AJE Best Practices Workshop USP

BEST PRACTICES FOR
WRITING AND PUBLISHING
YOUR RESEARCH
Amy Beisel
Strategic Partnerships Manager
www.aje.com
support@aje.com
© AJE

MORNING SESSION
9h30 – 10h: Opening and Scholarly Publishing Report
10h – 12h: Best Practices for Reading and Writing Scholarly Articles
• Keeping up with the literature
• Best practices for writing each section:
Introduction, Materials and Methods, Results, Discussion
• English editing basics
• Avoiding plagiarism

AFTERNOON SESSION
13h30 – 15h: Best Practices for Reporting Your Research
and Submitting Your Manuscript
• Selecting data and formatting figures
• Writing a title and abstract
• Choosing a journal
• Writing a cover letter
15h20 – 16h20: Roundtable with Experts
• Cases, Questions, and Answers
16h20: Closing Remarks

WHO WE ARE
We help researchers successfully communicate their work.

WHO WE ARE
• PhDs: 100 on staff and 2500 in expert network
• Editors recruited from top US graduate programs
• Subject-matter experts in 400 areas of study
• Native English speakers
• 60k manuscripts / year, 400k since 2004
• Proprietary software matches manuscripts with experts
• Multilingual support staff
• Partnerships with major publishers and societies

WHO YOU ARE
Raise your hand if you are…
• Principle Investigator / Faculty Member
• Post-Doctoral Researcher
• Graduate Student
• Undergraduate Student

WHO YOU ARE
Raise your hand if you have ever…
• Been an author on a published paper
• Written a manuscript
• Formatted a manuscript
• Created figures for a manuscript
• Had a manuscript rejected…
so you had to start all over again!

PUBLISHING IS TIME CONSUMING
http://indico.cern.ch/event/332370/session/10/contribution/24

THE EXPERTS
Theresa Anderson, PhD – Scientific Illustrator
Ariana Bevilacqua, MS – Editing Team Manager
Paul Klenk, MBA/PhD – Financial Analyst
Luciana Leopold, PhD – Editing Team Manager
Tony Macias, MA – Academic Translation Advisor
Ben Mudrak, PhD – Communications Manager
Michaela Panter, PhD – Academic Editor
Silvia Santos, PhD – Translation Team Manager
Ashley Smith, PhD – Scientific Illustrator
Kurt Spurlock, MA – Quality Manager
April Troester, PhD – Customer Service Director

AJE SCHOLARLY PUBLISHING
REPORT 2015
Trends around the world and in Brazil

PUBLISHING TRENDS 2015
Publication output is rapidly increasing
China is contributing a larger share every year

TEN YEARS IN REVIEW: 2005-2015
84% increase in publications:
• >900,000 more in 2015 than 2005
Emerging markets playing a large role:
• 204% increase in Brazil’s output
• 220% increase in India’s output
• 191% increase in China’s output
Medical papers have skyrocketed, with over 266,000 more published in
2015 than in 2005

PUBLISHING TRENDS: BRAZIL
Brazil’s growth has been slower but steady:
>50,000 papers for 2 years running

PUBLISHING TRENDS: BRAZIL
www.scimagojr.com
Brazil’s research output has increased relative to Latin America:
now the majority

PUBLISHING SNAPSHOT: BRAZIL 2015
Brazil has an outsize influence on Agricultural fields
Fields represented here?

PUBLISHING SNAPSHOT: BRAZIL 2015
Universidade de São Paulo was 2nd in the world in terms of publication output
by a research institution (after Chinese Academy of Science)

SNAPSHOT: BRAZIL 2015
Brazilian researchers published most frequently in
• PLOS ONE
• Espacios
• Seminas: Ciências Agrárias
• Ciência e Saúde Coletiva
• Ciência Rural

LOOKING BACK: BRAZIL 2005-2015
• Overall, 204% increase in publications (over 26,000 more papers
last year than 2015)
• Brazil has nearly doubled its share of publications worldwide, to
~3% of the total
• Brazil has maintained its position as the largest research producer in
Latin America

BEST PRACTICES FOR
READING AND WRITING
SCHOLARLY ARTICLES

BEST PRACTICES: OVERVIEW
• Keeping up with the literature and evaluating credibility
• Writing each section of your manuscript:
• Plagiarism in academic papers

KEEPING UP WITH THE LITERATURE

KEEPING UP WITH THE LITERATURE
2 million articles
28,000 journals
every year
…
How can I keep up with this amount of material?
How can I be sure to read the most relevant articles for my field?

