7 paper writing v2
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Scientific Paper Writing:
Guidelines and Tips
A. S. M. A. HaseebDept. of Mechanical Engineering
University of MalayaOffice: Room 13, Level 5, Engineering Tower Bldg.
Tel: 7967 4492, E-mail: [email protected]
Elsevier, Author Workshop 2008-11-6, How to prepare a manuscript for an international journal, Xiamen
University
K. E. Barrett, How to Write (and Review) a Scientific Paper, http://www.the-
aps.org/careers/careers1/mentor/workshop/2001/Barrett.doc,
S. Bloomer and M. J. Haas, How to write a scientific paper, inform, Volume 15 (12), December 2004.
Sami K. Solanki, How to Write a Research Paper, Internet Source
K. E. Barrett, Publishing 101, Chair, APS Publications Committee, Internet Source
Ed BullmoreHow to Write a Scientific Paper, Internet Source
WRITING A RESEARCH PAPER: Some general guidelines
for students and postdocs, Internet Source
S. Cordova, How To Write a Scientifi c Paper, http:// www.nmas.org/JAhowt o.html
Daniel J. Jacob, HOW TO WRITE AN EFFECTIVE SCIENTIFIC PAPER
K. Gaafar, How to write a scientific paper
R. Elvik, How to write a successful paper, Institute of Transport Economics, Oslo, Norway, Young researchers
seminar, May 10-13, 2005
W. A. Zin, HOW TO WRITE A SCIENTIFIC PAPER
M. Mallia, How to Write a Scientific Manuscript, Scientific Publications, Texas Heart Institute, Houston, Texas,
USA, Cardiology Rounds, February 19, 2008 T. H. Adair,Writing and publishing a research article, Center of Excellence in Cardiovascular-Renal Research,
University of Mississippi Medical Center
Barbara Gastel, Writing a Scientific Paper: Basics of Content and Organization Texas A&M University
References(all from internet sources)
Contents
Introduction
Before you start
General
Sections: Title, Abstract, Keywords, Introduction,
Methodology, Results, Discussion, Conclusions,
Acknowledgements, References
Submission to a journal
Ethical issues
Submission to a journal
Language
Conclusions
http://www.the-aps.org/careers/careers1/mentor/workshop/2001/Barrett.dochttp://www.the-aps.org/careers/careers1/mentor/workshop/2001/Barrett.dochttp://www.the-aps.org/careers/careers1/mentor/workshop/2001/Barrett.dochttp://www.the-aps.org/careers/careers1/mentor/workshop/2001/Barrett.dochttp://www.the-aps.org/careers/careers1/mentor/workshop/2001/Barrett.dochttp://www.the-aps.org/careers/careers1/mentor/workshop/2001/Barrett.doc -
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Gerard Piel: co-founder and the long-term publisher of the
modern incarnation of Scientific American magazine
Origins of Scientific Writing
Knowledge is lost without written records
Cave paintings and inscriptions first attempts to leaverecords
2000 BC Papyrus paper as a medium of communication
190 BC parchment made from animal skin
105 AD Chinese invented paper
1100 AD Chinese invented movable type
1455 AD Gutenberg printed his 42-line Bible from movabletype on a printing press
By 1500 thousands of copies of hundreds of books (calledincunabula) were printed
1665 the first scientific journals were published
What is a scientific paper
a written and published report describing original researchresults
an addition to human knowledge
the first publication of original research results
peers can repeat the experiments and test the conclusions
published in a journal readily available within the scientificcommunity
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IMRaD Story
Early journals descriptive papers
By second half of 19th century reproducibility of experimentsconstitute a fundamental principle of philosophy of science
The methods section became all important
IMRaD format slowly progressed in the latter half of the 19 th
century
I = Introduction , what question was studied
M = Methods, how was the problem studied
R = Results, what are the findings
a = and
D = Discussion, what do these findings mean
Why write scientific papers?
