How to Review a Manuscript*
*And respond to reviewers’ comments

Jonathan M. Samet, MD, MS
Professor and Flora L. Thornton...
Things we did not talk about
last week
• 
• 
• 
• 

Selecting a journal
Authorship issues
Cover letters
Recommending/not r...
SELECTING A JOURNAL
Selecting a Journal
•  Should have potential readership and
journal in mind as writing begins
–  Who will care about your ...
Selecting a journal
•  The tiers:
–  The big ones: NEJM, Lancet, JAMA, and so on.
–  The big ones in your field: the Ameri...
General Guidance
•  If you have something that may be “big”
then give the first tier journals a try. They
reject quickly (...
Impact Factor
•  Definition: “In a given year, the impact
factor of a journal is the average number
of citations received ...
Impact Factor: Important?
•  Sadly---YES
•  For promotion at USC, we are submitting
impact factors for journals along with...
Journal Impact Factor
•  Journal Impact Factors are calculated on a yearly basis
by the Journal Citation Reports database ...
Impact Factor – All Journals
Impact Factor – Journals by specialty fields
(e.g., respiratory system)
H-Index
•  The h-index of a publication is the largest
number h such that at least h articles in
that publication were cit...
H-Index for author

Southern California
Clinical and Translational Science Institute
Translating Science into Solutions fo...
Citation analysis for author
(e.g., Samet JM)

Southern California
Clinical and Translational Science Institute
Translatin...
Citation analysis for author
(e.g., Samet JM)

Southern California
Clinical and Translational Science Institute
Translatin...
Southern California
Clinical and Translational Science Institute
Translating Science into Solutions for Better Health
AUTHORSHIP
Authorship Issues
• 
• 
• 
• 
• 
• 

Who should be an author?
What about author order?
Multiple first and senior authors
D...
http://www.icmje.org/
ICMJE: Who is an Author?
1. Substantial contributions to the conception or
design of the work; or the acquisition, analysi...
Author Order
•  You might be first author if:
–  The project is your work
–  You are the PI and wrote the paper
–  You are...
Some examples of authorship
•  Pineles BL, Park E, Samet JM. Systematic review and metaanalysis of miscarriage and materna...
Consortium Papers
•  An emerging problem reflecting team
science and consortium mechanisms
•  Issues with consortia:
–  Po...
Southern California
Clinical and Translational Science Institute
Translating Science into Solutions for Better Health
Cover Letters
•  Not so important
•  Opportunity to say why paper is important,
but probably not receive much attention
• ...
Conflict-of-interest
“A conflict of interest exists when
professional judgment concerning a primary
interest (such as pati...
COI and Pat Buffler
In 2010, FMC paid Buffler nearly $200,000 in
cash and stock. Securities and Exchange
Commission record...
PEER REVIEW
Peer Review: The Ideal
•  Evaluation of scholarly work by several
peers with appropriate expertise.
•  Careful considerati...
Peer Review: The Reality
•  There are too many journals and too many
papers to be reviewed.
•  Typically, editors struggle...
Peer Review Comments
•  General comments:
– Significance of the findings
– Methodological issues
– Generalizability
– Link...
Peer Review Comments
•  Specific comments:
– The gamut
– Minor editorial stuff
– Points of disagreement
– Methodological f...
Things I Say
•  Important and makes a contribution
(unimportant and repetitive)
•  Substantive methodological concerns
(gi...
Things that annoy me!
•  Most annoying: priority claims (This is the
first study of______ or whatever).
•  Excessive relia...
Comments to the editor
•  Not much new here (hint: reject)
•  Fundamental problems with the data (hint:
be careful)
•  Muc...
An example of my review:
Obstructive sleep apnea and systemic hypertension
FIRST REVIEW
An example of my review:
Obstructive sleep apnea and systemic hypertension
SECOND REVIEW
An example of my review:
Obstructive sleep apnea and systemic hypertension
THIRD (AND FINAL) REVIEW
Another example of my review:
Chlamydia pneumoniae and asthma
Another example of my review (cont.):
Chlamydia pneumoniae and asthma
COMMENTS AND LETTERS
FROM THE EDITOR
What I do as editor
•  Initially scan the manuscript to find
reviewers.
•  When comments come, carefully read
them and go ...
Letter from the Editor
•  Should provide a roadmap for interpreting
the comments.
•  Provide an indication of those commen...
Responding to Comments
• 
• 
• 
• 
• 
• 