1) LITERATURE-BASED SEARCH ENGINES
These return citation results based on
keywords
author names
article title
journal type
Examples of free search engines:

PubMed: You can search 26 million biomedical citations from MEDLINE, life
sciences journals, and online books. May include links to full-text content.
PubCrawler scans daily updates to the PubMed and GenBank databases and
emails you an alert.
PubChase: You can search the biomedical literature, create libraries, and
receive recommendations based on saved articles.
Agris is a search engine for agricultural science and technology.
Google Scholar is one of the most widely used academic search engines. It’s
good for “free” versions but returns a lot of gray literature or irrelevant results.
Visit Wikipedia’s “List of academic databases and search engines”
for an extensive list, including discipline and access cost

2) RSS FEEDS
• Allow you to track particular websites by subscribing to automatic
updates of web content
• Headlines and summaries / abstracts are listed via a feed reader
• Readers are available as add-ons in internet browsers
• After you download the RSS reader, you can subscribe to the RSS
feed via journal webpages

3) TABLE OF CONTENT (TOC) ALERTS
• Publishers offer TOC alerts for newly published journal issues
• Include Early View and online articles
• Sign up at the publisher’s website
• SpringerAlerts, Wiley eTOC, Nature e-alert
• JournalTOCs – aggregator for 28k journals including SciELO

4) LISTSERVS
• Receive journal TOCs, calls for papers, and dataset
announcements via email distribution lists
• Listservs are often managed by universities and scientific
organizations
• Search for associations in your discipline and ask if they offer a
listserv

5) SOCIAL NETWORKS FOR ACADEMICS
Several benefits to engaging on academic networking sites:
• Identify relevant literature
• Contact with researchers in your field
• Building name recognition in your field
• Create opportunities to collaborate

SOCIAL NETWORKS FOR ACADEMICS
How many of you have heard of the following services? How many of
you use them?
• LinkedIn
• Twitter
• ResearchGate
• Academia.edu
• Google Scholar citation profile
• ORCID

LINKEDIN
• Networking
• Online CV
• Controlling your image

TWITTER
• Instantaneous
information
• Trading links
• Public Q&A

RESEARCHGATE
• Networking
• Sharing publications
• Q&A with other members

ACADEMIA.EDU
• Sharing full text
• Discovering other articles
• Searches that lead to you

GOOGLE SCHOLAR PROFILE
• Citations
• Alerts for similar
articles
• Largely automated

DISCUSSION
Turn to the person next to you and share one method that you often
use to learn about relevant research articles.
What is a new method that you plan to try?
Any suggestions that we haven’t listed?

EVALUATING RESEARCH CREDIBILITY
You’ve read the literature
You’re ready to cite it
…
But how do you know if it’s credible?

COMMON ASSESSMENTS OF CREDIBILITY
1) Journal’s reputation
1) Author’s reputation
1) Number of article citations

CAVEAT: JOURNAL REPUTATION
Even if a journal is prominent in your field, peer reviewed, highly
selective, and published by a well-regarded publisher, the article may
be flawed
Journals with high impact factors have higher retraction rates
High quality research may be published in lesser-known journals,
regional journals, specialized journals, or less selective journals
Other caveats?

CAVEAT: AUTHOR REPUTATION
An author’s seniority, reputation, publication record, education,
affiliation with a prominent institution, or training by a prominent
researcher do not guarantee that the article is credible
Why not? Your ideas?

