Nature Policy update
Linda J. Miller, U.S. Executive Editor
   Nature and the research journals
                     Septe...
Today‟s speakers
 Linda J. Miller, PhD
   Senior editor at Science 
   Launch editor of Nature Immunology 
   U.S. Ex...
Guide to today‟s talks
  General introduction to Nature journals
  Nature journal policies
  What is a good paper?
  What ...
Nature‟s mission circa 1869
Nature‟s mission today
 First, to serve scientists through prompt
 publication of significant advances in any branch
 of s...
Common Policies at Nature journals
 Authorship
 Deposition of data
 Sharing of materials
 Copyright
 Manuscript transfer s...
Authorship
 All authors are responsible for the paper
 Changes to authorship need to be approved by
 all authors
 Individu...
Deposition of data
  Sequences
  GenBank, EMBL, DDBJ
  Structures
  PDB, SWISS-PROT
  Genomes
  NCBI, ENSEMBL
  Microarray...
Sharing of materials
 Publication is a privilege & a pact
   Acceptance of manuscript implies
      o Author provides acc...
Copyright and author license
 Nature journal authors retain copyright on original research
 publications & grant NPG an ex...
MS Transfer Service
 Eliminates need for author to re-input a manuscript, if
 they are choose to submit their manuscript t...
Competing financial interests
 Authors required to fill out and sign a competing
 financial interests form before publicat...
Competing financial interests
 Published papers contain a standard statement
 indicating whether or not a competing intere...
Image integrity
Objective: Images in manuscripts accurately reflect
   the data
   Beautification - Photoshop or other gra...
What‟s wrong with this image?
Example 1: Gels
  The original cause for concern:
             -   +
                       ...
What‟s wrong with this image?

A close-up of
  the image
  revealed
  another
  potential                Artificially stra...
What‟s right with this image?

Editor requested explanation and author supplied
  unretouched experimental data
          ...
Guidelines for presenting gels
Publication-quality gels require that MW markers, negative
  and positive controls be run o...
Guidelines for presenting gels
Contrast should be set so that the background and
  „contaminating‟ bands are still visible...
Guidelines for presenting gels
Cut and repositioned („spliced‟) lanes are discouraged.
If absolutely unavoidable, gel disc...
Beautification becomes fraud when:
Graphic software is used to create images that
  misrepresent the actual data collected...
Fluorescence immunocytochemistry
Misleading manipulations include altering contrast or color
  in a portion of the photo o...
Image integrity
 What authors can do
  Provide more education to grad students and
   postdocs
  Insist on seeing origin...
Plagiarism
 Both self-plagiarism and plagiarizing others are
 increasing problems in science
 Papers already published in ...
Biosecurity
2001 anthrax attacks changed public‟s attitude, particularly
  in the US

Examples of papers that worried the ...
Biosecurity
Is „Censorship vs Openness‟
   equivalent to
   „Safety vs Risk‟?
First step
  January 2003 US National Academy of Sciences
    International journal editors

    Security experts

  Agr...
Joint journal statement
 All papers in peer-reviewed journals must contain
 enough information to adequately reproduce the...
What are „manuscripts of concern‟?
 October 2003 US National Academy of Sciences committee
 chaired by Gerald Fink
 Identi...
More „dual-use‟ publications
After the Jan 2003 meeting dual-use publication continues
   May 2003 Nature - anthrax genome...
Nature journal policy
 The editorial staff of Nature journals maintain a
 network of advisers on biosecurity issues.
 All ...
Journal‟s responsibilities
 Be alert to papers whose risks of publication might
 outweigh benefits.
 Be alert to papers wh...
Benefits of openness

 Search for mechanisms of pathogenic organisms is
 critical to continue to protect public health
 Op...
Science is international
 Overly harsh regulation of publication in one country will
 be ineffective
  International activ...
Don‟t throw out
the baby with the bathwater


“The traditions and structure of research in the U.S. today depends on
repli...
Immunology. All of it.
Nature Immunology is a multidisciplinary journal

Covers a wide range of subject areas in immunolog...
What are NI editors looking for?

 Novelty
 Interest to the general immunologist
 Sizeable step forward
 Impact in the fie...
Elements of a “strong contender”

 Clear presentation of an interesting question
 Intro creates interest – why should read...
Reasons for rejection
 Lack of mechanistic insight
 Catalog of data
 Data do not support conclusions
 Raises many interest...
Nature Medicine editorial structure

                   Editor
             (Juan Carlos Lopez)

           6 manuscript e...
What are we looking for?
 Important question, new concepts
 Therapeutic advances, even in the absence of
   conceptual adv...
How does
“translational research” fit in?
 Definitions:
   “The process of applying ideas, insights and discoveries
    g...
Probably not right for NM
Create new disease model, but have not yet used it to learn
something new about the biology of t...
What happens to submitted papers?

 ~280 papers received per month
 Each paper read in detail by one editor, discussed by ...
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  1. 1. Nature Policy update Linda J. Miller, U.S. Executive Editor Nature and the research journals September 2005
  2. 2. 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
  3. 3. 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
  4. 4. Nature‟s mission circa 1869
  5. 5. 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.
  6. 6. Common Policies at Nature journals Authorship Deposition of data Sharing of materials Copyright Manuscript transfer service Competing financial interests Plagiarism Image integrity Biosecurity
  7. 7. 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:
  8. 8. Deposition of data Sequences GenBank, EMBL, DDBJ Structures PDB, SWISS-PROT Genomes NCBI, ENSEMBL Microarrays GEO, ArrayExpress
  9. 9. 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
  10. 10. 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.
  11. 11. 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.
  12. 12. Competing financial interests Authors required to fill out and sign a competing financial interests form before publication
  13. 13. 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
  14. 14. 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
  15. 15. 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
  16. 16. What‟s wrong with this image? A close-up of the image revealed another potential Artificially straight problem boundary between lanes - indicative of lane splicing
  17. 17. 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
  18. 18. Guidelines for presenting gels Publication-quality gels require that MW markers, negative and positive controls be run on the same gels (preferably full length)
  19. 19. 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
  20. 20. 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.
  21. 21. 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
  22. 22. 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
  23. 23. 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
  24. 24. 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.
  25. 25. 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
  26. 26. Biosecurity Is „Censorship vs Openness‟ equivalent to „Safety vs Risk‟?
  27. 27. 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
  28. 28. 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.
  29. 29. 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
  30. 30. 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
  31. 31. 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.
  32. 32. 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
  33. 33. 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
  34. 34. 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
  35. 35. 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
  36. 36. 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
  37. 37. 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
  38. 38. 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
  39. 39. 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
  40. 40. 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
  41. 41. 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
  42. 42. 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)
  43. 43. 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)
  44. 44. 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
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