Getting published advice for graduate students and postdoctoral scientists
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Getting published advice for graduate students and postdoctoral scientists

Getting Published: Advice for Graduate Students and Postdoctoral Scientists

Alison O’Brien, Ph.D.

Professor and Chair

Uniformed Services University Bethesda, Maryland


Disclaimer

Disclaimer

  • The opinions or assertions contained herein are the private ones of the author and are not to be construed as official or reflecting the views of the DOD or the Uniformed Services University.


Getting published advice for graduate students and postdoctoral scientists

So…


Why should i listen to her

Why Should I Listen to Her?

  • Editor-in-Chief of Infection and Immunity 1999-2007

  • Previously Editor for Microbial Pathogenesis and then for Infection and Immunity

  • Published 144 peer-reviewed manuscripts and 54 invited chapters and reviews


But you should know

But You Should Know…

  • that on occasion I still get papers rejected.

  • Why? Either I have aimed too high in the journal world or there are additional data requested by the reviewers.

  • The preparation or clarity of the manuscript are usually not at issue.


Outline

Outline

  • Overview

  • Choice of journal

  • Constructing a manuscript

  • Ethics of scientific publishing

  • Revisions, resubmissions, rejections


Outline1

Outline

  • Overview

  • Choice of journal

  • Constructing a manuscript

  • Ethics of scientific publishing

  • Revisions, resubmissions, rejections


Quotes from robert a day s how to write and publish a scientific paper 5 th edition

Quotes from Robert A. Day’s How to Write and Publish A Scientific Paper (5th edition)

“The goal of scientific research is publication.”

“A scientific experiment, no matter how spectacular the results, is not complete until the results are published.”


Outstanding manuscripts

Outstanding Manuscripts

  • Present a complete scientific story.

  • Are organized so that the logic and hypotheses are easy to follow.

  • Are written in simple straightforward sentences.


What is scientific writing

What is Scientific Writing?

“The best English is that which gives the sense in the fewest short words."(from previous Instructions to Authors in the Journal of Bacteriology)

“Literary devices, metaphors, and the like, divert attention from the substance to the style.”(from R. Day)


Outline2

Outline

  • Overview

  • Choice of journal

  • Constructing a manuscript

  • Ethics of scientific publishing

  • Revisions, resubmissions, rejections


Which journal

Which Journal?

  • Ask yourself whether the information shifts any paradigms in the field. If yes, aim for a high impact, broader scope journal.

  • If no, but the findings are solid and the study complete, go for the specialty journal in your field that is read by most investigators in that area.


Journal selection students

Journal Selection & Students

  • Graduate students and fellows need to publish.

  • Try for a brief communication in a higher impact journal if there is a single message.

  • It is OK to submit to a lower impact journal.


Journal selection continued a tip

Journal Selection Continued: a Tip

  • If in doubt, email the editor with a brief description of the paper or an abstract.

  • Ask if the work would be considered for that journal.

  • This approach works with Cell and many ASM journals.

  • Abide by the answer even if it is No.


Outline3

Outline

  • Overview

  • Choice of journal

  • Constructing a manuscript

  • Ethics of scientific publishing

  • Revisions, resubmissions, rejections


Sequence for preparing a manuscript one model

Sequence for Preparing a Manuscript: One Model

Outline

Abstract

Title

References

Materials and Methods

Acknowledgements

Introduction

Results

Discussion


Language issues

Language Issues

  • Watch syntax or word order.

  • Use the active voice.

  • Keep your results in the past tense.

  • Put conclusions in the present tense.

  • Avoid “ing” words like “using”.

  • Compose simple sentences.

  • Punctuate correctly.


Why an outline

Why an Outline?

  • Helps with the flow of the paper.

  • Lets you know whether you have completed all the pieces to the story.

    • i.e. Do you have a good enough Western?

  • A good way to convince an advisor that it is time to write.


