This document provides an overview and outline for a presentation on writing research papers and managing reviews. It discusses frameworks for timely presentation of research and reviews, including the Writer's Algorithm which outlines good writing habits and the typical sections of a paper. The presentation style is meant to be interactive, encouraging attendees to interrupt and share. Key aspects that will be covered include determining the audience and journals, writing the title, abstract, introduction and conclusion, and organizing the methods, results and discussion sections. Guidance is provided on writing each section and ensuring a logical flow that clearly presents the findings and their implications.

1. A Writer s Algorithm
or
Papers Without (too much) Pain
and the sequelae that are Reviews…
October 7, 2011
Amy J. Markowitz, JD
Consulting Editor/Scientific Writing Specialist
UCSF Clinical and Translational Research Career Development Program
Managing Editor, Care of the Aging Patient JAMA
amyjmarkowitz@alum.wellesley.edu
415-307-0391

2. Markowitz Bio
http://ksc-ctsi.ucsf.edu/profile/amy
Amy J. Markowitz, JD, is the Consulting Consulting Editor/Scientific
Writing faculty for the UCSF Clinical and Translational Research Career
Development (K) Program. She teaches the Publishing and Presenting
Research (EPI 212) course as part of the TICR curriculum.
She is the Managing Editor of JAMA’s case-based geriatric series, Care
of the Aging Patient: From Evidence to Action.
She is a freelance editor, writing mentor, and curriculum development
consultant, with particular expertise in medicine and health policy.
She is an editor-for-hire on book, grant, Web site content, curriculum, and
manuscript projects, and provides on-site writing instruction.

3. Today's agenda
• A framework for presenting research and
managing reviews timely
• The Writer s Algorithm
– The basics of good writing habits (and
suggestions for teaching them to others)
– The sections of a paper
– The basics of effective self-editing

4. Today s style
• Please interrupt frequently
• Share with others - research and writing are not
solitary pursuits - at least not mostly

5. Most research involves a simple
finding
A>B
Weight of experimental mice > Weight of control mice
Bone density with TT genotype > Bone density with tt genotype
Survival after surgery > Survival with medical therapy
Health care in UK > Health care in US

6. Who cares?
• Who is your audience?
• Which journals are “reach” schools?
• Where have you published before?
- Have you served as a reviewer?

7. Title
• Based on the research question
• Try to make it interesting (catchy),
declarative, maybe even provocative
• Remember the magic words
– Randomized, blinded, prospective, etc.

8. The 4 basic parts of an abstract,
paper,
or presentation
• Introduction: Why would it matter if you could
show that A > B?
• Methods: How you will show that A > B.
– (Effect size: Comparing A with B)
• Results: Show that A > B.
• Discussion: What is the implication, now that we
know that A >B?

9. Begin Before the Beginning
• Scribble or type a list of topics, themes,
ideas, conclusions, in any order
• Work for about 15 minutes and then
reward yourself with a latte, and a quick
peek at the TIVO d Daily Show

10. Create a Scaffold
• Using the Instructions for Authors
contained on the Web site of every journal,
set up the major headings/sections of the
paper
• You are now not looking at a blank screen
and can treat yourself to a snack and a latte

11. Put on the Sorting Hat
• Insert fragments from the scribbled list into the
scaffolding sections, eg, background? result?
discussion?
• Pen a meaningful topic sentence for the fragments.
Note: meaningful means an original idea that sets
up the issue to be discussed in that section or
paragraph
• Continue to fill in the space under the topic
sentences by moving entries around, and by
adding entries from the scribbled list
• Open Endnote or other reference library and look
around

12. Put on the Sorting Hat
(continued)
• Note ideas for tables, boxes, figures
• Re-check rules for authors as to formatting
requirements
• Note areas that require further thought or
discussion
• Go for a run or a bike ride

13. Write an Introduction
• Do not reinvent the wheel - go back to the grant,
proposal, RFP
• Content: The introduction is your promise to the
reader
• Use a writing resource, style manual, dictionary,
grammar guide
American Medical Association Style Manual www.amamanualofstyle.com/
Merriam Webster online dictionary http://www.merriam-webster.com/
Stedman s Medical Spellchecker and dictionaries www.stedmans.com/
Nuts and Bolts of Scientific Writing- Constance Baldwin, PhD http://www.academicpeds.org/
espauthoring/page_01.htm

14. Content of Introduction
• The introduction is your promise to the reader (in
3 paragraphs or less - PRESENT TENSE FOR
ESTABLISHED KNOWLEDGE)
• Describe:
– Background, the raison d etre of the study (why the
problem was compelling)
– State of the field (relevant literature to date)
– The reason your findings will be relevant, and (if
you re feeling brave) the contribution you have made
• Close with a road map of what the reviewer/
reader will find in the paper:
– Hypothesis, Design, Sample, Methods

15. Introduction: The Final Test
• After reading it, could someone not familiar with the field
understand…
– Why you did the study
– How it advances the current state of the evidence

