How to write and publish a biomedical research paper Ahmed Negida

How to write and publish

a biomedical research paper

An easy guide for medical researchers

Prepared by

Ahmed Said Negida

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How to write and publish a biomedical research paper Ahmed Negida

Biography of the lecturer: Ahmed Negida

Education
Fifth-year medical student (2016/2017)
at Faculty of Medicine, Zagazig University, Egypt

Research Experience
▪ >4 years of diverse clinical research experience
▪ >40 international research publications
▪ Collaborator with many researchers in Egypt worldwide (UK, USA,
Australia, Iran, KSA, and Japan)
▪ Reviewer and editor in many international peer-reviewed journals
▪ Clinical research advisor for some hospitals and health companies
▪ Biostatistician for some CROs within and outside Egypt
▪ National Clinical Research Coordinator of GlobalSurg-1 project
(2014-2015), Research department, Royal College of Surgeons, UK
▪ Founder and chairman of Medical Research Group of Egypt

Teaching experience
In his spare time, he gives research workshops to researchers and
doctors. Since 2014, he has taught >400 researcher through his workshops
in different Egyptian governorates and universities. He is widely involved
in clinical research designing, medical statistics, scientific writing, and
evidence synthesis.

Contact Information
▪ Personal website: www.ahmed-negida.net
▪ Email: ahmed01251@medicine.zu.edu.eg
▪ Tel: +201125549087

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How to write and publish a biomedical research paper Ahmed Negida

1 Manuscript components

Title page

Abstract page

Manuscript TEXT

References

Appendices

2 Title page
❖ Criteria of good titles
• identify the main issue of your paper
• begin with the subject of your paper
• are accurate, unambiguous, specific, and complete
• do not contain abbreviations
• attract readers

❖ Types of titles

❖ Components of the title page

1. Manuscript title
2. Short running title
3. Authors
4. Affiliations
5. Correspondence details

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How to write and publish a biomedical research paper Ahmed Negida

3 Writing an abstract
It is a summary of the research paper in about 200-400 words (according to
journal/conference instructions). The abstract may be structured (Introduction,
Methods, Results, and Conclusion) and may be unstructured (one paragraph). The
importance of the abstract is that it helps the readers understand the general outline
about your paper. Also, the abstract is used in the meta-data for indexing purpose in
search databases and is made freely available by subscription journals (readers do
not need to pay money to read abstracts in subscription journals). The abstract can
be submitted to a conference and be presented in scientific meetings.

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How to write and publish a biomedical research paper Ahmed Negida

❖ Example for a structured abstract

❖ Example for an unstructured abstract

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How to write and publish a biomedical research paper Ahmed Negida

4 Writing the manuscript text

❖ IMRaD structure
Scientific research papers follow the structure (Introduction, Methods, Results, and
Discussion), abbreviated as IMRaD structure. The IMRaD structure has evolved in the
course of twentieth century and is currently the common structure of articles
published in scientific journals. However, the arrangement of the IMRaD structure is
rarely substituted in some journals as Nature publishing group.

❖ Types of scientific publications that do not follow the IMRaD structure

• Literature reviews • Editorials
• Expert opinion • Letters to Editor
• Piece of my mind • Case reports/Case series
NB: Systematic but not traditional reviews are reported according to the IMRaD
structure.

❖ Introduction

• The importance of introduction is to provide sufficient basic knowledge about

the topic to help getting the readers into the scope of your article
• The introduction shows the scientific rational of conducting your research study
in continuous flow and in a reasonable sequance
• The last paragraph of the introduction should include the aim of your research
study
• The introduction is composed of the following paragraphs: [1] a paragraph
showing overview about the study condition/disease; [2] a more specific
pargraph about the subject of the study (drug/gene/…); [3] gap of
knowledge; and [4] aim of the work.

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How to write and publish a biomedical research paper Ahmed Negida

❖ Methods and materials

• This is the most important section in your paper

• Methods and materials should be adequantly discribed to an extent that
allows replication and validation of your work
• Unlike other sections of the paper, errors in the methods section might not be
changeable and usually lead to the rejection of your manuscript

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How to write and publish a biomedical research paper Ahmed Negida

• Methods section accounts for about 80% of rejections of scientific research

papers
• Methods section is usually written in the past tense (work has been already
done) while if you are writing a study protocol, the methods will be in the future
• Whenever possible, standard diagnosis, processing, and measurement

❖ Results

• In this section, you present the findings of your study

• Methods of displaying the results are: (1) narrative paragraphs, (2) tables, and
(3) charts and figures
• Use one form of data presentation (i.e data reported in table should not be
repeated in the text or displayed as figure)
• Results are displayed in a reasonable flow from simple to complex (univariate
analysis, bivariate analysis, then multivariate analysis)
• Study outcomes even if not-statistically significant should be reported in the
results
• Do not interpret results or commen on their significance in practice

❖ Discussion

• The aim of this section is to discuss the findings of your study

• In this section, you discuss the statistical and clinical significance of your study
results
• Avoid repeating the results again
• This section should not contain new results
• The main parts of the discussion section are: [1] summary of findings of this
study, [2] justification of study resluts whnenever possible, [3] previous studies,
[4] agreement/disagreement with previous studies, [5]study strengths and
limitations, and [6] final conclusion.

