How to write… How to review… a paper

1. How to write… How to review… a paper January 30, 2006

2. Objectives Create / further develop your skills as a scientific writer Sharpen your skills as a reviewer of manuscripts Who has experience in critically reviewing a paper? Your top three considerations in deciding if a paper should have been published?

3. When I read / review / write a paper, the three things that make me decide if it is “good”(publishable) are… Novelty(Anything new here? Why spend my time on this one? ) Topicality (Is the area hot / Is my data related to something of interest to others? What is the “hook”? ) (Scanning the Newspaper analogy ) Convincing presentation(two components) Is the rationale for doing the work, and the chain of evidence supporting the story that runs through the paper clear? 2. Is the take home message understandable or is it a laundry list of anecdotal data proving you did a lot of work but haven’t constructed a noteworthy STORY?

4. Getting started: Before writing your first word, you need to know : Do you have an interesting story planned? Enough data? Are they convincing enough for a paper? If yes: Target audience? Preferred journal (or range of jnls) ? Order of writing: Results; M/M, Intro; Disc. M. Zeiger Essentials of Writing Biomedical Research Papers (or theses…) NJM Library Geoff Hicks NTP website

5. Renee –the Intro • Monther- Results • Anita –Discussion • Kent - The Abstract and Title • Discussion: When it’s returned…

6. The Good, The Revised &The Ugly… • GOAL: Novelty, originality and topicality Is it new and are we interested? • MESSAGE: Clear, concise and well written Can we understand what you are telling us? • STORY: Well designed, explained and significant Is what you are telling us believable and relevant?

7. When the going gets tough…the tough find help! • Essentials of Writing Biomedical Research Papers • By Mimi Zeiger, 2nd Edition • How I review an original scientific article. • By FG Hoppin • At the Bench: A Laboratory Navigator • By Kathy Barker • A DICTIONARY and Spell Check!!!

8. The Introduction The Lit • Capture the reader’s interest! • Prepare reader with the basics to understand your paper • The opening scene of your story Known Unknown Question Approach

9. Which introduction is better? It is known that general anesthetics depress the bronchomotor response to vagus nerve stimulation. However, the site of this depression has not been determined. To determine which site in the vagal motor pathway to the bronchioles is most sensitive to depression by barbiturates, we did experiments in which we stimulated this pathway at four different sites before and after exposure to barbiturates. Barbiturates depress the bronchomotor response to vagus nerve stimulation. However, the site of this depression has not been determined. Barbiturate treatment can also depress patients. To determine which site in the vagal motor pathway to the bronchioles is most sensitive to depression by anesthetics, we did experiments in isolates rings of ferret trachea in which we stimulated this pathway at four different sites before and after exposure to barbiturates. A B

10. Quick tips for writing introductions… • Tell the story of where the question came from • State or strongly imply the unknown • State the question or hypothesis • Make sure the importance of your work is evident • Do not answer the question, include results or implications • Be sure the experimental approach evident • Specify molecule, cell, animal or human population studied Aim to awaken interest, not kill it off!

11. Materials and Methods • Experiments done to answer the question • Cookbook for reproducibility

12. Quick guide for writing M&Ms Materials • Reagents • What was examined Methods • What you did (Study design) • In what order • How you did it • Why you did it • How you analyzed it Remember to include the source Include references if applicable State assumptions Written in PAST tense

13. Results

14. Things you should know • Journal your are targeting • Full length or short paper? • Read the “instructions for Authors” - know your limit (word numbers, figures) • Style (results OR results and discussion) • How much details (figure legends or result section) • Papers from that journal

15. Function • Present your key findings - Answer the hypothesis/question you addressed - Presented in a sequence that will logically support (or provide evidence against) the hypothesis - Include obvious trends, important differences, similarities, correlations, etc • Sequence - Major finding first > mechanism(s) - Follow up on previous findings first and keeping your most striking figure to the end

16. Should I report all findings? • Report your key findings (positive results) that support your hypothesis • Data not shown • Use supplementary section to show relevant results • Report negative results - they are important! - If you did not get the anticipated results • Your hypothesis was incorrect and needs to be reformulated • Stumbled onto something unexpected that warrants further study • Importance to others even though they did not support your hypothesis • Do not thinking that unanticipated results are necessarily "bad data" • If you carried out the work well, they are simply your results and need interpretation Many important discoveries can be traced to "bad data".