16. Dictionary of Useful Research
Phrases
• "It has long been known..." <-> I didn't look up the original
reference.
• "A definite trend is evident..." <-> These data are practically
meaningless.
• "Of great theoretical and practical importance..." <-> Interesting
to me.
http://writedit.wordpress.com/category/biomedical-writingediting/

17. Finishing the Introduction
• Read your introduction aloud to yourself to
see if it rings true and sounds sensible
• Click SAVE and pack up your
computer for the night

18. Write the Easy Parts First
• Good bets for knocking off sections are the
Methodology and Results sections
• Methods: Carefully track the research protocol,
and if you repeat or reproduce a part of the
protocol as stated in your original proposal, do not
paraphrase or change verbiage (PAST TENSE
FOR WHAT YOU DID)

19. Methods: How will you show that A > B?
• Who (what) did you study?
• What, if anything, did you do to them?
• How did you make your measurements?
• How did you compare A with B?
• Statistical tests to show that A ≠ B

20. Methods Checklist: The 4 Parts
• Design: Define the type, e.g., retrospective, case-
control, RCT, prospective
• Subjects: population, inclusion/exclusion criteria,
controls
• Measurements: survey instruments, assays,
physical measurements
• Analysis: Statistical plan and rationale

21. Measurements: A Way to
Organize
• Predictors before outcomes
• Medical presentation
– History, physical, simple lab, complex matters
• Explain odd decisions or missing data
• Appropriate level of detail - know your
audience

22. Analysis
• Don t list tests: explain why you used them
• Tell how measurements became variables
• How did you estimate the effect size?
• How did you determine the precision and significance of
the effect size?
– Univariate
– Multivariate (say what you adjusted for)

23. Results: Showing that A > B
• Make sure the main result is obvious
– Don t bury it in the middle of a long paragraph, an 8 x
6 table, or a complex figure
• Use alternative definitions of A and B
– Different measurement techniques or times
– Multivariate adjustment
– In various subgroups

24. Results, continued
Order of presentation:
– Collected sample first
– Follow order of hypothesis, chronology or
design elements
• Simple results before complex
• Strongest findings first
• Use subsection headings as a roadmap

25. Results/Discussion
(Pull out the scribbled list again)
Framing the Content (GENERALLY, PAST TENSE
FOR WHAT YOU FOUND)
• What grabbed you about your results?
• Was there an expected or unexpected finding? If you are
presenting something new, build the case in a logical order –
eg, is this study the result of a long line of similar research
that is confirmatory, but ?
• Is it presenting a new theory to explain an old phenomenon?
Is it rebutting a long-held belief in the field?
• Does it have implications for research policy or social policy?
• Will it be a useful tear-out with pragmatic clinical utility?

26. Discussion
• Actually speak to the reader (PRESENT
TENSE)
• Argue your case with the facts that you ve set
forth formulaically in the Results sections
• Use I.A.C. (Idea - Analysis - Conclusion)
• Check each paragraph against the next: be certain
that you are connecting the dots for the readers,
not bludgeoning them

27. Discussion Content
• Highlight key findings as they relate to the
study s purpose (was your hypothesis
proved?)
• Evaluate findings in relation to literature
• Discuss limitations
• Conclude with recommendations

28. Styling Your Discussion
Using the topic sentences you ve already drafted,
write stand-alone paragraphs following the I.A.C.
rubric:
• Idea (the topic sentence)
• Analysis (the clinical, microbiologic, biochemical,
social, economic, explanation of the result)
• Concluding sentence which sums up the analysis,
and often will serve as a transition to the next
paragraph

29. Styling Your Discussion
(continued)
• If you find that you are stuck, and cannot create an
I.A.C. paragraph for a particular result, go back to the
topic sentence, and make sure that it is worthy of a
whole finding/result
• Consider whether you have enough (interesting)
results to merit another paper (after this one is
completed)

30. Avoid Throwaway
Observations
The Sarah Arron Rule:
Do Not Give Reviewers the Opportunity to
Review the Paper You Didn’t Write

31. Anticipate Possible Criticism
• Careful, not defensive, explanation
• Anticipate critique of your methodology or
study design and present the reasoning
behind your choices
• Your design and study criteria were well
thought out in the beginning – now is not
the time to have a crisis of confidence

32. Conclude With a Send-off
• A conclusion is not a repetition
• Take the bully pulpit
• Set a research agenda; get others interested
in your field
• Create some controversy that is well-
founded on the basis of your findings

33. Some Practical Advice
• Return to the Instructions for Authors
– re-check style formatting requirements, word limit, format of
references, number of references, graphics format, the works
• Print hard copy of the manuscript, and proof it for
substance by reading it aloud once, making hard copy
corrections (you will be amazed at what you will find to
self-edit)
• Then, and only then, run spell check
• Wait a day, re-read, and with a sigh of relief, hit the
send key to your co-authors, or friendly readers

34. Credit Where It I$ Due
"This project was supported by Grant
Number KL2 RR024130 from the
National Center for Research
Resources (NCRR).

