Writing scientific

articles and scientific

publishing

'Scientific publishing. How (or how

not) to publish your paper?'

Dale Seaton, Journal Manager, Elsevier

Brian M Cooke, Editor-in-Chief, IJP
Introductions
Dale Seaton
 BSc in Zoology, and PhD in
Parasitology
 I have worked in scientific and
medical publishing for 20 years
and for Elsevier for 14 years in
various roles.
 As Executive Publisher I am
responsible for the management of
18 journals in the areas of
Parasitology + Entomology. I also
develop and organise new
scientific conferences.
 I manage approximately 60 Editors
around the world.
Brian M Cooke
 B.Sc. Biomedical Science and Ph.D.
in Clinical Haematology
 I have worked at Monash
University for more than 20 years
and am Professor of Microbiology
 I’ve been deputy Editor of IJP for 4
years and Editor-in-Chief since
April 2015
 My research focuses on red blood
cells, the parasites that infect
them, and the diseases that follow
 I published my first paper during
my honors year in The Journal of
Clinical Pathology in 1988
Trends in
publishing
Peer-reviewed journal growth 1665-2001
No of titles launched and still published in 2001

> 10M
articles
10000

Philosophical Transactions
100 of the Royal Society (London)

1
1665 1765 1865 1965
Year Source:
M A Mabe The number and growth of
journals, Serials 16(2). 191-7, 2003
 | 5

Peer-reviewed journal growth 1990-2013

 | 6

Scholarly publishing today

Scientific, technical and medical

(STM) publishing

2,000 STM
publishers

1.4 million ~30,000

peer-reviewed peer-reviewed
articles journals
 January 2015 | 7

Academic publishing

The publishing cycle 30-60

Solicit &%
rejected
manage by
> 13,000
submissions
editors

>700 million
downloads by
Publish &
>11 million 557,000
Manage +
Disseminate
researchers in Peer Review
reviewers
>120 countries!

12.6 million
Production
365,000
Edit &
articles prepare
articles
available accepted
The publishing industry over time …

Tim Berners-Lee
Henry Oldenburg

1665 1880 1989

2000 Today

1580 1998-1999
Trends in publishing
Electronic submission
Increased manuscript inflow

 1997: print only

 2009: 55% e-only (mostly e-collections)
25% print only
20% print-plus-electronic
 2014: 95+% e-only (life sciences field over 99%)
 2017: ???

Experimentation with new publishing models

E.g. “author pays” models, “delayed open access”, etc.

And a much greater requirement for mobile access and

Smartphone and tablet availability and functionality

Scope for many innovations in electronic published article

Innovations within articles
Content innovation initiative enables scientists to disseminate
their research in its full digital richness in Elsevier articles.
 3D geometric shapes and models
 3D molecular and crystallographic
models
 3D neuroimaging data
 Arabidopsis Gene Viewer
 AudioSlides
 Author videos
 Astronomy Databases
 BrainLink application
 Database linking
 Editorial Podcast Player
 Energy Terms and Definitions
 Generic Image Linking App
 Genome Viewer
 Gene Expression Omnibus (GEO) app
 Interactive maps
 Interactive pathways
 Interactive plots
 Inline supplementary material
 JEL Classifications
 Mol files and InChI keys
 Nomenclature App
 PANGAEA Data Maps
 Peer-Review Innovation
 Phylogenetic trees
 Protein Interaction Viewer
 Protein Viewer
 PubChem compounds
 SD-Reaxys
 Featured Multimedia for this Article
 Transportation DB Center App
 U3D models
 Virtual Microscope
Role of publishing
Journal publishing has thrived for over 340 years but the
fundamental role of Publishers remains unchanged

Registration

Certification

Dissemination

Elzevirianas circa 1629

Preservation
First scientific journals published
in 1665
Ready to Publish?
What are your personal reasons for publishing?

Valid reasons, however, editors, reviewers, and the research

community do not consider these reasons when assessing your work.
Are you ready to write a paper?

You should consider publishing if you have information that

advances understanding in a certain scientific field.