CAVEAT: CITATION COUNT
Citation numbers can be inflated or deflated based on the factors we
just mentioned:
readers’ perceptions of the journal’s reputation and author’s reputation

RISKS OF RELYING ON THESE
ASSESSMENTS
1) Citing questionable studies
May undermine the credibility of your study and perpetuate
inaccuracies in the scholarly record
2) Omitting credible studies
May weaken your study by overlooking findings that support
or refute your work

ASSESSING CREDIBILITY
• Was the research design appropriate for the question? Were proper
controls used?
• Is the work still relevant? Are there any retraction notices, errata, or
negative citations?
• Are the references in the paper credible and properly interpreted?
• Is the reference list comprehensive?
• How do the post-publication peer reviews evaluate the quality of the
study? (comments, PubPeer, PubMed Commons, Open Review)

ASSESSING CREDIBILITY
Taking a closer look at the research design and context will help you to
become more familiar with the literature and more confident in the
credibility of your sources.
DISCUSSION:
Turn to the person next to you and describe an example of a research
article you have read where the journal, author, or citation count was
not an accurate indicator of the quality of the research.
Please share an example with the large group.

BEST PRACTICES FOR
WRITING YOUR MANUSCRIPT
Keeping up with the literature
Evaluating research credibility
Writing Introduction, Materials and Methods, Results, Discussion

HOW TO TURN A LAB NOTEBOOK INTO A
SCIENTIFIC MANUSCRIPT
Carefully maintaining your lab notebook will make writing easier
For all experiments, record the following:
• Objective
• Materials and methods
• chemical reagents, analytical techniques, theoretical
calculations, actual measurements, etc.
• Experimental procedure
• Outcome / results
• Any notable observations (especially if unexpected)
Do this for the 100th time for every procedure, not just the 1st –
you never know which details will be significant

CHOOSING THE RIGHT STORY
1) Find all of your data and sort it – select the ones that tell this story
• You can put each experiment on a card or post-it so you can
shuffle them around when planning
2) Next, create the figures for each point you want to make
3) Now, think about the narrative that connects each card – this will
help you organize your arguments
Let’s look at some tips, section by section

ANATOMY OF A SCIENTIFIC
RESEARCH ARTICLE
1) Introduction
2) Materials and Methods
3) Results
4) Discussion and Conclusions
5) References
6) Figures
7) Title and Abstract

Cetin and Hackam (2005) Journal of Surgical Research

THE INTRODUCTION
Setting the stage

PURPOSE OF THE INTRODUCTION
Overview of the manuscript but distinct from the Abstract
• Abstract summarizes the entire paper
• Introduction places the results in the context of the larger
field of study

QUESTIONS TO GUIDE YOUR
INTRODUCTION
What is known about this topic?
What is not yet known?
How does this manuscript add to the body of literature in my field?
What was the purpose or hypothesis of the study?

THREE PARTS TO THE INTRODUCTION
1) Overview of previous research
What do we know?
2) Description of gaps in the current literature
What don’t we know?
3) Summary of the hypothesis underlying the study
What does this study contribute?

BE GENERAL FIRST, THEN SPECIFIC
“Individuals differ radically from one another in the degree to which
they are willing and able to express their emotions.”
“Indeed, the popular view is that such emotional expressiveness is a
central difference between men and women.... But the research
evidence is mixed...”
“There is even some evidence that men may actually...”
“In this study, we recorded the emotional reactions of both men and
women to filmed...”
(Bem 2003)

INTRODUCTION TIPS
Assume that no one has read the Abstract
Define all abbreviations
“Solid-state fermentation (SSF) is defined as the cultivation of
microorganisms…”
Define key terms
“surface-attached communities termed biofilms, in which the
bacterial cells surround themselves with a self-produced matrix
of sugar, protein, and DNA”
“relative to planktonic (free-living) counterparts”
Connect the Title and Introduction

CITING PREVIOUS WORK:
STRIKE A BALANCE
Provide enough detail to place the results in context
…but not so much that you bore the reader
Present both sides of the previous literature
• Aim for an objective review
• If you seem to be hiding some prior results, reviewers
may criticize it
• Acknowledge different perspectives

CITE RECENT LITERATURE
Recent = past 5 years in most cases
Pitfalls of older literature:
• The paper may have been disproven
• The paper may not tell the whole story anymore
• Readers may think you are not truly acquainted with the field
Exception: citing historically important references or theories
“Since the isolation of O139 Vibrio cholerae in 1993 [Smith et al.]”