A scientific career expansion of human knowledge
Academic and public sectors scientific papers ARE the meansfor this expansion
Publish or Perish You dont publish, youre out
Quality of a scientific paper? (now routinely- perhaps unfortunatelymeasured by the citation index)
Originality and importance of ideas
Effectiveness of communication, particularly when it comes to
planting the flag for new ideas
Before you
start
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Before you start
Before you start
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Before you start
Authorship
Decide on authors, and their order, as early as possible
Authors
- made a substantive intellectual contribution- participate sufficiently to take responsibility for the content
- can defend the data and conclusions publicly
Before you start
Criteria for authorship
Generate at least part of the intellectualcontent
Conception or design of the work
Data analysis and interpretation Draft, critically review, or revise the intellectualcontent
Approve the final version to be submitted
All three
criteria
should be
satisfied
Before you start
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Before you start
Before you start
Contents
Introduction
Before you start
General
Sections: Title, Abstract, Keywords, Introduction,
Methodology, Results, Discussion, Conclusions,
Acknowledgements, References
Submission to a journal
Ethical issues
Submission to a journal
Language
Conclusions
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General
Paper Writing:
A part of your research, not a post-research
activity !
Start writing papers as soon as possible view it as a tool ofyour research
Iterate and agonize over the paper as part of your research
The paper is not a description of the
work, it IS the work
Richard Feynman
Starting Out
Know your working style versus computer, time, place
Set a deadline
Just put something down and edit itafterwards
Easiest to startMATERIALS and
METHODS and RESULTS
Start writing the data as if you were
describing them to your colleagues
Lay out general arguments and then go
into details
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Decide on the key conclusions - the importantmessage that you want to put across
Do you have all the data AND the figures to prove
your point ?
If possible, give an informal ORAL presentation of
the work before you start to write the paper
Starting Out
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Contents
Introduction
Before you start
General
Sections: Title, Abstract, Keywords, Introduction,
Methodology, Results, Discussion, Conclusions,
Acknowledgements, References
Submission to a journal
Ethical issues
Submission to a journal
Language
Conclusions
Title
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The Title
Extremely important and must be chosen with great care will be
read by thousands Good title fewest possible words that adequately describe the
contents of the paper.
Accuracy of the title Indexing and abstracting
Concise, specific and informative
Contain the keywords that reflect the contents of the paper
Capture the fundamental nature of the experiments and findings
Waste words (studies on, investigations on, a, an, the etc) shouldnot be used
Make a list of the most important keywords
Think of a title that contains these words
Could state the conclusion of the paper
NEVER contains abbreviations, chemical formulas,proprietary names or jargon
Think, rethink of the title before submitting the paper
Be very careful of the grammatical errors due to faulty word
order Avoid the use of the word using
How to Prepare the Title
The Title
The Title
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The Title
Abstract
Very important part of the paper manyreaders will read just that
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A good abstract should contain in a very very precise form the
following elements:
Introduction:State the principal objectives and scope of the
investigation
Method:Describe the methods employed
Results:Summarize the results
Discussion/conclusion:State the principal conclusions
Abstract
An abstract is a brief summary of each ofmain sections (IMRAD) of the paper
No figures, no tables
No references (usually), no footnotes
Avoid abbreviations, equations and symbols
Make sentences short
It should not exceed about 250 words
Written usually in one paragraph
Written usually in the past tense as it refers to work done
Should never give any information or conclusion that is not
stated in the paper
Focus on what is new - essential ideas, essential numbers
Abstract
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Keywords
Contents
Introduction
Before you start
General
Sections: Title, Abstract, Keywords, Introduction,
Methodology, Results, Discussion, Conclusions,
Acknowledgements, References
Submission to a journal
Ethical issues
Submission to a journal
Language
Conclusions
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Introduction
Sets the scene for your unique contribution and place it in context
Not meant to be an exhaustive review
Formulate the problem to be addressed
Introduction
Introduction
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Why was the problem undertaken? Historical and current relevance
What is its significance?
What is known or has been done before?
- Be selective and critical
- Give credit to intellectual pioneer as well as to best prior work
- Some criticism of earlier work may be necessary be mildand very respectful, and show professional manners
- Cite peer-reviewed scientific literature or scholarly reviews
Avoid general reference work such as textbooks
Say why the present work needs to be done
Definitely needed: Goals of your paper. If similar papers exist: what isnew in the method or results
Introduction
Often done, but not necessary: give structure of remainingpaper in last paragraph of introduction
Important: The sentences within a paragraph should follow
a logical sequence
Introduction
Signalling the research question at the end of Introduction
To determine whether . . .
The purpose of this study was . . .
Therefore, we tested the hypothesis . . .
This report describes experiments designed to determine
whether . . .
Therefore, our first objective in these studies was to
determine whether . . .
In this study, we sought to extend our observations and to
specifically test . . .
