1. Scientific Writing in Medical Sciences Payam Kabiri, MD. PhD. Epidemiologist Department of Epidemiology & Biostatistics School of Public Health Tehran University of Medical Sciences

2. Research Output Three different research output are expected from research proposals: 1- Paper 2- Patent 3- Change

3. Adopted from: “Islam and Science: the data gap”, Nature, 2006, 444(7115):26-7

4. مقايسه فراواني مقالات و ارجاعات صورت‌گرفته به مقالات منتشرشده دانشگاه علوم پزشکي تهران و دانشگاه تهران با دانشگاه‌های رتبه يکصدم و دويستم دنيا در مجموعه Scopus در رتبه‌بندی سال 2009 تايمز THS-QS رتبه دانشگا ه نام دانشگاهکشور تعداد مقالات 5 ساله در Scopus تعداد ارجاعات به مقالات 5 ساله اخير Scopus تعداد اعضاي هيئت علمي نسبت ارجاع به عضو هيئت علمي نسبت ارجاع به مقاله 100 دانشگاه Rice آمريکا 62546634377285/910/61 200 دانشگاه Twente هلند 619337403100037/46/04 201 دانشگاه اندونزیاندونزی 549209343210/483/81 368 دانشگاه علوم پزشکي تهران و دانشگاه تهران ايران 1135931030 32439/62/37

5. Why “Scientific Writing”? The purpose of scientific writing is to convey ideas and facts about scientific work. Scientists understand and criticize each other's work through their articles. Thus, scientific writing should be intelligible to readers at the first reading.

6. Why Publish? Knowledge contributions Ensures scientific rigor Allows feedback (improves work) Promotes career  Document productivity  Document impact on field/reputation  Advertises your lab for future trainees Improves chances of funding Fulfills an obligation (public monies)

7. Evaluating an Academic Person though his/her CV Papers Number of papers Rate of publication Quality of journals Position in list of authors Focus

8. The Art of Scientific Writing Publish or Perish!

9. Steps in Scientific Writing Design well Decide politics Choose journal Read instructions to authors/papers Set framework Prepare drafts Distribute Polish Submit

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

11. Two Types of Studies Primary Study Secondary Study

12. Primary studies Experiments Clinical trials Surveys

13. Reviews (Overviews) Narrative reviews Systematic reviews & Meta-analyses Guidelines Decision analyses Economic analyses Review Article Secondary studies

14. Types of Medical articles Original Article Review Article Case Reports Editorial Short Communication (short papers) Letter to Editor Personal Views

15. Letter Stick to the point State the problem, issue or hypothesis Give the context Outline your comment, solution, viewpoint Give a strong conclusion Note limitations

16. Editorial Write for your readership (broad?) Be controversial and thought provoking Being subtle is often more powerful

17. Short communication Increasingly common Concise introduction Present data and discuss it shortly Only a few tables or figures Number of words limitations

18. Is your paper a paper, a brief or a research letter? Easier to get letters & briefs accepted. They make you indexed easier ! Decide whether you should submit it as a brief or letter firstly.

19. Case Reports Medical history of a single patient in a story form. Lots of information given which may not be seen in a trial or a survey. Often written and published fast compared to studies e.g. Thalidomide

20. The Hierarchy of Evidence 1.Systematic reviews & meta-analyses 2.Randomised controlled trials 3.Cohort studies 4.Case-control studies 5.Cross sectional surveys 6.Case reports 7.Expert opinion 8.Anecdotal

21. Hierarchy of studies

22. The traditional IMRaD  Introduction  Methods  Results  Discussion

23. The Basic Structure of an Article TITLE (S)Summary (Structured Abstract) (I) Introduction (What Question was asked?) (M)Methods (How was it Studied?) (R)Results (What was Found?) (A)Analysis (How data was analysed?) (D)Discussion(What Do the Findings Mean?) Acknowledgements References

24. Main Components of an Article Introduction: Why did you start? Methods: What did you do? Results:What did you find? Discussion: What does it all mean?