HOW MANY REFERENCES?
Include enough references to support your hypothesis
The Introduction does not need to be an exhaustive review
Each reference should support a statement, not simply be an example
Avoid a string of references at the end of one sentence
“have been examined using a variety of assays, mutagens, and strain
backgrounds (31, 38, 41, 53, 56, 59).”
Many journals will allow the use of (e.g., [31] and [53])

NOTE “GAPS” IN THE LITERATURE
Each field has an infinite number of open questions –
mention a few that your manuscript answers
Don’t just mention a gap –
explain why anyone should fill it
“Understanding how the P127 oncogene contributes to the
transformation of epithelial cells could lead to the discovery of
novel anticancer therapeutics.”

“GAPS”: OTHER THOUGHTS
If others have mentioned the question you’re answering,
cite them:
this supports the importance of your project
Focus on gaps that are well defined
“need to cure cancer”  too broad
“as yet, the portion of lipopolysaccharide bound by heat-
labile enterotoxin is unknown”  better

RECAP YOUR STUDY
Highlight what prompted you to perform the study
Connect your study to the gaps you defined earlier
“Because little is known about the types of V. cholerae
that cause disease in non-epidemic settings, we
investigated the infectious doses of several non-
O1/non-O139 serogroups.”

HYPOTHESIS/PROBLEM QUESTION
Hypothesis:
Specific prediction for results given current knowledge
Problem question:
Unanswered question or gap that you will fill
Hypotheses are encouraged
Otherwise, reviewers may think you were “fishing”
Use clear, unambiguous language
“If competition lowers reproductive output, then we expect fruit
size to be smaller when tree density increases.”

SUMMARIZE RESULTS BRIEFLY
Commonly, one sentence for methods
No numerical data or statistics
“In the present study, a SUP4-o forward-mutation system was
used to reexamine the relationship between MMR and Polη in
preventing GO-associated mutagenesis in yeast.”
And one sentence for a major conclusion
“The results reported here demonstrate that Polη can function
independently of MMR to prevent GO-associated mutagenesis,
presumably through its ability to bypass these lesions in an
error-free manner.”

DON’T OVERSELL THE RESULTS
In mathematics proofs are common,
but in biology, nothing is “proven”
Use words that soften your text
likely
indicates
contributes to our understanding of
suggests
further elucidates

INTRODUCTION: SUMMARY
Introduction provides context for your results:
why did you write the paper?
Three parts:
• Overview of results of previous studies
• Description of key “gaps”
• Summary of the current hypothesis and results
Be sure to include a hypothesis or problem question

INTRODUCTION: SUMMARY
When your Introduction is written, ask yourself:
Have I described the context for my work and created a
convincing narrative using references?
Your reader will look for an answer to the question:
Why did the authors write this paper?

MATERIALS AND
METHODS
What did you do? How did you do it?

WHY SPEND TIME ON THE
MATERIALS AND METHODS SECTION?
The ultimate form of peer review is reproduction of
published results
The importance of the results cannot be interpreted if the
study methods are unclear
A good Methods section leads to
reproducibility and credibility

WHY SPEND TIME ON THE
MATERIALS AND METHODS SECTION?
To keep the manuscript organized:
this is the framework for the Results section
To avoid rejection
“One of the more common reasons for rejection of a
manuscript is that the reviewers cannot fully understand
how the study was conducted.”
Provenzale (2007) American Journal of Roentgenology
Other reasons?

WHEN IS IT BEST TO WRITE THE M&M?
While you are performing your experiments:
• Record key details
• Perform important controls
• Plan the next experiments logically
• Save time when you start writing manuscript(s)

PROPER ORDER
Order is important
Organize the section on two levels:
Basic characteristics of the entire study
… leading to details of individual experiments
Match the order of methods and results reported

OVERALL FRAMEWORK
Study subjects
• Human subjects, animals, bacterial strains, etc.
• Approval and ethical statements
Interventions (for clinical trials)
Experimental details
Data analysis
• Statistical methods

