1. Scientific Writing: A step forward
Arash Etemadi, MD
Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences

2. Why Writing Is Important?
No publication, no project
Make information available for others
No publication, no promotion
Yardstick of productivity
No publication, no funding
What have you done for me lately?

3. Intrinsic Causes of Writing Problems
Internal Censors
Fears of Failure
Perfectionism
Procrastination

4. Intrinsic Blocks to Writing (I) Inability to Start Writing
“First, there is the difficulty of writing at all”
D. Brande Becoming a Writer
Perfectionism, self-consciousness, procrastination

5. How to Start Daily 30 minutes to one hour
Do not pay attention to structure, grammar, spelling

6. Stimulus Control Few regular places to work Close the door
Unplug the phone No
Arrange the site
But do not clean up the office

7. (II) Inability to Finish Writing
Multiple revisions
Multiple analyses
“Each time I think I am finished, I see there is a lot more to do”
Similar roots as inability to start (perfectionism)
Different people
Lack of insight

8. TUMS workshops on scientific writing
Level 1: Basics
Level 2: Focus on international publications
Level 3: Specialized writing

9. An overview

10. The traditional IMRaD
Introduction
Metods
Results
Discussion

11. A full paper consists of:
Title
Authors and Affiliation
Abstract
Introduction
Methods
Results
Discussion
Acknowledgments (optional)
References

12. Target your paper at a particular journal
Familiarise yourself thoroughly with potential journals
what sort of papers do they publish? (original articles, briefs, reviews, commentaries, iconoclastic pieces?)
What is the “culture” of the journal?
National or international focus?
Write for that journal

13. If for a general medical journal..
Mostly read by clinicians, so “practical”, useful, papers highly regarded.

14. If a specialist journal...
Cut to the chase!
Do not waste time with elementary ABC introductory sections -- it is being read by people who know the field
locate your paper precisely in what has gone before

15. Design well
Decide politics
Choose journal
Read instructions to authors/papers
Set framework
Prepare drafts
Distribute
Polish
Submit

16. What is the gestational period for a clinical science publication?
START
PROTOCOL/IRB 2-4 months
STUDIES/
EXPERIMENTS
4-24 months
WRITE AND
SUBMIT
14-44
Months!
2-4 months
REWRITE AND
RESUBMIT
2-4 months
2-4 months
WAIT
2-4 months
PUBLISHED!
BEST GUESS

17. Order of writing? Results Methods Introduction Discussion Abstract
References

18. Order of writing? Methods Results Introduction Discussion Abstract
References

19. Getting Started Do you have enough data for a manuscript?
Do you have a complete story to tell?
Write a list of the figures and tables that you would include in your paper
Write a brief, skeleton outline of the paper (1-2 pages) and show it, along with the list of figures, to your coworkers and discuss

20. TIPS…. Be enthusiastic about your data and your story
Be sure you convey what “problem” you have addressed in your study
Be sure to describe the area of research you are studying as fascinating and important

21. First Steps Analyze your data critically Do statistical analyses
Prepare figures
make graphs
take photographs, get prints, label
Prepare tables
Be sure your data is internally consistent
Show the final data figures (and tables) to your co-authors for comment

22. Effective Data Presentation
Figures are almost always better than tables
Look at published figures (in papers that have data similar to yours) to get ideas about how to compose graphs, and how to frame and label blots, gels and photomicrographs
Learn how to use graphics programs (Sigma Plot or Excel)
Learn to use Adobe Photoshop
Photomicrographs - color is expensive!

23. Instructions to the Authors
Guidelines for writing the paper
Usually found in January issue of journal
Almost always found on the web site for the journal

24. Mechanics of Writing- Title, Abstract and Introduction
Title- be as specific as possible; include design
Abstract is a summary of the paper (therefore write last); check for a word limit; structure it.
Introduction – Importance, a brief review of the literature, information gaps, statement of hypothesis
Introduction- about 3 to 4 paragraphs

25. Mechanics of Writing - Methods
Use subheadings to organize
Details - use sufficient detail for another investigator to be able to reproduce your results
Reference methods used previously
Be precise with respect to measurements and definitions
Statistics

26. Mechanics of Writing-Results
Tell a story
Use the most logical sequence to present the data (not necessarily the order in which you did the experiments)
Just report the data - do not include interpretation or comparison to literature
No duplication of data