Crafting a title

Crafting a Title

  • Shorter is better.

  • No jargon or abbreviations.

  • Put the main message in the title.

  • Avoid words like investigation, characterization, analysis.

  • TAKE TIME TO DEVISE THE TITLE.


Materials and methods

Materials and Methods

  • Look at published Material and Method sections in the journal to which you are submitting; note style.

  • Do not repeat verbatim published procedures that are readily accessible; note modifications to the method.

  • Organize into sections with like experiments together.


Materials and methods cont

Materials and Methods, Cont.

  • Do not start sentences with Arabic numbers or lower case letters.

  • Spell out the composition of all buffers the first time they are mentioned.

    • i.e. Phosphate Buffered Saline (PBS)

  • AVOID JARGON.


Introduction should contain

Introduction Should Contain

  • A synopsis of literature pertinent to the paper.

  • Purpose of the study.

  • A statement of the general methodological approach used.

  • Major results and conclusion.


Results

Results

  • Essence of the paper.

  • Avoid redundancy between text and figures/tables.

  • Don’t repeat Materials and Methods; just give an overview.

  • Lead the reader from section to section by stating your reasoning.


Results questions to ask

Results: Questions to Ask

  • Are statistics appropriate for the type of data analyzed (common error)?

  • Are the data shown truly “representative”?

  • Are the tables and figures formatted correctly?

  • Are lanes in scanned gels enhanced proportionately?


Discussion

Discussion

  • Hardest section to write.

  • OFTEN TOO LONG AND TOO WORDY Message obscured.

  • Suggestion: point out key findings in first paragraph, follow up with data interpretation/model.


The abstract cont

The Abstract, Cont.

  • NEXT TO THE TITLE, THE MOST CRITICAL PART OF THE PAPER IN THE INITIAL REVIEW PROCESS.


The abstract should quoted from day

The Abstract Should (Quoted from Day)

  • State the principal objectives and scope of the investigation.

  • Describe the methods employed.

  • Summarize the results.

  • State the principal conclusions.

  • Be written in the past tense.

  • Not include references.


Literature cited

Literature Cited

  • Reference the original discoverer of a finding.

  • List only significant references that have been published.

  • Check the citation against the original.

  • Make sure that all citations are in the reference list and that all references are cited.


Outline4

Outline

  • Overview

  • Choice of journal

  • Constructing a manuscript

  • Ethics of scientific publishing

  • Revisions, resubmissions, rejections


Authorship versus acknowledgement taken from iai instructions to authors

Authorship Versus Acknowledgement (taken from IAI instructions to authors)

“An author is one who made a substantial contribution to the overall design and execution of the experiments”

“Individuals who provided assistance, supplied reagents, or critiqued the paper need not be listed as authors but may be recognized in the Acknowledgments section”


Ethics trouble and i didn t know

Ethics, Trouble, and I Didn’t Know

  • ASM considers all authors responsible for the entire paper; know your collaborators.

  • Common ethics issues:

    • Fraudulent figures

    • Failure to acknowledge paper was previously rejected

    • Adding someone as an author without their knowledge, and many more.

  • Ignorance is not an excuse.


Outline5

Outline

  • Overview

  • Choice of journal

  • Constructing a manuscript

  • Ethics of scientific publishing

  • Revisions, resubmissions, rejections


Responding to critiques

Responding to Critiques

  • Address every point and make the corresponding changes in the text.

  • Do the requested experiments if they make sense. Trying to argue your way out of doing an important control is self-defeating.

  • Be polite.


When to resubmit

When to Resubmit

  • If the editor encourages you to do so.

  • If the criticisms indicate that the reviewers generally liked the paper but found an experimental flaw/lack of control.

  • Call/email the editor if you are really in doubt.


Sources

Sources

INFECTION AND IMMUNITY

2011 INSTRUCTIONS TO AUTHORS

SCOPE


Questions

Questions?


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