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“How to write a scientific paper”

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Scuola di Dottorato in Scienze Ingegneria Medicina
Seminario metodologico (Seminar on Professional Skills)
led by Marina Bentivoglio and Luca ViganГІ
30 June 2011
“How to write a scientific paper”
For those who have never published yet a scientific paper:
• Did you start writing one?
If you did: which difficulties did you encounter?
• Do you regularly read scientific articles in your field?
If so: what do you think is especially difficult to replicate in
such writing?
Key facts
• “verba volant, scripta manent”
• A scientific paper is the way to communicate/deliver
permanently your data to the scientific community
• Your only richness, in the scientific community, is your
name and your reputation: use it properly
• The community to which you address your work did not
discuss with you (data/concepts) previously, did not
participate in the study planning and data collection and
(did not participate in your failures, torment, discussions
with your supervisor)
• Scientific papers should be written in English
(“scientific English”, which is some kind of “jargon”
and has, however very precise rules)
• This is a disadvantage if English is not your mother tongue
• Is the scientific community “indulgent” concerning this?
Absolutely not!
•Therefore one should get organized. What to do?
Write your text in your mother tongue and find a translator?
What else?
Learn how to write your paper in English: it is feasible
and mandatory!
• Selection of the journal: “top journal”,
peer-reviewed indexed journal, non-indexed journals (no IF),
on-line publications
Format (in biomedical literature/life sciences):
Presenting your “primary” (unpublished) data (highest
“filter”of reviewers):
•Short communication
•Original research article
Reviewing a topic (including your own data):
•Review article
•Comments, opinions, “letters”
•Chapters in volumes, conference/symposium proceedings
• Computer science: different targets
Classical publication sequence in computer science:
• Workshop
• Conference
• Journal
Paper categories
• Original work
• Survey (only/mainly for journal)
” interesting data, but is presented
• An article that contains
in a “sloppy” form (typos, mispelled words, bad or excessive
use of abbreviations, etc) gives to reviewers (who represent the
first filter) a bad impression: the editing should be professional!
Editing tips:
- Read carefully the Instructions for Authors of the journal
- Select carefully the key words (words in the title are
automatically indexed)
- Use of acronyms: too many abbreviations may make
the text difficult to read; a term can be abbreviated only
if used more than 3 times and should be abbreviated when
first mentioned (and therein should no longer be used
in extenso)
Editing tips:
- Figures should be numbered consecutively and according
to citation in text; figures have legends
- Tables have a title and their own numbering (no legend)
-Obviously, all refs quoted in text should be listed in the
reference list and vice versa.
Scientists have in general little time, many of them are
under big pressure (grants, career, etc.)
The article should be an “appealing” and “user-friendly”
• very clear
•not verbose or repetitious, should be “effective”
•nicely illustrated with well readable figures
(graphics, formulae, etc.: avoid too small labels and
lettering; organize properly space avoiding blank space;
evaluate the image reduction for paper formatting/
printing, etc.)
What is “appealing”?
• “Novelty”:
• if “these observations are here reported for the first time”: specify it
clearly (and, of course, make sure that it is true!)
• if the methodological approach is novel: present your approach properly
and explain its advantages (as well as its limitations)
• “Impact” on knoweldge:
• Explain the impact of your findings on current knowledge/interpretation:
explain it clearly (no over-statements, no arrogance!)
Start raising these issues in the Introduction, but do properly
highlight them in the Discussion (and in the Abstract)
• Title
• Authors and affiliation/s
• Key words
Essential for indexing: think about it
(words in title are automatically indexed)
• Abstract
Body text:
• Introduction
• Material and Methods
• Results
• Discussion (including
• Acknowledgements
• References
• Figure legends
• For an “original research
article” (different, of course,
for review articles);
• Format/section subdivision
may vary, but all these
parts are anyhow included
• Title
• Authors and affiliation/s
• Abstract
•Key words
Body text:
• Introduction
•Basic definitions (background, pre-existing defs)
• Theoretical results (new defs, theorems,…)
• Experimental results (data and their analysis)
• Discussion
• Acknowledgements
• References
• [Appendix]
•Provides the first impression to the reader and
influences whether a reader is interested in reading
the manuscript
(while doing an e-search, the title determines whether
who does the search will go ahead and read the
abstract…. and then the paper)
•Avoid long titles
•Avoid titles which begin with redundant words
such as “A study of…”
Who is an Author of an abstract/scientific publication?
Authorship should be based on a substantial intellectual
contribution! (can be reflected in the order of names)
International Committee of Medical Journal Editors:
definition of authorship as being based on:
1) Substantial contribution to conception and design, acquisition
of data, or analysis and interpretation of data
2) Drafting the article or revising it critically for important
intellectual content
3) Final approval of the version to be published
(NB all authors are equally responsible and should approve the
version to be submitted)
Acquisition of funding or general supervision of the research
group alone does not constitute authorship...