17. Figures • Best format - Figure (bar graph with actual numbers, fold, normalized) - Table - FACS histogram/dot plot (show your gate and analysis) - Picture (microscope, Western blot, etc) • Provide clarifying information - Figure should be clear (self explanatory) - Use the text to clarify and highlight the key results that each conveys • A good strategy: - Make a note, on a draft of each Table or Figure, of the one or two key results you want to address in the text portion of the results - Make sure to get these points across in the text

18. Statistical Significance • Do not:marked or tremendous increase, enhance, ……. etc alone • Do:write statistical analysis sections (M & M) • report statistical test summaries (test name, p-value and numbers done) • example: t-test, ***p < 0.001, * p <0.05 • report statistical significance in conjunction with the results they support. Example: (180.5 ± 5.1 ug/ml; n=34) • Significant to what? (control, other group ..etc)

19. Things to avoid • Do not: Reiterate each value from a Figure or Table - only the key result or trends that each conveys • Do not: Present the same data in both a Table and Figure – redundant, waste of space - Decide which format best shows the result and go with it • Do not: Report raw data values (descriptive) - summarize as means, percents, etc

20. Writing Scientific Papers Anita L Kozyrskyj, PhD National Training Program in Allergy and Asthma January 30, 2006

21. What’s there to Discuss? • Function • Content • Organization • Length

22. Function • Main • To answer questions posed in Intro • Other • To explain how results support answer • To explain how answers fit existing knowledge

23. Content • State answers to the questions • Support the answers with results • Explain why answer is plausible • Defend your answer • Explain the newness of your answer • State importance of the answer

24. Content • Explain any results that do not support your answer • Explain discrepancies with published results • Explain unexpected findings • State limitations of design/methods • Explain validity of assumptions (strengths)

25. Organization • A beginning (power position) • Focus the story • A middle • Tell the story • An end • Make a point

26. Organization - Beginning • Present most important idea which is to answer the question. • Support/explain/defend your answer • Precede answer by a signal • State the animal or study population and important design features (Our cohort study of 14,000 children..) • Use a transition phrase/clause/topic sentence to link results to answer

27. Organization – Support Answer • The answer is a generalization of the results. To convince the reader that the answer is valid, present relevant results after stating the answer. • Highlight important statistic(s) reported in results, results that you want reader to remember (should not be the first time you report these statistics) • Cite figure or table

28. Organization - Signals • Before the answer is stated, it should be signaled, so that the reader knows it is the answer. • This study shows that • Our results indicate/demonstrate/show • In this study, we provide evidence that • In this study, we have shown/found that

29. Organization - Transitions • Other than “because” which creates a very long sentence, you must create a transition phrase/clause to link results to answer • In our experiments/study • Evidence that (answer) is that • We found that • Or use a topic sentence • (answer) has been demonstrated in two ways….First…..Second

30. Organization - Beginning • Example: • In a complete cohort of 14,000 children born in Manitoba in 1995, we found an association between antibiotic use in the first year of life and asthma at age 7. Children receiving more than 4 courses of antibiotics were at one and half times the risk of developing asthma.

31. Organization - Beginning • Example: • Our cohort study of 14,000 children born in Manitoba in 1995 documented evidence of an association between antibiotic use in the first year of life and asthma at age 7. We found that children receiving more than 4 courses of antibiotics were at one and half times the risk of developing asthma.

32. Organization - Beginning • DO NOT begin the Discussion with • A second introduction • A summary of the results • Secondary information • DO give credit to yourself • If you are the first or the missing link than say so, but be cautious • Be neither too modest or too boastful

33. Organization - Middle • Organize topics in order of most to least important answer • For each answer, support, explain, defend (results consistent with X, adjusted for Y) • THEN explain results that do not support answer, discrepancies with other results, unexpected findings, limitations of design/ methods & validity of assumptions • State importance of the answer last

34. Organization - Middle • Tell a story on 2 levels: individual stories within each paragraph and an overall story thruout using either of these techniques • OVERVIEW: topic sentence at the beginning of each subsection & transition topic sentence at the beginning of each paragraph • STEP-BY-STEP: topic sentence which repeats key term from previous paragraph, at the beginning of each paragraph

35. Organization: Overview Method • Subsection topic sentence announces • Our study design has several strengths.. • Transition topic sentence (paragraphs within section) keeps the story going • One (first), second (another), third, final • Transition topic sentence (between sections) keeps the story going • Despite these strengths, our study was limited

