Transcript Document

Competências Básicas de Investigação
Científica e de Publicação
Lecture 6: How Publishing works
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Publishing drives the scientific process
New consensus
view
Old consensus
view
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For you, getting published is important…
• Attribution of priority via peer review
– It’s new (probably), you were the first !
• Verification via peer review
– Your conclusions are clear and plausible
– Your methodology is appropriate
• Communication
– Integration into the consensus view
– Permanent archive
– Replication
• Professional advancement !!
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Broad readership
High rates of citation (= recognition)
CAPES Qualis points
$$$$$
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So, the Editor has two choices…
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Rejection: Royal Society for Chemistry
• “Articles submitted to our journals are prescreened so the editor that is handling the
article decides that the article is either out of
the journal scope or that the article is clearly
below the quality level of the journal.
• The pre-screening rates of our journals varies
a lot. Our high quality journals have a pre
screen rate of about 80%.”
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Reasons for rejection
• Mismatch with journal aims and scope [submit to
wrong journal]
• Failure to follow journal’s instructions to authors
• Badly written, bad English, bad Portuguese
• Lack of originality, novelty or significance [weak
hypothesis]
• Flaws in study design [poor experimental design]
• Several of these problems are easily avoidable!
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Lost in translation
• “Poor English” often used as a euphemism for
“badly written”
• Poor Portuguese translates as poor English
• If the science is clear (title, abstract, intro,
results) the chances of rejection are reduced
Which journal should I choose?
Selecting the best journal is important
The mycology journal ‘ecosystem’
– Important journals - Mycology Dept, UFPE (2006)
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Journal of Invertebrate Pathology
Phytopathology
Plant Pathology
Mycological Research
Plant Disease
Applied and Environmental Microbiology
Current Microbiology
Genetics and Molecular Biology
Molecular Plant Pathology
Medical Mycology
Mycopathology
Applied Soil Ecology
………..and at least 10 more journals!
– Note: only three titles contain a reference to mycology !
– Define your journal ecosystem carefully
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Journal selection criteria
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Your hypothesis
Aims and scope of journal
Impact Factor
Speed and ease of publication
Publisher’s statistics on circulation, downloads
Colleagues
Qualis ranking
What is an Impact factor?
• For a given year, the impact factor is the average
number of citations per paper published during the
two preceding years.
– A = number of times articles published in 2006 and 2007
were cited by other indexed journals during 2008.
– B = total number of articles published in 2006 and 2007.
– 2008 impact factor = A/B.
• Used as a proxy for the relative importance of a
journal within its field
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Frequency
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Frequency
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Try to publish in international journals with good
impact factors
0
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Total citations 2007-2012
300
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Total citations 2007-2012
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Author
Challenges
Survey
Journal Selection - Asia
Aimed at
Reaching Target
Audience and
Gaining
Recognition
69%
Convenience
20%
n=333
A Publisher’s View of the Cell Biology Ecosystem
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Example: Nature press release July 2013
• “The 2012 Journal Citation Report (JCR) places
Nature Communications at #3 and Scientific
Reports at #8 in the top 10 Multidisciplinary
Sciences titles.
• Nature remains #1 in the Multidisciplinary
Sciences, with an Impact Factor of 38.597, and
is the most cited science journal in the world
with 554,745 citations in 2012.”
Example: RSC press release June 2013
• The Royal Society of Chemistry's publishing
portfolio has once again shown outstanding
excellence, with the publication of the latest
Impact Factors (IF) report from Thomson
Reuters.
• Six out of the top 20 multidisciplinary
chemistry journals are published by the RSC more than any other publisher.
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So getting published isn’t easy…
• Journal editors are fiercely competitive
• They only want to publish articles that will
improve the standing of their journal
• So they select only those articles that they
think will be highly cited…
• And reject the majority of articles sent to
them [up to 90+%]
Implications for you!
• Identify the most important journals in your field
• Check their impact factors, Qualis rankings
• Read the ‘Aims and Scope’ statements for each
journal carefully
• Does your hypothesis fit the Aims and Scope?
• Can you find similar articles in recently published
issues?
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Cell: Aims and Scope
• Cell publishes findings of unusual significance in any
area of experimental biology, including but not
limited to cell biology, molecular biology,
neuroscience, immunology, virology and
microbiology, cancer, human genetics, systems
biology, signaling, and disease.
• The basic criterion for considering papers is whether
the results provide significant conceptual advances
into, or raise provocative questions and hypotheses
regarding an interesting biological question.
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Genomics: Aims and Scope
• The goal of Genomics is to promote the understanding of the structure,
function, and evolution of genomes in all kingdoms of life and the
application of genome sciences and technologies to challenging problems
in biology and medicine. The scope of the journal is broad and we
welcome original, full-length, and timely papers in all of the following
areas:
– Comparative genomics analysis that yields valuable insights into conserved
and divergent aspects of function, regulation, and evolution
– Bioinformatics and computational biology with particular emphasis on data
mining and improvements in data annotation and integration
– Functional genomics approaches involving the use of large-scale and/or highthroughput methods to understand genome-scale function and regulation of
transcriptomes and proteomes
– Identification of genes involved in disease and complex traits, including
responses to drugs and other xenobiotics
– Significant advances in genetic and genomics technologies and their
applications, including chemical genomics
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Gastroenterology: Aims and Scope
• Gastroenterology publishes novel clinical and basic
studies on all aspects of the digestive system,
including the liver and pancreas, as well as nutrition.