This could be in the form of:

• Presenting new, original results or methods

• Rationalizing, refining, or reinterpreting published results
• Reviewing or summarizing a particular subject or field

If you are ready to publish, a strong manuscript is needed

next….but what type?
Type of manuscript?
Further determinations...
• Full articles / Original articles;
• Letters / Rapid Communications / Short communications;
• Review papers / perspectives
•Self-evaluate your work: Is it sufficient for a full article? Or
are your results so thrilling that they need to be shown as
soon as possible, perhaps through a rapid communication?
•Ask your supervisor and colleagues for advice on manuscript
type. Sometimes outsiders see things more clearly than you!

If you are ready to publish, next consideration…..

Choosing a journal
Where to publish?
Do not just descend the Impact Factor ladder
‘Top' journals, Nature, Science, Lancet, Cell…

Field/discipline-specific top journals

Other field-specific journals

National/local journals
 Journal selection
It is not (only) the Impact Factor, it is (mainly) the right
audience!
Consult the Journal homepage/recent issues/on-line Guide to
Authors to learn:
• Aims and scope of the journal
• Accepted types of articles
• Readership
• Current hot topics
Go through the abstracts of recent publications
Articles in your references will likely lead you to the right journal

DO NOT gamble by submitting your manuscript to

more than one journal at a time
What should I look for in a journal?

 A journal that is read by colleagues that work in the same field.

Is it reaching your community?

 A journal that has the highest impact for that particular field
(not necessarily the highest IF!)

 A journal that has fast turnaround times

 A journal that is easy to find on the web

 Ask around: your colleagues may already have experience of

the journal (or the Editor!)
Ready to Write ?
What do Editors look for?

 Is it within the purview of the journal?

 Is it novel? (if not, the kiss of death!)
 Is it of broad (or specific) interest?
 Is your data compelling – and does it
support your conclusions?
 How big a step is it in new parasitological
insight?
 Does it provide new directions for research?
A good manuscript…

 Contains a scientific message that is novel, clear,

useful, relevant and exciting.
 Conveys the authors’ thoughts in a logical way such
that the reader arrives at the same conclusions as
the author.
 Makes the editor feel like (s)he is handling
something exciting, meaningful, useful and relevant
to the journal.
 Is well-organized and focused, and best of all, ONLY
AS LONG AS IT NEEDS TO BE.
First a simple truth ….

No matter how fascinating your experimental results or

how intriguing your observations, your work must be
published if it’s going to impact science and advance the
field

Even if your discovery is brilliant, bad writing can render

your findings unpublishable or delay publication until it is
extensively revised – that can cost you !

“It’s not science until it’s published!”

Language does make a difference

“It is quite depressive to think that we are

spending millions in grants for people to perform
experiments, produce new knowledge, hide this
knowledge in an often badly written text and then
spend some more millions trying to second guess
what the authors really did and found.”

Amos Bairoch, Nature Precedings,

2009: doi:10.1038/npre.2009.3092.1
Do publishers correct language?
• No. It is the author’s responsibility to make sure their
paper is in its best possible form when submitted for
publication – Reviewers and Editors don’t do it!
• (a few journals offer editing ‘added value’ – but after
acceptance!)
• Publishers often provide resources for authors
– If English is not your native tongue, invest in some
help!
– http://webshop.elsevier.com/languageservices
Manuscript language – overview

Accurate

Concise

Clear

Objective
Sentence structure

Write direct and short sentences

One piece of information per sentence

and one concept per paragraph

Avoid multiple statements in one

sentence
Tip: Read your manuscript out loud when proofreading.
You will pick up on more errors and run-on sentences.
Fact ……

Most people cant write well. You are not unusual….

or hopeless!

Write your draft, read it, re-write it - before sending

it to your co-authors for comment.

Then revise it, revise it, revise it …….

Get input from as many people as you can.

What constitutes a strong manuscript?

