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A Writer’s Algorithm or
Papers Without (too much) Pain
A Rubric to Efficiently Organize and Write a Manuscript
Amy J. Markowitz, JD
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 or a quick peek at the Tivo’d Daily Show
Create a Scaffold
• Using the Instructions for Authors/Grant Instructions contained on the Web site of every journal/funding agency, 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 or a latte
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
• Pull out your Endnote Library and troll around
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 ride
Write an Introduction
• Do not reinvent the wheel - go back to the grant, proposal, RFP
• Content: The introduction is your promise to the reader
• Style: Write the way that you speak, but not conversationally
Content of Introduction
• The introduction is your promise to the reader (in 3 paragraphs or less)
• Describe the background, raison d’etre of the study, the reason your findings are relevant, and (if you’re feeling gutsy) the contribution you have made
• Close the intro with a road map of what the reviewer/reader will find in the paper
Style of Introduction• Write the way that you speak, but not
conversationally• Be economical in your articulation: Avoid
connectors, descriptors, or transitions that you would not feel comfortable saying aloud, or presenting orally (eg, hence, thusly)
Specific Aims
• A roadmap or table of contents• Well-focused objectives and milestones
– Formulate aims in anticipation of publication titles
• Test your hypothesis– list no more than one or two sets of experiments
for each aim– briefly state how the aim helps prove your
hypothesis
• Evolve as the Research Plan evolves
Specific Aims, con’t.
• Write with experts and non-experts in mind
- use terms a broad audience will understand
• Don’t draft a hypothesis that you are unable to
test
• Draft and Redraft
Linking Aims to Hypotheses
Aim 1. To prospectively determine the relationship between recent cigarette smoke exposure and the development of ALI in a cohort of trauma patients at high risk for ALI.
We will analyze clinical and biological data from an ongoing prospective cohort of 350 trauma patients at SFGH to determine whether active and/or passive smoking, as reflected by serum cotinine levels on admission, are associated with ALI. This cohort provides a unique opportunity to study a population with a high prevalence of smoke
exposure and at high risk for ALI. • Hypothesis 1: Recent active or passive exposure to
cigarette smoke will be associated with an increased incidence of ALI in trauma patients.
Aim 2. To determine the relationship between biomarkers of longer-term cigarette smoke exposure and ALI in a prospective cohort of mixed medical and
surgical patients.We will use the resources of an ongoing cohort study to
perform a nested case-cohort study of 340 ALI patients and critically ill controls. Novel biomarkers in urine, hair, and toenails that reflect longer-term CSE will be used to compare exposure in cases and controls, controlling for important confounders. This sample will reflect the broad range of
clinical conditions associated with ALI.
• Hypothesis 2: Active and secondhand smoking, as reflected by biomarkers of cigarette smoke exposure, will be associated with ALI in a broad population of critically ill adults.
Aim 3: To test the mechanistic relationship between cigarette smoke exposure and ALI by measuring
biomarkers of endothelial injury, lung epithelial injury, and disordered coagulation in patients with ALI.
We will measure key biomarker levels in plasma samples from patients enrolled in Aim 2 to determine which biomarkers are particularly associated with CSE. These analyses will provide important insights into the mechanisms by which smoking promotes the development of ALI in patients at risk.
• Hypothesis 3: Exposure to cigarette smoke will be associated with elevated markers of endothelial injury, lung epithelial injury, and disordered coagulation in patients with ALI.
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/
Finishing the Introduction
• Read your introduction aloud to yourself to see if it rings true and sounds sensible
• Call it a day
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
Results/Discussion(Pull out the scribbled list again)
Framing the Content• 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?
Discussion
• Actually speak to the reader • 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
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
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)
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
Conclude With a Send-off
• A conclusion is not a repetition
• Take the bully pulpit, and set a course
• Set a research agenda; get others interested in your field
• Create some controversy that is well-founded on the basis of your findings
Some Practical Advice
• Return to the Instructions for Authors and re-check formatting requirements, word length, formatting of references, suggested number of references, advice about graphics, 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
Credit Where It I$ Due
"This project was supported by Grant Number KL2 RR024130 from the National Center for Research Resources (NCRR).”
Access Where It Is Due
The NIH Public Access PolicyThe Policy implements Division G, Title II, Section 218 of PL 110-161(Consolidated Appropriations Act, 2008) which states:
SEC. 218. The Director of the National Institutes of Health shall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine’s PubMed Central an electronic version of their final peer-reviewed manuscripts upon acceptance for publication, to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law.
Well-organized information about the NIH Public Access policyhttp://publicaccess.nih.gov/.http://publicaccess.nih.gov/FAQ.htm#b1
Compliance: a three-step processI) Address Copyright. Before you sign a publication orcopyright transfer agreement, make sure that the agreement allows the paperto be submitted to NIH in accordance with the Public Access Policy.
II) Submit the paper to NIH. a. Some publishers make the final published version of every NIH-fundedarticle publicly available in PubMed Central within 12 months of publicationwithout author involvement. See http://publicaccess.nih.gov/submit_process_journals.htm for a list of these journals. b. Deposit a copy of the final peer-reviewed manuscript in the NIHManuscript Submission (NIHMS) system (http://www.nihms.nih.gov/).c. Someone else (e.g., a research assistant or librarian), orpublisher, may deposit the final peer-reviewed manuscript files in theNIH Manuscript Submission system for you.
III) Cite. As of May 25, 2008, when citing a paper in NIH applications, proposals, and progress reports that falls under the Policy, authored or co-authored by you or arose from your NIH award, you must include the PubMed Central reference number. This policy includes applications submitted to the NIH for the May 25, 2008 due date and subsequent due dates.