27. Guidelines for Writing Results - The Study as it was Conducted
Specify the dates of the study
Provide a schematic summary
Describe the characteristics of each group
Indicate if the sample is representative
Indicate if randomization was successful
Describe duration and nature of follow up
For observations based on judgment, provide assessment of consistency

28. Guidelines for Writing Results: The Study Outcomes
Present the results for all primary endpoints
Report statistical findings in detail
Report actual p values , 95% CI , etc.
Report the main findings in figures or tables
- you don’t need to also report them in the text
Report confounders

29. Mechanics of Writing- Discussion
Construct parallel to results
Interpretation of data
Relate your results to the findings of other investigators
Summary paragraph at end - include significance of results
Avoid redundancy with results and introduction sections

30. Good discussions--- Address every key finding of the study
Present the finding in terms of what is known
State why this study is different
State why the results concur/ disagree with current knowledge
Justify differences
Point out future directions/ continued knowledge gaps

31. References Aim for about 30 references
Use recent review papers where appropriate to decrease the number
Get a hard copy of every reference in the manuscript and make sure the referenced paper says what you say it does! Don’t use abstracts!
Proof-read the reference list especially carefully as one of your reviewers may be cited!
Use End Note or other bibliographic software
Use the Internet

32. A Few Rules The first time you use an abbreviation, define it
When you give the commercial source for a reagent, the first time you cite the source include the location of the company (city and state)
Make sure the subject and verb agree in every sentence
No contrac. or exclamation points!

33. A Few Rules - continued Look for redundancy within the manuscript
Try not to use “it” or “they” - be specific!
No jargon
Two shorter sentences are frequently much more effective than a long, complex sentence
“Data” is plural not singular, i.e., “the data are…” NOT “ the data is…”

34. A Few Rules - continued
Capitalize people’s names, i.e., Golgi apparatus
Never, ever plagiarize! (even from yourself!)
Use numbers when expressing measurements, except when the number would begin a sentence

35. Common Errors in Manuscripts
The Title
is misleading/ does not set limits
Gives away the punch line
The Abstract
reports different measures/ methods
results are not the same as the paper
conclusions are not the same

36. The Introduction
question, hypothesis, study objectives are not specified, or are confused
importance, novelty, originality of the study not shown
presentation is not intriguing
(ie, the introduction is boring)

37. The Methods
Probably the most important section
reported methods not used
details are missing so you cannot understand
entire methods are omitted

38. Common Errors When Reporting RESULTS
Errors of Omission:
Not accounting for all study subjects
Not naming which statistical tests were used for specific analyses
Not presenting the results in clinically relevant terms

39. Errors in the Analysis
Lack of power
Failure to adjust for multiple comparisons
Analysis by treatment received and not by intention to treat
Errors in Interpretation
Not recognizing the limits/meaning of p
Clinical significance ignored in the face of statistics

40. The Discussion
logic is loose
is too expansive, wanders
is biased, omits key findings
key results are poorly explained
references are outdated
speculation is not identified
implications/ importance are overstated
limitations are not described

41. The Conclusions
simply restate the results
do not answer the study question
do not set limits for application

42. General Tips Just START !! Follow the instructions for authors
Apply research analytical principles
Adhere to scientific and writing ethics
Be patient - centered and not numbers centered
Write with vigor and write vividly

43. General Tips Write for readers and not to please peer reviews
- readers read to learn; reviewers, to improve
Avoid self plagiarism
Update the literature review
Have a clinical colleague read your draft
Seek out criticism

44. More reading
Hall GM, ed. How to write a paper. London: BMJ Publishing Group.
Peat J. Scientific Writing Easy when you know how. BMJ Publishing Group
The Vancouver Group. Uniform requirements for manuscripts submitted to biomedial journals

45. Finding and choosing an appropriate journal
Where to look for the journal:
Personal experience
Colleagues’ experience
Library
Citations
Online

46. Appropriate Journal General versus Specialty
International versus Local
High versus Low impact
LOOK AT THE JOURNAL
LOOK AT THE AUDIENCE

47. 1. What type of paper you wrote ?
research report (“original article”)
review paper
special article
editorial
case report
letter to the editor

