How to write and publish research - a one day workshop held by Ahmed Negida on 20/07/2016 for undergraduate and postgraduate researchers.

1. Ahmed Said Negida
Faculty of Medicine, Zagazig University, Egypt
School of Medicine, Liverpool University, UK
Founder and Chairman of Medical Research Group of Egypt
How to write and
publish research
An interactive, extensive, one-day workshop

2. 1. Structure of the research paper
2. Golden Rules of scientific writing
3. Common Errors in scientific writing with examples
4. Tips to make a world-class research paper
5. How to write a conference abstract
6. How to select a suitable journal
7. Flow of the publication process
8. How to address reviewers' comments
Learning Objectives

3. Session no.1
Structure of
Scientific Research
Paper

4. IMRaD
1. Introduction
2. Methods
3. Results
4. Discussion
1. Structure of research paper
Abstract
Text
Appendices
References

5. Manuscript text (IMRaD)
Exceptions
• Case report
• Case Series
• Literature Review
• View Point
• Editorial
• Letter to Editor
INTRODUCTION
METHODS
RESULTS
DISCUSSION

6. • What we know
• What we do not know
(Gap of Knowledge)
• Aim of this work
INTRODUCTION

7. METHODS
1. Study design (How?)
2. Where?
3. When?
4. Population
5. Inclusion/Exclusion
6. Sampling
7. Sample size
8. Intervention/Condition being observed
9. Outcome measurement
10. Data collection
11. Data entry
12. Statistical analysis

8. • Descriptive statistics
• Univariate analysis
• Bivariate analysis
• Multivariate analysis
• Figures, charts and captured images
RESULTS

9. DISCUSSION
• Interpretation of results
• Are results statistically significant?
• Are results clinically significant?
• Give possible justifications
(why drug X was better than drug Y?)
• What did previous studies
concluded about this topic?
• Is your study in accordance with
previous studies?
• If not, justify this contradiction
• Study strength points
• Study limitations
• Generalizability
• Implications for clinical practice
• Implications for future researchers
• Final conclusion

11. Session no.2
Rules of Scientific Writing

12. • Put actions in verbs
• Put characters in subjects
• Keep subjects near verbs
• Put new information last
• Use active voice
• Make sure the first and last sentences of a paragraph match
• Omit needless words
• Prefer simple words
• Use simple subjects

13. • Use short sentences
• When starting the sentence, don't overdo using “But” or “And”. “But” has become
quite acceptable; 'And' less so.
• Always try to put the words that relate to one another as close together as possible.
• Use common, everyday words rather than obscure or complex words.

14. Rules for reporting numbers
• Numbers less than 10 are words.
• Number 10 or more are numbers.
• Words not numbers begin a sentence.
• Be consistent in lists of numbers.
• Numbers less than 1 begins with a zero.
• Do not use a space between numbers and its percent sign.

15. • Use one space between a number and its unit.
• Report percentages to only one decimal place if the sample size is larger than 100.
• Do not use decimal places if the sample size is less than 100.
• Do not use percentage if the sample size is less than 20.
• Do not imply greater precision than your measurement instrument.
• For ranges use "to" or a comma but not "-" to avoid confusion with the minus sign and
use the same number of decimal places as the summary statistic.
• Rules for data numbers do not apply to citations to the literature.

16. The decision to begin the treatment regimen requires certain prerequisites, one of the most
important is the determination of liver fibrosis stage by pathological examination of a liver
tissue sample which remain the gold standard to evaluate the stage of liver fibrosis (3,4).
Determining the stage of live fibrosis is a prerequisite to start the treatment regimen. Till
the moment, pathological examination of a liver tissue is the gold standard method to
determine the stage of fibrosis.

