering a period of rapid discovery, because the
mammalian homologs for the many yeast genes that affect
autophagy have very recently been identified. Some of these
have generated new markers for this previously difficult-todiagnose process. I recently attended the first Gordon
Conference on autophagy, and the list of its roles in
development, cancer and host responses to pathogens was
impressive. It reminded me of 10-15 years ago, when the
genes that affect apoptosis were first available as a result of
nematode genetics…”
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“We have been able to use some of these newly available
reagents to show that the biochemical constituents of
cellular autophagy are used to form the membrane
components of the RNA replication complexes of both
poliovirus and rhinovirus. This is of especial interest
because, as yet, the process of autophagy has been
reported to be antiviral, and numerous reports are in
preparation that document the role of autophagy in host innate
immune responses. Therefore, the ability of a virus to
subvert this process, and not just evade it by, for example,
inhibiting PKR, provides a new example of host-pathogen
interaction. Furthermore, the ability of pathogens to provide
molecular inducers of autophagy, such as poliovirus proteins
described in the present manuscript, will be extremely helpful in
its dissection…”
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“PLoS Biology would be an outstanding forum for this
paper due to its intention of featuring interdisciplinary
research publications; we believe that this paper will be of
interest to cell biologists, due to the identification of viral
inducers of autophagy, and to microbiologists and
virologists, because it is being recently appreciated that
several bacterial, including Legionella pneumophila and
Brucillus abortus may also subvert the cellular autophagy
pathway. Furthermore, other RNA viruses, including murine
hepatitis virus, a close relative of the human SARS virus,
have been shown to replicate on double-membraned
vesicles that resemble those found in poliovirus-infected
cells.
“I have attached a summary of the manuscript. Thank you in
advance for considering this pre-submission inquiry.”
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Editing and follow up
• If you are writing to several journals at once,
check that you have inserted the appropriate
journal name into the letter…
• If you don’t hear back within 72 hr, feel free to
follow up with a second email or a phone call
• If you have queried several journals and
received several positive responses, it is good
form to let the journal editor know you have
chosen to submit the paper elsewhere (at least
before it comes out in the other journal)
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The Cover Letter
• Sometimes you will find it easier to convey why the
work is interesting and important in a cover letter than
you were able to do in the paper itself. The contents
are very similar to a presubmission inquiry, including
– The important question being answered by your paper, and
why it’s important
– The significance of your results to and beyond your field
– Why you think the scope and significance might make the
paper appropriate for the journal
– Any special needs, such as quick review, if you have them, but
also recommendations for reviewers or reviewer
exclusions, nontraditional peer review, etc., if you want to
provide them.
– Any related work that is in preparation or under
consideration at another journal
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“Dear Molecular Biology of the Cell Editor,
“Thank you for considering our manuscript “Identification of Histoplasma
capsulatum Transcripts Induced in Response to Reactive Nitrogen
Species” for publication in Molecular Biology of the Cell. Reactive
nitrogen species (RNS) such as nitric oxide are potent antimicrobial effectors used by the immune system to destroy
microbes. The ability of persistent organisms such as H.
capsulatum to resist killing by RNS and establish latent infections
in the host is thought to be important for pathogenesis. However,
the molecular response of H. capsulatum to RNS has not been
previously elucidated. Here we use a combination of two different
microarray technologies to identify 153 transcripts that are induced
in response to treatment with RNS. These genes are candidate
virulence factors that might affect the ability of H. capsulatum to
survive in the host. We show that expression of one of these genes
is sufficient to increase resistance to RNS in culture.”
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“The primary significance of this work is four-fold. First, this is the only largescale analysis of the transcriptional response of the fungus H. capsulatum, a
major pathogen of humans, to reactive nitrogen species (RNS). (The only other
example of transcriptional profiling in H. capsulatum was performed by our
laboratory and published in Molecular Biology of the Cell (Hwang et al., 2003. Mol
Biol Cell 14, 2314-2326).) Because molecular genetic tools in H. capsulatum are
limited, and because the genome sequence is not yet available, the identification of
a large set of genes that contribute to the nitrosative stress response is a highly
significant step forward for the field. Second, we have identified the first
candidate nitric oxide reductase in H. capsulatum, which will allow future analysis
of the role of nitric oxide detoxification in H. capsulatum pathogenesis. Third, we
used high density oligonucleotide tiling arrays generated by CombiMatrix
Corporation to precisely determine the boundaries of RNS-induced transcripts. This
technology is under-utilized, financially accessible to small academic labs, and
relevant to a variety of applications—and thus of great interest to a number of
researchers. Fourth, this work is being co-submitted with two other papers that
elucidate the global transcriptional response to RNS in two other fungi: the model
eukaryote Saccharomyces cerevisiae (Sarver et al.) and the fungal pathogen
Candida albicans (Hromatka et al.). We observed interesting similarities and
differences between the transcriptional responses to RNS for these three fungi,
each of which inhabits a unique environmental niche. As a whole, these three
papers greatly enhance our understanding of how eukaryotic microbes
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respond to nitrosative stress..”