48. 2. Is the paper really worth being published?
Is the message new, or new to a particular audience?
Search the literature to make sure you are not repeating history ++
Determine the odds that a particular journal will appreciate the newness and importance of your manuscript in the context of the existing medical literature

49. 3. Be realistic
This is your first manuscript or you have already a real track of publications on the topic ?
Are the co-authors or the Institution were you are based recognized in the field ?
Are you an Iranian author submitting to a national, a European or an American journal ?
Reviews are mostly only by invitation but national journals can be quite open

50. 4. Know your journal targets?
Impact factor and prestige
Normal content of one of the journal issues
Which kind of manuscripts are published ?
What are the preferred formats ?
Style and recent trends in the journal
Who is the editor-in-chief ? Can you contact him ?
Who are the members of the editorial-board ? They are very aware of the journal’s publication policy…you can try to contact some of them with questions

51. 1. Impact Factor: Oncology
J Natl Cancer Institute
J of Clinical Oncology
Cancer Research
Clinical Cancer Research
Oncogene
Gene Chromosome Cancer
Int Jrnl Cancer
Cancer
Annals of Oncology

52. 2. Normal content of the journal ?
Is the topic within the scope of the journal?
Is the topic represented in the journal frequently, or only rarely?
Would the journal offer the best match of audience and topic?
What formats are acceptable to the journal?

53. 3. Style and recent trends
Do look at a recent issue of the journal you plan to submit to
Do read the Instruction to authors of the journal
(links to 3500 journals’ Instructions at
Be aware of word/figure/table limits
Use the appropriate reference and citation styles
Help Editors and Referees (and yourself) – Number all pages

54. 4. Editor in chief and editorial board
Who is the editor-in-chief ?
If you can contact him, query the editor
be specific
sell your product
Editorial board members?

55. 5. Ask your mentor He may belong to a specific editorial board
He senses new opportunities
Launching of a new journal
Accurate format to sell your product
Provides a more realistic point of view

56. 6. What is your own agenda when publishing ?
Colleagues
Prestige journal vs. rapid publication
National visibility vs international fame
Issues of timeliness and in-depth track do matter

57. 7. Timeliness and friendliness of the submission process
Hot topic?
You can query about the average reviewing time (assistant of the editors)
Is there an online submission process?
Can you track your manuscript status online

58. Target your paper at a particular journal
Familiarise yourself thoroughly with potential journals
what sort of papers do they publish? (original articles, briefs, reviews, commentaries, iconoclastic pieces?)
What is the “culture” of the journal?
National or international focus?
Write for that journal

59. Anatomy of a submission
Compose a title page
determine who is the first author (you) vs. the senior author (last in the list of authors)
Be sure to cite the source of funding for the project

61. Study design and ethical approval
Data analysis
Authorship
Conflicts of interest
Peer review
Redundant publication (and duplicate submission)
Plagiarism and fraud
Dealing with misconduct

63. An “author” is generally considered to be someone who has made substantive intellectual contributions to a published study, and biomedical authorship continues to have important academic, social, and financial implications.
Some journals now request and publish information about the contributions of each person named as having participated in a submitted study, at least for original research.
Editors are strongly encouraged to develop and implement a contributorship policy, as well as a policy on identifying who is responsible for the integrity of the work as a whole (guarantorship).

64. Authorship credit should be based on
1) substantial contributions to conception and design, or acquisition of data, or analysis and interpretation of data;
2) drafting the article or revising it critically for important intellectual content;
and 3) final approval of the version to be published.
Authors should meet conditions 1, 2, and 3.

65. Acquisition of funding, collection of data, or general supervision of the research group, alone, does not justify authorship.
All persons designated as authors should qualify for authorship, and all those who qualify should be listed.
Each author should have participated sufficiently in the work to take public responsibility for appropriate portions of the content.
The order of authorship on the byline should be a joint decision of the co-authors. Authors should be prepared to explain the order in which authors are listed.

