Scientific Writing 101Scientific Writing 101

“In science the credit goes to the man who convinces the world, not to the man to whom the idea first occurs.”

-Sir Francis Darwin

Parham Mirshahpanah 20 July, 2007

Process

1. Journal

2. Data & Figures

3. Results

4. Materials & Methods

5. Introduction

6. Discussion

7. Abstract

8. Formatting & Submission

9. Reviewer Response

Process

1. Journal

2. Data & Figures

3. Results

4. Materials & Methods

5. Introduction

6. Discussion

7. Abstract

8. Formatting & Submission

9. Reviewer Response

Journal Selection

Aims & Scope

Reference Relevance

Impact Factor

Editorial Board

Scientific class:i.e. biology,

chemistry, etc…

Clinical application:derm, oncology,cardiology, etc…

Quality of data:novelty, value to

scientific community

Utilize familiar names:references &associations

Correspondence type:letter, original article,

review…

Similar journal as themajority of your

references

Getting started: formatting

Refer to journal home page for individual formatting styles; varies by journal

Immunity

1. Title

2. Authors & Affiliations;

corresponding author

3. Running Title (displayed

in Journal TOC)

4. Abstract/ Summary

5. Introduction

6. Results

7. Discussion

8. Materials & Methods

9. References

10. Figure Legends

11. Tables & Figures

• Total number of display

items• High resolution images

(300-500 dpi minimum)• color versus b/w• MS Word/ Excel/ PPT/

PDF• Display item

configuration: heading,

body, description• References: textual

reference and

bibliography formatting

Additional factors to consider:

Getting started: formatting

JBC Contact Dermatitis Gene Therapy

Different journals have varying aesthetic properties that are handled by publisher and not to be considered by author

Getting started: formatting

Submission Proof

Process

1. Journal

2. Data & Figures

3. Results

4. Materials & Methods

5. Introduction

6. Discussion

7. Abstract

8. Formatting & Submission

9. Reviewer Response

Getting started: data

Choose the course of presentation based on the highest added value to the scientific community, which will also yield

the optimal journal

Develop an outline & order data to support story

What information do you have and how can you best present it?

Animal model ChemistryMolecular biology

Figures: basics

After your abstract, readers will look to figures to gain the most information with the least time

investment; therefore your figures should accurately depict and explain your findings in the

simplest possible form

Consider:• axes/ titles

• labeling• values

• breaks to amplify points of interest

• balanced amount of information

• consistency (colors and symbols)

Mirshahpanah et al. Exp Dermatol 2007

light gray = MF

dark gray = MPA

Figures: breaks & dual axes

Edema

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Dual axes allows incorporation of two relevant parameters into a single graph,

which allows for better comparison

break decreases the amount of space used for irrelevant info and allows for expansion

of point of interest

sparse graph

Figures: tables

Maintain consistency, simplicity, and completeness

Mirshahpanah et al. Exp Dermatol 2007

Informative title clear labeling across headings (along with measurement parameters) consistent presentation of information: mean ± SD Legend describes fundamental properties necessary to read table

Figures: titles & legends

• First sentence summarizes results of figure• Followed by a brief “materials and methods” explanation specific for this figure• Then describes actual results with values and significance where appropriate (p-values)• Ends with statistical evaluation methods and representative value definition

Zollner et al. JCI 2002

Process

1. Journal

2. Data & Figures

3. Results

4. Materials & Methods

5. Introduction

6. Discussion

7. Abstract

8. Formatting & Submission

9. Reviewer Response

Results: basics

• Describes findings that are presented in figures, without duplicating

the figures

DO provide guided description of findings, including trends or

correlations

DO cite other papers that are directly relevant to your data; not in

terms of implications but pure results

DO provide basic interpretation of results without alluding to larger

implications

DO NOT simply restate that which is clearly presented in the figures

DO NOT discuss the role of results in the greater scheme of your

paper – save this for the discussion

Language: use past tense to describe events that have occurred in your

experiment and present tense for conclusions you draw from the results

Results: example

Zollner et al. JCI 2002

• Leading sentence summarizes results

• Transitory sentence from previous section links different paragraphs and guides reader in the intended direction and flow of information (data presentation)

• References used to support results

• Minimal interpretational statements allow for unbiased presentation of data with subtle guidance from the author to address the issue: why do I care?

