Publication of Research Article

Dr. S. Umesha, PhD.

Associate Professor
DOS in Biotechnology
University of Mysore
Manasagangotri
Mysore- 570006
 Table of Contents

• Introduction
• Part I: Publication & Peer Review
– Deciding to Publish
– Submitting Your Paper
– After Submission
– Overview of Peer Review
– Purpose of Peer Review
– How It Works
– The Role of Editor
– Limitations and Issues
 Table of Contents Cont’d
• Part II: Writing a Scientific Manuscript
– The Scientific Manuscript
– Word Choice
– The Abstract
– The Introduction
– The Methods & Materials Section
– The Results Section
– The Discussion Section
– Figures, Tables, Equations, and References
“There is no way to get
experience except through
experience.”
 Scientific Publication is a Team Effort

Editorial Office

Author Reviewer

Submission, Editorial Screening, Reviewing and Editorial Decision

Processes are similar to those presented in previous talks
Scientific Publication is a Team Effort

Journal

Authors Reviewer
 Part
PartI:I:Publication
Publication &
& Peer
Peer
Review:
Review:
Deciding to Publish and Submitting Your Paper
• What to publish?
– abstract vs. full report
• Choosing your forum
– Which type of journal is best for you?
– What audience are you targeting?
• Research the journal
– Publication guidelines
– Article style
 Publish and perish
“The Seven Deadly Sins”
1. Data manipulation, falsification
2. Duplicate manuscripts
3. Redundant publication
4. Plagiarism
5. Author conflicts of interest
6. Animal use concerns
7. Humans use concerns
 What constitutes redundant
publication?
Data in conference abstract? No
Same data, different journal? Yes
Data on website? Maybe
Data included in review article? OK if later
Expansion of published data set? Yes
 What makes a good research
paper?

 Good science
 Good writing
 Publication in good journals
What constitutes good science?
Novel – new and not resembling something
formerly 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.
What constitutes a good journal?

Impact factor –
average number of times published papers
are cited up to two years after publication.

Immediacy Index –
average number of times published papers
are cited during year of publication.
 Journal Citation Report

Journal Impact Factor Immediacy Index

Nature 30.979 06.679

Science 29.162 05.589

Hypertens 05.630 00.838

AJ P Heart 03.658 00.675
Physiol Rev 36.831 03.727

Am J Math 00.962 00.122

Ann Math 01.505 00.564
Things to consider before writing
1. Time to write the paper?
- has a significant advancement been made?
- is the hypothesis straightforward?
- did the experiments test the hypothesis?
- are the controls appropriate and sufficient?
- can you describe the study in 1 or 2 minutes?
- can the key message be written in 1 or 2 sentences?

“Those who have the

most to say usually say
it with the fewest words”
Things to consider before writing
1. Time to write the paper?
- has a significant advancement been made?
- is the hypothesis straightforward?
- did the experiments test the hypothesis?
- are the controls appropriate and sufficient?
- can you describe the study in 1 or 2 minutes?
- can the key message be written in 1 or 2 sentences?

2. Tables and figures

- must be clear and concise
- should be self-explanatory

3. Read references
- will help in choosing journal
- better insight into possible reviewers
Things to consider before writing
4. Choose journal
- study “instructions to authors”
- think about possible reviewers
- quality of journal “impact factor”

5. Tentative title and summary

6. Choose authors
 After Submission

• Publication Procedure (6-12 months)

– Author submits
– Editor is assigned to manuscript
– Editor assigns reviewers (associate editors) to inspect
– Reviewers decide on whether to review paper
– Several reviewers inspect and edit
– Editor decides on accuracy of revisions and whether to
accept paper
– If accepted, editor sends paper back to author with
revisions
– Author revises paper and sends it back
– Possibility of second review process
– Publication!
 Authorship

Guidelines on authorshop, International committee of Medical Journal Editors,

Reprinted by kind permission of the Editor of the British Medical Journal of Sept
14, 1985. J Clin Pathol 39: 110, 1986
 What is Peer Review?

• Review process for scientists by scientists

• Purpose
– To filter what is published as “science”
– To provide researchers with perspective
• Where is peer review used?
– Scientific publication
– Grant review
– Tenure promotion
 Constraints of Peer Review
• Slow
• Conflicting views
– Confronting theory bias
• Personal views
– Objective vs. personal edits
• Fraud
– Data manipulation and
invention
“Editors and scientists portray
peer review as a quasi-sacred
process that helps to make
science our most objective truth
teller. But we know that the system
of peer review is biased, unjust,
unaccountable, incomplete, easily
fixed, often insulting, usually
ignorant, occasionally foolish, and
frequently wrong.”
-- Richard Horton, editor of The
Lancet,
 Scientific Misconduct
• Gift Authorship
• Redundant Publication
• Plagiarism
• Fabrication
• Falsification
• Conflict of Interest
Part II: Writing a Scientific
Manuscript
 Writing Style and Audience

• Checklist:
• Void of anecdotes or stories
• Reports facts not outlandish conclusions
• No misspellings
• Grammatical accuracy
• Meets formatting guidelines
• Avoids using the first person
• Who’s the audience?
• Write for your target audience
Words and expressions to avoid