• Has a clear, useful, and exciting message

• Presented and constructed in a logical manner

• Editors and reviewers and can easily grasp the

significance

Make it easy on the editor and reviewers to

understand your story
Building an article from the ground up

Title & Abstract

Introduction Methods
Results Discussion Conclusion

Figures / tables (your data)

Make a decision about which journal you would like to submit to

first, even before beginning to write. In that way, you can follow
the style of the journal, and shape the focus of the paper.
Article title

• A good title should contain the fewest possible words

that adequately describe the content of a paper.
• Effective titles:
• Identify the main issue of the paper
• Begin with the subject of the paper
• Are accurate, unambiguous, specific, and complete
• Are as short as possible

Strong (and accurate) titles: attract the

reader’s attention
Some good recent titles
Some good recent titles
Some good recent titles
Some good recent titles
Some good recent titles
Some good recent titles
Titles – different for review articles
Titles – different for review articles
Titles – different for review articles
Titles – different for review articles
Humour – OK, but be careful !!
Good titles, good covers !
The power of social media ?

852 friends (since March)

52% women
47% men
13-65+ yrs
(mode 25-34 yrs)
Sudan
Australia
Egypt
Pakistan
Good titles also rank well on social media ! – Altmetrics
(www.altmetric.com)
Abstract
An effective abstract is almost always just one paragraph :
What has been done and what are the main findings?
The advertisement for your article and freely available in PubMed,
Medline, Embase, SciVerse Scopus, etc.

Most important section of the article — It will be read by the most

people

It should include important data (sample size, statistics)

and results

Often best to write the abstract last

Some journals now also ask for a graphical abstract

Introduction

Introduction is especially important!

A high proportion of “lack of novelty” rejections are
made after reading abstract, introduction and
conclusions (often the last paragraph!)

• Remember, you are telling a story. The Introduction sets the scene.
• What was the purpose of your work? Introduce your scientific
question immediately – and clearly.
• Do not attempt to summarize the whole field (it is not possible!)
• Quote what is necessary for background and give credit to previous
works [Your reviewer could have written a seminal article in the
past!].
Introduction (continued)
• Give a clear motivation for the work. Explain why before
explaining how.
• Explain what is novel compared to what is already
available in the literature
• High level description of your approach. Why is it
important? Why is it difficult? Why is this new ?
• What are the alternatives? Why is yours different or
better?
• What are the gaps and how are you going to plug them?
• At the end of the introduction the reader knows the
problem and maybe the solution/approach you propose
Methods
Describe how the problem was studied

• Often the easiest place to start writing a paper

• Describe how the research was done – accurately.
Don’t copy and paste….
• When using methods that have been published before,
reference the publication without repeating the
description in detail – but merely citing a previous
article may not be sufficient
• Describe the statistical methods used – accurately !
Results
• Describe your findings in a logical sequence
• Should parallel your Methods section
• Provide some structure with subheadings – if necessary
• Don’t repeat what you’ve already stated
• Emphasis is on the observations of your research -- NOT
the implications
• Check and recheck your data for accuracy and consistency
— make sure the numbers add up!
• Results of statistical analyses – correctly performed
• Figures and tables – make them clear and readable
• Can often be one of the shortest sections of your paper
Results

Do not try to fit

everything in!
But this is what
should end up in the
paper

This may be your total

work.. !!
Discussion
This is where you interpret what your results mean. Provide critical
appraisal. This is the most important (and difficult) section of your
manuscript.

 Does not require complete review of the literature but should

place the study in context for the reader – but don’t repeat what
is in the Introduction.
 Why are your findings new and different?
 How are they relevant? Can you identify a mechanism to explain
your results or hypothesis?
Include:
 Interpretation of results taking into account any sources of bias or
imprecision. Acknowledge the weaknesses.
 Context of results with current evidence and in relation
to the purpose of your study.
Discussion continued

Be careful not to use statements that go beyond

what the results can support

Try to end on a positive tone

Don’t ever plagiarise – anywhere in your

manuscript !! You will be caught…
References
Cite the main scientific publications on which your work is based

Do not use too many references - but don’t be lazy

and only cite most recent reviews
Always ensure you have fully absorbed
material you are referencing

Avoid excessive self-citations

Avoid excessive citations of publications

from the same journal
Conform strictly to the style given in
the guide for authors
47
Acknowledgments