Introduction
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Contents
Introduction
Before you start
General
Sections: Title, Abstract, Keywords, Introduction,
Methodology, Results, Discussion, Conclusions,
Acknowledgements, References
Submission to a journal
Responding to reviewers
Ethical issues
Submission to a journal
Language
Conclusions
Methodology
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Clear and sufficiently complete other scientists, eventhose not familiar with your specialty, could repeat the
Work
Assembe a simple collection of procedural outlines turnthis into prose
Use past tense
Provide references as necessary
Use subheadings if necessary
Do not include results in Methods
Often a figure can illustrate and clarify the method
Methodology
Find the balance between: Describing everything important andLeaving out everything not needed.
Rule of thumb:
- New method, new instrument, new type of data Describe
in detail, since required for reproducibility
- Known method or instrument, previously used and
described in other paper(s) Often a reference is sufficient
Do not repeat descriptions
For chemicals exact technical specifications and source or
method of preparation
Avoid trade names of chemicals
Methodology
Examples of alternative titles:
Computational technique (appropriate for a numerical
paper)
Instrument and measurements (e.g. if a new
instrument is being described or used, or an instrumentis used in a non-standard mode)
Data and analysis technique (e.g. if the special
technique of analysing the data is essential for the
results)
Often studied carefully by the refereeDecides whether the results can be trusted or not
The paper will be rejected based on methodology
Methodology
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Results
John Wesley Powell (March 24, 1834 September 23, 1902): a
U.S. soldier, geologist, and explorer of the American West
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How to write the Results
Written in the past tense
Heart of the paper needs to be clearly and simply stated orderly and logical sequence, without interpretation
guide the reader through the findings, stressing the major points
Do not describe methods that have already been described inthe Methodology section
structure this section is to write it around the figures. However,do not forget to make a logical order
Results
The core of the paper, where the results obtained duringthe long labour of research are presented.
Be concise. Pre-select the results (i.e. identify the
important and new results) before writing about them in
the results section
Keep in mind: The fool collects facts, the wise man selects
them (John W. Powell)
Avoid repetition!
Assemble draft FIGURES and lay them out in order on a tableor desk
Decide what are the key points that you need to make, and
write them out
More Results
Decide on what to put into the Results section and what tomove to the Discussions section
General rule (but not a very hard and fast one)
Results section only describe the results, but do
not interpret them very much
Discussion section provide the interpretation and the
comparison with the literature, without repeating all theresults
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Results: Figures
Each figure must be referred to in the text must have a
caption
Captions short, but self-explaining
only clarify what is plotted and not try to interpret the
figure
For photomicrographs Dont forget scale bars!
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Axes
- Minimize tick marks
- Dont number each tick Lettering
- Uniform, lower case- Minimize, avoid bold
- After reduction, 2-3 mm high
Legend
- Gives message
Results: Tables
Make a table if you have multiple numbers to show andyou cannot put them into a figure, or if the exact
numbers are important
Remember, figures are generally easier to read than
tables.
Each table must have a title. Keep it short.
must be referred to in the text.
Never put the same data in the form of both table andfigure
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Contents
Introduction
Before you start
General Sections: Title, Abstract, Keywords, Introduction,
Methodology, Results, Discussion, Conclusions,
Acknowledgements, References
Submission to a journal
Ethical issues
Submission to a journal
Language
Conclusions
Discussion
Hardest section to write !
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How to write the Discussion
Primary purpose interpretation, synthesis, predictive speculation
Interpret your results present the principles, relationships,and generalizations shown by the Results
How your results and interpretations agree or contrast with
previous work
Theoretical implications of your work, and any possiblepractical applications
Point out any exceptions or any lack of correlation and define
unsettled points Present ambiguity and discrepancies
objectively
Explain what is new without exaggerating
Discuss key studiesonly those relevant to your work
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Last paragraph- In summary (2-3 entences)
- In conclusion (biggest
message, return to Intro, avoidspeculation, avoid need more
work
Middle paragraphs- Base each on a major result
Always focus on your results
Never discuss prior work withoutreference to your work
Refer Tables and Figures
First paragraph- State major findings
- Paraphrase abstract
Structure and contents
Contents
Introduction
Before you start
General
Sections: Title, Abstract, Keywords, Introduction,
Methodology, Results, Discussion, Conclusions,
Acknowledgements, References
Submission to a journal
Responding to reviewers
Ethical issues
Submission to a journal
Language
Conclusions
Conclusions
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Conclusions
can wait to be written until rest of paper is
mature
First paragraph: focus on what you did. Begin with We haveused, We have investigated
Following paragraphs: one major finding per paragraph. First
sentence states the finding, following sentences elaborate.