Many journals now request specification of the
contribution of each Author
For example:
Author Contributions
Conceived and designed the experiments: M.B., K.K.,
A.K.N. Performed the experiments: A.K.N., A.A., J.Y.F.,
D.M. N., J-J.M. Analyzed the data: A.K.N., S.P., P.F.S.E.
Wrote the paper: M.B., A.K.N., K.K., P.F.S.E.”
• Limited length (every word is precious!)
• Very important: openly accessible
• It is the first text part encountered by the reviewer
(and by the reader); it could be the last part to write,
when the main “take home” message and its “novelty
and impact” are fully clear to you
Sometimes reviewers are picked based on the abstract
• Should contain, very synthetically, all the elements
of the study:
rationale (or motivation), methods, main results,
conclusions and “take-home message”
• One or two sentences (at the beginning)
of background information
• The question/s asked
• What was done to answer the question/s
• Findings that answer the question/s (in a logical order)
• The answer to the question/s
It must make sense when read in isolation for those who only read the abstract
(NB e-searchers may only retrieve the abstract!)
It must also provide a clear and accurate recapitulation of the manuscript
for readers who read the entire manuscript (must not contain data which
are not included in the Results)
(From: Sue Jenkins, 1994 – and still valid!)
• “Sets the stage”
•Present very clearly the rationale for the study (essential),
in the framework of current knowledge (NB but should not be
a “discussion”, should be an “introduction”)
•Introduce the methods you have adopted to solve your problem
and start emphasizing the original contribution/s of the study
Background to the topic (past verbe tense)
• What is known or believed about the topic
• What is still unknown or problematic
• Findings of relevant studies (past verbe tense)
• Importance of the topic
Statement of the research question
“To determine whether…”
“The purpose of this study was to…”
“This study tested the hypothesis that…”
“This study was undertaken to…”
Approach taken to answer the question (past verbe tense)
(From: Sue Jenkins, 1994 – and still valid!)
• NB: your work should be “reproducible”
(replication of the study is a requisite of a scientific work and
its richness!)
• Specify all the sources of reagents:
manufacturer/company, city, country;
website for softwares, etc;
the providing colleague/laboratory (kindly supplied by…)
• Remember ethical statements related to animal experiments
• Should be precise, complete, synthetic
• Pay attention (throughout the text) to use/selection of words:
“show, indicate, suggest, demonstrate”
“obvious, evident, important*”, etc.
(*what would really be “not important”?)
• Guide the reader in identifying the data you consider key
• Should be precise, complete, synthetic
• Definitions: define each notion before use
• Theorems: proof must be understandable/convincing
(reader should be able to follow all the steps)
• Algorithms: readable, appropriate level of abstraction
• Pay attention (throughout the text) to use/selection of words:
“show, indicate, suggest, demonstrate”
“obvious, evident, important”, etc.
• Experimental data: HW, SW, cpu time, memory, program
options/parameters, choice of algorithms/strategies, input data
NB: data should be interpreted/analyzed (not just reported)
• It could help to start with a “summary” of results/contributions
(in the order in which they are then discussed)
• Divide into subsections (possibly according to logical reasoning)
• DO NOT REPEAT THE RESULTS (or the Introduction)
• Discuss your data comparing them with previously published
Computer science: compare with related works
• End, possibly, with “Conclusions” or “Concluding remarks”
in which the study impact and the “take-home message” should be
very clear.
Computer science: also directions for future research, open problems
Life sciences: the same, making it clear in which “directions for
future research” are your own findings inserted
To remember:
• Indication of the novelty/impact/relevance/implications
of the study (originality/uniqueness of the work), i.e.,
the priority of the study
• Explanations of:
- Any results that do not support the answer/s to your question/s
- How the findings concur with those of others
- Any discrepancies of the results with those of others
- Eventual unexpected findings
- The methodological limitations of the study which may
affect the study validity and/or generalization of the study
•Grant/Funding support (all details: grant number)
• All help should be acknowledged (be generous in thanking!):
technical advice/assistance/support, help in the preparation
of the manuscript, etc.)
When you start writing a paper, try to finish it
within a relatively short period of time, not to loose
concentration and contact with the pertinent literature
(which keeps being published…)
But when you think that the paper is ready, let it “rest”
for at least a couple of days and read it again
with “new eyes”……
Who are they?
Friends, enemies…?
Young, old?
Lots of information / guidelines / manuals are
available, e.g.
•William Strunk, Jr. and E.B. White – The elements of
For those who have already published a scientific paper:
Which difficulties did you encounter in writing
- and then getting accepted for publicationyour paper/s?
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