Transcript A step forward (level 2) - Ferdowsi University of Mashhad

Scientific Writing: A step
forward
Arash Etemadi, MD
Department of Epidemiology and Biostatistics, School
of Public Health, Tehran University of Medical Sciences
[email protected]
Why Writing Is Important?
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No publication, no project
 Make information available for others
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No publication, no promotion
 Yardstick of productivity
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No publication, no funding
 What have you done for me lately?
Intrinsic Causes of Writing
Problems
 Internal
Censors
–Fears of Failure
 Perfectionism
 Procrastination
Intrinsic Blocks to Writing
(I) Inability to Start Writing
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“First, there is the difficulty of writing at
all”
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D. Brande Becoming a Writer
Perfectionism, self-consciousness,
procrastination
How to Start
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Daily
30 minutes to one hour
Do not pay attention to structure,
grammar, spelling
Stimulus Control
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Few regular places to work
Close the door
Unplug the phone
No e-mail
Arrange the site
– But do not clean up the office
(II) Inability to Finish Writing
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Multiple revisions
Multiple analyses
“Each time I think I am finished, I see
there is a lot more to do”
Similar roots as inability to start
(perfectionism)
Different people
Lack of insight
TUMS workshops on
scientific writing
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Level 1: Basics
Level 2: Focus on international
publications
Level 3: Specialized writing
An overview
The traditional IMRaD
–Introduction
–Metods
–Results
–Discussion
A full paper consists of:
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Title
Authors and Affiliation
Abstract
Introduction
Methods
Results
Discussion
Acknowledgments (optional)
References
Target your paper at a
particular journal
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Familiarise yourself thoroughly with
potential journals
what sort of papers do they publish?
(original articles, briefs, reviews,
commentaries, iconoclastic pieces?)
What is the “culture” of the journal?
National or international focus?
Write for that journal
If for a general medical
journal..
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Mostly read by clinicians, so
“practical”, useful, papers highly
regarded.
If a specialist journal...
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Cut to the chase!
Do not waste time with elementary
ABC introductory sections -- it is being
read by people who know the field
locate your paper precisely in what
has gone before
1.
2.
3.
4.
5.
6.
7.
8.
9.
Design well
Decide politics
Choose journal
Read instructions to authors/papers
Set framework
Prepare drafts
Distribute
Polish
Submit
What is the gestational period for a clinical science publication?
START
PROTOCOL/IRB 2-4 months
STUDIES/
4-24 months
EXPERIMENTS
WRITE AND
SUBMIT
REWRITE AND
RESUBMIT
2-4 months
2-4 months
WAIT
PUBLISHED!
14-44
Months!
2-4 months
BEST GUESS
2-4 months
Order of writing?
1.
2.
3.
4.
5.
6.
Results
Methods
Introduction
Discussion
Abstract
References
Order of writing?
1.
2.
3.
4.
5.
6.
Methods
Results
Introduction
Discussion
Abstract
References
Getting Started
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Do you have enough data for a
manuscript?
Do you have a complete story to tell?
Write a list of the figures and tables
that you would include in your paper
Write a brief, skeleton outline of the
paper (1-2 pages) and show it, along
with the list of figures, to your
coworkers and discuss
TIPS….
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Be enthusiastic about your data and
your story
Be sure you convey what “problem”
you have addressed in your study
Be sure to describe the area of
research you are studying as
fascinating and important
First Steps
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Analyze your data critically
Do statistical analyses
Prepare figures
– make graphs
– take photographs, get prints, label
Prepare tables
Be sure your data is internally consistent
Show the final data figures (and tables) to
your co-authors for comment
Effective Data Presentation
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Figures are almost always better than tables
Look at published figures (in papers that have
data similar to yours) to get ideas about how
to compose graphs, and how to frame and
label blots, gels and photomicrographs
Learn how to use graphics programs (Sigma
Plot or Excel)
Learn to use Adobe Photoshop
Photomicrographs - color is expensive!