66. All contributors who do not meet the criteria for authorship should be listed in an acknowledgments section. Examples of those who might be acknowledged include a person who provided purely technical help, writing assistance, or a department chair who provided only general support. Financial and material support should also be acknowledged.
Groups of persons who have contributed materially to the paper but whose contributions do not justify authorship may be listed under a heading such as “clinical investigators” or “participating investigators”

67. When a large, multi-center group has conducted the work, the group should identify the individuals who accept direct responsibility for the manuscript.
These individuals should fully meet the criteria for authorship defined above.
When submitting a group author manuscript, the corresponding author should clearly indicate the preferred citation and should clearly identify all individual authors as well as the group name.
An example: GEMINI

68. Conflicts of interest
Conflicts of interest comprise those which may not be fully apparent and which may influence the judgment of author, reviewers, and editors.
They have been described as those which, when revealed later, would make a reasonable reader feel misled or deceived.
They may be personal, commercial, political, academic or financial.
“Financial” interests may include employment, research funding, stock or share ownership, payment for lectures or travel, consultancies and company support for staff.

69. (1) Such interests, where relevant, must be declared to editors by researchers, authors, and reviewers.
(2) Editors should also disclose relevant conflicts of interest to their readers. If in doubt, disclose. Sometimes editors may need to withdraw from the review and selection process for the relevant submission.

70. Redundant publication/ duplicate submission
Redundant publication occurs when two or more papers, without full cross reference, share the same hypothesis, data, discussion points, or conclusions.
Duplicate submission is when the same manuscript has been sent to journal while still under evaluation by another.

71. (1) Published studies do not need to be repeated unless further confirmation is required.
(2) Previous publication of an abstract during the proceedings of meetings does not preclude subsequent submission for publication, but full disclosure should be made at the time of submission.
(3) Re-publication of a paper in another language is acceptable, provided that there is full and prominent disclosure of its original source at the time of submission.
(4) At the time of submission, authors should disclose details of related papers, even if in a different language, and similar papers in press.

72. What is fraud? Fabrification: Invention of data or cases
Falsification: Wilful distortion of data
Ignoring outliers?
Not admitting that some data are missing.
Post hoc analyses that are not admitted?
Not including data on side effects in a clinical trial

73. What is fraud? Plagiarism: Copying of data or papers But by how much?
Stealing ideas?
Redundant publication
Gift authorship.
Not attributing other authors.
Not publishing research
Not disclosing a conflict of interest

74. Plagiarism
Plagiarism ranges from the unreferenced use of others’ published and unpublished ideas, including research grant applications to submission under “new” authorship of a complete paper, sometimes in a different language.
It may occur at any stage of planning, research, writing, or publication: it applies to print and electronic versions.
All sources should be disclosed, and if large amounts of other people’s written or illustrative material is to be used, permission must be sought.

75. Dealing with misconduct
(1) The general principle confirming misconduct is intention to cause others to regard as true that which is not true.
(2) The examination of misconduct must therefore focus, not only on the particular act or omission, but also on the intention of the researcher, author, editor, reviewer or publisher involved.
(3) Deception may be by intention, by reckless disregard of possible consequences, or by negligence. It is implicit, therefore, that “best practice” requires complete honesty, with full disclosure.
(4) Codes of practice may raise awareness, but can never be exhaustive.

76. Investigating misconduct
(1) Editors should not simply reject papers that raise questions of misconduct. They are ethically obliged to pursue the case. However, knowing how to investigate and respond to possible cases of misconduct is difficult.
(2) COPE is always willing to advise, but for legal reasons, can only advise on anonymised cases.
(3) It is for the editor to decide what action to take.

77. Serious misconduct
Less serious misconduct
Sanctions, blacklists

78. Feedback Ask your co-authors to read the manuscript critically
Give the paper to informed colleagues (1or 2 max) to read
A real friend will give you lots of ideas for improvement
Read your own paper as if you were a reviewer, with the figures in front of you as you read it

79. Final Preparations for Submission
Proof-read, proof-read, proof-read!
Make sets of figures for submission but also keep a set of original figures for your files
Make copies of the submitted manuscript, including the figures, for every author
Write a cover letter, short and direct, addressed to the editor
Make a list of suggested reviewers, if this is requested by the journal

80. Dr. Michael Holtzman,
American Journal of Respiratory Cell
and Molecular Biology,
Editorial Office
American Thoracic Society
1740 Broadway, New York, NY
Tel
Fax
Dear Dr. Holtzman,
Please find enclosed an original manuscript entitled, “……………………...” by [authors]. The material presented in this paper is original and has not been submitted for publication elsewhere. No part of the research presented in this manuscript has been funded by tobacco industry sources. We verify that all the authors have read the manuscript and approve its submission. To aid the review process, may we suggest the reviewers listed on the following page.
We hope that you will find our manuscript acceptable for publication in the American Journal of Respiratory Cell and Molecular Biology.
Thank you for your attention.
Sincerely
…….
Corresponding author

