This was the presentation of (How to write a biomedical research day workshop) given by Ahmed Negida as a part from MRGE continuous research activities in Egypt. The course was joined by 45 medical students and seniors from different Egyptian Universities and it was more than 6 hours of exciting learning activities. Major Learning Objectives were: 1- Structure of biomedical Research Paper 2- How to Write a conference Abstract 3- Scientific Writing Rules 4- Research Protocol 5- Referencing Using Mendeley software 6- Scientific Publication

1. Ahmed Said Negida
Faculty of Medicine, Zagazig University
Founder and Chairman of Medical Research Group of Egypt
How to write a Biomedical
Research Paper
An interactive, extensive, one-day workshop

2. 1. Structure of biomedical research papers
2. How to write a conference abstract
3. Scientific writing rules
4. Research Protocols
5. Referencing using Mendeley
6. Scientific Publication
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
How to write
a conference
abstract

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

13. • 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

14. Types of titles

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

16. 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

17. 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.

18. 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.

19. 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).’’

20. ABSTRACT: Results

21. ABSTRACT: Results

22. 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.

23. Fitting abstracts into space

24. Fitting abstracts into space

25. Fitting abstracts into space

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

27. Writing
Abstract
It is your turn now!

28. Write an Abstract for the following titles
Caffeine for patients with Parkinson’s disease: A Phase III,
Randomized, Double Blind, Placebo Controlled Trial of
Neuroprotective effects of c-ABL inhibitors in MPTP induced
mouse model of Parkinson’s disease
PARK 20 gene polymorphism is associated with increased risk of
Parkinson’s disease: A Case control study in Cairo

29. 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

30. 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.

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

32. Session no.3
Scientific Writing
Rules

33. 3- Scientific Writing Rules
• 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

34. • 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.

35. 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.

36. • 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.

37. 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.

38. Avoid Long Phrases

39. Parallel Sentences

40. Omit Needless Words

41. Creating a flow between sentences

42. Avoid Repetition

43. Sneaky Plurals

44. Avoid Gender Specific Pronouns

45. Use because to mean "because"

46. Correct use of Verbs

47. 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 …

48. 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.

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

50. Session no.4
Research
Protocols

51. 4- Research Protocol
Protocol vs. proposal

52. Importance of study protocol
 Enhances the scientific integrity
 Providing a better study documentation, efficiency, and communications.
 Ethical approval (IRB or Ethics Committee)
 Applying to a funding agency “Proposal”.
 International Registration

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

54. 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 - +

55. Parts of Research Protocol (WHO template)

62. Session no.5
Referencing
Using
Mendeley

63. Separate
Presentation

64. Mendeley
workshop
It is your turn now!

65. File 1
• Cite the paper of
Baratloo et al in the
text using AMA style.
• Change to
(Harvard style)
File 2
• Open the printed handouts
page no.4.
• Write the paragraph of
“Current Treatments of
Migraine”
– All reference files are
available and numbered (x5
to x12) in different file
formats.
File 3
• Change to
(Harvard Style)
• Change to (Vancouver
style)
• Alter the two
paragraphs

66. Session no.6
Scientific
Publication

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

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

69. 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.

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

71. 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

72. UNIFORM REQUIREMENTS
Use double spacing
throughout the
manuscript

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

74. 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

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

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

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

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

79. 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

80. 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.

81. 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.

86. 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

87. 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

88. 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
• Direct Object Identifier