Ensures that those who helped in the research are recognised

Advisors/people
Suppliers who
who have Financial Proofreaders
may have
provided useful supporters and and graphic
donated
scientific funding bodies artists
materials
discussion
Authorship
 Policies regarding authorship can vary.
 One example: the International Committee of Medical Journal
Editors (“Vancouver Group”) declared that an author must:
 substantially contribute to conception and design, or
acquisition of data, or analysis and interpretation of data;
 draft the article or revise it critically for important
intellectual content; and
 give their approval of the final full version to be published.
 ALL 3 conditions must be fulfilled to be a credited author!
 Your institution will/should have a policy or guidelines
 Many journals now require an authorship declaration
 Disputes are common and of the difficult to resolve
 Try to get this sorted out early on in the work
Cover letter

Very important:
Your chance to speak 'directly' to the Editor

• Often overlooked by authors and filled cursorily (a big mistake!).

• You have spent months working in your paper – Don’t rush it now!
• Explain the main findings and your motivation – what gaps in
current knowledge have you filled?
• Highlight the novelty and significance of results
• Note special requirements (suggest not to contact a particular
referee, for example)
• Suggest referees: experts, not collaborators (say why)
• State any conflicts of interest
Ready to go..?

Don’t underestimate how long this is going to take

The peer review process
Peer review
Four possible outcomes

Accept as it is

Accept with minor or

moderate revision,
usually not back to
referees

Major revision, revised

manuscript usually goes
back to referees

Reject
First Decision: “Accepted” or “Rejected”
Accepted
• Very rare, but it happens
• Congratulations!
– Cake for the department
– Now wait for page proofs
and then for your article
online and in print
Rejected
• Probability 40-90% ...
• Do not despair
• It happens to everybody
• Try to understand WHY
• Straight out rejection without
peer review
• Consider reviewers’ advice
• Be self-critical
• If you submit to another journal,
begin as if it were a new manuscript
• Take advantage of the reviewers’
comments. They may review
your (resubmitted) manuscript
again!
• Read the Guide for Authors of
the new journal, again and again.
Reasons for upfront rejection…

Outside of the aims and scope of the journal.

Not of general interest.

A catalogue of data – no new insight. Confirms the

results of others.

No broad conclusion – many interesting possibilities but

nothing solid.

Geographically-specific.
First decision: “Major” or “Minor” revisions
Major revision
– The manuscript may finally be published in the journal
– Significant deficiencies must be corrected before
acceptance
– Usually involves (significant) textual modifications and/or
additional experiments

Minor revision
– Basically, the manuscript is worthy to be published
– Some elements in the manuscript must be clarified,
restructured, shortened (often) or expanded (rarely)
– Textual adaptations – alterations to figures
– “Minor revision” does NOT guarantee acceptance after
revision!
Manuscript revision: a great learning opportunity!

Prepare a detailed letter of response. Copy-paste reviewer comments

and address them one by one.
State specifically what changes you have made to the manuscript.
Give page and line number.
Provide a scientific response to the comment you accept; or a
convincing, solid and polite rebuttal to the point you think a reviewer
is wrong.
If extensive changes are required revise the whole manuscript not just
the parts the reviewers point out.
Minor revision does NOT guarantee acceptance after revision.
Do not count on acceptance, but address all comments carefully
Rejection: not the end of the world

Everyone has papers rejected.

Do not take it personally. Do not become abusive!
Try to understand why the paper was rejected.
Note that you have received the benefit of the editors and
reviewers’ time: take their advice seriously!
Re-evaluate your work and decide whether it is
appropriate to submit the paper elsewhere.
Rejection: if you decide to go elsewhere…

When you re-submit the paper elsewhere, modify it

appropriately to fit the new guidelines.

Don’t copy and paste from your original cover letter !!

‘I am submitting our manuscript to Nature

Communications …. when re-submitting to the IJP !!
ACCEPTED!
Congratulations…
Ethics in publishing
 Publish AND Perish! – if you break ethics rules

• International scientific ethics

have evolved over centuries,
and are commonly held
throughout the world.

• Scientific ethics are not

considered to have national
variants or characteristics
– there is a single ethics
standard for science.