STUDY SUBJECTS AND ETHICS
Provide all relevant information about study subjects
Humans: age, sex, how they were recruited,
inclusion/exclusion criteria, medical conditions, control
groups, sample size
Animals: species, breed, housing/feeding, sample size
Microorganisms: species, strain, serotype
“Institutional review boards at the University of Manitoba in Winnipeg,
Canada and St. John’s Medical College and Hospital in Bangalore, India
approved the study and the verbal consent process. ”

INTERVENTIONS
For clinical trials or studies involving animals
• Drugs, hormones, antibiotics used (with manufacturer)
• Method of administration (dose, route)
For studies involving microorganisms, list antibiotics used to
maintain cultures
“All strains containing the inducible plasmid construct were grown in Luria-
Bertani broth supplemented with ampicillin (100 µg/ml).”

EXPERIMENTAL DETAILS
Using the past tense, describe how each experiment
was carried out and how data were measured
• Report methods in the same order as the corresponding
results
• Make sure all results have methods described
• When using methods that are described in a previous paper,
include a proper citation
• When modifying previous methods, include a citation and
fully describe the changes

EXPERIMENTAL DETAILS WITH CITATIONS
Total sugar content was measured by a colorimetric
method using phenol and sulfuric acid according to Taylor
(1995).
“using the method of Taylor et al. (1995)”
“as previously described (Taylor, 1995)”
“using a previously described method (Taylor, 1995)”
“HESN status in the sexually exposed Colombian cohort
was defined as previously described [9].”

PROVIDE SUFFICIENT DETAILS
Some terms (e.g., “analyzed”) can be vague –
always state exactly what you measured or assessed
“Each fraction was analyzed for oxygen content”
“Each fraction was assessed for the presence of oxygen”
“The oxygen content in each fraction was measured”
Don’t confuse what was measured with what was performed
“Cd binding capacity was performed”
“Cd binding capacity was measured”
“Measurement of Cd binding capacity was performed”

STATISTICAL ANALYSIS
Fully describe all statistical tests
“An independent, two-tailed Student’s t-test for equal variance was
used to compare the branch length in each group.”
If more than one test was used, specify when and how you decided to
use one or the other
“Competition indices with a normal distribution, as determined by the
Kolmogorov-Smirnov test, were tested for differences by Student’s t-
test. Data sets without a normal distribution were tested for
differences using the Mann-Whitney U test.”
Define the threshold for statistical significance
“p-values < 0.05 were considered statistically significant.”

Materials and Methods
This section is a common cause of rejection for lack of detail
Important questions:
• Have I explained my methods sufficiently so that they can be reproduced
by others?
• Do I cite all previously described methods?
• Do I have too much text?
• Do I have the appropriate controls?
• Did my choice of methods introduce any bias into the results?
• Have I chosen the correct techniques to address my research question,
and used the correct statistical analyses?

Materials and Methods:
Final Considerations
Check journal requirements:
• Animal studies (ARRIVE guidelines, IACUC approval)
• Human subjects (CONSORT guidelines, IRB approval)
• Source of reagents
Consider: Do the results of the methods I chose
answer my hypothesis?

RESULTS, DISCUSSION,
CONCLUSION
Closing the case

RESULTS: KEY COMPONENTS
• The results should relate to the study objective
• Tie experiments together
“Having shown that salamanders prefer cool water over warm water, we
next determined whether water was preferred to other liquids.”
• Highlight important data, but include anything relevant
Present p-values
Trim data that don’t fit your objective
• Follow the most logical order
Not necessarily chronological
Reread for any gaps

DISCUSSION AND CONCLUSIONS
Label the final paragraph Conclusions
• Highlight major findings
• Restate the study’s importance
• Clarify the “takeaway message”
Address limitations
• Balance with strengths
• Don’t dwell on limitations that are outside of your control
• End on a positive note

DISCUSSION AND CONCLUSION:
FINAL CONSIDERATIONS
Base your conclusions only on the data
• What do the results allow you to conclude?
• Assumptions about what might be happening should be
clearly presented as speculation
Remember that…
If your experimental design doesn’t answer your objective…
If you generalize your results too far…
If your conclusions are not supported by your data…
…the journal editor will not consider the work publishable

