How to write a scientific manuscript michael terns

1.

How To Write A
Scientific Manuscript
Michael Terns
BCMB 8030

2.

Anatomy of a Research Paper
Title
Authors
Abstract
Keywords
Need to be accurate and informative for
effective indexing and searching
Main text (IMRaD)
Introduction
Methods
Results
Discussion (Conclusion)
Acknowledgements
References
Supplementary material
Each has a distinct function

3.

Tell a Story!
Steps in Story line
Section of the Paper
Question
Introduction
Experiments done to
answer question
Methods
Results found to
answer question
Results
Answer
Discussion
The story also includes why question and answer
are important and how they fit with previous work

4.

Introduction
Primary functions:
1. Identifies the research question(s).
2. Provides background information
(context) that a reader needs to understand
your experiments.
3. Catches and holds reader’s interest
(justifies why the work is important).

5.

Introduction
A Funnel-like Organization
Known (general area)
Unknown (specific topic)
Question (make this obvious)

6.

Introduction
• States purpose of study and describes why it matters.
• Funnels from:
Known (the big picture significance and previous work) to
Unknown (the specific gap in knowledge) to
Question (this should be important, specific, and unresolved).
• Keep introduction focused, brief (3-4 paragraphs) and relevant
to your work.
• Not an extensive literature review! (summarizes background
information only for specific aspect of the topic being addressed).
• Past tense (previous findings and to state question) and
present tense (for what is currently true).
• Ends by stating question and general approach or by
summarizing principal results and conclusions suggested.

7.

Tell a Story!
Steps in Story line
Section of the Paper
Question
Introduction
Experiments done to
answer question
Methods
Results found to
answer question
Results
Answer
Discussion

8.

Materials
Primary functions:
1. To tell reader what experiments you did to answer
the question(s) posed in the introduction.
2. Should include sufficient details and references
to permit a trained scientist to evaluate your work
fully or to repeat the experiments exactly as you
have done them.

9.

Methods
• Describe in detail what was done to answer the research question.
• Give sources (company, etc.) and detailed description of reagents
and equipment used.
• Use subheadings (e.g. Immunoblotting, Plasmid constructs, etc.)
• Usually written in chronological order (i.e. same order as in Results)
• Use past tense.
• Understand what are common vs. specialized techniques.
(provide more detailed information for specialized/new techniques).
• Do not include results in Methods section.

10.

Tell a Story!
Steps in Story line
Section of the Paper
Question
Introduction
Experiments done to
answer question
Methods
Results found to
answer question
Results
Answer
Discussion

11.

Results
Primary functions:
1. Objectively state results/findings of the
experiments described in the Methods section.
2. Direct reader to figures or tables that present
the supporting data.
The Results Section is
the Core of your Paper!

12.

Results
Objectively describe the findings (significant data interpretation
and conclusions belong in Discussion).
For each set of experiments:
1. Why you did the experiment (rationale).
2. How you did it (without repeating details found in Methods).
3. Presentation of representative data (what you did and found).
Use subheadings.
Use past tense.
Do not include detailed experimental information (Methods).
Provides foundation for Discussion.
Don’t assume that readers read previous sections. At start,
re-orient reader to the main question and general methods.

13.

Figures and Figure Legends
Design effective (clear and simple) figures, graphs, images,
tables, etc. from the raw data.
Figures should “stand-alone”- a reader should be able to look at
a figure and it’s legend and be able to understand how the
experiment was done as well as see the results (without
reference to the text).
Give each figure and table a simple, self-explanatory title in the
form of a sentence. (Most of the content of paper should be
evident from reading these titles alone).
2 approaches for writing figure legend titles:
1. State what figure represents.
(e.g. levels of p53 in human lymphocytes).
2. Gives the conclusion of a figure.
(e.g. p53 expression is absent in most human lymphocytes).

14.

Tell a Story!
Steps in Story line
Section of the Paper
Question
Introduction
Experiments done to
answer question
Methods
Results found to
answer question
Results
Answer
Discussion

15.

Discussion
Primary functions:
1. To answer the question(s) posed in the Introduction.
2. To explain how results support the answer(s).
3. To explain how answer(s) fit in with existing knowledge
on the topic.
Be sure to convey the significance of your work
and emphasize unique contributions.

16.

Discussion (Content)
Answers to question(s) posed in introduction (provide your
interpretation of results).
Accompanying support, explanation, and defense of answers.
(point out principals, relationships, generalizations – DO NOT
simply rehash/restate results but discuss the results).
Explanation of novelty of work (compare with previously
published work).
Explanations of any unexpected findings, discrepancies with
other’s related work, and limitations of methods or study design.
Explanation of importance/significance of work (e.g. applications,
implications, speculations). Answer the question….So what?
Use present tense except when describing previous work (past).
Discussion (like a good story) has a beginning, middle, and end.

17.