What did this cover letter have
– The important question being answered by the paper,
and why it’s important
• Understanding how persistent organisms resist killing
by nitrosative stress and thereby establish latent
infections is important for our understanding of
pathogenesis (and in potential treatment).
– The significance of the results to and beyond the field
• candidate virulence factors
• Utility of approach
• Increase our understanding of how eukaryotic microbes
respond to nitrosative stress
– Special need
• cosubmission with other papers
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Choices at the evaluation stage
• Reject without review (expect a letter outlining
the reasons for the decision)
• Review, but with a strong editorial
perspective that will influence the ultimate
decision
• Review, without a strong editorial
perspective; reviewers will determine the
outcome of the decision making process
• (At some journals, such as JBC, editors can
decide to accept papers without further review)
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Rejection without review
• The journal form letter
– “The field has advanced to the point where
the work is no longer appropriate for Cell…”
– “We have come to the view that papers
describing new components of signal
transduction pathways are no longer
appropriate, and that for us to consider such a
paper, there would need to be some
mechanistic insight…”
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“Custom” letters
• “Previous work has shown…Your paper
extends this work by
demonstrating…given the results that
have already been published, such a
finding, while of some interest to the field,
is not unanticipated…”
• Hopefully constructive
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If there is a strong editorial opinion
at the outset…
• Some editors will tell you before review,
and you can encourage this level of
communication during the presubmission
inquiry or as part of the cover letter
• The editors may send a special letter to
the reviewers asking that particular
attention be paid to a particular aspect of
the work.
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The Peer Review Stage
If the paper seems appropriate and logically
sound, who would be best to assess the
technical aspects of a paper?
Methodologies
Model Systems
Big Picture
Sense of Journal
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What can you do to help?
• Don’t be afraid to suggest reviewers, along
with their expertise (esp. for papers that
use unusual methodologies)
• If there are conflicts that would lead to a
reviewer not being able to offer an
objective opinion, don’t be afraid to ask
that this person be excluded, but explain
why.
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Do not…
• Exclude an entire field from reviewing your
paper (editors will generally respect 2 or 3
exclusions, but if you exclude everyone,
then they will have a hard time reviewing
the paper)
• Offer as potential reviewers only people
who have collaborated with you in the past
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Types of Peer Review
• Traditional: Authors are known to
reviewers, but reviewers are anonymous
• Open peer review (reviewers are known to
authors, usually policy is set by journal but
can be modified on request from reviewer)
• Double-blind peer review (can be
requested by author)
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The decision
• Depending on the nature and strength of the
editorial opinion, and what other papers are
being considered by the journal, the role the
reviews play in the ultimate decision will vary.
• The editor’s letter will hopefully convey (as much
as it can given the confidential nature of the
review process) any discrepancies between the
reviewer and editorial opinions on the paper.
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Types of Decisions
• Accept without revision
• Accept with revision (major or minor)
• Reject
This should be clear from the letter, and
don’t let wishful thinking get in the way of
figuring out which one it is.
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Recognizing rejection
“I am really sorry that we cannot be more
positive on this occasion but hope that you find
our referees' comments helpful.”
“Our review of your manuscript…is now
complete. I regret to say we have decided
against publication in Science…We hope you
find the referees’ suggestions helpful and we
hope you will consider Science for future papers.
I’m sorry we couldn’t bring better news this
time.”
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Clear invitation to resubmit
“As you will see below, all three reviewers liked
your study quite a lot. Although two of them
raise some issues, I suspect that they won't be
too difficult to address (though it will require
some thought and effort). Assuming you can
address their concerns in a satisfactory manner,
I hope to be able to make a final decision on a
revised manuscript without re-review. (That's
not a promise, but my expectation.) Please let
me know if any of my comments or the
reviewer's comments needs clarification.”
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Do the editors want it back?
“As with all papers submitted to the journal,
yours was seen by the PLoS editorial staff as
well as by an academic editor with relevant
expertise. In this case, your article was also
evaluated by two independent reviewers…The
reviewers appreciated the attention to an
important problem. Based on the reviews, we
will not be able to accept this manuscript for
publication in the journal, although we would
be willing to review again a much-revised
version, based on the review comments. We
cannot of course promise publication at that
time…”
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“While Reviewer #2 points out that other [related] efforts
have been made…, the editors and the academic editor
feel that this work is the most definitive to date, and as
such, that it in principle merits publication in PLoS
Biology. However, several experimental issues remain to
be addressed before the manuscript could be considered
suitable for publication in the journal. In particular….