BE CONCISE
Readers focus on beginnings and ends
Longer sentences = larger “forgotten” middle
Rutgers University

LENGTHY SENTENCES
Take a moment to read this sentence:
“On the tops of crinoids is a circle of plates called
radials, which in some primitive crinoids is further
divided into a lower inferradial and an upper
superradial, and below the radials is a circlet of plates
called basals.”
39 words
(Carpenter, 2001)

LENGTHY SENTENCES
Now read the following:
“On the tops of crinoids is a circle of plates called
radials. In some primitive crinoids, these radials are
divided into lower inferradials and upper superradials.
Below the radials is a circlet of plates called basals.”
12, 14, and 13 words
(Carpenter, 2001)

LENGTHY SENTENCES
Long introductory dependent clause
Because…
Because only certain proteins are transported into the nucleus of
the cell, and many such proteins contain nuclear localization
signals (NLSs) that are recognized by importins, we searched the
primary sequences of the two novel proteins for homology to
canonical NLSs.
Only certain proteins are transported into the nucleus of the cell,
and many such proteins contain nuclear localization signals
(NLSs) that are recognized by importins. We therefore searched
the primary sequences of the two novel proteins for homology to
canonical NLSs.
40
words
24 and 16
words

LENGTHY SENTENCES
Flesch reading ease and Flesch-Kincaid grade level scores can be
used to objectively evaluate readability.
Flesch reading easy guidelines:
- 90.0-100.0 Easily understood by an 11-year-old student
- 60.0-70.0 Easily understood by 13- to 15-year-old students
- 0.0-30.0 Best understood by university students
https://en.wikipedia.org/wiki/Flesch%E2%80%93Kincaid_readability_tests#cite_note-7

CUT OUT EXTRANEOUS WORDS
Short, clear sentences are easier to digest and make the
point stronger
As seen
Currently
Because
To
Whether
Shorter versionLengthy version
As can be seen
At the present time
Due to the fact that
In order to
Whether or not

REDUNDANT PHRASES
Avoid extra words that add no meaning
Absolutely essential  essential
Aggregate together  aggregate
Completely filled  filled
End result  result
Fewer in number  fewer
Throughout the entire study  throughout the study

FORMAL TONE
Scientific writing does not really involve English as we
normally speak it
Jargon (transfect)
Specialized meanings (transform)
Unique conventions (gender vs. sex)
Deviating from this tone will stand out to reviewers and
readers –
It’s important to maintain formality

FORMAL TONE – THINGS TO AVOID
Possessive forms
The material’s melting point was…
The melting point of the material was…
Contractions
Can’t Isn’t
It’s Haven’t
“Ghost quotes”
Nicknames (e.g., calling oncogenes “time bombs”)
Quotation marks are appropriate for direct quotes.

FORMAL SYNONYMS
Addresses
Approximately
Large
Currently
Performed/conducted
Such as
Observed
Formal synonymInformal term
Deals with
About/around
Big
Nowadays
Done
Like
Seen/saw

WORDS WITH LITTLE MEANING
Has/is
Cd nephrotoxicity is tubular dysfunction
Cd nephrotoxicity manifests as tubular dysfunction
The species has three toxins
The species secretes three toxins
Interesting
One of its interesting functions is…
One of its relevant functions is…
One unique function of this protein is…

WORDS WITH LITTLE MEANING
Important
Rice is one of the most important crops
Rice is one of the most commonly consumed crops OR
Rice is a critical food source for billions
Superior
This method is superior to previous protocols
This method is faster than previous protocols OR
This method requires less starting material than previous
protocols

PRONOUN USAGE
Avoid ambiguity with demonstrative pronouns
This, that, these, those
These correspond to…
These features of the cells correspond to…
And other pronouns
It was not active in the absence of Mg2+.
The enzyme was not active in the absence of Mg2+.

PRONOUN USAGE
Who vs. that
Use ‘who’ to introduce information about human beings
Use ‘that’ or ‘which’ to introduce information about
inanimate objects or other nouns
Patients who presented with three of the following
symptoms were included.
The final two subjects, who were recruited from the
same site, both tested negative.

