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Ahmed Said Negida
Faculty of Medicine, Zagazig University
Founder and Chairman of Medical Research Group of Egypt
How to w...
1. Structure of biomedical research papers
2. How to write a conference abstract
3. Scientific writing rules
4. Research P...
Session no.1
Structure of
Scientific Research
Paper
IMRaD
1. Introduction
2. Methods
3. Results
4. Discussion
1. Structure of research paper
Abstract
Text
Appendices
Referenc...
Manuscript text (IMRaD)
Exceptions
• Case report
• Case Series
• Literature Review
• View Point
• Editorial
• Letter to Ed...
• What we know
• What we do not know
(Gap of Knowledge)
• Aim of this work
INTRODUCTION
METHODS
1. Study design (How?)
2. Where?
3. When?
4. Population
5. Inclusion/Exclusion
6. Sampling
7. Sample size
8. Inter...
• Descriptive statistics
• Univariate analysis
• Bivariate analysis
• Multivariate analysis
• Figures, charts and captured...
DISCUSSION
• Interpretation of results
• Are results statistically significant?
• Are results clinically significant?
• Gi...
Session no.2
How to write
a conference
abstract
ABSTRACT = ‫الملـخص‬
Conference Submission
Indexing in databases
Subscription Journals (non-OA)
For readers: Get quick ove...
• Identify the main issue of your paper
• Begin with the subject of your paper
• Accurate, unambiguous, specific, and comp...
Types of titles
ABSTRACT Structure
• Introduction
• Methods
• Results
• Conclusion
• Aim (Purpose)
• Methods
• Results
• Conclusion
• Cont...
ABSTRACT: Introduction
Sentence no 3
Aim of this study
Sentence no 2
A more specific sentence about the Factor/Agent
Sente...
ABSTRACT: Methods
The methods section of the abstract should describe the study
design, who was studied, what you measured...
ABSTRACT: Results
• Make sure you emphasize the main finding of the study.
• Concentrate on various aspects of that single...
ABSTRACT: Results
For example, suppose you find that hypertensive patients who take calcium
channel blockers are more like...
ABSTRACT: Results
ABSTRACT: Results
ABSTRACT: Conclusion
• Do not repeat the results in slightly different words, or make
superfluous declarations such as ‘‘T...
Fitting abstracts into space
Fitting abstracts into space
Fitting abstracts into space
Fitting abstracts into space
Last choice: Delete sentences
(irrelevant to conclusions or appear several times)
Writing
Abstract
It is your turn now!
Write an Abstract for the following titles
Caffeine for patients with Parkinson’s disease: A Phase III,
Randomized, Double...
Why Abstracts are rejected
1.Dull topic (not interesting or a lot of previous research)
2.Small Sample Size
3.All numbers,...
Sentences that invite rejection
There are two phrases that will almost always result
in your abstract being rejected: ‘‘Da...
What is different colleagues want to
present the same abstract?
Dishonest behavior …
Session no.3
Scientific Writing
Rules
3- Scientific Writing Rules
• Put actions in verbs
• Put characters in subjects
• Keep subjects near verbs
• Put new infor...
• Use short sentences
• When starting the sentence, don't overdo using “But” or “And”. “But” has become
quite acceptable; ...
Rules for reporting numbers
• Numbers less than 10 are words.
• Number 10 or more are numbers.
• Words not numbers begin a...
• Use one space between a number and its unit.
• Report percentages to only one decimal place if the sample size is larger...
The decision to begin the treatment regimen requires certain prerequisites, one of the most
important is the determination...
Avoid Long Phrases
Parallel Sentences
Omit Needless Words
Creating a flow between sentences
Avoid Repetition
