Scientific Writing Mehmet Tevfik DORAK, MD PhD Robert Stempel College of Public Health and Social Work Department of Environmental & Occupational Health February 5, 2013

https://www.coursera.org/#course/sciwrite

https://www.coursera.org/#course/sciwrite

http://writingcenter.fiu.edu/about-us/services-for-graduate-students/ (www)

http://plagiarism.org/citing-sources/citation-styles

http://plagiarism.org/citing-sources/citation-styles

Scientific Writing Link: http://www.aacc.org/publications/clin_chem/ccgsw/Pages/default.aspx#

Scientific Writing Main source: 2nd edition: http://www.amazon.com/Publishing-Presenting-Clinical-Research-Second/dp/0781795060/ref=sr_1_4?s=books&ie=UTF8&qid=1360030583&sr=1-4 3rd edition: http://www.amazon.com/Publishing-Presenting-Clinical-Research-Browner/dp/1451115903/ref=sr_1_2?s=books&ie=UTF8&qid=1360030583&sr=1-2

Scientific Writing Outline Basic principles of scientific writing Advice on sections of a scientific article Additional advice on good practice Uniform requirements for manuscripts submitted to biomedical journals Appendix: Additional sources

Scientific Writing: Basics Link: http://www.nature.com/scitable/topicpage/effective-writing-13815989

Scientific Writing: Basics DO NOT: - Make long, complicated sentences; just say it - Use longer words when there is a simpler alternative (utilize vs. use; perform vs. do) - Use jargon; just say it in plain English - Try to overwhelm the reader with your knowledge; making sense and putting across your ideas in a conmprehensible way is more important Examples: - http://www.nature.com/scitable/topicpage/effective-writing-13815989 - https://cgi.duke.edu/web/sciwriting (https://cgi.duke.edu/web/sciwriting/index.php?action=lesson3) - http://www.writingfix.com/PDFs/IPod/Podcasting_Science_Scientific_Writing_Tips.pdf - http://writingcenter.unc.edu/handouts/writing-concisely

Scientific Writing: Basics Link: http://www.columbia.edu/cu/biology/ug/research/paper.html

Title and Abstract TITLE ABSTRACT - Are the title and research question closely related? - Is the title objective in tone? - Are special features of the study mentioned? ABSTRACT - Are there introduction, methods, results and conclusions sections even if they are not explicitly labelled as such? - Are the main features of the study mentioned? - Are the key results of the study stated in words? - Do the conclusions flow from the results? - Did you follow all the rules of the journal?

Standard abstract model: http://www. nature

Structured abstract model: http://humrep. oxfordjournals

Characteristics of a Good Abstract Stands on its own without need to read the paper States the hypothesis, question, or objective of the study Completes the story by answering the hypothesis, question, or objective Contains the same key words and terms as the title and the introduction Follows the correct style and format Follows the order of the main text Stays within the allowed word count Does not contain information absent in the paper Does not make conclusions unsupported by the data Limits the use of abbreviations Does not include references Does not cite tables or figures Paper: http://www.clinchem.org/content/56/4/521.full Table: http://www.clinchem.org/content/56/4/521/T1.expansion.html

Conference Abstract What to avoid: Lack of originality No background, no implications Small study, lack of statistical power, inconclusive results No numbers, too much talk All numbers, no words Too short, too different Sloppiness as a proxy for lack of care and quality Too many abbreviations Inappropriate statements (present your data and discuss your results rather than promising to do so)

Abstract Writing Exercise IL-6 and β-selectin as prognostic markers for atherosclerotic disease Background: Atherosclerotic disease is a major cause of death in the United States. We investigated which analyte, IL-6 or β-selectin, would be a better prognostic marker for atherosclerotic disease. Methods: We divided patients into 4 groups. Specimens from each patient were tested for interleukin-6 and β-selectin and matched against the patient’s disease group. During the study period, these analytes were measured again to determine whether concentrations changed with disease severity. Mortality was also monitored for each group to investigate any relationship between IL-6 or β-selectin and the risk of death. Results: The IL-6 concentrations were different between groups, with the IL-6 concentrations significantly different between groups 1 and 3, and 1 and 4. Although IL-6 and β-selectin concentrations both changed, β-selectin changed by only 10% to 30%. Changes in disease severity were reflected in changes in IL-6. IL-6 values were the same for men and women and did not show any relationship with patient age. Intraindividual variation for IL-6 was much lower than that for β-selectin. Conclusions: IL-6 and β-selectin concentrations change with a change in heart disease severity. Intraindividual variation of IL-6 was also much lower than β-selectin, further validating the use of IL-6 over β-selectin. Further work is needed to confirm this observation. Link: http://www.clinchem.org/content/56/4/521.ful

Abstract Writing Exercise Interleukin-6 as a prognostic marker for atherosclerotic disease Background: Serum concentrations of the vascular inflammation marker β-selectin correlate with atherosclerotic disease severity, but β-selectin has a large intraindividual variation. We investigated whether interleukin-6 (IL-6), another marker of vascular inflammation, could predict disease severity and mortality risk. Methods: Consecutive outpatients undergoing evaluation for peripheral vascular disease (PVD) were divided into categories ranging from no functional impairment (group 1) to severe functional impairment (group 4). Blood was collected at baseline and quarterly over 3 years. Serum IL-6 and β-selectin were quantified to calculate intraindividual variation and to assess the relationships of these markers to disease severity and mortality. Results: Baseline median IL-6 concentrations were 12, 26, 96, and 144 μg/L for categories 1 to 4, respectively (P < 0.001 for categories 3 and 4 vs 1) and were not found related to age or sex. Median β-selectin concentrations increased 30% across the 4 categories. Increased disease severity and mortality were associated with higher IL-6 concentrations (P < 0.01 for both), but not β-selectin. Intraindividual variation for group 1 was 14% for IL-6 and 36% for β-selectin. Conclusions: IL-6 appears to be a better marker of disease severity and mortality than β-selectin in patients with PVD, with lower intraindividual variation and significant concentration changes with increasing disease severity. Link: http://www.clinchem.org/content/56/4/521.full

Introduction - Are the four major elements (background, existing research, problems with that research or gaps in knowledge, your improvements) covered in four or fewer paragraphs? - Is it possible for a reader to tell why you did the study and why it is an improvement over existing knowledge? - Do you use an objective tone when criticizing previous work? - Do you describe how your study addresses the problems of previous research? - Is there anything extraneous in your introduction?