PRONOUN USAGE
That vs. which
‘That’ introduces essential information
“The car that is parked next to mine has a bird painted on it.”
“The cells that were transfected glowed green.”
‘Which’ introduces additional nonessential information
“Uruguay, which won the first FIFA world cup, will play against
Venezuela later this summer.”
“Vibrio cholerae, which causes the deadly diarrheal disease cholera,
is endemic to many tropical regions.”

ANTHROPOMORPHISM
Human emotions or behaviors projected onto other animals
or to inanimate objects
It is unclear why cows in the US choose to face north
when they eat.
It is unclear why cows in the US only eat when facing
north.
Bacteria in rich soil regularly attack each other.
Bacteria in rich soil frequently secrete compounds that
kill neighboring bacteria.

MISPLACED MODIFIERS
Put explanatory phrases near what they modify
The patient experienced severe pain in his right arm when
lifting objects for three months.
For three months, the patient experienced severe pain in his
right arm upon lifting objects.
Copper enters the environment in high concentrations due
to agricultural activity in the form of copper sulfate.

PARALLEL STRUCTURE
Match elements in a series so that they serve the same
grammatical purpose
Words
Phrases
Clauses
Sentences
• Possible therapeutic approaches include surgery, undergoing
radiation therapy, and to give chemotherapy.
• Better: Possible therapeutic approaches include surgery, radiation
therapy, and chemotherapy.
noun
passive
voice/
gerund
infinitive

AVOIDING PLAGIARISM
Giving credit where it is due

WHAT IS PLAGIARISM?
U.S. Office of Research Integrity defines plagiarism as
“the appropriation of another person’s ideas, processes, results, or
words without giving appropriate credit”
Academic misconduct that can result in
• Diminished credibility
• Rejection / retraction from a journal
• Dismissal from a university or research

MAIN TYPES OF PLAGIARISM
Verbatim plagiarism:
Copying text word for word from someone else’s work without citing the
source
Plagiarism of ideas:
Mentioning someone else’s unique idea – theory, interpretation, data,
method, opinion, or new terminology – without citing the source

OTHER TYPES OF PLAGIARISM
Loose paraphrasing
Paraphrasing someone else’s work with only slight changes,
maintaining the author’s logic and ideas, without citing the source
Plagiarism from alternate sources
Failing to cite the source of publicly available knowledge, such as
websites, blogs, lectures
Self-plagiarism and duplicate publication
Recycling your own previously published text, whether a paragraph or a
whole article

WHY PLAGIARIZE?
Discussion: turn to the person next to you and discuss why someone may
purposely or accidentally plagiarize
Your thoughts?
Some possibilities:
• Pressure to publish
• Desire to advance in career
• Anxiety about writing original work in English
• Struggle to express complex ideas in their own words
• Carelessness while writing
• Heavy reliance on few sources
• Belief that “imitation is the sincerest form of flattery”
• Lack of understanding of norms around plagiarism

HOW TO AVOID PLAGIARISM
IN YOUR WRITING
1) As you read the literature, keep careful records of your sources
Citation software can help: Zotero, ReadCube, EndNote

IN YOUR WRITING
2) Draw on multiple sources to ensure content diversity, and err on the
side of citation

3) After writing, review your manuscript and reference list to ensure that
all appropriate citations are included
Plagiarism software can help: Turnitin, iThenticate, eTBLAST (free)
IN YOUR WRITING

WHEN TO CITE
When including verbatim text
• Also place it inside quotation marks
When paraphrasing unique ideas, logic, information – regardless of
the source
When mentioning your previously published work
When reproducing / adapting others’ graphs or tables
• Request permission first

WHEN NOT TO CITE
When describing your own work for the first time
When mentioning common knowledge
• Information in general reference texts
• If you are not sure, cite it

MORNING SESSION
9h30 – 10h: Opening and Scholarly Publishing Report
10h – 12h: Best Practices for Reading and Writing Scholarly Articles
• Keeping up with the literature
• Best practices for writing each section:
• Avoiding plagiarism in academic papers