“Additionally, the academic editor points out that more work
is needed to improve the clarity and presentation of the
data; the Results and Discussion could both be significantly
shortened (as much as 50%), and modified to remove
excessive speculation and overly detailed description of
experiments. Please note that we consider it essential
that you address both the experimental concerns as
well as the issues of presentation in a revised
manuscript.
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“Should you decide to revise the manuscript for further
consideration here, your revisions should address the
specific points made by each reviewer. You should also
send along a cover letter, indicating your response to the
review comments and the changes you have made in the
manuscript. You should also cite any additional relevant
literature that has been published since the original
submission and highlight any additional citations in your
response. The editors will consider the advance your revised
manuscript represents over work published prior to its
submission in reaching a final decision regarding publication.”
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Reviewers always ask for more
• Think about what you might be able to
include in a revised paper, and whether it
might make sense to hold back an
experiment from the original submission
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Split reviews: what is the outcome?
• If an Editor hasn’t already formed an opinion, it
is likely to be rejected. Publishing is a very
visible act. If you accept a paper and it’s widely
thought to be rubbish, the whole world knows it.
If you reject a paper that turns out to change the
world as we know it (or to be published in
another journal of comparable stature), the
mistake is usually pretty private.
• If an Editor is already interested in the paper
prior to review, it is more likely to be accepted.
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You’re much better off if the editors rather
than the reviewers control the final decision.
Why?
• The editor can decide which of the reviewers’
comments are critical and which are not.
Otherwise, you might just have to do everything
the reviewers say.
• The editor is building a relationship with you and
an appreciation for the field. At some point, the
editor may decide it’s time to “invest” in the area
in which you work.
• The editor can ensure that decisions are
consistent from paper to paper. Reviewers
(since they change from paper to paper) cannot.
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There are two parts to a decision
letter
• Letter from the Editor
– Can you address the major concerns raised
by the editor?
• Reviewer’s comments
– Can you address all or only a subset of
concerns raised by the reviewers?
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Revising the Paper
If you can respond to everything, great. If
not, check with your editor first about your
plan of action before resubmitting the
paper
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Responding to Rejection
• Give yourself time to digest the reason for the
rejection. Do not call the editor minutes after you
get the decision.
• See if the decision make sense. If you feel too
emotional, ask a colleague you respect to help
you assess this.
• Sometimes editors do make mistakes, and, if
they do, you may be able to persuade them to
change their minds. Don’t be afraid to write an
appeal letter or call the editor (it IS part of their
job), but you may wish to have a colleague look
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at it before you send it.
If you decide to appeal
• Stick to the science. Arguments about the
number of postdoc years the paper took or
the effect this publication will have on your
career will not help.
• Treat the editor as your colleague, not
your enemy.
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Responding to criticism
• Recognize that there is something to learn from every
criticism, and act respectful (even if you don’t feel it).
Assume that the editors and reviewers worked hard to
reach this decision, so if you want them to be open
minded, you should not insult their intelligence or ability
to do their job.
-For example, a requested experiment might actually
be in the paper, but was missed by the reviewer. Simply
point out that the experiment has been done (and offer to
make it more prominent) without voicing your frustration
over the fact it wasn’t noticed.
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Response to Reviews
(Example)
“This letter is a point-by-point response to
the reviewer's comments. Our responses
are in blue. We eagerly await your final
decision on our manuscript…”
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“NOR1 experiments in Figure 8: The most strongly induced NOR1 transcript
is the shortest one which initiates within the coding sequence. Can you say
anything about whether the part of the protein that would be missing in the
short transcript is known to be non functional? The truncation would appear
to remove some conserved amino acids as depicted in Figure 8C. So is this
highly induced transcript even likely to encode a functional protein?”
“We have no way of knowing whether the shortest NOR1 transcript encodes a
functional protein. It is possible that it encodes a protein with altered localization
when compared to the full-length protein, or that the truncated protein plays
some type of regulatory role. The protein that is predicted to be translated from
the short transcript is missing 2 amino acids that were shown to be critical for
NADH binding in the Fusarium oxysporum P450nor protein. Therefore, it is
possible that the short-form is unable to bind NADH and reduce nitric oxide. The
function of all of the NOR1 transcripts will be one focus of future studies.”
45
“When they express a NOR1 gene to check for increased resistance to
RNS, do they express the short transcript? That would have been the
better way to do it. How do the levels of the transcript induced by copper
compare to the induction they see of the endogenous transcript? Perhaps
they can do a Northern to check. The concern I have is that they are
inducing abnormally high levels of the full length gene, and the phenotype
of this may not reflect that of the modest induction of the shorter
transcript.”