Discussion (Organization)
BEGINNING: States answer and summarizes main findings.
Start with very brief one paragraph summary that provides the
answer (main conclusions) to the question and gives main lines
of evidence that supports the answer.
The answer can be stated in the first sentence or after one
sentence that re-states the question or gives brief context.
MIDDLE: Explains answer and how it fits in with previous work.
Includes your interpretations of results.
Generally organized from most to least important answers.
Use clear topic sentences at the beginning of each paragraph,
Compares your work to relevant studies of others.
END: Gives final conclusion(s).
Two standard ways to conclude: 1) Restate answer and/or
2) Indicate importance of work by stating implications,
applications, speculations, (possibly) suggest future work.

18.

Acknowledgments
Acknowledge and thank colleagues who contributed
to the work but do not meet the criteria of authorship.
Intellectual assistance (including reviewing manuscript).
Technical help.
Special equipment.
Materials (e.g. cell lines, antibodies,genes,etc.).
Acknowledge financial support (list grant information).

19.

References
Primary functions:
1. To give credit to the ideas and findings of others.
2. To direct readers to sources of further information

20.

References
1. Include only significant, published work.
2. Must be accurate (you should not cite a reference that
you have not read).
3. Keep in mind your likely reviewers.
4. Use correct format for specific journal.
5. Use bibiography software such as “END NOTE”.

21.

Abstract
Primary functions:
1. To provide an overview and clear preview of paper.
2. Must be understandable by itself and accurately
reflect the paper.
IS VITALLY IMPORTANT:
A reader uses an abstract to quickly understand
the purpose, methods, results, and significance
of your work and will only read further if their
interest is captivated by the Abstract.

22.

Abstract
1. Typically 100-250 words (journal-specific).
2. Is a single paragraph, condensed version of entire paper.
3. Should specifically and selectively pull-out (“abstract”)
the highlights from each section of the paper (IMRaD).
I: background and question.
M: what experiments were done.
R: what results were found.
D: the overall answer/conclusion.
4. Usually starts with a sentence or two of background info
and ends with a sentence stating the importance of answer.
5. Past tense.
6. Is typically the last section of paper written.

23.

Title
Primary functions:
1. To identify the main topic and message (answer)
of paper (accurately, completely, and specifically).
2. To attract readers.
Keep in mind that few people will read your entire paper
but many will read the title (also used in search terms).
Be concise, revealing, and exciting.
Be direct and as big picture as the data can justify.

24.

Writing Style
Your main goal should be to make a reader comfortable
in understanding the information presented.
Write simply, clearly, and without ambiguity (Effective
organization is key).
Assume the reader is NOT an expert in the subject of paper.
Words: must be chosen and arranged so that their
meaning is clear (are precise, simple, and necessary).
Sentences: should address one idea (simple and direct).
Paragraphs: should be treated as a single topic with a clear
message (use topic, supportive, and transition sentences)
Flow: Make logical connections/transitions between end of
each sentence, paragraph, or section and the next.
General approach: overview first, then details.

25.

Common Errors (Don’ts)
Title/Abstract: Too vague or detailed, not captivating
reader’s interest, over-stating or over-generalizing.
Introduction: Too much information (random summarization
of papers on subject) or failure to point out gap/question.
Methods: Insufficient detail to enable replication by others.
Results: Confusing figure design, not telling an easy to
follow story, redundancy* with other sections of paper.
* discussing results (save for Discussion)
* including detailed methodology (save for Methods)
Discussion: Highly redundant with Results, too much
information, poor transitions, ommission of related work, not
thoughtful.
Not following specific journal instructions

26.

Tips (Do’s)
It is wise to begin writing the paper while the work is still
in progress (writing process itself can help focus the
experiments).
Copious Self-Editing!!!!
* cut, cut, cut……main route to clarity.
* carefully check organization, grammar, and spelling.
* review how well you fulfilled the purposes of each main
section of paper (avoiding redundancy between sections).
* make sure that the significance of your work is emphasized
throughout the paper.
* check to see compliance of specific journal instructions.

27.

The C3 Principle
Good writing contains the following:
• Clarity
• Conciseness
• Correctness (accuracy)
The key is to be as brief and specific as
possible without omitting essential details

28.

Know Thy Enemy
Good writing avoids the following:
• Repetition
• Redundancy
• Ambiguity
• Exaggeration
These are common annoyances for reviewers and editors

29.

Plagiarism
UNDERSTAND AND AVOID IT!!!
Do not use the exact wording (or phrasing) from
another paper - even when you cite the source.
Put all papers far away when you write.
Insufficient acknowledgement of ideas or work
is a form of plagiarism.

30.

Main Sources
“How to Write and Publish a Scientific Paper”.
Sixth edition. Day and Gastel. Greenwood Press.
“Essentials of Writing Biomedical Research
Papers”. Second edition. Zeiger. McGRAW-Hill.