Sneaky Plurals
Avoid Gender Specific Pronouns
Use because to mean "because"
Correct use of Verbs
TENSES
Introduction
 Present: to refer to present
evidence
 Past: to refer to previous studies,
aim and hypothesis
 It ...
Standard Reporting Guidelines
Standard guidelines for reporting research studies have been
developed and undergo acronyms ...
http://www.equator-network.org/
Session no.4
Research
Protocols
4- Research Protocol
Protocol vs. proposal
Importance of study protocol
 Enhances the scientific integrity
 Providing a better study documentation, efficiency, and...
Importance of IRB approval
Protect Research Subjects
Protect Investigators
Protect your research idea (registry ID)
Essent...
How much does a study protocol
differs from the final manuscript
Protocol Research Paper
Scientific Rational +++ +
Aims an...
Parts of Research Protocol (WHO template)
Session no.5
Referencing
Using
Mendeley
Separate
Presentation
Mendeley
workshop
It is your turn now!
File 1
• Cite the paper of
Baratloo et al in the
text using AMA style.
• Change to
(Harvard style)
File 2
• Open the print...
Session no.6
Scientific
Publication
Draft Manuscript Paper
Revision/Polishing Peer-review
Authors Journal
Publication
Conference
National
International
Journal
Peer-reviewed
Predatory
ABSTRACT
FULL TEXT
Vancouver guidelines for authorship
The (ICMJEs) stated that each author should have participated sufficiently in the work...
Editors may ask authors to justify
authorship and state contributions
of each author.
Acknowledgment = ‫عرفان‬ ‫و‬ ‫شكر‬
 General support by a department head or an institution
 Technical help, laboratory w...
UNIFORM REQUIREMENTS
Use double spacing
throughout the
manuscript
UNIFORM REQUIREMENTS
Pages should have margins at least 25 mm and be numbered
UNIFORM REQUIREMENTS
Follow the sequence of title page, abstract, keywords, text,
acknowledgements, references, tables, le...
UNIFORM REQUIREMENTS
Title page should include
(title, short running title, funding,
authors, affiliation, correspondence)...
UNIFORM REQUIREMENTS
Text (Introduction, Methods, Results and Discussion)
Introduction Methods Results Discussion
UNIFORM REQUIREMENTS
Begin each section
on a new page
Each table should
be on a new page
UNIFORM REQUIREMENTS
• Get permission to reproduce previously published materials.
• Enclose a transfer of copyright.
• Ke...
Four methods to select a Journal for publication
1- Asking an Expert co-worker/colleagues
2- Look at references of your ma...
Ask a colleague to have a look on the
quality of the manuscript, then list
relevant journals in three groups
Likely to acc...
1. Search PubMed using your keywords
2. Limit results to your publication type
3. Arrange results alphabetically
By visual...
COVER LETTER
Correspondence details
Dear Editor,
We are sending you the manuscript entitled: ….
What have you done in this...
Is acceptable for publication
Is acceptable for publication following minor revisions
Is acceptable for publication follow...
Summary of Important Terms
• Draft
• Manuscript
• Paper
• Article
• Author
• Co-author
• First Author
• Senior Author
• Co...
How to write a biomedical research paper
How to write a biomedical research paper
How to write a biomedical research paper
How to write a biomedical research paper
How to write a biomedical research paper
How to write a biomedical research paper
How to write a biomedical research paper
How to write a biomedical research paper
How to write a biomedical research paper
How to write a biomedical research paper
How to write a biomedical research paper
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How to write a biomedical research paper