5 Appendices
• Acknowledgement ………..?
• Funding source ………..?
• Conflict of interest ………..?
• Tables ………..?
• Figures and Figures' legends ………..?
• References ………..?

6 Rules of scientific writing

• Put actions in verbs
• Put characters in subjects

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How to write and publish a biomedical research paper Ahmed Negida

• Keep subjects near verbs

• Put new information last
• Use active voice
• Make sure the first and last sentences of a paragraph match
• Omit needless words
• Prefer simple words
• Use simple subjects
• Numbers less than 10 are words.
• Number 10 or more are numbers.
• Words not numbers begin a sentence.
• Be consistent in lists of numbers.
• Numbers less than 1 begins with a zero.
• Do not use a space between numbers and its percent sign.
• Use one space between a number and its unit.
• Report percentages to only one decimal place if the sample size is larger than
100.
• Do not use decimal places if the sample size is less than 100.
• Do not use percentage if the sample size is less than 20.
• Do not imply greater precision than your measurement instrument.
• For ranges use "to" or a comma but not "-" to avoid confusion with the minus
sign and use the same number of decimal places as the summary statistic.
• Rules for data numbers do not apply to citations to the literature.
• Examples for avoiding long phrases
• Correct use of parallel sentences
• Creating a flow between sentences
• Avoid repetitions
• Correct use of the sneaky plurals
• Avoid gender-specific pronouns
• Using because to mean "because"

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How to write and publish a biomedical research paper Ahmed Negida

7 Preparing the manuscript file

• Use double spacing throughout the manuscript

• Provide at least 25 mm margins

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How to write and publish a biomedical research paper Ahmed Negida

• Pages should be numbered

• Begin each section in a new page

• Begin each table in a new page

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 How to write and publish a biomedical research paper Ahmed Negida

8 Selecting a relevant journal

1. Asking a colleague with experience in the topic, make three lists ….
2. Checking the references of your manuscript
3. Search PubMed using your manuscript keywords then ….
4. Use journal selector tools (Edanz, Cofactor, Elsevier, BMC, ….)

9 Reading the Instructions to authors

On its website, each journal has specific requirements regarding: manuscript types,
types of submitted files and their formats, word count, abstract style, table/figure
count, reference style, items reporting, … etc.

Make sure you have read the instructions to authors carefully before submitting to
the journal. If you did not comply to these instructions, your submission will be returned
back to the author by the editorial assistant. Non-complying to the journal
requirements makes a bad impression in the editorial office.

10 Authorship
ICMJEs criteria of authorship (Vancouver criteria)

The authors should meet ALL the 3 criteria:

1. Have substantial contribution to the work

2. Participated in drafting OR revising the manuscript
3. Agree on the publication of the final manuscript

Those who do not qualify for authorship are acknowledged.

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How to write and publish a biomedical research paper Ahmed Negida

11 Writing a cover letter

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How to write and publish a biomedical research paper Ahmed Negida

12 Submitting the manuscript to the journal system

13 Upload files

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How to write and publish a biomedical research paper Ahmed Negida

14 Suggesting reviewers
1. Asking a colleague with expertise in the topic
2. Suggest people with significant contribution to the topic
3. Search PubMed and suggest authors of previous work

15 After submission (Flow of the publication process)

16 Peer-review process
The process of peer review guarantees that submitted manuscripts are revised be
experts and peers in the field who submit their review report to the editor. The
editor can select one, two, three, or more reviewers to revise your manuscript;
sometimes one of the selected reviewers is from the suggested reviewers by the
authors during the submission. Each reviewer is asked to submit his report within 2-
3 weeks from accepting the invitation to review the manuscript. The peer review
process can take from few weeks up to several months (average 2-3 months).

❖ Types of the peer-review

1. Blinded peer review
2. Unblinded peer review (open review)

17 Replying to reviewers' comments

1. Be calm and objective
2. Deconstruct each message into individual items
3. Address each item separately
4. Always be polite even if the reviewer is NOT correct
5. Try to make all suggested changes
6. Try to negotiate the radical points
7. Do not ignore any of the reviewers' comments

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How to write and publish a biomedical research paper Ahmed Negida

8. Organize your response in a tabular manner

Number Comment Location Amendment/ Response

1 xxx Page no . xx We added ….
2
3

9. Support your response with relevant references

10. Be clear and very simple
11. Take a positive attitude
12. It is time to win the editor to your side!

18 Editorial decisions
- Acceptance
- Conditional acceptance (accepted following revisions)
- Might be considered for publication after minor/major revisions
- Considered for publication as a short communication or letter
- Rejected

