Basic Skills for Scientific
Research and Publishing.
Segment 8. Getting a scientific
article published
28 August 2012
Ganesha Associates
1
What is scientific publishing ?
• Scientific publishing is the process by which scientific
progress is communicated to the community.
• So it is an essential part of the scientific process
• If it isn’t published, it isn’t science…
• …and you’ve wasted a lot of the tax-payer’s money
• Scientific publishing is a commercial enterprise
28 August 2012
Ganesha Associates
2
Publishing drives the scientific process
New consensus
view
Old consensus
view
28 August 2012
Ganesha Associates
3
Getting published is important for
you because…
• 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
appropriate
– But your conclusions may still later be proved to be incorrect…
• Communication
– Replication, integration into the consensus view
– Permanent archive
• Evaluation !!
– $$$$$
– CAPES Qualis
28 August 2012
Ganesha Associates
5
Which journal will you publish in ?
(Field: developmental neuroscience)
– Tier A: high profile, broad readership journals such as Nature,
Science and Cell
– Tier B: the “highest quality” specialized journals, or less high
quality broader journals such as Neuron, Nature Neuroscience,
Genes & Development, and Development. If going for breadth,
PNAS, Current Biology, EMBO Journal
– Tier C: “safe bet” journals, such as Developmental Biology, J.
Neuroscience, BioMedCentral journals
– Tier D: the “just publish it” titles, such as Mechanisms of
Development, Experimental Brain Research. Some authors
would never publish in these journals – they would just as soon
put their work in a drawer
28 August 2012
Ganesha Associates
6
Which journal will you publish in ?
(Field: developmental neuroscience)
– “If I have a paper which I believe demonstrates a fundamental
advance in our understanding of neural differentiation – what
path do I take ?”
– “….there are two underlying pressures determining the place to
publish: the prestige of the journal and the need to be first.”
– “….if the aim is to ‘establish turf’, if someone else comes out
before you in any ‘respectable journal where you trust the quality
of the science, then you have lost your ability to stake your claim
to that particular piece of ‘turf’.
– If there is more time, authors may go from one top tier journal to
another before choosing to go to the next level.”
28 August 2012
Ganesha Associates
7
Which journal will you publish in ?
(Field: cell biology)
28 August 2012
Ganesha Associates
8
The mycology journal ‘ecosystem’
– Important journals - Mycology Dept, UFPE (2006)
•
•
•
•
•
•
•
•
•
•
•
•
•
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 !
28 August 2012
Ganesha Associates
9
Ecosystems
28 August 2012
Ganesha Associates
10
Journal hierarchies
• General discoveries of high fundamental importance
– Nature
• Discoveries of high fundamental importance within a
specialist discipline or field
– Journal of Neuroscience
• Confirmatory studies
– Generalisation to other species
– Qualification of boundary conditions
– Brain Research
• Me-too studies, esoteric fields
– Brain and Cognition
28 August 2012
Ganesha Associates
11
Implications of discipline-specific journal
ecosystems
• Identify the most important journals in your field
• Check the impact factor
• Remember, every journal has a well-defined role
• So read the ‘Aims and Scope’ statements for
each journal carefully
• At the same time, make a copy of the journals’
‘Instructions for Authors’, they will be different too
28 August 2012
Ganesha Associates
12
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.
28 August 2012
Ganesha Associates
13
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
high-throughput 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
28 August 2012
Ganesha Associates
14
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.
28 August 2012
Ganesha Associates
15
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.
28 August 2012
Ganesha Associates
16
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 ten 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
28 August 2012
Ganesha Associates
17
Cell’s editorial structure
• In-house Editor
– 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
28 August 2012
Ganesha Associates
18
Editorial evaluation process - Cell
• All submissions are initially evaluated in depth by the
Editor-in-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.
28 August 2012
Ganesha Associates
19
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 ?
28 August 2012
Ganesha Associates
20
The most likely outcome of the editorial
process is rejection
• Nature, Science, Cell and other top ranking journals
have rejection rates of over 95%
• Most high quality journals have a rejection rate of over
80%
• Most journals with an Impact Factor >1 have a rejection
rate > 66%
• All Editors want their journals to be better than their
rivals.
• So they select only the best articles to publish.
• Some manuscripts may not even be sent for full peer
review
• Authors of accepted papers will often be asked for
revisions and reductions in length
28 August 2012
Ganesha Associates
21
Define: Triage
A system for allocating scarce resources; it
provides the maximum resources to
individuals of highest priority, and few or no
resources to individuals of lowest priority.
Derived from practices used to prevent medical
systems from being overwhelmed when there
are many sick or injured.
28 August 2012
Ganesha Associates
22
Triage quality varies
• Journal of Biological Chemistry, Biochemistry,
and Biochimica Biophysica Acta all have
rejection rates > 80%
• Impact Factors of 7.4, 5.1. 2.5
• 21%, 34%, 55% of published articles receive 1
or 0 citations
• High Impact Factor journals have higher false
negative rates – they reject a lot that is good
• Low Impact Factor Journals have higher false
positive rates – they publish a lot that is not good
28 August 2012
Ganesha Associates
23
The importance of rejection rates
28 August 2012
Ganesha Associates
24
How to avoid rejection ?
