7 Paper Writing V2

8/13/2019 7 Paper Writing V2

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Scientific Paper Writing:

Guidelines and Tips

A. S. M. A. HaseebDept. of Mechanical Engineering

University of MalayaOffice: Room 13, Level 5, Engineering Tower Bldg.

Tel: 7967 4492, E-mail: [email protected]

Elsevier, Author Workshop 2008-11-6, How to prepare a manuscript for an international journal, Xiamen

University

K. E. Barrett, How to Write (and Review) a Scientific Paper, http://www.the-

aps.org/careers/careers1/mentor/workshop/2001/Barrett.doc,

S. Bloomer and M. J. Haas, How to write a scientific paper, inform, Volume 15 (12), December 2004.

Sami K. Solanki, How to Write a Research Paper, Internet Source

K. E. Barrett, Publishing 101, Chair, APS Publications Committee, Internet Source

Ed BullmoreHow to Write a Scientific Paper, Internet Source

WRITING A RESEARCH PAPER: Some general guidelines

for students and postdocs, Internet Source

S. Cordova, How To Write a Scientifi c Paper, http:// www.nmas.org/JAhowt o.html

Daniel J. Jacob, HOW TO WRITE AN EFFECTIVE SCIENTIFIC PAPER

K. Gaafar, How to write a scientific paper

R. Elvik, How to write a successful paper, Institute of Transport Economics, Oslo, Norway, Young researchers

seminar, May 10-13, 2005

W. A. Zin, HOW TO WRITE A SCIENTIFIC PAPER

M. Mallia, How to Write a Scientific Manuscript, Scientific Publications, Texas Heart Institute, Houston, Texas,

USA, Cardiology Rounds, February 19, 2008 T. H. Adair,Writing and publishing a research article, Center of Excellence in Cardiovascular-Renal Research,

University of Mississippi Medical Center

Barbara Gastel, Writing a Scientific Paper: Basics of Content and Organization Texas A&M University

References(all from internet sources)

Contents

Introduction

Before you start

General

Sections: Title, Abstract, Keywords, Introduction,

Methodology, Results, Discussion, Conclusions,

Acknowledgements, References

Submission to a journal

Ethical issues


Language

Conclusions
http://www.the-aps.org/careers/careers1/mentor/workshop/2001/Barrett.dochttp://www.the-aps.org/careers/careers1/mentor/workshop/2001/Barrett.dochttp://www.the-aps.org/careers/careers1/mentor/workshop/2001/Barrett.dochttp://www.the-aps.org/careers/careers1/mentor/workshop/2001/Barrett.dochttp://www.the-aps.org/careers/careers1/mentor/workshop/2001/Barrett.dochttp://www.the-aps.org/careers/careers1/mentor/workshop/2001/Barrett.doc


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Gerard Piel: co-founder and the long-term publisher of the

modern incarnation of Scientific American magazine

Origins of Scientific Writing

Knowledge is lost without written records

Cave paintings and inscriptions first attempts to leaverecords

2000 BC Papyrus paper as a medium of communication

190 BC parchment made from animal skin

105 AD Chinese invented paper

1100 AD Chinese invented movable type

1455 AD Gutenberg printed his 42-line Bible from movabletype on a printing press

By 1500 thousands of copies of hundreds of books (calledincunabula) were printed

1665 the first scientific journals were published

What is a scientific paper

a written and published report describing original researchresults

an addition to human knowledge

the first publication of original research results

peers can repeat the experiments and test the conclusions

published in a journal readily available within the scientificcommunity


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IMRaD Story

Early journals descriptive papers

By second half of 19th century reproducibility of experimentsconstitute a fundamental principle of philosophy of science

The methods section became all important

IMRaD format slowly progressed in the latter half of the 19 th

century

I = Introduction , what question was studied

M = Methods, how was the problem studied

R = Results, what are the findings

a = and

D = Discussion, what do these findings mean

Why write scientific papers?