• Only data points that are relevant to the point of the study are discussed, not every single point needs to be mentioned

• Correlations may be drawn to support other data or to gain support from other results

Process

1. Journal

2. Data & Figures

3. Results

4. Materials & Methods

5. Introduction

6. Discussion

7. Abstract

8. Formatting & Submission

9. Reviewer Response

Materials & Methods: basics

• Accurately and concisely summarizes materials and methods used to carry out

experimental procedures Animals and models employed along with appropriate authorization statement Reagents used including company name and location (city, state/country) Provides enough detail to reproduce results in another lab of similar capacity; write

with a general scientific audience in mind:

not necessary to write: We poured 50% sodium dodecyl sulfate (SDS) buffer into a graduated cylinder until the bottom of the meniscus was at the 20ml line. We then poured 80ml de-ionized water to make 10% SDS buffer and divided it into five equal tubes.

instead summarize:We aliquoted 20ml of 10% SDS to 5 tubes.

You may cite other papers for detailed explanation of methods and briefly state the

main points to align the reader Order methods according to the logical flow of the experiment, often paralleling the

order of results and figures Include Statistics – these are methods used to evaluate data

Language: past tense, passive voice (the reader is not interested in who did the

experiment, but instead what was done) - i.e. avoid “we”

Materials & Methods: example

Concise descriptions

Approval for animal model statement

Topic sentence summarizing

subsequent method description

Referencing of detailed descriptions

instead of re-writing it

Brief description summarizing main

experimental procedure

Statistics used in various steps; often

involves several procedures; again,

referencing other sources saves space

and allows reader to locate detailed

description if necessary

Mirshahpanah et al. Exp Dermatol 2007

Process

1. Journal

2. Data & Figures

3. Results

4. Materials & Methods

5. Introduction

6. Discussion

7. Abstract

8. Formatting & Submission

9. Reviewer Response

Introduction: format

Basic background: what clinical implication does your study fit into? Introduce history

Past studies and their results; what information is still unknown/ what questions arose?

Description of specific parameters addressed in your study, align reader

with language and readouts

State your objective, process and allude to the significance your

results aim to provide

Introduction: basics

• Guides reader into the specific material you are about to discuss Where does the clinical implication of your study lay?

• disease-specific? • Basic biological process? • Drug discovery?

Introduce basic background and concepts: history and references• characterize the background of the issues you will address in your study• outline the evolution of the topic of interest by discussing previous study’s

results and conclusions; use primary references• i.e. drug/ therapy development, animal models, molecular biology, etc…

What studies already exist that are similar to your investigation• what were their conclusions?• what are they lacking; what still requires elucidation?• describe how your study fits into the larger picture of these previous findings

The final paragraph should briefly describe what you did, why you did it, and how

you did it – all with relevance to the previous studies you have mentioned• allude to your broader implicated findings: what have you done that makes this

an important study that adds value, what gap have you filled? Intro should give reader a working knowledge of history, implications, some

specifics, and providing the reason your study adds value

Process

1. Journal

2. Data & Figures

3. Results

4. Materials & Methods

5. Introduction

6. Discussion

7. Abstract

8. Formatting & Submission

9. Reviewer Response

Discussion: constituents

results

literature

theory

clinical applications

Discussioncontradictions

patternsfuture studies

Discussion: format

Summarize your findings

Discuss each major result in the context of previous studies, pointing out

supportive and contradictory findings

Suggest implications and practical applications of results; extend to other species if appropriate

Provide “big picture” conclusion of results; integrating results, literature, theory and future direction for further studies

Discussion: basics

• Innovative facet of scientific article, allowing for guided interpretation of results First paragraph summarizes findings in a clear manner Draw conclusions from each major result

• Briefly describe results without repeating previous sections• Cite literature that your results build upon or contradict • Explain possible reasons for your findings (appropriately supported by data or

references); provide reasons for deviations• Provide evidence for conclusions combining previous work with current

findings• Suggest future studies to further elucidate or verify your results

Be open about your results, describe deviations from hypothesis or expected

results, what future experiments would clarify these issues? Broader implications

• Suggest theoretical implications of your results• Suggest practical application of your results• Discuss findings in a broader topic – extend to clinical situations if applicable

