Transcript Company Briefing - Fudan University

Nature Policy update
Linda J. Miller, U.S. Executive Editor
Nature and the research journals
September 2005
Today’s speakers
Linda J. Miller, PhD
 Senior editor at Science 
 Launch editor of Nature Immunology 
 U.S. Executive Editor for Nature and the Nature
research journals
J. Myles Axton, PhD
 Oxford University investigator and lecturer 
 Editor of Nature Genetics
Guide to today’s talks
General introduction to Nature journals
Nature journal policies
What is a good paper?
What do we expect from out referees?
Some specifics about
 Nature Medicine
 Nature Immunology
 Nature Genetics
 Nature Biotechnology
Nature’s mission circa 1869
Nature’s mission today
First, to serve scientists through prompt
publication of significant advances in any branch
of science, and to provide a forum for the
reporting and discussion of news and issues
concerning science.
Second, to ensure that the results of science are
rapidly disseminated to the public throughout the
world, in a fashion that conveys their
significance for knowledge, culture and daily life.
Common Policies at Nature journals
Authorship
Deposition of data
Sharing of materials
Copyright
Manuscript transfer service
Competing financial interests
Plagiarism
Image integrity
Biosecurity
Authorship
All authors are responsible for the paper
Changes to authorship need to be approved by
all authors
Individual contributions can now be
acknowledged in the published paper:
Deposition of data
Sequences
GenBank, EMBL, DDBJ
Structures
PDB, SWISS-PROT
Genomes
NCBI, ENSEMBL
Microarrays
GEO, ArrayExpress
Sharing of materials
Publication is a privilege & a pact
 Acceptance of manuscript implies
o Author provides access to readers of all new reagents described
in the paper
o Reagents provided by biotech or other corporate partners be
made available to all
o If access is conditional (such as small fees, Material Transfer
Agreements, etc), conditions must be made explicit
If journal receives complaints, we will take action
 Contact author for explanation
 Contact funding agencies and institutes if warranted
 Post Editor’s Note with paper
Copyright and author license
Nature journal authors retain copyright on original research
publications & grant NPG an exclusive license-to-publish.
Authors can post the accepted version on their personal
website and can republish in books or reviews they are writing
- cite original source.
Funding agencies and their institutions can post the accepted
author’s version of the manuscript in their online archives 6
months after publication in a Nature journal.
Nature journals are coordinating access policies with the
deposition policies of major science funding agencies such as
the US National Institutes of Health and the UK Wellcome
Trust.
MS Transfer Service
Eliminates need for author to re-input a manuscript, if
they are choose to submit their manuscript to another
NPG journal
Authors provided with a link in their decision letter
Authors can choose any of the NPG or Nature journals
If the manuscript had been reviewed at the first Nature
journal, and the author chooses to send the manuscript
to another Nature journal, the reviews are automatically
forwarded to the next Nature journal - this can save time
in the evaluation of the manuscript at the second journal.
Competing financial interests
Authors required to fill out and sign a competing
financial interests form before publication
Competing financial interests
Published papers contain a standard statement
indicating whether or not a competing interest
exists
Details of the competing financial interests are
given online
Image integrity
Objective: Images in manuscripts accurately reflect
the data
Beautification - Photoshop or other graphic
tools used to alter a portion of an image
(changing colors, brightness, contrast) in an
attempt to make data clearer or remedy
unsightly data
Deliberate fraud - manufacturing data that was
never obtained experimentally
What’s wrong with this image?
Example 1: Gels
The original cause for concern:
-
+
Bands in lanes
marked “+” and “-”
were almost
identical, but text
stated that they
were different
What’s wrong with this image?
A close-up of
the image
revealed
another
potential
problem
Artificially straight
boundary
between lanes indicative of lane
splicing
What’s right with this image?
Editor requested explanation and author supplied
unretouched experimental data
-
+
Two problems resolved:
 Lanes not cut
 Controls now run on
same gel
Guidelines for presenting gels
Publication-quality gels require that MW markers, negative
and positive controls be run on the same gels (preferably
full length)
Guidelines for presenting gels
Contrast should be set so that the background and
‘contaminating’ bands are still visible. Immunoblots often
need boxes to demarcate the edge of the filter
Blot with
indeterminate
edges
Gel of too high
contrast with
box
Guidelines for presenting gels
Cut and repositioned (‘spliced’) lanes are discouraged.
If absolutely unavoidable, gel discontinuities should be
indicated with boxes or inserted white space - and noted
in the Figure legend.
Beautification becomes fraud when:
Graphic software is used to create images that
misrepresent the actual data collected
Band sections cut and pasted into new positions- green
Bands flipped and pasted into another lane - red
Fluorescence immunocytochemistry
Misleading manipulations include altering contrast or color
in a portion of the photo or adding/deleting elements in
photo
Manipulated image
Manipulation of added cells revealed by
contrast adjustment
Image integrity
What authors can do
 Provide more education to grad students and
postdocs
 Insist on seeing original data from which a
figure was built
What editors can do
 Develop clearer guidelines and post in online
Guides for Authors and Referees
 Initiate internal inspections of all papers to
detect problems before publication
Plagiarism
Both self-plagiarism and plagiarizing others are
increasing problems in science
Papers already published in non-English
journals are unlikely to be published in high
profile English-language journals; the original
publication must always be cited
Give credit where credit is due
If in doubt, err on the side of too many, rather
than too few, citations.
Biosecurity
2001 anthrax attacks changed public’s attitude, particularly
in the US
Examples of papers that worried the media & public
2002 J. Virol. paper - created a mousepox virus lethal
even to mice already vaccinated against mousepox
2002 Science paper - de novo synthesis of polio virus
without cells
Biosecurity
Is ‘Censorship vs Openness’
equivalent to
‘Safety vs Risk’?
