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How to write…
How to review…
a paper
January 30, 2006
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?
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)
1. 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?
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
Renee –the Intro
• Monther- Results
• Anita –Discussion
• Kent - The Abstract and Title
• Discussion: When it’s returned…
TheThe Good, Good, TheThe Revised Revised && TheThe Ugly… Ugly…
•GOAL: Novelty, originality and topicalityIs it new and are we interested?
•MESSAGE: Clear, concise and well writtenCan we understand what you are telling us?
•STORY: Well designed, explained and significant
Is what you are telling us believable and relevant?
When the going gets When the going gets tough…tough…the tough find help!the tough find help!
• Essentials of Writing Biomedical Research PapersBy Mimi Zeiger, 2nd Edition
• How I review an original scientific article.By FG Hoppin
• At the Bench: A Laboratory NavigatorBy Kathy Barker
• A DICTIONARY and Spell Check!!!
The IntroductionThe Introduction
• Capture the reader’s interest!
• Prepare reader with the basics to understand your paper
• The opening scene of your story
The Lit
Known
Unknow
n
Questio
n
Approac
h
Which introduction is Which introduction is better?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.
AA
BB
Quick tips for writing Quick tips for writing introductions…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!
Materials and MethodsMaterials and Methods
• Experiments done to answer the question
• Cookbook for reproducibility
Quick guide for writing Quick guide for writing MM&&MsMs
MaterialsMaterials
• Reagents
• What was examined
MethodsMethods
• 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
Results
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
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
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".
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
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)
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
Writing Scientific PapersWriting Scientific Papers
Anita L Kozyrskyj, PhDAnita L Kozyrskyj, PhDNational Training Program in National Training Program in
Allergy and AsthmaAllergy and AsthmaJanuary 30, 2006January 30, 2006
What’s there to Discuss?What’s there to Discuss?
Function Content Organization Length
FunctionFunction
Main– To answer questions posed in Intro
Other– To explain how results support answer– To explain how answers fit existing
knowledge
ContentContent
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
ContentContent
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)
OrganizationOrganization
A beginning (power position) Focus the story
A middle Tell the story
An end Make a point
Organization - BeginningOrganization - 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
Organization – Support AnswerOrganization – 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
Organization - SignalsOrganization - 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
Organization - TransitionsOrganization - 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
Organization - BeginningOrganization - 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.
Organization - BeginningOrganization - 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.
Organization - BeginningOrganization - 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
Organization - MiddleOrganization - 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
Organization - MiddleOrganization - Middle
Tell a story on 2 levels: individual stories within each paragraph and an overall story thruout using either of these techniques
A. OVERVIEW: topic sentence at the beginning of each subsection & transition topic sentence at the beginning of each paragraph
B. STEP-BY-STEP: topic sentence which repeats key term from previous paragraph, at the beginning of each paragraph
Organization: Overview MethodOrganization: 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
Organization: Step by Step MethodOrganization: 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
Organization - MiddleOrganization - 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
Organization - EndOrganization - 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
LengthLength 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
Structured abstract provides a good way for you to look at your work. (know rules, word limits, the take home message).
The Abstract
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)
The question. “Here we asked…” precisely what?. May follow citation of your or the field’s hypothesis.
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 AbstractResults:
1. 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.
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 !
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?
The Title
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”
Goals: 1. Describe what you contributed—what is your message2. Attract readers.
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!
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?