Author
Journal staff
Rejection
Editor-in-Chief
Rejection
Referees
Rejection
Publication
28 August 2012
Ganesha Associates
25
Major reasons for rejection - Editors
• Subject falls outside of the aims and scope of
the journal
• Subject is not of sufficient importance or novelty
for publication in the journal so it will not appeal
to a broad audience
• Manuscript not written in the appropriate style or
format for the journal
• Manuscript too long
• Manuscript incomplete
• Quality of English not perfect
28 August 2012
Ganesha Associates
26
The role of peer review
–
–
–
–
–
–
–
History
Anonymous
Multiple, to avoid bias
Validation/accreditation
Selecting the best
Or de-selecting the worse ?
Alternatives
• Nature
• PLos One
28 August 2012
Ganesha Associates
27
The role of peer review
• A peer is someone who is of the same or equal standing
as another. Thus peer review is review performed by
individuals considered to be professional equals.
• The process forces authors to meet the standards of
their discipline and achieve scientific objectivity.
• Publications and awards that have not undergone 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.
This is just as true for professional scientists as it is for
students.
• Peer review can result in acceptance, conditional
acceptance or rejection
28 August 2012
Ganesha Associates
28
Peer review – the pros
– A peer is someone who is of the same or equal
standing as another. Thus peer review is review
performed by individuals considered to be
professional equals.
– The process forces authors to meet the standards of
their discipline and achieve scientific objectivity.
– Publications and awards that have not undergone
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. This is just as true for professional scientists
as it is for students.
– Peer review can result in acceptance, conditional
acceptance or rejection
28 August 2012
Ganesha Associates
29
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
– “There is increasing concern that most current
published research findings are false” John Ioannidis,
PLoS 2005
28 August 2012
Ganesha Associates
30
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.
28 August 2012
Ganesha Associates
31
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?
28 August 2012
Ganesha Associates
32
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
28 August
2012 severity
Ganesha Associates
33
the
disease
A Referee’ Check List
• Taken from the journal Respiratory Care
• Structured to focus on each section of the
manuscript
28 August 2012
Ganesha Associates
34
PLoS One
• PLoS ONE is an international, peer-reviewed, openaccess, online publication. PLoS ONE welcomes reports
on primary research from any scientific discipline. It
provides:
–
–
–
–
–
–
Open-access—freely accessible online, authors retain copyright
Fast publication times
Peer reviewed by expert, practicing researchers
Post-publication tools to indicate quality and impact
Community-based dialogue on articles
Worldwide media coverage
• “All papers that make a valuable contribution to the
scientific literature, that are replicable, that are clearly
written, and whose conclusions are supported by the
data deserve publication.”
28 August 2012
Ganesha Associates
35
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 —which may
have been rejected solely because of space or scope
limitations— 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.
28 August 2012
Ganesha Associates
36
Introduction
• Is the background information adequate to
introduce the research problem ?
• Are the references adequate ?
• Are specific study objectives or
hypotheses stated ?
• Is the writing in this section clear and
concise ?
28 August 2012
Ganesha Associates
37
Methods
• Are there outcome variables described for each
study objective or hypothesis ?
• Are there appropriate descriptions of how
calculated values were determined ?
• Are outcome variables that do not relate to the
objectives or hypotheses avoided ?
• Are the measurement procedures appropriate
for the study objectives or hypotheses ?
• Is there enough detail to judge validity and for
readers to replicate the study ?
• Were appropriate statistical methods chosen for
this study design ?
• Is the writing in this section clear and concise ?
28 August 2012
Ganesha Associates
38
Results
• Are there complete data for each procedure or
test described in the Methods section ?
• Do the data, or descriptions on the data, appear
to be valid ?
• Are data that do not relate to the study
objectives or hypotheses avoided ?
• Are the tables and illustrations adequate ?
• Does the text avoid presenting the same data as
the Tables and Illustrations ?
• Is the writing clear and concise ?
28 August 2012
Ganesha Associates
39
Discussion
• Is there an explanation of how the results address the
problem statement or hypothesis ?
• Are theoretical and practical aspects of the results
discussed ?
• Do you agree with the interpretation of the results ?
• Is there a comparison of this study with previously
published studies ?
• Are the references adequate ?
• Is there a discussion of the limitations of the study ?
• Is there a section that clearly states the authors
conclusions ?
• Is the writing of this section clear and concise ?
28 August 2012
Ganesha Associates
40
Major reasons for rejection - Referees
•
•
•
•
•
•
•
•
•
•
Inappropriate or incomplete statistics
Over-interpretation of results
Inappropriate instrumentation
Sample too small or unbiased
Text too difficult to follow
Insufficient problem statement
Inaccurate or inconsistent data reported
Incomplete, inaccurate, or outdated literature review
Insufficient data presented
Defective tables or figures
28 August 2012
Ganesha Associates
41
Main reasons for rejection - Brasil
•
•
•
•
Submitted to the wrong journal
Journal aims and scope not followed
Purpose of the work unclear
Work does not relate to current areas of
research interest
• Too long
• English
28 August 2012
Ganesha Associates
42
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
28 August 2012
Ganesha Associates
43
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
28 August 2012
Ganesha Associates
44
Some more suggestions to help you get
published
– Choosing a problem
• Something that you have a personal interest in
• is based on a current experimental paradigm recognized by the
international scientific community
• for which experimental resources are available, affordable
• and for which you have intellectual support, e.g. experimental design,
data interpretation, etc
– Mestrado/Doutorado projects
•
•
•
•
•
•
Choose a supervisor with a good research track record
Specify the research problem 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
28 August 2012
Ganesha Associates
45