17. Session no.3
Common Errors in
scientific writing

18. Avoid Long Phrases

19. Parallel Sentences

20. Omit Needless Words

21. Creating a flow between sentences

22. Avoid Repetition

23. Sneaky Plurals

24. Avoid Gender Specific Pronouns

25. Use because to mean "because"

26. Correct use of Verbs

27. TENSES
Introduction
 Present: to refer to present
evidence
 Past: to refer to previous studies,
aim and hypothesis
 It is known that ….
 Therefore, we investigated …
Methods  Past  Patients were recruited, …
Results
 Past for results
 Present for referring to tables or
figures
 We found that…
 Figure x shows..
Discussion
 Present to answer the research
question
 Present to discuss the literature
 Past to discuss the results
 Our findings suggest..
 Evidence from previous studies
shows…
 We found that …

28. Session no.4
Tips to make a world-
class research paper

29. .. Before it is too late ..
• Clear / Novel / Interesting .. Why?Research Question
• Study Design: Prospective or retrospective?
• Sample Size? Sampling method? Randomization?
• Outcome measure – standard?
Design
• Errors in implementation? Non-response? Loss of
follow up?Implementation
• Correct English Language use
• Well-structured, clear, manuscript
Writing

30. Follow the Standard Reporting Guidelines
Standard guidelines for reporting research studies have been
developed and undergo acronyms such as CONSORT, MOOSE,
QUOROM, STRAD, STROBE and PRISMA. Highly ranking
journals in addition to the International Committee of Medical
Journal Editors (ICMJEs) recommends standard reporting of
research studies according to these guidelines.
When you start writing

31. http://www.equator-network.org/

32. Session no.5
How to write
a good abstract

33. ABSTRACT = ‫الملـخص‬
Conference Submission
Indexing in databases
Subscription Journals (non-OA)
For readers: Get quick overview
Why is abstract
important?

34. • Identify the main issue of your paper
• Begin with the subject of your paper
• Accurate, unambiguous, specific, and complete
• Do not contain abbreviations
• Attract readers
Criteria of a good title

35. Types of titles

36. ABSTRACT Structure
• Introduction
• Methods
• Results
• Conclusion
• Aim (Purpose)
• Methods
• Results
• Conclusion
• Context
• Evidence Aquatisation
• Results
• Conclusion
NOT structured
(one single paragraph)

37. ABSTRACT: Introduction
Sentence no 3
Aim of this study
Sentence no 2
A more specific sentence about the Factor/Agent
Sentence no 1
About the General Topic/Disease/Condition

38. ABSTRACT: Methods
The methods section of the abstract should describe the study
design, who was studied, what you measured, and how you
analyzed the data. If it matters, you should mention where the
subjects came from and how they were selected. Specify the
number of subjects, by group if appropriate. All important
measurement techniques should be described.
You can leave out obvious methods (‘‘Subjects were asked their
age and sex’’), as well as intricate details, unless they absolutely
matter.

39. ABSTRACT: Results
• Make sure you emphasize the main finding of the study.
• Concentrate on various aspects of that single result, such as the
effects of adjusting for potential confounders, of using
alternative definitions, or of looking for dose-response effects.
• It is better to be profound/deep than broad-based.
• Do not just present P values, F statistics, or regression
coefficients. Make sure your effect size is clear.
• State your key results in words, followed by the numbers.

40. ABSTRACT: Results
For example, suppose you find that hypertensive patients who take calcium
channel blockers are more likely to have strokes. It is more important to present
your results by type of calcium channel blocker (long-acting vs. short-acting) and by
type of stroke (ischemic vs. hemorrhagic), and to show that patients taking other
antihypertensive medications did not have an increased risk, than to present
extraneous data with small P values such as the finding that ‘‘patients who took
diuretic medications had more gallstones (P<0.01).’’
For example:
‘‘Patients treated with Gentamycin were nearly twice as likely to require dialysis as
those treated with other aminoglycosides (20% vs. 11%; RR=1.9; 95% CI=1.3 – 2.8).’’

41. ABSTRACT: Results

42. ABSTRACT: Results

43. ABSTRACT: Conclusion
• Do not repeat the results in slightly different words, or make
superfluous declarations such as ‘‘These results may have clinical
importance,’’ ‘‘Our results should be confirmed by other investigators,’’ ‘‘Our
findings support our hypothesis,’’ or ‘‘Further research is needed.’’
• Make a reasonable statement about the implications of your results.
• If the results have, or may have, clinical meaning, then say how.
• If another study is needed, then state what sort of study it should be.