Final paragraph should have some forward-looking
perspective. Dont let paper finish on a whimper!
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Reference
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A few words about references
Extensive referencing scholarly and ethical thing to do
useful to readersmakes your paper more accessible by search engines!
Be serious about literature search and reading papers devote a bit of time to this each day
Never cite a paper for which you havent read at least therelevant part
Cite papers in a context that makes it clear what the paper did
Dont cite textbooks
Theres nothing wrong with citing yourself or your group
extensively. But dont ignore what others have done!
Contents
Introduction
Before you start
General
Sections: Title, Abstract, Keywords, Introduction,
Methodology, Results, Discussion, Conclusions,
Acknowledgements, References
Submission to a journal
Ethical issues
Submission to a journal
Language
Conclusions
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Dealing withreviewers
Dealing with referees reports
anticipate revision: it is almost inevitable and generally beneficial
Complete additional experiments if needed
At first sight referees reports often look more negative than
they really are.
Read the report and then put it away for a week before looking at itagain (to calm down).
Discuss it with your supervisor and make the changes to the paperasked by the referee
Point by point reply to the refereehow you have taken his/her
comments into account
If you disagree with the referee and havent taken one of his/her
suggestions into account you explain why.organise the final version
of the paper and all ancillary data carefully before submission
Referees are not always stupid. If the referee does not
understand something, then it is likely that the paper is not
clear on this point. Make it clearer.
Do not respond to reviewers while upset
try not to take criticism personally or as a reflection ofincompetence on the part of reviewers
their failure to understand is your lack of clarity
be respectful, exact and direct in responding to the editorRemain polite. Even if the referee is nasty, there is usually
nothing to be gained by showing your anger.
If you feel that you are being unfairly treated by the
referee you can ask for a second opinion.
Sincerely thank the editor and reviewers for helping you to
improve your work
They have invested a lot of time, mostly on a voluntary basis
Ask a neutral colleague to review your response
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Ethical issues in
publication
Ethical responsibilities of a scientist
Intellectual honesty
Accurate assignment of credit
Fairness in peer review
Collegiality in scientific interactions
Transparency in conflicts of interest
Protection of human and animal subjects
Common ethical issues
Redundant publication Authorship disputes
Duplicate publication
Human welfare concerns
Data fabrication/falsification Increasingly, includes inappropriate manipulation of
figures
Plagiarism
Conflicts of interest
Others (e.g., reviewer bias, submissionirregularities)
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Prior publication
Defined as:
Data
Extended verbatim text passages
Tables or illustrations
Redundant publication
Definition
Using text or data from
another paper/prior
publication (usually
your own) in a new
paper
Also called auto- or
self-plagiarism
How to avoid
Do not include
material from a
previous study in a
new one, even for
statistical analysis
Repeat control groups
as needed
What constitutes redundant publication?
Data in conference abstract?
Same data, different journal?
Data on website?
Data included in review article?
Expansion of published data set?
No
Yes
Maybe
OK if later
Yes
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Authorship disputes
Definition
Disputes arising from
the addition, deletion,or change in the order
of authors
How to avoid
Agree on authors and
their order beforestarting the study
Ensure all authors
meet criteria for
authorship
Sign publishers
authorship forms
Duplicate publication
Definition Submission of or
publication of thesame paper orsubstantial parts of apaper in more thanone place
How to avoid Do not submit a paper
to more than onejournal at a time
Wait until your paper isrejected beforesubmitting elsewhere
Withdraw a paper ifyou decide not to re-submit after being
invited to do so
Data fabrication/falsification
Definition
Changing or makingup data in amanuscript
Intended to improvethe results
Includes digitalmanipulation ofimages (blots,micrographs, etc.)