Material/Subjects & Methods - Did you mention the design of the study? - Could a reader reproduce your study based on the details you provide? - Did you mention the design of the study? - Are the setting, source and number of subjects, and inclusion/exclusion criteria for subjects clear? - Are the measurements described in a logical order? Are quality issues addressed? - Did you state how you measured the effect size, and how you determined whether it was statistically significant?

Results - Did you provide the basic results of the study (including descriptive characteristics)? Did you continue with main results, other important findings and additional results? - Are the effect sizes for the main outcomes of the study easy to find? - Does the text complement the tables and figures? - Are unusual or surprising results in their proper place? *** THE MOST IMPORTANT SECTION ***

Figures & Tables TABLES FIGURES - Is the title sufficiently descriptive without being Tolstoyesque? - If the table tidy? (Rows and columns line up, each column centred under its heading, headings italicised, etc.) - Are there any unneeded data, repeated Ns, excessive precision or ambitious abbreviations? - Is the meaning of every item obvious without referring to the text? - Can any two of them be combined? - Are all the tables cited in the text and in the right order? FIGURES - Does every figure make its point clearly? - Are the axes, lines bars and points labelled? Are the scales correct and comparable? - Does each figure have a legend, not a title? - Are the figures numbered and are they cited in the right order? - Does the text and figures complement each other or create redundancy?

Discussion - Did you discuss the key findings and explain why they matter? - Have you indicated the strength of your convictions? - Did you mention alternative interpretations of your results? - Have you included the limitations and strengths of the study? - Did you make recommendations about what should happen next? - Did you present any new data in the discussion? If so, move them to the results section. - Does each paragraph flow from the previous one and do you make your point in the beginning of each paragraph? - Are there trivial points that can be eliminated?

Structured discussion example: http://www. nature

References - Did you provide a reference for all non-obvious statements of fact? - Did you follow the instructions of the publisher for unpublished data, abstracts or personal communications? - Did you cite only the references that you have read and understood? - Did you prepare the reference list in the special format for the target journal? - Did you update thereference list before submission? - If no special format is indicated, have you been consistent?

Conflict of interest statements Reviewer suggestions and exclusions Other Bits Running title Keywords (MESH) Author contributions Conflict of interest statements Acknowledgements Reviewer suggestions and exclusions Cover letter

Looking Back When the manuscript is finished, look back to see: - Does the title make sense or the text has changed drastically and you need a new title? - Have you made your research question clear? - Have you provided an answer? - Have you made it clear: (a) how your work adds to the previous knowledge, and what gap it fills, and (b) what progress does your work represent? In other words: Do not bother with a statistical exercise based on a convenience sample. In the Discussion, all you have to say should not be just how many other studies are out there and how inconsistent the results are, and your study is just another inconclusive addition to the mix.

Good Practice Even if not required: - Prepare key messages - Try to summarize your work for lay people Read the review criteria of the journal Do not ask anyone to review your paper without providing a title and an abstract! Structured abstract model: http://humrep.oxfordjournals.org/content/28/2/462.abstract.html

Typical Review Criteria - Importance of research subject studied - Originality - Appropriateness and adequcy of study design - Strength of evidence supporting conclusions - Quality and length of presentation - Duplication of data in text, tables and figures - Appropriate and adequate citing of previous work

Uniform Requirements Link: http://www.icmje.org

Scientific Writing Thank you for Your Attention! Mehmet Tevfik DORAK This presentation will be posted at this site: http://www.dorak.info/fiu/sci_write.html Mehmet Tevfik DORAK Robert Stempel College of Public Health and Social Work Department of Environmental & Occupational Health February 5, 2013

Scientific Writing Appendix: Additional Resources

http://www.dorak.info/fiu/sci_write.html http://www.dorak.info/fiu/sci_write.html

Link: http://www. nature

Link: http://writing. bitesizebio eBook: http://bitesizebio.com/ebooks/writing-your-first-or-next-paper

http://www. americanscientist http://www.americanscientist.org/issues/pub/the-science-of-scientific-writing

https://cgi.duke.edu/web/sciwriting/index.php Presentation in PDF: https://cgi.duke.edu/web/sciwriting/resources/201108_DukeScientificWritingWorkshop.pdf

https://cgi.duke.edu/web/sciwriting/index.php?action=lesson3

Link: http://writingcenter.unc.edu/handouts

Link: http://abacus. bates

http://www.scidev.net/en/practical-guides/how-do-i-write-a-scientific-paper-.html

http://cbc.arizona.edu/sites/default/files/marc/Sci-Writing.pdf

http://classweb.gmu.edu/biologyresources/writingguide/index.htm

Link: http://www.fhsu.edu/biology/Eberle/BIOL825Lecture2

Link: http://www. amazon

Link: http://www. amazon

Link: http://www. amazon

Link: http://www. amazon

Link: http://www. amazon