44. Fitting abstracts into space

45. Fitting abstracts into space

46. Fitting abstracts into space

47. Fitting abstracts into space
Last choice: Delete sentences
(irrelevant to conclusions or appear several times)

48. Writing
Abstract
It is your turn now!

49. Why Abstracts are rejected
1.Dull topic (not interesting or a lot of previous research)
2.Small Sample Size
3.All numbers, No talk
4.All talk, No numbers
5.Too short
6.Too many abbreviations and too much data
7.Sentences that invite rejection
8.Many P values; Less focus on effect sizes
9.Overuse of Respectively

50. Sentences that invite rejection
There are two phrases that will almost always result
in your abstract being rejected: ‘‘Data will be
presented’’ and ‘‘Results will be discussed.’’
Never include either of these phrases in an abstract
unless you have been invited to make a presentation
at the meeting and were asked to submit an abstract
for the audience’s benefit.

51. What is different colleagues want to
present the same abstract?
Dishonest behavior …

52. Session no.6
Scientific
Publication

53. Draft Manuscript Paper
Revision/Polishing Peer-review
Authors Journal

54. Publication
Conference
National
International
Journal
Peer-reviewed
Predatory
ABSTRACT
FULL TEXT

55. Vancouver guidelines for authorship
The (ICMJEs) stated that each author should have participated
sufficiently in the work to take full responsibility of the content.
Substantial
contributions
Drafting the
article and
revising it
critically
Final approval
of the version
to be
published.

56. Editors may ask authors to justify
authorship and state contributions
of each author.

57. Acknowledgment = ‫عرفان‬ ‫و‬ ‫شكر‬
 General support by a department head or an institution
 Technical help, laboratory work, and data collection
 Input of students, trainees, and research assistants
 Provision of clinical details of patients
 Statistical, graphics, or library support
 Critical review of the drafts
 Financial support from granting bodies, drug companies etc.
 Financial interests that may pose a conflict of interest

58. UNIFORM REQUIREMENTS
Use double spacing
throughout the
manuscript

59. UNIFORM REQUIREMENTS
Pages should have margins at least 25 mm and be numbered

60. UNIFORM REQUIREMENTS
Follow the sequence of title page, abstract, keywords, text,
acknowledgements, references, tables, legends to figures.
Title
page
Abstract
And
Keywords
Text
Acknowledgement
Conflict of interest
Funding
References
Tables
Figures’
Legends

61. UNIFORM REQUIREMENTS
Title page should include
(title, short running title, funding,
authors, affiliation, correspondence)
Title
Short running title
Authors
Affiliation
Correspondence

62. UNIFORM REQUIREMENTS
Text (Introduction, Methods, Results and Discussion)
Introduction Methods Results Discussion

63. UNIFORM REQUIREMENTS
Begin each section
on a new page
Each table should
be on a new page

64. UNIFORM REQUIREMENTS
• Get permission to reproduce previously published materials.
• Enclose a transfer of copyright.
• Keep an exact copy of everything submitted.

65. Session no.7
Flow of the
publication
process

66. Submitted
Check for Journal
requirements
Check for Quality + meeting
the Journal scope
Revise the manuscript
Author
Editor Assistant
Editor in Chief
Reviewer(s)
COMMENTS
Take Decision
Send Decision email
FLOW OF THE PUBLICATION PROCESS (Brief summary)

67. Notify the publishing editor
Put manuscript into Journal
template – For publication
Send to author to check for
errors during processing
Editor Assistant
Publication Editor
Author
Author comments/Revisions
After Acceptance of your manuscript
Uncorrected proof

68. Session no.6
Selecting
Suitable Journal

69. Four methods to select a Journal for publication
1- Asking an Expert co-worker/colleagues
2- Look at references of your manuscript
3- Search PubMed using your keywords
4- Using Journal Finder tool at Elsevier and BMC

70. Ask a colleague to have a look on the
quality of the manuscript, then list
relevant journals in three groups
Likely to accept
(>60%)
Realistic Possibility
(10%-60%)
Less Likely
(<10%)
If you are in a hurry,
submit to a journal from
(Likely to accept >60%)
category. Otherwise,
submit to journals of
Realistic Possibility.

71. 1. Search PubMed using your keywords
2. Limit results to your publication type
3. Arrange results alphabetically
By visual inspection, you can identify the most
frequent journals (the most relevant)
If there are so much results, export them to
excel file and present the frequency of journals
graphically. Select the most relevant ones.