How to avoid Present the exact
results obtained
Do not withhold datathat dont fit yourhypothesis
Dont try to beautifyimages withPhotoshop anymanipulations mustapply to the wholeimage
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Unacceptable figure manipulation
Improper editing
Improper grouping Improper adjustmentAuthors should not:
Move
Remove
Introduce
Obscure
Enhance
any specific feature within a image. Imagesshould appear as captured in the lab
Improper editingBoxes revealed during processing for publication; removal reveals debris
Bottom image from Rossner and Yamada, J. Cell Biol. 166: 11-15 (2004)
Plagiarism
Definition
Taking the work ofanother
Copying a figure,table, or even wordingfrom a published orunpublished paperwithout attribution
How to avoid
Provide citation to thework of others
Obtain copyrightpermission if needed
Do not copy exactwording from anothersource, even ifreferenced, unless inquotes
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Conflicts of interest
Definition
Real or perceived
conflict due to
employment,
consulting, or
investment in entities
with an interest in the
outcome of the
research
How to avoid
Disclose all potential
conflicts to the Editor
and within the
manuscript
The Seven Deadly Sins1. Data manipulation, falsification
2. Duplicate manuscripts
3. Redundant publication
4. Plagiarism
5. Author conflicts of interest
6. Animal use concerns
7. Humans use concerns
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ACKNOWLEDGMENTS
Include
Intellectual assistance
echnical help, including writing and data
analyses Special equipment or materials
Outside financial assistance (including
grants, contracts, or fellowships)
Contents
Introduction
Before you start
General
Sections: Title, Abstract, Keywords, Introduction,
Methodology, Results, Discussion, Conclusions,
Acknowledgements, References
Submission to a journal
Ethical issues
Submission to a journal
Language
Conclusions
Submission to
a journal
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Completion of research
Preparation of manuscript
Submission of manuscript
Assignment and review
Decision
Rejection Revision
Acceptance
Resubmission
Re-review
PUBLICATION!
Rejection
Adapted from a figure by Dale Benos
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Most common reasons for rejection
of a manuscript
Major reasons for rejection
Inappropriate for the journal Do your homework
Merely confirmatory/incremental Avoid LPUs
Describes poorly-designed or inconclusivestudies Focus on your hypothesis
Poorly written
Great science in an ugly package can still be rejected
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What makes a good research
paper?
Good science
Good writing
Publication in good journals
What constitutes good science?
Novel
new and not resembling somethingformerly known or used (can be novel but not
important)
Mechanistic testing a hypothesis - determining
the fundamental processes involved in or
responsible for an action, reaction, or other natural
phenomenon
Descriptive describes how are things are but
does not test how things work hypotheses are
not tested.
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What constitutes a good journal?
Impact factor
average number of times published papersare cited up to two years after publication.
Immediacy Index average number of times published papersare cited during year of publication.
Outlineoriginality and
important
findings
Language
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Contents
Introduction
Before you start
General Sections: Title, Abstract, Keywords, Introduction,
Methodology, Results, Discussion, Conclusions,
Acknowledgements, References
Submission to a journal
Ethical issues
Submission to a journal
Language
Conclusions
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A scientific paper clear, objective, to the point
Strive for logical, linear flow. Put yourself in the perspective of the
reader
Be as short as possible. Every word must hurt
Be on the lookout for unnecessary words and sentences
Use short words (e.g., use vs. utiilize)
Remove value judgments: Surprising, interesting,
unfortunately have no place in a scientific paper.
Use scientific words as much as possible but with their precisemeaning
Avoid slang and jargon
Use the active voice whenever possible usually less wordy and is
unambiguous
First person is acceptable when the meaning is clear
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Avoid Wordiness Delete Unnecessary Words
Delete phrases which do not contribute to the
meaning of a sentence
Past or present tense preference is to some extent personal
Past tense is OK for describing results of an experiment but use
present tense for a general conclusion
WHATEVER TENSE IS USED, BE CONSISTENT AND
DONT SWITCH BACK AND FORTH IN THE SAMEPARAGRAPH !! !
Tense
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Some Common Problems
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Examples
Not correct: Our results suggest that Hoxa3 may be involved in
thymus development
Correct: Our results suggest that Hoxa3 is involved in thymus
development
Not correct: It is possible that Shh in the endoderm may regulate
Bmp4 expression in the mesoderm
Correct: It is possible that Shh in the endoderm regulatesBmp4 expression in the mesoderm
Use of suggest that ; hypothesize that possible thatThese phrases do not need may, might
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Proofreading Unimportant details tend to
be overlooked
BEFORE GIVING THE DRAFT TO YOUR
SUPERVISOR
Check the Figures versus the textCheck the References versus the text
Check the Figure legends
In general, edit a paper after printing it out and reading it
as a whole, rather than editing it on a computer screen
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