Stay calm and be respectful.
Express gratitude/thanks.
Do NOT be combative, even...
Responses to Comments
•  Respond to each comment, identified in
some systematic way.
•  Embed responses into comments.
•  ...
Example #1: Response to Review – Smoking and TB
Example #1: Manuscript Revision – Smoking and TB

48
Example #2: Response to Review – Smoking and DM
Example #2: Manuscript Revision – Smoking and DM

50
Example #2: Manuscript Revision – Smoking and DM
What to do if rejected!
•  Don’t take it personally.
•  Do not call the editor or send an email
(generally).
•  Look throu...
Why would your manuscript be
rejected?
•  Not notable or newsworthy: the “big
journals.”
•  Not novel: any journal.
•  Not...
LETTERS TO THE EDITOR
(FROM READERS OF ARTICLE)
Samet, Straif, Schuz, Saracci. Epidemiology 2014;25:23-7
Letters to the Editor

Southern California
Clinical and Translational Science Institute
Translating Science into Solutions...
Letters to the Editor –
Author’s Response

Southern California
Clinical and Translational Science Institute
Translating Sc...
Letters to the Editor –
Author’s Response (cont.)

Southern California
Clinical and Translational Science Institute
Transl...
Exercises

Southern California
Clinical and Translational Science Institute
Translating Science into Solutions for Better ...
You receive the following
comments on your
manuscript. Write responses:

Southern California
Clinical and Translational Sc...
1. While the study findings are of
interest, the generalizability of
these findings based on Hispanic
patients at LAC, is ...
2. This is an elegant experimental
model of addiction. However, I
hardly see any relevance to
alcoholism in people.

South...
3. The main finding, increased risk
for diabetes in those drinking more
coffee is of interest (RR = 1.8, 95%
CI 0.98-2.70)...
GENERAL RESOURCES
http://www.icmje.org/
http://www.equator-network.org/reporting-guidelines/
How to Review a Manuscript_Slides_JS_02.24.2014
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How to Review a Manuscript

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How to Review a Manuscript_Slides_JS_02.24.2014