76. What should you do after
selecting a Suitable Journal?

77. Instructions for Authors
Go to
Guidelines for Author

78. Instructions for Authors

79. Title Title length
Title page
Requirements?
Remove authors’ names?
Conflict of interest statement?
Length of manuscript?
Number of tables?
Number of figures?
Source of Funding
Abstract page
Structured? One paragraph?
Maximum words?
Keywords?

80. Manuscript TXT
Structure?
Length?
Font?
Spaces?
Numbering of pages?
Tables
Separated?
Within text?
In End of manuscript?
Figures
File type?
Legends?
In text? Or Separate? Or both?

81. References
Style?
Maximum number of references?
Additional
Conflict of interest form?
Conflict of interest statement?
Agreement on publication form?
Copyright transfer form
Acknowledgement?
Authors contributions?

82. • Go to the Submission system
• Start submitting your manuscript
• Upload the files and manuscript details
! COVER LETTER?
Recommend Reviewer?

83. How to get recommended reviewers
- Go to PUBMED
- Search with Keywords
- Fine most relevant articles
- Select authors of these articles
- Get their information email/affiliation
Usually the Journal editor select one of the recommended
reviewers and one additional reviewer from the Journal database

84. COVER LETTER
Correspondence details
Dear Editor,
We are sending you the manuscript entitled: ….
What have you done in this paper?
Strength points
Key conclusions
• All authors meet ICMJE criteria and agree on this
publication.
• This work has not been published before (in whole
or in part).
• This paper is not being considered elsewhere.
Check our examples

85. Peer-Review
Blinded Unblinded
One, Two, Three reviewers might evaluate your paper
ACCORDING TO JOURNAL POLICY

86. Peer-Review
Reviewers do NOT accept/reject manuscript
They Revise + Recommend a decision for the Editor
Reviewer states
- Strength points
- Week points
- Methodological limitations?
- Statistical errors?
- Scientific writing errors?

87. Peer-Review
Authors have the right to “decline revision” if they believe
reviewer comments are not realistic/ will make undesirable
substantial changes in the results? Conclusions?
- Weak points in the methodology >> Usually your paper will be rejected
- Weak points in writing? Can be corrected? Can be revised? A figure to
improve/add? Additional analysis to consider? Checking manuscript language?
>> Acceptance after Revision

88. Is acceptable for publication
Is acceptable for publication following minor revisions
Is acceptable for publication following major revision
May be reconsidered for publication following major revisions
May be considered for publication as a letter or a short report
Is unacceptable for publication
EDITORIAL
DECISIONS

89. Session no.8
How to address
reviewer
comments

90. It is NORMAL that your work be criticized by other peers in the field
Be Calm and Objective
Deconstruct each message into individual items
that you can handle and respond to

91. Try to make the majority of changes requested
Try carefully to negotiate the radical points ??

92. Editors take it seriously!
Do NOT ignore any of the reviewer comments

93. - Make your responses VERY CLEAR and VERY SIMPLE. Why?
- It is time to get the editorial panel on your side ! And persuade
them with your work ! So, simplify it ..
- Take a positive attitude ! -> Why?
- Try to make a table for responses ..
- This will help you organize your thoughts and responses!

94. Number Comment Location Amendment/ Response
1 xxx Page no . xx We added ….
2

95. You do not have to accept all changes
But you need to give reasons to
convince the editor that your situation
is reasonable

96. Always be POLITE
Even if the reviewer is not correct

97. Additional Notes

98. Summary of Important Terms
• Draft
• Manuscript
• Paper
• Article
• Author
• Co-author
• First Author
• Senior Author
• Corresponding Author
• Referee/Reviewer
• Editor
• Editorial Office
• Reference
• Citation
• Impact Factor
• H-Index
• Reference
• In Press (Online First)
• Issue
• Volume
• Copyright transfer
• Conflict of interest
• Funder
• Sponsor
• Reprint
• Peer-review
• Predatory
• Retraction of publication
• Article Processing Charges
• Publication fee
• Open Access Journal
• Non-OA Journal
• Indexing
• Digital Object Identifier

99. Importance of IRB approval
Protect Research Subjects
Protect Investigators
Protect your research idea (registry ID)
Essential for International Publication

100. How much does a study protocol
differs from the final manuscript
Protocol Research Paper
Scientific Rational +++ +
Aims and objectives +++ +
Ethics “How you protected
research subjects”
+++ +
Timeline/Budget +++ -
Results - +