First step
January 2003 US National Academy of Sciences
 International journal editors
 Security experts
Agreed:
 Editors uphold integrity of scientific literature & ensure
reproducibility and verifiability
 Editors agreed to assess ‘manuscripts of concern’ for
risk of misuse vs benefit to public health
Joint journal statement
All papers in peer-reviewed journals must contain
enough information to adequately reproduce the
results
Commitment to identification of papers before review
and/or publication that have the potential for abuse
Formation of clear policies as to the process to which
such papers would be subjected
If a paper is deemed inappropriate for publication as
is, it would either be modified without compromising
its reproducibility or communicated to the scientific
community through other avenues.
What are ‘manuscripts of concern’?
October 2003 US National Academy of Sciences committee
chaired by Gerald Fink
Identified some categories of experiments should be cause for
concern:
 Render vaccines ineffective
 Confer resistance to useful antibiotics or antivirals
 Enhance virulence of microorganisms
 Increase transmissibility of pathogens
 Alter host range of a pathogen
 Render a pathogen harder to detect
 ‘Weaponize’ biological agents or toxins
More ‘dual-use’ publications
After the Jan 2003 meeting dual-use publication continues
May 2003 Nature - anthrax genome
May 2003 Science - SARS sequence
Mar 2004 Science - crystal structure of 1918 pandemic
influenza HA
Oct 2004 Nature - construction of virulent flu with 1918
HA and/or NA
Nature journal policy
The editorial staff of Nature journals maintain a
network of advisers on biosecurity issues.
All concerns on that score, including the
commissioning of external advice, will be shared
within an editorial monitoring group consisting of the
Editor-in-Chief of Nature publications, the Executive
Editor of the Nature research journals, the Chief
Biological Sciences Editor of Nature, and the chief
editor of the journal concerned.
Once a decision has been reached, authors will be
informed if biosecurity advice has informed that
decision.
Journal’s responsibilities
Be alert to papers whose risks of publication might
outweigh benefits.
Be alert to papers whose research materials’
dissemination might cause hazard.
Ensure papers’ protocols adhere to local ethics rules
Keep in touch with debate
Be transparent
News section: scrutinize biodefense developments
Benefits of openness
Search for mechanisms of pathogenic organisms is
critical to continue to protect public health
Open publication of genomes, as SARS genome has
already proven, can have almost immediate health
benefits
Science is international
Overly harsh regulation of publication in one country will
be ineffective
International activities like science need international
consensus in deciding what constitutes appropriate
action
Editors and scientists both have the responsibility for
protection of public health with minimal disruption of
openness
Don’t throw out
the baby with the bathwater
“The traditions and structure of research in the U.S. today depends on
replication and refutation, which means that sufficient data and methods to
allow that must be published in peer-reviewed journals. Such publication
also mitigates fraudulent results, sloppy science, and political biases
guiding important policy decisions. Recent, well-publicized incidents of
scientific misconduct underscore the merits of this system.”
MRC Greenwood
Chancellor, UC Santa Cruz
Immunology. All of it.
Nature Immunology is a multidisciplinary journal
Covers a wide range of subject areas in immunology, from
immune receptor signaling to microbial immunopathology
Human immunology welcome
nature
immunology
What are NI editors looking for?
Novelty
Interest to the general immunologist
Sizeable step forward
Impact in the field
Provide new directions for research
Provide fundamental insights into the workings of the
immune system
nature
immunology
Elements of a “strong contender”
Clear presentation of an interesting question
Intro creates interest – why should reader care?
Strong, well-controlled data
Rules out some alternative explanations
Speculation doesn’t “stretch the data”
Discussion puts paper in perspective
Data is significant step forward with broader implications
nature
immunology
Reasons for rejection
Lack of mechanistic insight
Catalog of data
Data do not support conclusions
Raises many interesting possibilities, but doesn’t begin
to distinguish between them
New, but not a large enough step in field
Lacking in significant novelty
Only of interest to specialists in a subfield
Experiments all performed in cell lines
No broad conclusions
nature
immunology
Nature Medicine editorial structure
Editor
(Juan Carlos Lopez)
6 manuscript editors
New York, London, San Francisco
• Cardiovascular
• Infectious disease, immune system
• Cancer
• Metabolic disease
• Neuroscience
• And others
What are we looking for?
Important question, new concepts
Therapeutic advances, even in the absence of
conceptual advance
Technically convincing
Direct relevance to human disease
Mechanistic and molecular insight
 Mechanisms involved in disease processes



Relevant animal models
Human clinical samples or data from patients
New therapeutic agents or strategies

Mechanism of action in vivo
How does
“translational research” fit in?
Definitions:
 “The process of applying ideas, insights and discoveries
generated through basic scientific inquiry to the treatment or
prevention of human disease” (NIH)
 Taking ideas from clinical research back into experimental settings
We are eager to publish translational research
 Research involving humans is difficult
 High standards should be maintained
September 2004 editorial (10:879)
Probably not right for NM
Create new disease model, but have not yet used it to learn
something new about the biology of the disease
Experiments all done in cell lines, ex vivo
Compound works great, but mechanism is unclear
Gene or protein profiling
 Provocative changes, but functional importance in vivo is unclear
 For diagnostics, need prospective study, blinded samples
Mutation identification
 Effect of mutation on protein function or expression not clear
 Provides limited new insight into disease process
January 2004 editorial (10:1)
What happens to submitted papers?
~280 papers received per month
Each paper read in detail by one editor, discussed by all
~75-85% returned without review in 1-2 weeks
~15-25% are sent for review, 2-4 referees
Decision for reviewed papers takes 4-6 weeks
~ 5% of submitted papers are published
 Most reviewed more than once
 Most are substantially revised