  1. 1. How to Review a Manuscript* *And respond to reviewers’ comments Jonathan M. Samet, MD, MS Professor and Flora L. Thornton Chair Department of Preventive Medicine Director, ECDE, SC CTSI Career Development Seminar Series Feb 24, 2014 Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  2. 2. Things we did not talk about last week •  •  •  •  Selecting a journal Authorship issues Cover letters Recommending/not recommending reviewers •  Acknowledgements •  Conflict-of-interest Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  3. 3. SELECTING A JOURNAL
  4. 4. Selecting a Journal •  Should have potential readership and journal in mind as writing begins –  Who will care about your findings? –  For whom are they relevant? •  The impact consideration •  Tiers of journals –  First level: NEJM etc. –  Second level: Good ones in your field –  Third level: the “undesirables and new journals Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  5. 5. Selecting a journal •  The tiers: –  The big ones: NEJM, Lancet, JAMA, and so on. –  The big ones in your field: the American Journal of whatever and so on. –  The little ones in your field: the American Journal of your particular niche. –  The latest on-line creation (beware “predatory publishing”) Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  6. 6. General Guidance •  If you have something that may be “big” then give the first tier journals a try. They reject quickly (and often without review). •  Then turn to the best journals in your field —and write for them. •  And if rejected, start down the hierarchy. •  Should you ever give up? Remember, the papers are “forever” on your CV. Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  7. 7. Impact Factor •  Definition: “In a given year, the impact factor of a journal is the average number of citations received per paper published in that journal during the two preceding years.” •  Should you care? Unfortunately, you probably should. •  Citation analysis increasingly part of promotion process. Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  8. 8. Impact Factor: Important? •  Sadly---YES •  For promotion at USC, we are submitting impact factors for journals along with citation counts •  In some countries, CVs list journal impact factors and citation counts •  High impact journals receive great weight at USC Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  9. 9. Journal Impact Factor •  Journal Impact Factors are calculated on a yearly basis by the Journal Citation Reports database ( http://wokinfo.com/products_tools/analytical/jcr/) •  The Impact Factor of a journal is the average number of times that articles published in that journal in a two year period have been cited in the following “JCR year” 2012 Impact Factor = Total citations made in 2012 to papers published in that journal in 2010 & 2011 Total papers published in that journal in 2010 & 2011 Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  10. 10. Impact Factor – All Journals
  11. 11. Impact Factor – Journals by specialty fields (e.g., respiratory system)
  12. 12. H-Index •  The h-index of a publication is the largest number h such that at least h articles in that publication were cited at least h times each. For example, a publication with five articles cited by, respectively, 17, 9, 6, 3, and 2, has the h-index of 3. •  The h5-index is the h-index of only those of its articles that were published in the last five complete calendar years. Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  13. 13. H-Index for author Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  14. 14. Citation analysis for author (e.g., Samet JM) Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  15. 15. Citation analysis for author (e.g., Samet JM) Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  16. 16. Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  17. 17. AUTHORSHIP
  18. 18. Authorship Issues •  •  •  •  •  •  Who should be an author? What about author order? Multiple first and senior authors Dealing with student authors Dealing with disputes about authorship Consortium papers Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  19. 19. http://www.icmje.org/
  20. 20. ICMJE: Who is an Author? 1. Substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data for the work; AND 2. Drafting the work or revising it critically for important intellectual content; AND 3. Final approval of the version to be published; AND 4. Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  21. 21. Author Order •  You might be first author if: –  The project is your work –  You are the PI and wrote the paper –  You are a trainee and carried out the work and wrote the paper •  You might be the senior author if: –  You are the PI –  Your trainee is the first author –  A junior colleague is first author Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  22. 22. Some examples of authorship •  Pineles BL, Park E, Samet JM. Systematic review and metaanalysis of miscarriage and maternal exposure to tobacco smoke during pregnancy. Am J Epidemiol. 2014; in press. •  Peng RD, Samoli E, Pham L, Dominici F, Touloumi G, Ramsay T, Burnett RT, Krewski D, Le Tertre A, Cohen A, Atkinson RW, Anderson HR, Katsouyanni K, Samet JM. Acute effects of ambient ozone on mortality in Europe and North America: results from the APHENA study. Air Qual Atmos Health. 2013; 6(2): 445-453. •  Giovino GA, Mirza SA, Samet JM, Gupta PC, Jarvis MJ, Bhala N, Peto R, Zatonski W, Hsia J, Morton J, Palipudi KM, Asma S; GATS Collaborative Group. Tobacco use in 3 billion individuals from 16 countries: an analysis of nationally representative cross-sectional household surveys. Lancet 2012; 380(9842): 668-79. Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  23. 23. Consortium Papers •  An emerging problem reflecting team science and consortium mechanisms •  Issues with consortia: –  Positioning yourself on writing committees –  Multiple/multiple authorship •  How will they count for recognition of scholarship and advancement? Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  24. 24. Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  25. 25. Cover Letters •  Not so important •  Opportunity to say why paper is important, but probably not receive much attention •  With regard to suggesting reviewers: –  If there is someone to be avoided, then reasonable to let the editor know and –  Giving suggestions for reviewers may be helpful, particularly if the article is in a particular niche Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  26. 26. Conflict-of-interest “A conflict of interest exists when professional judgment concerning a primary interest (such as patients’ welfare or the validity of research) may be influenced by a secondary interest (such as financial gain). Perceptions of conflict of interest are as important as actual conflicts of interest.” (ICJME 2013) Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  27. 27. COI and Pat Buffler In 2010, FMC paid Buffler nearly $200,000 in cash and stock. Securities and Exchange Commission records show that when she sold the stock the company gave her, mostly in 2010, Buffler made more than $2 million. A review of public records shows that in publishing her results in scientific journals or in applying for government funding from the National Institutes of Health, Buffler did not disclose that she owned stock in FMC or served as one of its directors. Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  28. 28. PEER REVIEW