36. Organization: Step by Step Method • Paragraph topic sentences which include key terms picked up from previous paragraph • 1st pr: …association with antibiotic use remained in rural children… • 2nd pr: Why would rural children be at increased risk? • 3rd pr: We offer an alternate explanation for increased sensitivity of rural children… • Using a question as a topic sentence provides variety, but ONCE is enough

37. Organization - Middle • Check that outline of overall story is apparent from reading the chain of topic sentences at the beginning of each paragraph. The reader should be able to read the first sentence of every paragraph and follow the story. • For a point that does not fit the story, either: • Use an ordinary topic sentence without transition or key term and put point in a separate paragraph • Use a subtopic sentence and include the point in another paragraph

38. Organization - End • Conclude by making a point. Options are: • Restate answer to the question. Precede answer by a signal (In conclusion…..) • Indicate importance of the research by stating applications, recommendations, implications and speculations • Restate answer and indicate importance of the work

39. Length • Do not obscure or overwhelm the message. Make the Discussion no longer than necessary to state, support, explain and defend the answers. • Short as possible • Do not use unnecessary words • Do not add unnecessary detail, such as overwhelming details on what others have found • Do not include side issues, such as citing literature which is not directly relevant to your findings

40. Structured abstract provides a good way for you to look at your work. (know rules, word limits, the take home message). The Abstract Limit introductory rationale to 1 (max 2) short, focused sentences on topic you’ll be presenting new data on (not the general area of research or broadly related topics). - Ex: Hygiene hypothesis vs Ag purity… The question.“Here we asked…” precisely what?. May follow citation of your or the field’s hypothesis. Limit methodology to what you need to tell them for them to understand your broad approach—not everything you did. - Don’t bury them in detail. Forest vs Trees - Accent novelty or distinguishing characteristics that distinguish yours from exptl approach taken by others. (if there is)

41. The Abstract Results: • What is the logical thread of the story you are telling? (This and “Significance” are decisive in acceptance/rej’n) 2. What are the most exciting things you found that address your research question ? Needs to be a Precise but Coherent story-- not list of IL1 up, IL 2 down, IL3 unchanged, 4 undetectable, lots of proliferation… If you’ve got it flaunt it (if anyone would be expected to care). “Significantly” vs p<0.0001; “We saw” vs “In 74 subjects, we saw” Conclusions / Significance:What has this paper added? What does the world now know that they would not if you had not submitted this paper? Why should we care? Translation: Why my paper must be published.

42. Abstract Tactics • Clear story? Read aloud to assess continuity and impact. • Short sentences. Simplicity. • Every word essential? (extra adjectives, articles that add little?) Detail buries impact. • PPF Verb tenses. Consistency. • Ask someone to read it and tell you what they got from it • Omitting, or putting in vague, hypothesis/question turns this into a blind guessing game (by reader/reviewer) that you’ll lose. Why did they do the work? • Target your style for the type of paper: Methods, Hypothesis testing, Descriptive… See Mimi !

43. The Title The most important part of your whole paper. Some people read only title, or only abstracts. Your data may never be seen. Shorter is better What is the goal of a title?

44. The Title Goals: 1. Describe what you contributed—what is your message 2. Attract readers. Tips on accomplishing this: • Want it to be: Accurate, complete, specifically targeted to your paper, memorable. (take home msg) • ONE message (paper too!) • Look at other successful titles in your area. • Begin with the important term: “RSV is linked to… “Excessive Leukotriene production causes…” “Maternal smoking associated with…” • Declarative sentence: “Maternal stress is linked with increased pediatric asthma” vs. • “The effect of maternal stress in development of pediatric asthma”

45. General tips you’ve found useful • Writing a paper is a daunting experience. Three weeks effort can turn into three years. Set weekly timelines and stick to them—it’s not going away until you get it done. • Get regular feedback from your colleagues, and advisor… Initial 1p Overview; Draft figures/ results (what else is missing?); M and M; … • Take care. Poor spelling/grammar/organization (ie. Fig 1,3,2,5) indicates a lack of interest to advisor, reviewers. If you don’t care enough, why will anyone else? Read it aloud!

46. Tips Importance of negative data—not only positive findings count! IF there was no change in a readout or if it was undetectable AND the audience is expected to care about it, you need to tell them. Ex. Increased IL-13 selective vs Type 2 expression upon parasite exposure… (result: no change in IL-4,5,9). • However—watch out for laundry list. Don’t assume that everyone knows your area and your literature in detail. “While it is widely believed that…” explain true state, caveats. Mimi Chapter 12—The Big Picture. More?