A scientific career expansion of human knowledge

Academic and public sectors scientific papers ARE the meansfor this expansion

Publish or Perish You dont publish, youre out

Quality of a scientific paper? (now routinely- perhaps unfortunatelymeasured by the citation index)

Originality and importance of ideas

Effectiveness of communication, particularly when it comes to

planting the flag for new ideas

Before you

start


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Before you start

Before you start


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Before you start

Authorship

Decide on authors, and their order, as early as possible

Authors

- made a substantive intellectual contribution- participate sufficiently to take responsibility for the content

- can defend the data and conclusions publicly

Before you start

Criteria for authorship

Generate at least part of the intellectualcontent

Conception or design of the work

Data analysis and interpretation Draft, critically review, or revise the intellectualcontent

Approve the final version to be submitted

All three

criteria

should be

satisfied

Before you start


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Before you start

Before you start

Contents

Introduction

Before you start

General





Ethical issues


Language

Conclusions


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General

Paper Writing:

A part of your research, not a post-research

activity !

Start writing papers as soon as possible view it as a tool ofyour research

Iterate and agonize over the paper as part of your research

The paper is not a description of the

work, it IS the work

Richard Feynman

Starting Out

Know your working style versus computer, time, place

Set a deadline

Just put something down and edit itafterwards

Easiest to startMATERIALS and

METHODS and RESULTS

Start writing the data as if you were

describing them to your colleagues

Lay out general arguments and then go

into details


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Decide on the key conclusions - the importantmessage that you want to put across

Do you have all the data AND the figures to prove

your point ?

If possible, give an informal ORAL presentation of

the work before you start to write the paper

Starting Out


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Contents

Introduction

Before you start

General





Ethical issues


Language

Conclusions

Title


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The Title

Extremely important and must be chosen with great care will be

read by thousands Good title fewest possible words that adequately describe the

contents of the paper.

Accuracy of the title Indexing and abstracting

Concise, specific and informative

Contain the keywords that reflect the contents of the paper

Capture the fundamental nature of the experiments and findings

Waste words (studies on, investigations on, a, an, the etc) shouldnot be used

Make a list of the most important keywords

Think of a title that contains these words

Could state the conclusion of the paper

NEVER contains abbreviations, chemical formulas,proprietary names or jargon

Think, rethink of the title before submitting the paper

Be very careful of the grammatical errors due to faulty word

order Avoid the use of the word using

How to Prepare the Title

The Title

The Title


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The Title

Abstract

Very important part of the paper manyreaders will read just that


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A good abstract should contain in a very very precise form the

following elements:

Introduction:State the principal objectives and scope of the

investigation

Method:Describe the methods employed

Results:Summarize the results

Discussion/conclusion:State the principal conclusions

Abstract

An abstract is a brief summary of each ofmain sections (IMRAD) of the paper

No figures, no tables

No references (usually), no footnotes

Avoid abbreviations, equations and symbols

Make sentences short

It should not exceed about 250 words

Written usually in one paragraph

Written usually in the past tense as it refers to work done

Should never give any information or conclusion that is not

stated in the paper

Focus on what is new - essential ideas, essential numbers

Abstract


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Keywords

Contents

Introduction

Before you start

General





Ethical issues


Language

Conclusions


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Introduction

Sets the scene for your unique contribution and place it in context

Not meant to be an exhaustive review

Formulate the problem to be addressed

Introduction

Introduction


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Why was the problem undertaken? Historical and current relevance

What is its significance?

What is known or has been done before?

- Be selective and critical

- Give credit to intellectual pioneer as well as to best prior work

- Some criticism of earlier work may be necessary be mildand very respectful, and show professional manners

- Cite peer-reviewed scientific literature or scholarly reviews

Avoid general reference work such as textbooks

Say why the present work needs to be done

Definitely needed: Goals of your paper. If similar papers exist: what isnew in the method or results

Introduction

Often done, but not necessary: give structure of remainingpaper in last paragraph of introduction

Important: The sentences within a paragraph should follow

a logical sequence

Introduction

Signalling the research question at the end of Introduction

To determine whether . . .

The purpose of this study was . . .

Therefore, we tested the hypothesis . . .

This report describes experiments designed to determine

whether . . .