  29. 29. Peer Review: The Ideal •  Evaluation of scholarly work by several peers with appropriate expertise. •  Careful consideration of the comments by an editor who has read the manuscript. •  Transmission of comments and suggestions for revision to the authors. •  Revision followed by acceptance Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  30. 30. Peer Review: The Reality •  There are too many journals and too many papers to be reviewed. •  Typically, editors struggle to identify peer reviewers. •  Peer reviewers may not do their jobs well. •  Comments from editors may be limited and give too little guidance. Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  31. 31. Peer Review Comments •  General comments: – Significance of the findings – Methodological issues – Generalizability – Links to other studies – Implications Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  32. 32. Peer Review Comments •  Specific comments: – The gamut – Minor editorial stuff – Points of disagreement – Methodological fine points – Errors Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  33. 33. Things I Say •  Important and makes a contribution (unimportant and repetitive) •  Substantive methodological concerns (give it up) •  Additional analyses needed (data are not well analyzed) •  Findings over-interpreted (Not much here —but!) Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  34. 34. Things that annoy me! •  Most annoying: priority claims (This is the first study of______ or whatever). •  Excessive reliance on statistical significance. •  Failure to discuss limitations and generalizability. •  Silly discussions of implications of findings. •  MRIN (more research is needed) Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  35. 35. Comments to the editor •  Not much new here (hint: reject) •  Fundamental problems with the data (hint: be careful) •  Much needed to make this ready for publication (hint: be careful) •  Writing needs careful editing (hint: this manuscript needs a rescue mission) •  New findings and well written (hint: accept!) Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  36. 36. An example of my review: Obstructive sleep apnea and systemic hypertension FIRST REVIEW
  37. 37. An example of my review: Obstructive sleep apnea and systemic hypertension SECOND REVIEW
  38. 38. An example of my review: Obstructive sleep apnea and systemic hypertension THIRD (AND FINAL) REVIEW
  39. 39. Another example of my review: Chlamydia pneumoniae and asthma
  40. 40. Another example of my review (cont.): Chlamydia pneumoniae and asthma
  41. 41. COMMENTS AND LETTERS FROM THE EDITOR
  42. 42. What I do as editor •  Initially scan the manuscript to find reviewers. •  When comments come, carefully read them and go back to the manuscript and read carefully. •  Make a decision and justify it in the letter. •  If revision, the letter highlights the points that must be addressed. Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  43. 43. Letter from the Editor •  Should provide a roadmap for interpreting the comments. •  Provide an indication of those comments that are most critical. •  Address conflicting comments. •  Provide the editor’s own insights. Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  44. 44. Responding to Comments •  •  •  •  •  •  Stay calm and be respectful. Express gratitude/thanks. Do NOT be combative, even if justified. Respond to every comment systematically. Provide analyses to support responses. Accept minor comments unless wrong to show your responsiveness. Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  45. 45. Responses to Comments •  Respond to each comment, identified in some systematic way. •  Embed responses into comments. •  Provide additional analyses and tables, and consider use of supplement to address concerns. Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  46. 46. Example #1: Response to Review – Smoking and TB
  47. 47. Example #1: Manuscript Revision – Smoking and TB 48
  48. 48. Example #2: Response to Review – Smoking and DM
  49. 49. Example #2: Manuscript Revision – Smoking and DM 50
  50. 50. Example #2: Manuscript Revision – Smoking and DM
  51. 51. What to do if rejected! •  Don’t take it personally. •  Do not call the editor or send an email (generally). •  Look through the comments—take advantage of the review. •  Quickly set out a strategy for revision and submission elsewhere. •  Remember that rejection happens to great work. Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  52. 52. Why would your manuscript be rejected? •  Not notable or newsworthy: the “big journals.” •  Not novel: any journal. •  Not well done: any journal. •  Not well written: any journal. •  Badly written: any journal. Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  53. 53. LETTERS TO THE EDITOR (FROM READERS OF ARTICLE)
  54. 54. Samet, Straif, Schuz, Saracci. Epidemiology 2014;25:23-7
  55. 55. Letters to the Editor Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  56. 56. Letters to the Editor – Author’s Response Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  57. 57. Letters to the Editor – Author’s Response (cont.) Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  58. 58. Exercises Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  59. 59. You receive the following comments on your manuscript. Write responses: Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  60. 60. 1. While the study findings are of interest, the generalizability of these findings based on Hispanic patients at LAC, is uncertain. Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  61. 61. 2. This is an elegant experimental model of addiction. However, I hardly see any relevance to alcoholism in people. Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  62. 62. 3. The main finding, increased risk for diabetes in those drinking more coffee is of interest (RR = 1.8, 95% CI 0.98-2.70) but the p-value (p=0.06) is not significant. Southern California Clinical and Translational Science Institute Translating Science into Solutions for Better Health
  63. 63. GENERAL RESOURCES
  64. 64. http://www.icmje.org/
  65. 65. http://www.equator-network.org/reporting-guidelines/

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