25. 25 “Bowtie” Model For a Scientific Paper Broad IdeasSpecific IdeasBroad Ideas

26. A full paper may contain: Title Authors and Affiliation Abstract Introduction Methods Results Discussion Acknowledgments (optional) References

27. Initial steps 1-Understand the type of manuscript you are writing. 2-Re-evaluate your project. 3-Plan the sections and subsections you need. 4-Match your content to your readers’ knowledge. 5-Keep information specific rather than general. 6-Write in plain language. Keep your sentences short. 7-Use tables, diagrams, flowcharts and graphs.

28. Politics first!

29. Order of writing? 1. Results 2. Methods 3. Introduction 4. Discussion 5. Abstract 6. References

30. Order of writing? 1. Methods 2. Results 3. Introduction 4. Discussion 5. Abstract 6. References

31. More reading Hall GM, ed. How to write a paper. London: BMJ Publishing Group. Advanced Writing, Floresita V.Bustamante, SAMT Essentials of Writing Biomedical Research Papers, Zeiger Scientific Writing Easy when you know how. Peat J. BMJ Publishing Group. 2002. The Vancouver Group. Uniform requirements for manuscripts submitted to biomedial journals. www.icmje.org

32. Questions

33. Writing Results Payam Kabiri, MD. PhD. Epidemiologist Department of Epidemiology & Biostatistics School of Public Health Tehran University of Medical Sciences

34. Results Simplecomplex Describe the population Start with positive findings Establish how comparable your groups were Use a mixture of text, tables and figures Mention units of measurement Mention what numbers, brackets, etc. refer to  9+4, 854 (12.3) Bring the P values

35. 35 "Males (180.5 ± 5.1 cm; n=34) averaged 12.5 cm taller than females (168 ± 7.6 cm; n=34) in the AY 1995 pool of Biology majors (two-sample t-test, t = 5.78, 33 d.f., p < 0.001)." Sample

36. Results Provide only enough interpretation to lead the reader from one experiment to the other  Avoid lengthy analysis and comparison to the work of others No need to follow chronology of study  Rather, provide a logical progression and tell a story

37. 37 1. Start with positive findings. 2. Do not compare the present data with previously published results. 3. Write the text of the Results section concisely and objectively. 4. The passive voice will likely dominate here, but use the active voice as much as possible Results

38. 38 Tables and Figures Consider using a table to present large amounts of data/results.  Must refer to all tables in text. Use figures to graphically represent significant results.

39. Results Use the “Stand alone” tables Make sure totals add to 100% Do not repeat the Tables and Figures in text  Summarize: e.g., there were no significant associations…  Describe: e.g. there was a three fold increase in the risk of..

40. 40 Each Table or Figure must include a brief description of the results being presented and other necessary information in a legend. Table legends go above the Table; tables are read from top to bottom. Figure legends go below the figure; figures are usually viewed from bottom to top Tables and Figures

41. 41 Tables and Figures are assigned numbers separately and in the sequence that you will refer to them from the text.  The first Table you refer to is Table 1, the next Table 2 and so forth.  Similarly, the first Figure is Figure 1, the next Figure 2, etc. Tables and Figures

42. 42 When referring to a table from the text, "Figure" is abbreviated as Fig.,e.g., Fig. 1. Table is never abbreviated, e.g., Table 1. Tables and Figures

43. 43 Example 1: Courtesy of Shelley Ball. Example 2: Courtesy of Shelley Ball.

44. 44

45. 45 Used when we want to distinguish a result & make it prominent into readers view Figures are visual presentations of results, including graphs, diagrams, photos, drawings, schematics, maps, etc. Graphs are the most common type of figure. Graphs show trends or patterns of relationship. Figures

46. 46 Avoid clutter (too many numbers or symbols) Should provide a clear statistical message Vertical (“Y”) axis: outcome/dependent variable Horizontal (“X”) axis: exposure/independent variable Name & define each axis Give the measurement unit of each axis Figures

47. 47

48. 48

49. Results Common mistakes  Raw data  Redundancy  Discussion and interpretation of data  No figures or tables  Methods/materials reported

50. Figure 1. Effect of total alkaloid fraction of methanolic extract on mean survival time

51. Figure 1. Effect of total alkaloid fraction of methanolic extract of unripe fruit of Solanum pseudocapsicum on mean survival time (MST) in tumor bearing mice.