Therefore, our first objective in these studies was to

determine whether . . .

In this study, we sought to extend our observations and to

specifically test . . .

Introduction


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Contents

Introduction

Before you start

General





Responding to reviewers

Ethical issues


Language

Conclusions

Methodology


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Clear and sufficiently complete other scientists, eventhose not familiar with your specialty, could repeat the

Work

Assembe a simple collection of procedural outlines turnthis into prose

Use past tense

Provide references as necessary

Use subheadings if necessary

Do not include results in Methods

Often a figure can illustrate and clarify the method

Methodology

Find the balance between: Describing everything important andLeaving out everything not needed.

Rule of thumb:

- New method, new instrument, new type of data Describe

in detail, since required for reproducibility

- Known method or instrument, previously used and

described in other paper(s) Often a reference is sufficient

Do not repeat descriptions

For chemicals exact technical specifications and source or

method of preparation

Avoid trade names of chemicals

Methodology

Examples of alternative titles:

Computational technique (appropriate for a numerical

paper)

Instrument and measurements (e.g. if a new

instrument is being described or used, or an instrumentis used in a non-standard mode)

Data and analysis technique (e.g. if the special

technique of analysing the data is essential for the

results)

Often studied carefully by the refereeDecides whether the results can be trusted or not

The paper will be rejected based on methodology

Methodology


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Results

John Wesley Powell (March 24, 1834 September 23, 1902): a

U.S. soldier, geologist, and explorer of the American West


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How to write the Results

Written in the past tense

Heart of the paper needs to be clearly and simply stated orderly and logical sequence, without interpretation

guide the reader through the findings, stressing the major points

Do not describe methods that have already been described inthe Methodology section

structure this section is to write it around the figures. However,do not forget to make a logical order

Results

The core of the paper, where the results obtained duringthe long labour of research are presented.

Be concise. Pre-select the results (i.e. identify the

important and new results) before writing about them in

the results section

Keep in mind: The fool collects facts, the wise man selects

them (John W. Powell)

Avoid repetition!

Assemble draft FIGURES and lay them out in order on a tableor desk

Decide what are the key points that you need to make, and

write them out

More Results

Decide on what to put into the Results section and what tomove to the Discussions section

General rule (but not a very hard and fast one)

Results section only describe the results, but do

not interpret them very much

Discussion section provide the interpretation and the

comparison with the literature, without repeating all theresults


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Results: Figures

Each figure must be referred to in the text must have a

caption

Captions short, but self-explaining

only clarify what is plotted and not try to interpret the

figure

For photomicrographs Dont forget scale bars!


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Axes

- Minimize tick marks

- Dont number each tick Lettering

- Uniform, lower case- Minimize, avoid bold

- After reduction, 2-3 mm high

Legend

- Gives message

Results: Tables

Make a table if you have multiple numbers to show andyou cannot put them into a figure, or if the exact

numbers are important

Remember, figures are generally easier to read than

tables.

Each table must have a title. Keep it short.

must be referred to in the text.

Never put the same data in the form of both table andfigure


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Contents

Introduction

Before you start

General Sections: Title, Abstract, Keywords, Introduction,




Ethical issues


Language

Conclusions

Discussion

Hardest section to write !


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How to write the Discussion

Primary purpose interpretation, synthesis, predictive speculation

Interpret your results present the principles, relationships,and generalizations shown by the Results

How your results and interpretations agree or contrast with

previous work

Theoretical implications of your work, and any possiblepractical applications

Point out any exceptions or any lack of correlation and define

unsettled points Present ambiguity and discrepancies

objectively

Explain what is new without exaggerating

Discuss key studiesonly those relevant to your work


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Last paragraph- In summary (2-3 entences)

- In conclusion (biggest

message, return to Intro, avoidspeculation, avoid need more

work

Middle paragraphs- Base each on a major result

Always focus on your results

Never discuss prior work withoutreference to your work

Refer Tables and Figures

First paragraph- State major findings

- Paraphrase abstract

Structure and contents

Contents

Introduction

Before you start

General





Responding to reviewers

Ethical issues


Language

Conclusions

Conclusions


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Conclusions

can wait to be written until rest of paper is

mature

First paragraph: focus on what you did. Begin with We haveused, We have investigated

Following paragraphs: one major finding per paragraph. First

sentence states the finding, following sentences elaborate.