81. List of Potential Reviewers
1) Dr. Joe Smith
Duke University Medical Center
Cell Biology
438 Nanaline Duke/Box 3709
Durham, NC 27710
Phone:
Fax:
2)Dr. Virginia Jones
Vanderbilt University
Pathology
th Ave S.
Nashville, TN
Phone: X 5499
Fax:
3)Dr. Tony D. Soprano
Southampton General Hospital
Child Health
Level G (803) Center Block
Tremona Rd.
Southampton, SO16 6YD United Kingdom
Phone:
Fax:
4) Dr. David Mitchell
Department of Pediatrics
Milton S. Hershey Medical Center
H085 Hospital
Hershey, PA 17033
Phone:
Fax:
5)Dr. Arnold Smith
University of Missouri-Columbia
Department of Molecular Microbiology and Immunology
M616 Medical Sciences Building DC 04400
Columbia, MO 65212
Phone:
Fax:

82. COVERING LETTER Polite Why Journal chosen Importance of paper
Concessions
Brief

83. Submitting the Paper Frequently done on-line via PDF files
If required, send the number of hard copies of the manuscript and figures required by the journal
Send a disk with files for the manuscript and figures, if required
Get the copyright form used by the journal signed by all authors, if required
Send all of this material by a reliable method, so that your precious manuscript is not lost in the mail!!

84. Peer review
Articles submitted to peer-reviewed journals (manuscripts) are reviewed by experts who advise the editor on whether they should be published and what changes are necessary.

85. Editorial decision Accepted as it is (rare)
Accepted on the condition of certain amendments (back to cycle)
Reconsidered if reviewers’ comments met (back to cycle)
Rejected

86. Peer Review - Functions To Protect i) The author from publishing & ii) The subscriber from reading Material of insufficient quality

87. Problems with peer review
Slow
Expensive
A lottery
Ineffective
Biased
Easily abused
Can’t detect fraud
Works for improving studies not selecting which to publish

88. Dealing with the Journal’s Response
Absolute Rejection
Don’t take it personal
Don’t write or call the editors (unless you know them well !)
Editorial rejection: send it out the next day to another journal
Reviewers comments:
Fix the easy ones
Fix the glaring ones
Unlikely to get much better sitting on your desk
Send it out the next day

89. Dealing with the Journal’s Response
Conditional acceptance (rejection)
It is yours to lose
First cool down (24-48 hours)
Within 1-2 weeks decide on responses
Make real changes, say you have done great changes (describe, highlight,etc)
Look for clues from the editor as to the extent of the revision needed.
Avoid arguments
Thank sincerely, but avoid being obsequious

90. Responding to reviews Swallow your pride!
You don’t have to accept all, but don’t over-reject
Ask editor about conflicting comments
However unreasonable the reviewers may seem: be polite!
Distinguish conditional acceptance from offer to reconsider (and from rejection of course!)
Appeals (for rejection)

91. Resubmission Letter Dr. Brian F. McCabe
Editor, Annals of Otology, Rhinology and Laryngology
Department of Otolaryngology-Head and Neck Surgery
The University of Iowa Hospitals and Clinics
Iowa City, IA 52242
Dear Dr. McCabe,
Please find enclosed a revised manuscript entitled, "Surfactant protein A in rabbit sinus and middle ear mucosa" by……….
We have addressed the comments of the reviewers as detailed below:
1)We have changed the title of the paper as suggested by the reviewer.
2)We have expanded the description of the animals used in the study (page 4, paragraph 1). All the animals except the pathogen-free, were naturally infected with Pasteurella multocida. The antibiotic treated animals were chosen randomly. The infections were observed postmortem and pathogen was identified by culture by the Animal Care Unit.
3)The lengths of the micron bars in Figures 5-8 have been added to the legends. A magnification bar has been added to Figure 10.
We hope that you will now find our manuscript suitable for publication in the Annals of Otology, Rhinology and Laryngology. Thank you very much for your prompt review.
Sincerely,