35. Responding to Reviews*,
Internal and External
*Formerly known as Anger Management

36. Reviews, internal and external
• Read through the reviews twice
• You will be offended by everything the first
time, and begin to appreciate some of the
merits by the second time
• Consult with your co-authors

37. Take a step-wise approach
• Begin the explanatory Response to Editor letter
simultaneously with your revisions
• The tone should be respectful but not obsequious
• Address each comment, in numeric order, citing
to the page and line where you ve made the
revisions - as relevant, add the actual text to the
letter once it is finalized in the manuscript
• Where logical, group comments so that they are
more easily addressed, eg, comments from each of
three reviewers that address the same issue in
methods, results, or discussion

39. What if the reviewer has
completely missed the point?
Consider whether:
• You have presented the idea abstrusely; try
rewriting unless this undermines the integrity of
the idea
• The reviewer (generally an expert in the field, wed
to their point of view) a) has a vested interest in
your being incorrect, b) has just been proven
wrong by your results, or c) did not read the
paper carefully

40. Re-consult
• Check your intra-reviewer-rater reliability
• What if MOM and DAD disagree????
• Get your gumption up, be thoughtful, and
make a decision - you must resubmit -
now s the time…

41. Greg s Reviewer s Misread
Some aspects of the results presentation could be clearer. Some of the presentation of results
such as those in figure 3 does not make it clear how many patients were seen at each follow-up
visit.
We have attempted to make the results more clear, with a special emphasis on the number of
subjects with follow-up. As suggested, we have changed figure 3 so that the numbers of patients
at each follow-up visit are clearer and have included those numbers in the figure itself.

42. Original Figure 3 and Legend

43. Abundance of Caution

44. Response and Lessons Learned
Dealing with easy fixes, eg, ad the n=

45. Ralph s Reviews
Reviewer #4:
First of all let me acknowledge that I appreciate the complexity of
evaluating any mass media campaign, particularly one that is very short
term with limited funding.
This is an interesting and complex paper as currently constructed. I
found many parts difficult to follow and lacking in methodological
details necessary to properly interpret the results. Having said that,
I think, with much revision, some parts merit publication (if not by
Medical Care, perhaps elsewhere). I am trying to make my comments
constructive.
I absolutely disagree that this campaign is an example of a wide-scale
MM campaign to affect office visit and antibiotic use... In summary, I think there is
too much in this one paper. … The MM campaign does not fly with me at all.

46. Ralph s Response
The easy fix:

47. I absolutely disagree that this campaign is an example of a wide-
scale MM campaign to affect office visit and antibiotic use... In
summary, I think there is too much in this one paper. … The MM
campaign does not fly with at all with me.
• Please see response to Reviewer #4, Comment #7 regarding media exposure/impressions.
• Both the preceding office and household educational intervention (Gonzales R et al. Health
Services Research 2005;40:101-16) and the mass media campaigns were based on the
logic that reducing office visits was one possible (and perhaps, most effective) means for
reducing inappropriate antibiotic use; the other key means was increasing appropriate
prescribing behavior by providers. The small media materials for households and patients
incorporated information that was designed to assist families to make appropriate decisions
about whether medical care was warranted for symptoms of colds or bronchitis, to challenge
assumptions that antibiotics are required for colds or bronchitis, and to put the issue of
antibiotic use for ARIs on the agenda for discussion with a provider. The mass media
messages contained less detail than the household and clinic materials for patients, but
were also designed to provoke questioning about the need for antibiotics for various
respiratory symptoms and illnesses. We recognized that if a healthcare decision-maker in
the family (e.g., the mother) no longer believed that antibiotics would help colds and coughs,
she might be less likely to seek care. This is based on the multitude of studies that have
found that desire and perceived need for antibiotics—for symptom relief—is a major reason
that patients seek care for these illnesses. In social marketing terms, in this project a critical
difference between doers and non-doers was the idea that antibiotics were necessary for
treatment of ARIs (see W Smith references below; also, William Smith was the chief AED consultant on
the Get Smart Campaign).
• Smith, W. (1998). Social marketing: What's the big idea? Social Marketing Quarterly, Vol. IV, Number 2,
5-17.
• AED. Social Marketing Lite: Ideas for Folks with Small Budgets and Big Problems.
http://www.aed.org/ToolsandPublications/upload/Social%20Marketing%20Lite.pdf or at
http://www.eric.ed.gov/ERICDocs/data/ericdocs2sql/content_storage_01/0000019b/80/17/30/ea.pdf

48. Response and Lessons Learned
Dear Dr. Gonzales,
I am pleased to inform you …
***************************************************************
How many papers have we got here?

49. What if the reviewer has
completely missed the point?
• Tough. You must explain to the journal editors
why it is that you have chosen not to revise in
accordance with the reviewer s comment, and be
prepared to support your point of view.

50. Response and Lessons Learned
• Submit elsewhere?
• Change the focus?
• Consult with a non-co-author colleague?

51. Shave and a Haircut
• Address stylistic editorial comments after the
substantive revisions
• Stylistic issues frequently relate to length
• Reduce to tabular or graphic form any appropriate
demographic descriptions of study subjects, or less
intrinsic data and descriptors
• Do not repeat in text what is best presented in a
table or figure
• Give your co-authors one last shot, WITH A
DEADLINE, then: pull the trigger