19 Rules of predatory journals and publishers!

No. Rule Interpretation
The scope of interest Look to the “aims and scope” section of a potential journal
includes non-biomedical website. If multiple, wide-ranging and unrelated fields of study
1
subjects alongside are combined (eg, agriculture, geology, astrophysics, health),
biomedical topics you should be concerned.
The website contains If you see multiple, obvious English-language typos and
2 spelling and grammar grammatical errors on a journal’s home page, this is probably a
errors sign of low quality (and poor translation).
Low-resolution or stretched images, screenshots or those that
Images are
resemble or replicate legitimate industry images are a likely sign
distorted/fuzzy, intended
of a low-quality, if not illegitimate, publishing entity. Obtaining
3 to look like something
knowledge of or referring to legitimate publishing industry logos
they are not, or are
in your field may be handy. The Google Chrome similar image
unauthorised
search feature may also be helpful here.
If the wording on a potential journal’s web page is aimed at
attracting authors and submissions (eg, prominently inviting
submissions, promoting quick peer review or publication), this is
The home page
4 probably a good warning to stay away. You likely want your
language targets authors
research to be read by a specific target audience. Publishing it
in a venue with little focus (ie, vastly different topic areas)
reduces this possibility.
A metric called the Index Copernicus Value (ICV) is associated
The Index Copernicus almost exclusively with illegitimate entities. Legitimate journals do
5 Value is promoted on the not appear to use this questionable metric. Not all illegitimate
website entities have it, but if you see this metric listed on a potential
journal’s website, it’s probably best to stay away.
Description of the
A journal should provide authors with details of what to expect
6 manuscript handling
after you submit your paper, including details about peer review.
process is lacking

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How to write and publish a biomedical research paper
Manuscripts are
7 requested to be
submitted via email
Rapid publication is
8
promised
There is no retraction
9
policy
Information on whether
and how journal content
10
will be digitally preserved
is absent
The article
processing/publication
11
charge is very low (eg,
<$150)
Journals claiming to be
open access either retain
12 copyright of published
research or fail to mention
copyright
The contact email
address is non-
professional and non-
13
journal affiliated (eg,
@gmail.com or
@yahoo.com)
Ahmed Negida
If you cannot find this information anywhere on the journal’s or
publisher’s website, be concerned.
In the submission area of a journal’s website, if you are instructed
to submit your manuscript via email to the journal/editor for
consideration, rather than through an electronic submission
system, this may be a sign that the journal is unfamiliar with
standard/legitimate practice. Submitting your manuscript via
email is probably unwise. If you encounter this, check with peers
about the norms in your field.
At this moment in time, most legitimate journals are unlikely to
make any indication that your manuscript will be published
rapidly. Whether or not an article is published at all typically
depends on the outcome of peer review.
Every journal should have a mechanism for recalling or retracting
an article. This information may be found in the journal policies
section, or even in instructions to authors. Even in the best of
journals, errors, omissions and fraud are possible. Journals should
have an explicit, transparent statement of how they intend to
handle such instances.
Perpetual preservation of content, following a variety of industry
digital archiving protocols, is a technical obligation of scholarly
journals. It is a prerequisite for any journal seeking to be indexed
in databases such as PubMed; it also a vital part of the inclusion
criteria for entities such as the Directory of Open Access Journals.
This information can be difficult to locate or to understand (if it is
located). A good indication of preservation is whether the
journal’s publisher deposits content to a central repository (in
medicine, PubMed Central is an example of this).
In open access biomedical journals or those with open access
options (hybrid) article processing charges (APCs) can be quite
high (upwards of $800, about £650). Information about APCs
may be found within journal sections on open access, journal
policies or instructions to authors. If a journal claiming to be open
access does not indicate a fee, or if the fee is very low (eg,
<$150), check with your peers about the going rate for article
processing charges in your area of research/publishing.
Pure open access journals do not require authors to sign over the
copyright for their manuscripts to the journal. Authors should be
able to retain copyright of published open access work. Look for
this information before submitting to or publishing in a journal. It
is often found in the journal policies or the instructions to authors
sections.
Journals, journal editors and journal staff should all have
institutional or journal-affiliated email addresses as a marker of
professionalism. Check the “contact us” email address(es) as a
first pass.
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How to write and publish a biomedical research paper Ahmed Negida

20 Assignment (1) Proofread the following paragraphs

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 How to write and publish a biomedical research paper Ahmed Negida

21 Assignment (2): Find two relevant journals for:

MS1: Safety and efficacy of Droxidopa for Neurogenic Orthostatic Hypotension

MS2: A review of the epidemiology and treatment of Zika virus

MS3: Coenzyme Q10 for patients with Parkinson's disease

22 Assignment (3) Suggest two reviewers for:

MS: Velpatasvir plus Sofosbuvir for the treatment of Hepatitis C virus infection
genotype 4

23 Additional links
Equator network: http://www.equator-network.org/

Beall's list: http://beallslist.weebly.com/

Referencing by Mendeley: https://www.youtube.com/watch?v=IPtSPnt5ZFY

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