Jargon Preferred use

a considerable amount of much
on account of because
a number of several
Referred to as called
In a number of cases some
Has the capacity to can
It is clear that clearly
It is apparent that apparently
Employ use
Fabricate make
Day, RA. “How to write and publish a scientific
paper,” 5th edition, Oryx Press, 1998.
 Word Choice

• Examine vs. Analyze

– Activity to gain knowledge vs. Describing the analysis of
that knowledge
• Bloom’s Taxonomy
– Knowledge
– Comprehension
– Application
– Analysis
– Synthesis
– Evaluation
 Word Choice
• Bloom’s Taxonomy
– Knowledge: Recitation of fact
• Found, identified, labeled
– Comprehension: State a problem or interpret fact
• Discuss, predict, compare
– Application: Apply old information to solve new problems
• Solve, show, examine, classify
– Analysis: Used to explain patterns or meaning
• Analyze, investigate, compare, contrast
– Synthesis: Making predictions or discussing possibilities
• Predict, plan, devise, propose
– Evaluation: Drawing conclusions, making recommendations
• Justify, verify, argue, recommend, determine
 Manuscript Structure

• Abstract
• Introduction
• Body of Article
• Results
• Discussion and Conclusions
• Acknowledgements
• References
• Figures and Tables
 Abstract
• Summary of Manuscript (200-300 Words)
• Problem investigated
• Purpose of Research
• Methods
• Results
• Conclusion
 Abstract
• Common Mistakes
– Too much background or methods information
– Figures or images
– References to other literature, figures or images
– Abbreviations or acronyms
 Introduction
• Broad information on topic
– Previous research
• Narrower background information
– Need for study
• Focus of paper
– Hypothesis
• Summary of problem (selling point)
• Overall 300-500 words
 Introduction
• Common Mistakes
– Too much or not enough information
– Unclear purpose
– Lists
– Confusing structure
– First-Person anecdotes
 Methods and Materials
• Provides instruction on exactly how to repeat experiment
– Subjects
– Sample preparation techniques
– Sample origins
– Field site description
– Data collection protocol
– Data analysis techniques
– Any computer programs used
– Description of equipment and its use
 Methods and Materials
• Common Mistakes
– Too little information
– Information from Introduction
– Verbosity
– Results/ sources of error reported
 Results
• Objective presentation of experiment results
– Summary of data
• NOT a Discussion!

• Common mistakes
– Raw data
– Redundancy
– Discussion and interpretation of data
– No figures or tables
– Methods/materials reported
 Discussion
• Interpret results
– Did the study confirm/deny the hypothesis?
– If not, did the results provide an alternative hypothesis? What
interpretation can be made?
– Do results agree with other research? Sources of
error/anomalous data?
– Implications of study for field
– Suggestions for improvement and future research?
• Relate to previous research
 Discussion

• Common Mistakes
– Combined with Results
– New results discussed
– Broad statements
– Incorrectly discussing inconclusive results
– Ambiguous data sources
– Missing information
 Figures and Tables

• Tables
– Presents lists of numbers/ text in columns
• Figures
– Visual representation of results or illustration of
concepts/methods (graphs, images, diagrams, etc.)
• Captions
– Must be stand-alone
 Figures and Tables
• Guidelines for Figures and Tables
– High resolution
– Neat, legible labels
– Simple
– Clearly formatted
– Indicate error
– Detailed captions
 References
• Check specific referencing style of journal
• Should reference:
– Peer-reviewed journal articles, abstracts, books
• Should not reference:
– Non-peer-reviewed works, textbooks, personal communications
• Common Mistakes
– Format, Format, Format
• (Figures & Tables, Equations, and References)
– Redundant Information
• Text, Figures, Tables, and Captions
– Type of Reference
Process of Research
Completion of research

Preparation of manuscript

Submission of manuscript

Assignment and review

Decision
Rejection Revision

Resubmission

Re-review
Acceptance
Rejection
Publication
 Resources
Day, RA. “How to write and publish a scientific paper,” 5th edition,
Oryx Press, 1998.

Fischer BA, Zigmond MJ. “Components of a research article.”

survival@pitt.edu
Marshal GS. “Writing a peer reviewed article.”
http://dor.umc.edu/ARCHIVES/GMarshallPublishingarticle.ppt

Hall, JE. “Writing research papers (and getting them published)”

http://dor.umc.edu/ARCHIVES/GMarshallPublishingarticle.ppt

Benos, D., Reich, M. “Peer review and publication in APS journals.”

http://www.the-aps.org/careers/careers1/EBSymposia/Benos2003.ppt
 What is open access?

• Free, immediate access online

• Unrestricted use
 What is open access?

• Free, immediate access online

• Unrestricted use
 What is open access?

• Free, immediate access online

• Unrestricted use
 What is open access?

• Free, immediate access online

• Unrestricted use
 Document

A network of literature
A network of literature and Document
Database
data
The life cycle of a research article

Research

Submission
2-3 Experts
Rejects

Is it rigorous?
Good enough?
Right audience?
Takes months/years
Peer review

Publication Journal name is key

New models of scholarly
communication

Research

2-3 Experts
Rejects

Submission Is it rigorous?
Good enough?
Right audience?
Peer review
Takes weeks/months

PLoS Publication Focus on the article

Currents

Enhanced article
Article-level metrics
Integrated with data
Organization in Hubs