53. 53 Something to avoid ! Do not present the same data in both a Table and Figure - this is considered redundant and a waste of space and energy. Decide which format best shows the result and go through it. Do not report raw data values when they can be summarized as means, percents, etc.

54. 54 Do NOT ! Use big words that you do not really mean  Attributable  Causality  Preferential  Significant (without statistical evidence)  Validity Mix incidence and prevalence Mix frequency, rate, proportion, ratio

56. گزارش نتايج آماري نوشتن تعداد فراواني همراه با درصدها وقتي تعداد نمونه اندك است. عدم نياز به نوشتن فرمول‌های حجم نمونه و آزمون‌های آماری ارائه پارامترهايی‌كه آزمون شده‌اند مانند ميانگين, نسبت يا درصد, ضريب همبستگي, حتي اگر آزمون‌ها معني‌دار نشده باشند. نوشتن شاخص آزمون و مقدار آن همراه با درجه آزادي و p-value نوشتن مقداردقيق p-value براي آزمون‌هاي معني‌دار وغيرمعني‌دار (تا دو رقم اعشار)

57. تعريف كردن علائمي كه براي نتايج معني‌دار به‌كار مي‌رود (مانند ستاره) و به‌كار بردن علائم مشابه نوشتن اعداد به‌صورت گرد شده با درنظرگرفتن دقت داده‌هاي اوليه (ميانگين تا يك رقم اعشار و انحراف معيار و خطاي معيار تا دو رقم اعشار بيشتر از داده‌هاي خام) درج درصدها تا يك رقم اعشار (گاهي حتي نياز به ارقام اعشاري هم نيست). نوشتن شاخص‌هايي مانند t,r تا دو رقم اعشار گزارش نتايج آماري

58. The p-value in a nutshell p < 0.05 a statistically significant result p = 0.05 or 1 in 20 result fairly unlikely to be due to chance 0 1 Could the result have occurred by chance? The result is unlikely to be due to chance The result is likely to be due to chance 1 20 p > 0.05 not a statistically significant result p = 0.5 or 1 in 2 result quite likely to be due to chance 1 2

59. Confidence Interval (CI) Is the range within which the true size of effect (never exactly known) lies, with a given degree of assurance (usually 95%)

60. Check list for Results Baseline data provided? Primary and other endpoints clear and complete? Does the text complement figures and tables? Are measures of uncertainty mentioned? (SD, SE, CI)

61. 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

62. 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

63. 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

64. 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 contract. or exclamation points!

65. 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…”

66. 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

67. Questions ?

68. Writing Discussion Section Payam Kabiri, MD. PhD. Epidemiologist Department of Epidemiology & Biostatistics School of Public Health Tehran University of Medical Sciences

69. 69 How to Write Discussion

70. 70  To write Briefly & summarize your principal finding  Implications of your results for other researchers  Interpret findings in light of the literature  Reconcile findings with the literature  Limitations of your study  Conclusions The function of the Discussion is:

71. Paragraphs in Disscussion 1st paragraph  Introduce broad Idea  State major findings 2nd paragraph Explicit rationale  Explicit rationale Last paragraph  Conclusion  Sugesstions

72. 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

73. Discussion Do your results provide answers to your testable hypotheses? If so, how do you interpret your findings? Do your findings agree with what others have shown? If not, do they suggest an alternative explanation or perhaps a unforeseen design flaw in your experiment (or theirs?)

74. Discussion Given your conclusions, what is our new understanding of the problem you investigated and outlined in the Introduction? Explain weaknesses, shortcomings. Be fair: this will build trust. Don’t over-criticize yourself, don’t go to unnecessary details.