“As shown in Fig. 8B, 3 NOR1 transcripts are observed when H.
capsulatum cells are exposed to nitric oxide. The largest transcript is
constitutive. The medium transcript and the smallest transcript are both
induced. Mapping studies indicate that the medium transcript likely
encodes the full-length protein as shown in Fig. 8C. We ectopically
expressed the medium NOR1 transcript. We chose to express the
medium transcript because the transcript is definitely induced during
nitrosative stress, and because it encodes a full-length protein that is
highly homologous to known nitric oxide reductases in other fungi. The
shortest transcript may not be functional, as described in point 1, above.
Although it might be interesting to overexpress the shortest transcript to
see if it affects RNS resistance, those experiments are beyond the 46
scope of this study…”
“We have performed Northern analysis to compare the levels of ectopic
expression of the NOR1 transcript with levels of endogenous induction
during nitrosative stress (data not shown) and the ectopic expression of
NOR1 is clearly at a higher level than the endogenous induced
transcripts. Because it can be difficult to overexpress a single gene and
observe a phenotype, it is often necessary to overexpress at a high level.
Future experiments could address whether lower levels of induction
would alter the resistance phenotype, but our feeling is that the key
experiments require generation of a gene disruption strain. Though
we have already spent a year trying to generate a NOR1 disruption
strain, some new technologic developments make us hopeful that
another year of effort might successfully yield a disruption of this
gene. Therefore, we will focus our efforts in this direction. (See
reviewer 3, point 1.)”
47
“The statement on p 9 (Materials and Methods) "we did not analyze
clones for which the sum of the ratio of the medians for the 635 nm and
532 nm channels was <= 500 intensity units" does not make sense.
What do they mean by sum of the ratio of medians?”
“The reviewer is absolutely correct. The sentence has been changed to
say ‘the sum of the median intensities’ rather than the ‘sum of the ratio
of the medians.’”
48
What do you think happened with
this paper?
• It was accepted without being sent back
for re-review
• Because an editor was given the authority
to make a decision on the paper
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Submitting your rejected paper to
another journal
• Respond to the concerns of the original
reviewers either in word or deed
– It will improve your paper
– You may get them again
• The pros and cons of telling a journal
you’ve been somewhere else first
– No one wants to be seen as taking rejects
– You may get a quick decision
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Building your reputation
A well-known scientist once said to me
that the only thing you have is your
reputation. If you are new to a field, people
will look at your paper with an open mind.
But once you have started publishing, your
reputation will precede you. Build the best
reputation by publishing work that is
scholarly and significant.
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Building your reputation with
editors: an old-boy’s network?
• What is the quality and significance of
work you have submitted to the journal in
the past?
• Where have you submitted your best work
in the past?
• How enjoyable has it been to work with
you?
• (Have you been helpful as a reviewer?)
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How does a journal attract good
papers?
• By publishing great ones.
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The quality of individual papers
varies
• The best papers
enhance the
reputation of the
journal
• The better your work
is, the more latitude
you’ll be given and
the more you can
request
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When you have a really “hot” paper, journals
will compete with each other for your work.
What kind of special treatment can you get?
•
•
•
•
•
Speed of review and publication
Relief of length restrictions
Division of work into multiple papers
Cover
Additional coverage (review, press
release, etc.)
• Change in access policy, etc.
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If you have a “borderline” paper, what
kind of special treatment can you get?
• Speed of review and publication, for good
cause
• Relief of length restrictions, for good cause
• Division of work into multiple papers
• Cover
• Additional coverage (review, press
release, etc.)
• Change in access policy, etc
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Playing the journals
• Collaborators submitting work together or
to separate journals
• Dividing results into multiple publications
• Going between journals
How do these things influence your
reputation? It depends on whether the act
is seen as a manipulation of the editorial
process.
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Editors travel to many scientific
meetings each year
• To learn about the latest results, and
recruit the top papers
• To develop an appreciation for a field that
is unfamiliar to them
• To identify good reviewers
• To identify topics for review
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When you meet an editor
• Share your perspective on work you found
particularly interesting
• Tell them about the work you’re doing and
why you’re doing it (invite them to your
poster)
• Offer feedback about or suggestions for
the journal
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You can also
• Ask about and discuss new areas the
journal finds particularly interesting
• Ask about and discuss changes in journal
policies that are important to you
• Ask about their research background, and
why they decided to become an editor
• Talk about mutual acquaintances
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Treat editors as your
colleagues
and they will become your
advocates
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Thank you.
[email protected]
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