• Ethics problems with scientific

articles are on the rise globally.
M. Errami & H. Garner
A tale of two citations
Nature 451 (2008): 397-399
Ethics issues in publishing

Scientific misconduct
– Falsification of results

Publication misconduct
– Plagiarism
• Different forms / severities
• The paper must be original to the authors

– Duplicate publication
– Duplicate submission
– Appropriate acknowledgement of prior research and researchers
– Appropriate identification of all co-authors
– Conflict of interest
Scientific misconduct

Data fabrication and falsification

• Manipulation of research materials, equipment, processes

• Changes in / omission of data or results such that the research is not
accurately represented in the research record

This can include selecting data to fit a preconceived hypothesis:

– do not include (data from) an experiment because ‘it did not work’, or
– show ‘representative’ images that do not reflect the total data set, or
– simply shelve data that do not fit.
Scientific misconduct
The most dangerous of all falsehoods is a slightly distorted truth
G.C. Lichtenberg (1742-1799)

“… the fabrication of research data … hits at the heart of our

responsibility to society, the reputation of our institution, the
trust between the public and the biomedical research
community, and our personal credibility and that of our mentors,
colleagues…”

“It can waste the time of others, trying to replicate false data or
designing experiments based on false premises, and can lead to
therapeutic errors. It can never be tolerated.”

Professor Richard Hawkes

Department of Cell Biology and Anatomy
University of Calgary
Data fabrication and falsification – you will be found out
Figure manipulation
Figure manipulation – example
different authors and experiments

Am J Pathol, 2001 Life Sci, 2004

Manipulation

Rotated 180o Zoomed out ?!

Ethics issues in publishing

Scientific misconduct
Falsification of results

Publication misconduct
– Plagiarism
• Different forms / severities
• The paper must be original to the authors

– Duplicate publication
– Duplicate submission
– Appropriate acknowledgement of prior research and researchers
– Appropriate identification of all co-authors
– Conflict of interest
Plagiarism detection tools
• Elsevier is participating in 2 plagiarism detection schemes
– Turnitin (for universities) & Ithenticate (for publishers and
corporations)
– Manuscripts are checked against a database of 20 million peer
reviewed articles which have been donated by 50+ publishers,
including Elsevier.
– All post-1994 Elsevier journal content is included, and pre-1995
content is being added week-by-week

• Editors and reviewers

• Your own colleagues…

• “Other“ whistleblowers
– “The walls have ears", it seems ...
Publication ethics – self-plagiarism
2003 2004

Same
colour
left and
right

Same
text
Retractions

Articles of which the authors have committed plagiarism or

fraud are not removed from ScienceDirect. Everybody who
downloads it will see the reason of retraction…
Publication ethics – how it can end ..
Some actual emails………..
“I deeply regret the inconvenience and agony caused to you by my
mistake and request and beg for your pardon for the same. As such I am
facing lot many difficulties in my personal life and request you not to
initiate any further action against me.

I would like to request you that all the correspondence regarding my

publications may please be sent to me directly so that I can reply them
immediately. To avoid any further controversies, I have decided not to
publish any of my work in future.”

“Dear Editor,
Good day! Today, I find my student (named xxx) submit a paper to you
without my agreement. However, this paper is an unethical practice. This
boy has been punished. Please forgive us. Again, we are very, very sorry
to waste your time and work. Please withdraw this paper as soon as
possible.”
What are your responsibilities as an author?

• Report data that is –

– Real
– Unfabricated
– Original
• Declare any conflicts of interest.
• Ensure proper authorship.
• Submit to one journal at a time.
• Make sure to cite others’ work carefully and properly.
 Packed with free online lectures and interactive courses, together with
expert advice and resources to help you or your students on their way to
publishing a world-class book or journal article.

Free courses include:

• Introduction to scholarly publishing
• How to get published in a journal
• Book publishing
• Peer review
• Publishing ethics
• Grant writing
• Getting your paper noticed

publishingcampus.com
Elsevier Publishing Campus colleges offer opportunities to get involved in
discussions, enhance research skills, build networks and more.

publishingcampus.com
Good Luck !