Instructions to the
Authors
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Guidelines for writing the paper
Usually found in January issue of
journal
Almost always found on the web site
for the journal
Mechanics of Writing- Title,
Abstract and Introduction
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Title- be as specific as possible; include
design
Abstract is a summary of the paper
(therefore write last); check for a word
limit; structure it.
Introduction – Importance, a brief
review of the literature, information
gaps, statement of hypothesis
Introduction- about 3 to 4 paragraphs
Mechanics of Writing Methods
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Use subheadings to organize
Details - use sufficient detail for another
investigator to be able to reproduce
your results
Reference methods used previously
Be precise with respect to
measurements and definitions
Statistics
Mechanics of Writing-Results
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Tell a story
Use the most logical sequence to present the
data (not necessarily the order in which you
did the experiments)
Just report the data - do not include
interpretation or comparison to literature
No duplication of data
Guidelines for Writing Results The Study as it was Conducted
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Specify the dates of the study
Provide a schematic summary
Describe the characteristics of each group
Indicate if the sample is representative
Indicate if randomization was successful
Describe duration and nature of follow up
For observations based on judgment,
provide assessment of consistency
Guidelines for Writing
Results:
The Study Outcomes
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Present the results for all primary endpoints
Report statistical findings in detail
Report actual p values , 95% CI , etc.
Report the main findings in figures or tables
- you don’t need to also report them in
the text
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Report confounders
Mechanics of WritingDiscussion
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Construct parallel to results
Interpretation of data
Relate your results to the findings of
other investigators
Summary paragraph at end - include
significance of results
Avoid redundancy with results and
introduction sections
Good discussions--
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Address every key finding of the study
Present the finding in terms of what is
known
State why this study is different
State why the results concur/
disagree with current knowledge
Justify differences
Point out future directions/ continued
knowledge gaps
References
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Aim for about 30 references
Use recent review papers where appropriate
to decrease the number
Get a hard copy of every reference in the
manuscript and make sure the referenced
paper says what you say it does! Don’t use
abstracts!
Proof-read the reference list especially
carefully as one of your reviewers may be
cited!
Use End Note or other bibliographic software
Use the Internet
A Few Rules
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The first time you use an abbreviation, define
it
When you give the commercial source for a
reagent, the first time you cite the source
include the location of the company (city and
state)
Make sure the subject and verb agree in
every sentence
No contrac. or exclamation points!
A Few Rules - continued
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Look for redundancy within the manuscript
Try not to use “it” or “they” - be specific!
No jargon
Two shorter sentences are frequently much
more effective than a long, complex sentence
“Data” is plural not singular, i.e., “the data
are…” NOT “ the data is…”
A Few Rules - continued
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Capitalize people’s names, i.e., Golgi
apparatus
Never, ever plagiarize! (even from
yourself!)
Use numbers when expressing
measurements, except when the
number would begin a sentence
Common Errors in
Manuscripts
The Title
 is misleading/ does not set limits
 Gives away the punch line
The Abstract
 reports different measures/ methods
 results are not the same as the paper
 conclusions are not the same
The Introduction
 question, hypothesis, study
objectives are not specified, or are
confused
 importance, novelty, originality of
the study not shown
 presentation is not intriguing
(ie, the introduction is boring)
The Methods
Probably the most important section
reported methods not used
 details are missing so you cannot
understand
 entire methods are omitted
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Common Errors When
Reporting RESULTS
Errors of Omission:
 Not accounting for all study subjects
 Not naming which statistical tests were
used for specific analyses
 Not presenting the results in clinically
relevant terms
Errors in the Analysis
 Lack of power
 Failure to adjust for multiple comparisons
 Analysis by treatment received and not
by intention to treat
Errors in Interpretation
 Not recognizing the limits/meaning of p
 Clinical significance ignored in the face
of statistics
The Discussion
 logic is loose
 is too expansive, wanders
 is biased, omits key findings
 key results are poorly explained
 references are outdated
 speculation is not identified
 implications/ importance are overstated
 limitations are not described
The Conclusions
 simply restate the results
 do not answer the study question
 do not set limits for application
General Tips
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Just START !!