75. Discussion If warranted, what would be the next step in your study, e.g., what experiments would you do next?

76. Discussion Reverse of Introduction (pyramid)

77. 1. Organize the Discussion to address each of the experiments or studies for which you presented results. 2. discuss each in the same sequence as presented in the Results, providing your interpretation of what they mean in the larger context of the problem. Discussion

78. Do not waste entire sentences restating your results; if you need to remind the reader of the result to be discussed, use "bridge sentences" that relate the result to the interpretation: "The slow response of the lead-exposed neurons relative to controls suggests that...[interpretation]". Discussion

79. 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

80. 80 active voice Use the active voice whenever possible in this section. concise Be concise and make your points clearly. first person Use of the first person is okay, but too much use of the first person may actually distract the reader from the main points. 2-3 paragraphs, <450 words Style

81. 81 Some notes How would you change your experiment to make it better? What new questions did this experiment make you think of? If you made mistakes in your experimental design, did you discuss them and how to fix it for next time.

82. Questions

83. Notes About Titles Payam Kabiri, MD. PhD. Epidemiologist Department of Epidemiology & Biostatistics School of Public Health Tehran University of Medical Sciences

84. Title First & most of the times the only part of an article that readers and editors see and read. Key elements that advertises the paper’s contents  Informative and Specific Maybe helpful to choose the title when the paper is complete

85. عنوان مقاله عنوان مقاله را هزاران نفر مي‌خوانند، درحالي که تعداد اندکي کل مقاله را بررسي مي‌کنند. عنوان مقاله در صفحه محتواي مجله و نيز در اندکس‌هاي پزشکي توسط بسياري خوانده مي‌شود. عنوان مانند تابلوي يک مغازه است و يا محصول يک کارخانه يا مزرعه است و لذا بايد جذاب باشد، تا افراد را براي خواندن مقاله جذب کند.

86. عنوان مقاله عنوان مقاله بايد با حداقل تعداد کلمات و درعين‌حال به‌طور کافي بيان‌گر محتواي مقاله باشد:  مبهم نبوده، دقيق باشد.  کلمه‌هاي اختصاصي بکار رود.  کلمه‌ها آشنا باشد.  کلمه‌هاي کوتاه انتخاب شود.

87. Title Short and simple State subject, not conclusion Include study design Include time and place if necessary Begin with a keyword Avoid abbreviations Remove empty phrases such as “ A study of…” Use Subtitles (notice number of words) “Exercise and Coronary Heart Disease: Framingham Offspring Study”

88. بهتر است که عنوان با کلمات کليدی و اصلی (Keyword) شروع شود. به‌عبارت ديگر بهتر است که عنوان شامل کلمات کليدی و اصلی باشد که بوسيله تعدادی حروف ربط درکنار يکديگر قرار گرفته‌اند. 1- Aortic Stenosis,Von Willebrand Factor, and Bleeding. 2-"Acquired Von Willebrand syndrome in Aortic Stenosis. 3-"Risk of Bacterial Meningitis in Children with Cochlear Implants. عنوان مقاله

89. گاهی اوقات بهتر است که عنوان مقاله به صورت سوالی مطرح شود که باعث ترغيب خواننده گردد. اصولا طرح عنوان مقاله به صورت سوال، يکی از الگوهای عنوان نويسی می‌باشد. 1-" Do Bisphosphonates Make Children’s Bones Better or Brittle ?" 2-" Use It or Lose It –Do Effortful Mental Activities Protect against Dementia?" 3-" Behind the Research : Death by Voluntary Dehydration –What the Caregivers Say ?" عنوان مقاله

90. Titles Guidelines 1- New England Journal of Medicine: Concise and descriptive (not declarative) 2- Lancet: Concise but informative 3- Annals of Internal Medicine: As brief as possible while conveying essential features of the article’s content 4- BMJ: Keep them concise

91. Routin suggestions for titles: Concise and precise Informative and descriptive Not misleading or unrepresentative Specific – for example, include type of study and numbers (if large) Words appropriate for classification Interesting not dull

92. & Finally check: Is it accurate? Is it in any way misleading? Does it contain essential key words? Is it interesting?