• The types of articles Gastroenterology publishes
include original papers, review articles, case reports,
and special category manuscripts.
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Agricultural and Forest Meteorology
• Agricultural and Forest Meteorology is an international
journal for the publication of original articles and reviews on
the inter-relationship between meteorology and the fields of
plant, animal and soil sciences, ecology, and biogeochemistry.
Emphasis is on basic and applied scientific research relevant
to practical problems in agriculture, forestry, and natural
ecosystems. Articles must appeal to an international
audience. Theoretical models should be tested against
experimental data. Special issues devoted to single topics are
also published.
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Inside a primary journal: Cell
• Cell was launched in 1974 as the
journal of exciting biology.
• Now a part of Elsevier’s Cell
Press, a family of 15 journals,
• Cell’s Ph.D.-trained scientific
editors work with authors,
reviewers, and editorial board
members with the goal of
publishing 26 issues of the most
interesting discoveries in biology
every year
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Cell’s editorial structure
• In-house Editors
– Employed by the journal’s publisher to carry out
administrative and copy-editing roles
• Editor-in-Chief
– Major figure in the field
• Editorial Board
– Represent all of the major sub-fields, act as advisors to the
Editor-in-Chief. Usually recognised experts in their
respective fields
• Referees
– Selected by the Editorial Board, usually an expert in the
specific area covered by the manuscript
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Editorial evaluation process - Cell
• All submissions are initially evaluated in depth by the Editorin-Chief or sent to an appropriate member of the Editorial
Board.
• Papers that do not conform to the general criteria for
publication will be returned to the authors without detailed
review, typically within 3-5 days.
• Otherwise, manuscripts will be sent to reviewers who have
agreed in advance to assess the paper rapidly.
• The editors will make every effort to reach decisions on these
papers within 3 weeks of the submission date.
• Accepted papers will be published within 3 months of
acceptance.
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What is the Editor looking for ?
• Plausibility
– Is the experimental design robust ?
– How effectively have the alternative hypotheses
been excluded ?
• Topicality
– Is the work original
– Is it interesting ?
– Is it relevant ?
– Is it useful ?
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Covering letter format
• Address to the editor personally
• State your manuscript title and publication
type
• Give a brief background, rationale and
description of your results
• Explain the importance of your findings and
why they would be of interest to the journal’s
target audience
• Provide corresponding author details
The role of peer review
– History
– Anonymous
– Multiple, to avoid bias
– Validation/accreditation
– Selecting the best
• Or avoiding the worse ?
– Alternatives
• Neuroscience
• PLos One
• Elsevier
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Peer review – the pros
– The process forces authors to meet the
standards of their discipline and achieve
scientific objectivity.
– Publications that do not involve peer
review are likely to be regarded with
suspicion by scholars and professionals in
many fields.
– Peer review is important to achieve clear,
precise writing.
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Peer review – the cons
– A peer is likely to be a competitor. How objective are they
going to be ?
– Most articles get published and the quality of articles
published in high impact titles such as Nature is highly
variable.
– Authors are encouraged by the publishing process to
exaggerate their claims and even be selective of the data
being published, leading to bias
– Negative findings are rarely published, leading to further bias
when judging the effectiveness say of new medical
technologies
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Alternatives: PLOS ONE
• PLOS ONE is a journal that publishes reports of
original research from all disciplines within science
and medicine.
• PLOS ONE will rigorously peer-review manuscripts
and will publish all papers that are technically sound.
• Judgments about the importance of any particular
paper are made after publication by the readership,
I,e, citations, article downloads.
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Alternatives: Neuroscience Peer-Review
Consortium
• The NPRC was created to reduce the inefficiency that arises when an
author submits a manuscript to a journal after the same manuscript
has been reviewed and rejected by another journal.
• In many cases, publication of good manuscripts is delayed as editors
from each journal attempt to find reviewers, send the reviews, and
wait for the reviews to be returned.
• Often the same reviewer is asked to review the same manuscript
multiple times.
• The NPRC streamlines this process by allowing reviews solicited by
one journal to be forwarded and re-used by other member journals.
• However, ultimate control of manuscript submission remains in the
hands of authors as reviews are forwarded only when the author
requests this service.
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A letter of rejection
Dear Author,
We have received the reports from our advisors on your manuscript
XYZ-D-13-00220 “Title********************************".
With regret, I must inform you that, based on the advice received, I have decided that your manuscript
cannot be accepted for publication in the Journal of Imaginary Microbiology.
Below, please find the comments for your perusal.