Follow the instructions for authors
Apply research analytical principles
Adhere to scientific and writing ethics
Be patient - centered and not numbers
centered
Write with vigor and write vividly
General Tips
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Write for readers and not to please peer
reviews
- readers read to learn; reviewers, to
improve
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Avoid self plagiarism
Update the literature review
Have a clinical colleague read your draft
Seek out criticism
More reading
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Hall GM, ed. How to write a paper. London: BMJ
Publishing Group.
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Peat J. Scientific Writing Easy when you know how.
BMJ Publishing Group. 2002.
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The Vancouver Group. Uniform requirements for
manuscripts submitted to biomedial journals.
www.icmje.org
Finding and choosing an
appropriate journal
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Where to look for the journal:
– Personal experience
– Colleagues’ experience
– Library
– Citations
– Online
Appropriate Journal
General versus Specialty
International versus Local
High versus Low impact
LOOK AT THE JOURNAL
LOOK AT THE AUDIENCE
1. What type of paper you
wrote ?
research report (“original article”)
review paper
special article
editorial
case report
letter to the editor
2. Is the paper really worth
being published?
– Is the message new, or new to a
particular audience?
– Search the literature to make sure you
are not repeating history ++
– Determine the odds that a particular
journal will appreciate the newness and
importance of your manuscript in the
context of the existing medical literature
3. Be realistic
– This is your first manuscript or you have already
a real track of publications on the topic ?
– Are the co-authors or the Institution were you
are based recognized in the field ?
– Are you an Iranian author submitting to a
national, a European or an American journal ?
– Reviews are mostly only by invitation but
national journals can be quite open
4. Know your journal
targets?
1. Impact factor and prestige
2. Normal content of one of the journal issues
 Which kind of manuscripts are published ?
 What are the preferred formats ?
3. Style and recent trends in the journal
4. Who is the editor-in-chief ? Can you contact
him ?
5. Who are the members of the editorial-board
? They are very aware of the journal’s
publication policy…you can try to contact
some of them with questions
1. Impact Factor: Oncology
1998
1999
2000
2001
2002
10.730
12.945
14.159
14.240
14.500
J of Clinical Oncology
8.228
7.963
8.773
8.530
9.868
Cancer Research
8.370
8.614
8.460
8.302
8.318
Clinical Cancer Research
2.941
3.442
4.643
5.076
5.991
Oncogene
6.192
6.517
6.490
6.737
5.979
Gene Chromosome Cancer
3.804
4.902
4.534
4.416
4.199
Int Jrnl Cancer
3.283
3.545
3.918
4.233
4.056
Cancer
3.660
3.362
3.611
3.909
3.941
Annals of Oncology
2.867
3.195
3.249
3.153
3.114
J Natl Cancer Institute
2. Normal content of the journal ?
• Is the topic within the scope of the
journal?
• Is the topic represented in the journal
frequently, or only rarely?
• Would the journal offer the best match of
audience and topic?
• What formats are acceptable to the
journal?
3. Style and recent trends
Do look at a recent issue of the journal you plan
to submit to
 Do read the Instruction to authors of the journal
(links to 3500 journals’ Instructions at www.mco.edu/lib/instr/libinsta.html)
 Be aware of word/figure/table limits
 Use the appropriate reference and citation styles
 Help Editors and Referees (and yourself) –
Number all pages
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4. Editor in chief and editorial board
– Who is the editor-in-chief ?
– If you can contact him, query the editor
be specific
 sell your product
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– Editorial board members?
5. Ask your mentor
– He may belong to a specific editorial
board
– He senses new opportunities
Launching of a new journal
 Accurate format to sell your product
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– Provides a more realistic point of view
6. What is your own agenda
when publishing ?