93. Title types Indicative (State what paper covers, not what it says) Informative (Good to start writing with)

94. عنوان مقاله 1. عنوان اصلیMain Title 2. عنوان مکرری Running Title

95. Check list for Introduction Is it clear why you did the study? How does your study add to knowledge? Is criticism justified and gentle? What can be left out?

96. Questions

97. References Payam Kabiri, MD. PhD. Epidemiologist Department of Epidemiology & Biostatistics School of Public Health Tehran University of Medical Sciences

98. 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 EndNote or other bibliographic software Use the Internet

99. References Appropriate format Only 1 or 2 references per point Don’t over self-cite Avoid textbooks & conference abstracts. Avoid referencing to thesis & dissertations Avoid using the references list of your reference Select carefully, balance authors used

100. Main Important Referencing Styles 1. Author-Date Style (Harvard Style) 2. Numeric Style (Vancouver Style)

101. Author-Date Style system In-Text citations Cite your sources within your text by giving the author’s surname(s), year of publication, and (when appropriate) page numbers: Examples:  Contrary to popular perception, violent crime has been shown to be decreasing (Johnson 2004)  James and Peters (2003) have argued that…

102. Author-Date Style Reference List Bibliography All references are listed in author/date alphabetical order: Example :  HOLLAND, M., 2002. Guide to citing Internet sources [online]. Poole: Bournemouth University. Available from: http://www.bournemouth.ac.uk/library/using/guide_to_citing_inter net_sourc.html [Accessed 4 November 2002]. http://www.bournemouth.ac.uk/library/using/guide_to_citing_inter net_sourc.html  OXFORD ENGLISH DICTIONARY, 1989. 2nd ed. Oxford: Clarendon Press.  UNESCO, 1993. General information programme and UNISIST. Paris: UNESCO, (PGI-93/WS/22).  WISEMAN, S., ed., 1967. Intelligence and ability. Harmondsworth: Penguin.

103. Numeric system In-Text Citations Each citation in the text is given a number in brackets: Example :  Ericson (1) and Milne (2) take the view that… but other authorities (3) argue that… References are listed in number order in the bibliography, & cited by that number each time they are referred to in the text.

104. Numeric system Reference List Bibliography Example : 1. ERICSON, E.E., 1991. The apocalyptic vision of Mikhail Bulgakov's ‘The Master and Margarita'. New York: Edwin Mellen, p.153. 2. MILNE, L., 1977. ‘The Master and Margarita’: a comedy of victory. Birmingham: University of Birmingham, pp.62- 3. 3. BARRATT, A., 1987. Between two worlds: a critical introduction to ‘The Master and Margarita’. Oxford: Clarendon Press, p.96. Each reference number points to a single reference only

105. “Vancouver” Style Now is the time for all good men to come to the aid of their country. 1 Four score and seven years ago our forefathers brought forth a new nation conceived in liberty and dedicated to the proposition that all men are created equal. 2 References 1.Alpay L, Russell A. Information technology training in primary care: the nurses' voice. Comput Inform Nurs. 2002;20(4):136-142. 2.Balen RM, Jewesson PJ. Pharmacist computer skills and needs assessment survey. J Med Internet Res. Mar 29 2004;6(1):e11.

106. APA Style Now is the time for all good men to come to the aid of their country.(Alpay & Russell, 2002) Four score and seven years ago our forefathers brought forth a new nation conceived in liberty and dedicated to the proposition that all men are created equal.(Balen & Jewesson, 2004) References Alpay, L., & Russell, A. (2002). Information technology training in primary care: the nurses' voice. Comput Inform Nurs, 20(4), 136-142. Balen, R. M., & Jewesson, P. J. (2004). Pharmacist computer skills and needs assessment survey. J Med Internet Res, 6(1), e11.

108. http://mulford.meduohio.edu

109. Questions

110. بزنید ! Email اگر میل داشتید payam.kabiri@gmail.com