You are kindly requested to also check the website for possible reviewer attachment(s).
I would like to thank you very much for forwarding your manuscript to us for consideration and wish you
every success in finding an alternative place of publication.
With kind regards,
Editor
What to do next
• Unconditional rejection
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Editor offers no opportunity for appeal
Show comments to colleagues
Revise as though the rejection was conditional
Submit to a different journal
• Conditional rejection
– Regard this as an opportunity to improve your paper
– Show comments to colleagues
– Respond to all comments and record your actions in a
covering letter
– Consider submitting to a better journal!
Reviewer comments - example
• The paper needs to be formatted properly for the journal.
• This reviewer was only able to find information for papers
submitted with Introduction, materials and methods,
results and discussion sections while much of this is in the
paper the format appears to be incorrect even for a short
communication.
• It was difficult to find the number of samples taken or to
understand the experimental set-up as written; changing
the style to a more traditional journal format as suggested
above would help with this.
• In addition the most important reference Brown et al 2013
is missing!
Reviewer comments - example
This paper describes clinical and cytogenetic finding in a child with
retinoblastoma who had an aggressive fatal course. The authors postulate
that this may be related to changes in chromosome 6. However, it is
difficult to see how the findings here either promote or negate that
hypothesis. In addition several other problems should be addressed:
a. Abstract, line 9: could (not should)
b. Abstract: define IO
c. Staging details at the time of initial diagnosis are inadequate. Were scans
done of the head? chest? abdomen? pelvis? bone?
d. One assumes that the right eye was normal at initial diagnosis but this is
not stated.
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Reviewer comments – example, cont’d
e. Staging details at the time of initial relapse are inadequate. Were scans done of
the head? chest? abdomen? pelvis? bones?
f. What was the csf cytology at the time of initial relapse?
g. What cytologic studies were performed on the ocular, marrow and other tumors
at the initial relapse to prove that this was retinoblastoma?
h. What is MADIT?
i. If the authors are going to postulate that chromosome 6 abnormalities are
important then other publications require more careful review and more detailed
presentation of findings. How does one more case advance the hypothesis?
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Reviewer Comments – main problems
Author’s Hypothesis:
This case represents a particularly aggressive form of retinoblastoma which can
be diagnosed by the observation of a rare chromosomal abnormality
Referees Hypotheses:
The initial treatment of the retinoblastoma was ineffective
But assuming it wasn’t:
Several chromosomal abnormalities described – no evidence that specific
chromosomal defect chosen was connected with the disease severity
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Why were the referee’s comments confusing?
Referee response letter
• Respond to all of the reviewers’ comments
• Describe all of the changes you have made in the letter
• Also describe the reasons why you have not made
suggested changes
• Make it easy to see the changes have made in the
manuscript itself
– Refer to line and page numbers
– Different color font
– Highlight the text
Referee response letter
• If you disagree with the reviewer with the reviewer be clear
why:
– Reviewer Comment: In your analysis of the data you have
chosen to use a somewhat obscure fitting function (regression).
In my opinion, a simple Gaussian function would have sufficed.
Moreover, the results would be more instructive and easier to
compare to previous results.
– Author response: We agree with the reviewer that a simple
Gaussian fit would facilitate comparison with the results of
other studies. However, our tailored function allows for the
analysis of the data in terms of the Smith model [Smith et al,
1998]. We have added two sentences to the paper (page 3
paragraph 2) to explain the use of this function and Smith’s
model.
Ten simple rules to help you get published
– Read many papers, and learn from both the good and the bad
work of others. It is never too early to become a critic
– The more objective you can be about your work, the better that
work will ultimately become.
– Good editors and reviewers will be objective about your work.
– If you do not write well in the English language, take lessons early;
it will be invaluable later.
– Learn to live with rejection.
– Philip E. Bourne, PLoS
– http://compbiol.plosjournals.org/perlserv/?request=getdocument&doi=10.1371/journal.pcbi.0010057
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Ten simple rules to help you get published
– The ingredients of good science are obvious - novelty of research
topic, comprehensive coverage of the relevant literature, good
data, good analysis including strong statistical support, and a
thought-provoking discussion
– Start writing the paper the day you have the idea of what
questions to pursue
– Become a reviewer early in your career.
– Decide early on where to try to publish your paper.
– Quality is everything
– Philip E. Bourne, PLoS
– http://compbiol.plosjournals.org/perlserv/?request=getdocument&doi=10.1371/journal.pcbi.0010057
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Some more suggestions to help you get published
– Choosing a problem
• Something that you have a personal interest in
• Based on a current experimental paradigm recognized by the international
scientific community
• And for which you have intellectual support, e.g. experimental design, data
interpretation, etc
• For which experimental resources are available, affordable
– Mestrado/Doutorado projects
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Choose a supervisor with a good research record
Specify the research problem early during the first year
Try to shape first year course work around these specific needs
Pay more attention to experimental design, not just statistics
Don’t attempt one big experiment, but plan several
Seek progress reviews at regular intervals
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