The final paragraph should state what your findings added to the scientific

community (why is this study important?) and provide suggestions for future

direction

Process

1. Journal

2. Data & Figures

3. Results

4. Materials & Methods

5. Introduction

6. Discussion

7. Abstract

8. Formatting & Submission

9. Reviewer Response

Abstract

Most frequently read section of your paper; must be concise and complete

1. Brief introductory sentence to topic – i.e. clinical issue addressed

2. Background/ purpose of experiment

3. Methods – brief description of study design

4. Results – using actual values or stating major trends and findings from results

5. Conclusion – summary of discussion stating the major contribution of your study

Notes: Do not include brand names and try to avoid abbreviations

Abstract: example

1. Introduction – topical glucocorticoids

2. Purpose – assessment of two leading compounds: function & side effects

3. Methods – in vitro and in vivo rodent models for compound

atrophogenicity

4. Results – one compound superior to the other in both respects

5. Conclusions – better drug in this test system, must be tested in clinic to

confirm

Mirshahpanah et al. Exp Dermatol 2007

Process

1. Journal

2. Data & Figures

3. Results

4. Materials & Methods

5. Introduction

6. Discussion

7. Abstract

8. Formatting & Submission

9. Reviewer Response

Formatting & Submission

Order • Cover Page• Key Words• Abstract• Introduction• Materials & Methods• Results• Discussion• References• Figure Legends• Figures• Supplemental data

Submission• Cover letter to the editor• Online electronic submission

& correspondences

Formatting & Submission: cover letter

Properly address the editorIntroduce manuscript including titleProvide a brief paragraph about your study

• relevance• scope• results

Conclude with reasoning for choosing this journal• Why is your study relevant and important for the readership of

this particular journal?• What conclusions can you draw from your study?

Process

1. Journal

2. Data & Figures

3. Results

4. Materials & Methods

5. Introduction

6. Discussion

7. Abstract

8. Formatting & Submission

9. Reviewer Response

Reviewer Response

•Thank each reviewer for his/her contributions, they volunteer their time to review papers and are ultimately responsible for accepting your manuscript

•Provide complete point-by-point response to detail exactly how you have adapted your manuscript or fully refuted comments; if necessary, break up reviewer’s paragraph to respond to each query

•Follow guidelines for review process in each journal; generally, track changes in MS Word and be prepared to provide original, changed, and revised versions

•Resubmit as soon as possible to ensure timely publication

EndNote: reference manager

•Create a new library for each publication; allows for simple reformatting

when necessary•Many available journal styles, which may be further formatted for those

missing from the database

connect to PubMed to search and directly download into database

format bibliography specifically for each journal

EndNote: remote searches

Multi-field searching capacity allows for specific location of topics by various search fields and associations

EndNote: output styles

Edit Output Styles Edit “current style” (use the style closest to your journal of interest)

SigmaPlot: basics

•Scaling

•Axes

•Breaks

•Grouping

•Error bars

Enhancing differences among datapoints

time (period)

0 1 2 3 4 5 6

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experimental group

SigmaPlot: scalingEnhancing differences among datapoints

time (period)

0 1 2 3 4 5 6

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experimental group

Enhancing differences among datapoints

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experimental group

resize scales to maximize data presentation

Enhancing differences among datapoints

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experimental group

Enhancing differences among datapoints

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insert break to enhance differences

SigmaPlot: breaks

SigmaPlot: enhancement

Basic Plot (original) Aesthetically Enhanced Plot

Enhancing differences among datapoints

time (period)

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Enhancing differences among datapoints

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General Tips

Use consistent tenses – don’t switch between past, present and future

Simple is preferred over complex – words/ sentences/ structure

Use the active voice (except in methods)

We found correlations… (active voice)

Correlations were found… (passive voice)

Subject-verb agreement (The mice from each study were sacrificed.)

Use affirmative (+) rather than negative (-) constructions

Numbers beginning a sentence must be spelled (Twenty-five vs. 25)

Avoid phrases such as:

• four different groups

• absolute essential

• in close proximity

• very close to zero

• much better

General Writing: flow

• Simple is better; writing should be easy

to read

• Flow of paper should follow an

hourglass shape

Introduction starts broadly (top),

narrows to specific point(s)

addressed (neck)

Materials, Results & Figures detail

exactly what was observed

(grains)

Discussion applies findings in a

broader setting (base)

General Writing: example

A good paragraph generally possesses several key features that contribute to its

clarity and effectiveness in presenting information. The first feature is a topic

sentence that provides the reader with a general overview of the topic covered in the

ensuing paragraph. The body of the paragraph should provide substantial

information with references and evidence supporting the topic sentence. The final

sentence serves to wrap up the ideas and prepare the reader for material to follow in the

next paragraph, also known as a transition sentence. Upon reading the final sentence,

the reader should be able to name the topic of the following paragraph.

Topic Sentence

Body:supporting evidence

Concluding/ transition sentence