Final paragraph should have some forward-looking

perspective. Dont let paper finish on a whimper!


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Reference


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A few words about references

Extensive referencing scholarly and ethical thing to do

useful to readersmakes your paper more accessible by search engines!

Be serious about literature search and reading papers devote a bit of time to this each day

Never cite a paper for which you havent read at least therelevant part

Cite papers in a context that makes it clear what the paper did

Dont cite textbooks

Theres nothing wrong with citing yourself or your group

extensively. But dont ignore what others have done!

Contents

Introduction

Before you start

General





Ethical issues


Language

Conclusions


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Dealing withreviewers

Dealing with referees reports

anticipate revision: it is almost inevitable and generally beneficial

Complete additional experiments if needed

At first sight referees reports often look more negative than

they really are.

Read the report and then put it away for a week before looking at itagain (to calm down).

Discuss it with your supervisor and make the changes to the paperasked by the referee

Point by point reply to the refereehow you have taken his/her

comments into account

If you disagree with the referee and havent taken one of his/her

suggestions into account you explain why.organise the final version

of the paper and all ancillary data carefully before submission

Referees are not always stupid. If the referee does not

understand something, then it is likely that the paper is not

clear on this point. Make it clearer.

Do not respond to reviewers while upset

try not to take criticism personally or as a reflection ofincompetence on the part of reviewers

their failure to understand is your lack of clarity

be respectful, exact and direct in responding to the editorRemain polite. Even if the referee is nasty, there is usually

nothing to be gained by showing your anger.

If you feel that you are being unfairly treated by the

referee you can ask for a second opinion.

Sincerely thank the editor and reviewers for helping you to

improve your work

They have invested a lot of time, mostly on a voluntary basis

Ask a neutral colleague to review your response


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Ethical issues in

publication

Ethical responsibilities of a scientist

Intellectual honesty

Accurate assignment of credit

Fairness in peer review

Collegiality in scientific interactions

Transparency in conflicts of interest

Protection of human and animal subjects

Common ethical issues

Redundant publication Authorship disputes

Duplicate publication

Human welfare concerns

Data fabrication/falsification Increasingly, includes inappropriate manipulation of

figures

Plagiarism

Conflicts of interest

Others (e.g., reviewer bias, submissionirregularities)


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Prior publication

Defined as:

Data

Extended verbatim text passages

Tables or illustrations

Redundant publication

Definition

Using text or data from

another paper/prior

publication (usually

your own) in a new

paper

Also called auto- or

self-plagiarism

How to avoid

Do not include

material from a

previous study in a

new one, even for

statistical analysis

Repeat control groups

as needed

What constitutes redundant publication?

Data in conference abstract?

Same data, different journal?

Data on website?

Data included in review article?

Expansion of published data set?

No

Yes

Maybe

OK if later

Yes


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Authorship disputes

Definition

Disputes arising from

the addition, deletion,or change in the order

of authors

How to avoid

Agree on authors and

their order beforestarting the study

Ensure all authors

meet criteria for

authorship

Sign publishers

authorship forms

Duplicate publication

Definition Submission of or

publication of thesame paper orsubstantial parts of apaper in more thanone place

How to avoid Do not submit a paper

to more than onejournal at a time

Wait until your paper isrejected beforesubmitting elsewhere

Withdraw a paper ifyou decide not to re-submit after being

invited to do so

Data fabrication/falsification

Definition

Changing or makingup data in amanuscript

Intended to improvethe results

Includes digitalmanipulation ofimages (blots,micrographs, etc.)