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Colleagues
Prestige journal vs. rapid publication
National visibility vs international fame
Issues of timeliness and in-depth track do
matter
7. Timeliness and
friendliness of the
submission process
• Hot topic?
• You can query about the average reviewing
time (assistant of the editors)
• Is there an online submission process?
• Can you track your manuscript status online
Target your paper at a
particular journal
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Familiarise yourself thoroughly with
potential journals
what sort of papers do they publish?
(original articles, briefs, reviews,
commentaries, iconoclastic pieces?)
What is the “culture” of the journal?
National or international focus?
Write for that journal
Anatomy of a submission
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Compose a title page
– determine who is the first author
(you) vs. the senior author (last in
the list of authors)
Be sure to cite the source of funding for
the project
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Study design and ethical approval
Data analysis
Authorship
Conflicts of interest
Peer review
Redundant publication (and duplicate
submission)
Plagiarism and fraud
Dealing with misconduct
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An “author” is generally considered to be someone
who has made substantive intellectual contributions
to a published study, and biomedical authorship
continues to have important academic, social, and
financial implications.
Some journals now request and publish information
about the contributions of each person named as
having participated in a submitted study, at least for
original research.
Editors are strongly encouraged to develop and
implement a contributorship policy, as well as a
policy on identifying who is responsible for the
integrity of the work as a whole (guarantorship).
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Authorship credit should be based on
– 1) substantial contributions to conception
and design, or acquisition of data, or
analysis and interpretation of data;
– 2) drafting the article or revising it
critically for important intellectual
content;
– and 3) final approval of the version to be
published.
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Authors should meet conditions 1, 2,
and 3.
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Acquisition of funding, collection of data, or general
supervision of the research group, alone, does not
justify authorship.
All persons designated as authors should qualify for
authorship, and all those who qualify should be
listed.
Each author should have participated sufficiently in
the work to take public responsibility for
appropriate portions of the content.
The order of authorship on the byline should be a
joint decision of the co-authors. Authors should be
prepared to explain the order in which authors are
listed.
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All contributors who do not meet the criteria for
authorship should be listed in an acknowledgments
section. Examples of those who might be
acknowledged include a person who provided
purely technical help, writing assistance, or a
department chair who provided only general
support. Financial and material support should also
be acknowledged.
Groups of persons who have contributed materially
to the paper but whose contributions do not justify
authorship may be listed under a heading such as
“clinical investigators” or “participating
investigators”
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When a large, multi-center group has
conducted the work, the group should
identify the individuals who accept direct
responsibility for the manuscript.
These individuals should fully meet the
criteria for authorship defined above.
When submitting a group author
manuscript, the corresponding author
should clearly indicate the preferred citation
and should clearly identify all individual
authors as well as the group name.
An example: GEMINI
Conflicts of interest
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Conflicts of interest comprise those which
may not be fully apparent and which may
influence the judgment of author, reviewers,
and editors.
They have been described as those which,
when revealed later, would make a
reasonable reader feel misled or deceived.
They may be personal, commercial, political,
academic or financial.
“Financial” interests may include
employment, research funding, stock or
share ownership, payment for lectures or
travel, consultancies and company support
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(1) Such interests, where relevant,
must be declared to editors by
researchers, authors, and reviewers.
(2) Editors should also disclose
relevant conflicts of interest to their
readers. If in doubt, disclose.
Sometimes editors may need to
withdraw from the review and
selection process for the relevant
submission.
Redundant publication/
duplicate submission
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Redundant publication occurs when
two or more papers, without full cross
reference, share the same hypothesis,
data, discussion points, or conclusions.
Duplicate submission is when the
same manuscript has been sent to
journal while still under evaluation by
another.
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(1) Published studies do not need to be repeated
unless further confirmation is required.
(2) Previous publication of an abstract during the
proceedings of meetings does not preclude
subsequent submission for publication, but full
disclosure should be made at the time of
submission.