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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

Published in: Science

How to write a biomedical research paper

  1. 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. 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. 3. Session no.1 Structure of Scientific Research Paper
  4. 4. IMRaD 1. Introduction 2. Methods 3. Results 4. Discussion 1. Structure of research paper Abstract Text Appendices References
  5. 5. Manuscript text (IMRaD) Exceptions • Case report • Case Series • Literature Review • View Point • Editorial • Letter to Editor INTRODUCTION METHODS RESULTS DISCUSSION
  6. 6. • What we know • What we do not know (Gap of Knowledge) • Aim of this work INTRODUCTION
  7. 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. 8. • Descriptive statistics • Univariate analysis • Bivariate analysis • Multivariate analysis • Figures, charts and captured images RESULTS
  9. 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
  10. 10. Session no.2 How to write a conference abstract
  11. 11. ABSTRACT = ‫الملـخص‬ Conference Submission Indexing in databases Subscription Journals (non-OA) For readers: Get quick overview Why is abstract important?
  12. 12. • 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
  13. 13. Types of titles
  14. 14. ABSTRACT Structure • Introduction • Methods • Results • Conclusion • Aim (Purpose) • Methods • Results • Conclusion • Context • Evidence Aquatisation • Results • Conclusion NOT structured (one single paragraph)
  15. 15. 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
  16. 16. 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.
  17. 17. 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.
  18. 18. 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).’’
  19. 19. ABSTRACT: Results
  20. 20. ABSTRACT: Results
  21. 21. 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.
  22. 22. Fitting abstracts into space
  23. 23. Fitting abstracts into space
  24. 24. Fitting abstracts into space
  25. 25. Fitting abstracts into space Last choice: Delete sentences (irrelevant to conclusions or appear several times)
  26. 26. Writing Abstract It is your turn now!
  27. 27. 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
  28. 28. 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
  29. 29. 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.
  30. 30. What is different colleagues want to present the same abstract? Dishonest behavior …
  31. 31. Session no.3 Scientific Writing Rules
  32. 32. 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
  33. 33. • 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.
  34. 34. 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.
  35. 35. • 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.
  36. 36. 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.
  37. 37. Avoid Long Phrases
  38. 38. Parallel Sentences
  39. 39. Omit Needless Words
  40. 40. Creating a flow between sentences
  41. 41. Avoid Repetition
  42. 42. Sneaky Plurals
  43. 43. Avoid Gender Specific Pronouns
  44. 44. Use because to mean "because"
  45. 45. Correct use of Verbs
  46. 46. 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 …
  47. 47. 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.
  48. 48. http://www.equator-network.org/
  49. 49. Session no.4 Research Protocols
  50. 50. 4- Research Protocol Protocol vs. proposal
  51. 51. 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
  52. 52. Importance of IRB approval Protect Research Subjects Protect Investigators Protect your research idea (registry ID) Essential for International Publication
  53. 53. 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 - +
  54. 54. Parts of Research Protocol (WHO template)
  55. 55. Session no.5 Referencing Using Mendeley
  56. 56. Separate Presentation
  57. 57. Mendeley workshop It is your turn now!
  58. 58. 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
  59. 59. Session no.6 Scientific Publication
  60. 60. Draft Manuscript Paper Revision/Polishing Peer-review Authors Journal
  61. 61. Publication Conference National International Journal Peer-reviewed Predatory ABSTRACT FULL TEXT
  62. 62. 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.
  63. 63. Editors may ask authors to justify authorship and state contributions of each author.
  64. 64. 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
  65. 65. UNIFORM REQUIREMENTS Use double spacing throughout the manuscript
  66. 66. UNIFORM REQUIREMENTS Pages should have margins at least 25 mm and be numbered
  67. 67. 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
  68. 68. UNIFORM REQUIREMENTS Title page should include (title, short running title, funding, authors, affiliation, correspondence) Title Short running title Authors Affiliation Correspondence
  69. 69. UNIFORM REQUIREMENTS Text (Introduction, Methods, Results and Discussion) Introduction Methods Results Discussion
  70. 70. UNIFORM REQUIREMENTS Begin each section on a new page Each table should be on a new page
  71. 71. UNIFORM REQUIREMENTS • Get permission to reproduce previously published materials. • Enclose a transfer of copyright. • Keep an exact copy of everything submitted.
  72. 72. 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
  73. 73. 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.
  74. 74. 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.
  75. 75. 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
  76. 76. 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
  77. 77. 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

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