How to avoid Present the exact

results obtained

Do not withhold datathat dont fit yourhypothesis

Dont try to beautifyimages withPhotoshop anymanipulations mustapply to the wholeimage


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Unacceptable figure manipulation

Improper editing

Improper grouping Improper adjustmentAuthors should not:

Move

Remove

Introduce

Obscure

Enhance

any specific feature within a image. Imagesshould appear as captured in the lab

Improper editingBoxes revealed during processing for publication; removal reveals debris

Bottom image from Rossner and Yamada, J. Cell Biol. 166: 11-15 (2004)

Plagiarism

Definition

Taking the work ofanother

Copying a figure,table, or even wordingfrom a published orunpublished paperwithout attribution

How to avoid

Provide citation to thework of others

Obtain copyrightpermission if needed

Do not copy exactwording from anothersource, even ifreferenced, unless inquotes


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Conflicts of interest

Definition

Real or perceived

conflict due to

employment,

consulting, or

investment in entities

with an interest in the

outcome of the

research

How to avoid

Disclose all potential

conflicts to the Editor

and within the

manuscript

The Seven Deadly Sins1. Data manipulation, falsification

2. Duplicate manuscripts

3. Redundant publication

4. Plagiarism

5. Author conflicts of interest

6. Animal use concerns

7. Humans use concerns


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ACKNOWLEDGMENTS

Include

Intellectual assistance

echnical help, including writing and data

analyses Special equipment or materials

Outside financial assistance (including

grants, contracts, or fellowships)

Contents

Introduction

Before you start

General





Ethical issues


Language

Conclusions

Submission to

a journal


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Completion of research

Preparation of manuscript

Submission of manuscript

Assignment and review

Decision

Rejection Revision

Acceptance

Resubmission

Re-review

PUBLICATION!

Rejection

Adapted from a figure by Dale Benos


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Most common reasons for rejection

of a manuscript

Major reasons for rejection

Inappropriate for the journal Do your homework

Merely confirmatory/incremental Avoid LPUs

Describes poorly-designed or inconclusivestudies Focus on your hypothesis

Poorly written

Great science in an ugly package can still be rejected


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What makes a good research

paper?

Good science

Good writing

Publication in good journals

What constitutes good science?

Novel

new and not resembling somethingformerly 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.


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What constitutes a good journal?

Impact factor

average number of times published papersare cited up to two years after publication.

Immediacy Index average number of times published papersare cited during year of publication.

Outlineoriginality and

important

findings

Language


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Contents

Introduction

Before you start

General Sections: Title, Abstract, Keywords, Introduction,




Ethical issues


Language

Conclusions


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A scientific paper clear, objective, to the point

Strive for logical, linear flow. Put yourself in the perspective of the

reader

Be as short as possible. Every word must hurt

Be on the lookout for unnecessary words and sentences

Use short words (e.g., use vs. utiilize)

Remove value judgments: Surprising, interesting,

unfortunately have no place in a scientific paper.

Use scientific words as much as possible but with their precisemeaning

Avoid slang and jargon

Use the active voice whenever possible usually less wordy and is

unambiguous

First person is acceptable when the meaning is clear


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Avoid Wordiness Delete Unnecessary Words

Delete phrases which do not contribute to the

meaning of a sentence

Past or present tense preference is to some extent personal

Past tense is OK for describing results of an experiment but use

present tense for a general conclusion

WHATEVER TENSE IS USED, BE CONSISTENT AND

DONT SWITCH BACK AND FORTH IN THE SAMEPARAGRAPH !! !

Tense


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Some Common Problems


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Examples

Not correct: Our results suggest that Hoxa3 may be involved in

thymus development

Correct: Our results suggest that Hoxa3 is involved in thymus

development

Not correct: It is possible that Shh in the endoderm may regulate

Bmp4 expression in the mesoderm

Correct: It is possible that Shh in the endoderm regulatesBmp4 expression in the mesoderm

Use of suggest that ; hypothesize that possible thatThese phrases do not need may, might


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Proofreading Unimportant details tend to

be overlooked

BEFORE GIVING THE DRAFT TO YOUR

SUPERVISOR

Check the Figures versus the textCheck the References versus the text

Check the Figure legends

In general, edit a paper after printing it out and reading it

as a whole, rather than editing it on a computer screen


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7 Paper Writing V2

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