(3) Re-publication of a paper in another language
is acceptable, provided that there is full and
prominent disclosure of its original source at the
time of submission.
(4) At the time of submission, authors should
disclose details of related papers, even if in a
different language, and similar papers in press.
What is fraud?
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Fabrification: Invention of data or
cases
Falsification: Wilful distortion of
data
– Ignoring outliers?
– Not admitting that some data
are missing.
– Post hoc analyses that are not
admitted?
– Not including data on side
What is fraud?
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Plagiarism: Copying of data or papers
– But by how much?
– Stealing ideas?
Redundant publication
Gift authorship.
Not attributing other authors.
Not publishing research
Not disclosing a conflict of interest
Plagiarism
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Plagiarism ranges from the unreferenced use of
others’ published and unpublished ideas, including
research grant applications to submission under
“new” authorship of a complete paper, sometimes
in a different language.
It may occur at any stage of planning, research,
writing, or publication: it applies to print and
electronic versions.
All sources should be disclosed, and if large
amounts of other people’s written or illustrative
material is to be used, permission must be sought.
Dealing with misconduct
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(1) The general principle confirming misconduct is
intention to cause others to regard as true that
which is not true.
(2) The examination of misconduct must therefore
focus, not only on the particular act or omission,
but also on the intention of the researcher, author,
editor, reviewer or publisher involved.
(3) Deception may be by intention, by reckless
disregard of possible consequences, or by
negligence. It is implicit, therefore, that “best
practice” requires complete honesty, with full
disclosure.
(4) Codes of practice may raise awareness, but can
never be exhaustive.
Investigating misconduct
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(1) Editors should not simply reject papers
that raise questions of misconduct. They are
ethically obliged to pursue the case.
However, knowing how to investigate and
respond to possible cases of misconduct is
difficult.
(2) COPE is always willing to advise, but for
legal reasons, can only advise on
anonymised cases.
(3) It is for the editor to decide what action
to take.
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Serious misconduct
Less serious misconduct
Sanctions, blacklists
Feedback
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Ask your co-authors to read the
manuscript critically
Give the paper to informed colleagues
(1or 2 max) to read
A real friend will give you lots of ideas
for improvement
Read your own paper as if you were a
reviewer, with the figures in front of you
as you read it
Final Preparations for
Submission
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Proof-read, proof-read, proof-read!
Make sets of figures for submission but also
keep a set of original figures for your files
Make copies of the submitted manuscript,
including the figures, for every author
Write a cover letter, short and direct,
addressed to the editor
Make a list of suggested reviewers, if this is
requested by the journal
Dr. Michael Holtzman,
American Journal of Respiratory Cell
and Molecular Biology,
Editorial Office
American Thoracic Society
1740 Broadway, New York, NY 10019-4374
Tel 212-315-6440
Fax 212-315-6456
Dear Dr. Holtzman,
Please find enclosed an original manuscript entitled, “……………………...” by [authors]. The material
presented in this paper is original and has not been submitted for publication elsewhere. No part of
the research presented in this manuscript has been funded by tobacco industry sources. We verify
that all the authors have read the manuscript and approve its submission. To aid the review
process, may we suggest the reviewers listed on the following page.
We hope that you will find our manuscript acceptable for publication in the American Journal of
Respiratory Cell and Molecular Biology.
Thank you for your attention.
Sincerely
…….
…….
Corresponding author
List of Potential Reviewers
1) Dr. Joe Smith
Duke University Medical Center
Cell Biology
438 Nanaline Duke/Box 3709
Durham, NC 27710
Phone: 919-684-8040
Fax: 919-684-8106
e-mail: [email protected]
2)Dr. Virginia Jones
Vanderbilt University
Pathology
1310 24th Ave S.
Nashville, TN 37212-2637
Phone: 615-327-4751 X 5499
Fax: 615-321-6305
e-mail: [email protected]
3)Dr. Tony D. Soprano
Southampton General Hospital
Child Health
Level G (803) Center Block
Tremona Rd.
Southampton, SO16 6YD United Kingdom
Phone: 44-23 8079 6161
Fax: 44-23 8079 6378
e-mail: [email protected]
4) Dr. David Mitchell
Department of Pediatrics
Milton S. Hershey Medical Center
H085 Hospital
Hershey, PA 17033
Phone: 717-531-5925
Fax: 717-531-8985
e-mail: [email protected]
5)Dr. Arnold Smith
University of Missouri-Columbia
Department of Molecular Microbiology and
Immunology
M616 Medical Sciences Building DC 04400
Columbia, MO 65212
Phone: 573-882-8989
Fax: 573-882-4287
e-mail: [email protected]
COVERING LETTER
Polite
Why Journal chosen
Importance of paper
Concessions
Brief
Submitting the Paper
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Frequently done on-line via PDF files
If required, send the number of hard copies
of the manuscript and figures required by the
journal
Send a disk with files for the manuscript and
figures, if required
Get the copyright form used by the journal
signed by all authors, if required
Send all of this material by a reliable method,
so that your precious manuscript is not lost
in the mail!!
Peer review
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Articles submitted to peer-reviewed
journals (manuscripts) are reviewed by
experts who advise the editor on
whether they should be published and
what changes are necessary.
Editorial decision
1.
2.
3.
4.
Accepted as it is (rare)
Accepted on the condition of certain
amendments (back to cycle)
Reconsidered if reviewers’ comments
met (back to cycle)
Rejected
Peer Review - Functions
To Protect
i) The author from publishing
&
ii) The subscriber from reading
Material of insufficient quality
Problems with peer review
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Slow
Expensive
A lottery
Ineffective
Biased
Easily abused
Can’t detect fraud
Works for improving studies not
selecting which to publish
Can’t detect fraud
Dealing with the Journal’s Response
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Absolute Rejection
– Don’t take it personal
– Don’t write or call the editors (unless you
know them well !)
– Editorial rejection: send it out the next day to
another journal
– Reviewers comments:
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Fix the easy ones
Fix the glaring ones
Unlikely to get much better sitting on your desk
Send it out the next day
Dealing with the Journal’s Response
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Conditional acceptance (rejection)
– It is yours to lose
– First cool down (24-48 hours)
– Within 1-2 weeks decide on responses
– Make real changes, say you have done great
changes (describe, highlight,etc)
– Look for clues from the editor as to the
extent of the revision needed.
– Avoid arguments
– Thank sincerely, but avoid being obsequious
Responding to reviews
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Swallow your pride!
You don’t have to accept all, but don’t overreject
Ask editor about conflicting comments
However unreasonable the reviewers may
seem: be polite!
Distinguish conditional acceptance from offer to
reconsider (and from rejection of course!)
Appeals (for rejection)
Resubmission Letter
Dr. Brian F. McCabe
Editor, Annals of Otology, Rhinology and Laryngology
Department of Otolaryngology-Head and Neck Surgery
The University of Iowa Hospitals and Clinics
Iowa City, IA 52242
Dear Dr. McCabe,
Please find enclosed a revised manuscript entitled, "Surfactant protein A in rabbit sinus and middle ear
mucosa" by……….
We have addressed the comments of the reviewers as detailed below:
1)We have changed the title of the paper as suggested by the reviewer.
2)We have expanded the description of the animals used in the study (page 4, paragraph 1).
All the animals except the pathogen-free, were naturally infected with Pasteurella multocida.
The antibiotic treated animals were chosen randomly. The infections were observed
postmortem and pathogen was identified by culture by the Animal Care Unit.
3)The lengths of the micron bars in Figures 5-8 have been added to the legends. A
magnification bar has been added to Figure 10.
We hope that you will now find our manuscript suitable for publication in the Annals of Otology,
Rhinology and Laryngology. Thank you very much for your prompt review.
Sincerely,