AFTERNOON SESSION
13h30 – 15h: Best Practices for Reporting Your Research
and Submitting Your Manuscript
• Data and figures
• Finishing touches: title and abstract
• Choosing a journal
• Writing a cover letter
15h20 – 16h20: Roundtable with Experts:
Cases, Questions, and Answers
16h20: Closing, Questions, and Final Observations

BEST PRACTICES FOR
REPORTING YOUR
RESEARCH

DATA AND FIGURES
Ashley Smith, PhD
Scientific Illustrator

FINISHING TOUCHES
Tips for writing a strong title and abstract

CHOOSING A TITLE
Most important part of the paper
• Many readers will only see the title
• First chance to make a good impression
How do I write a good, appropriate title?

KEEP IT SHORT…
Lengthy titles will not be completely read
• Research shows that papers with shorter titles are viewed
and cited more frequently (Paiva et al., 2012)
• 16 words is sufficient (Knight, 1996)
Remove filler terms
• ‘effects of’
• ‘comparison of’
• ‘a case of’/ ‘a study on’
Do not use abbreviations to save space

…BUT DON’T MAKE IT TOO SHORT
Too little information means readers will skip your paper
• They may not know it is relevant to them
• “Novel cancer biomarker” is short but not informative
Include enough information to make your study unique
“Compensatory evolution of net-charge in influenza A
virus hemagglutinin”

AVOID QUESTIONS AND LENGTHY
CONSTRUCTIONS
• Choose a descriptive phrase – no filler words
• Questions do not make good titles for scientific manuscripts
• You should be providing an answer
• Complete sentences often add excess words
“Red hens undergo spontaneous chromosome rearrangement
when exposed to ultraviolet light”
vs.
“Ultraviolet light-induced chromosome rearrangement in red hens”

DON’T OVERSELL THE MANUSCRIPT
Avoid bold terms unless they are absolutely true –
reviewers will be skeptical
• “novel”
• “first time”

TITLE TIPS
Make sure your paper relates to your title
“Molecular mechanism of chromosome rearrangement in red hens” should
provide a full mechanism
You may need to temper the language:
“Protein X contributes to chromosome rearrangement in red hens”
Only mention methods if they are the paper’s focus
Papers with methods-based titles are read less frequently
(Paiva et al., 2012)

KEYWORDS
Use keywords that a reader would search for
• Organism name
• Most common name for a gene
• Name of key technique
Place most important terms at the beginning and end

TITLE: FINAL THOUGHTS
Get your colleagues’ help!
• Offer three or four choices and see which grabs their
attention
Reevaluate the title after any revisions or resubmissions

THE ABSTRACT: FIRST AND LAST
The Abstract
is found at the beginning…
but write it last
Always select a journal first
• Word count
• Differences in format and other requirements

WRITING THE ABSTRACT
Summarize key points from every section
• Reason for the study
• Hypothesis
• Primary methods used
• Key results
• Importance of the study

WRITING THE ABSTRACT: WHAT TO AVOID
Never refer to the text
• “will be discussed further in the text”
Avoid citations if at all possible
• Citations clutter the abstract and draw attention away from
your work
Leave out numbers and statistics
• Focus on conclusions from data/overall results
Minimize abbreviations
• But always define the ones you use

UNNECESSARY INFORMATION
Make every word count:
• Remember to stay on topic. Avoid mentioning
interesting findings or experiments if they aren’t
relevant to this story.
• Choose effective verbs
• Critically examine each word/phrase: does it convey
important information?

TELLING READERS THEY ARE
READING A PAPER
Is it necessary to remind readers that you are describing
your results?
We found that neither group showed a statistically
significant increase over the course of the experiment.
Our results indicate that protein X is not functional in
the absence of magnesium.
Note: this is okay when contrasting with others’ findings in
the Introduction and Conclusion
X
X

TELLING READERS THEY ARE
IN THE PRESENT
Is it necessary to remind your readers that you are
describing current knowledge?
In the present day, numerous archaeal genomes have
been fully sequenced.
There are currently known to be seven components of
the ATC complex.
Note: this is okay if you are directly contrasting the findings
with what was previously thought
X
X

EXAMPLES OF WORDINESS
There were several subjects who completed…
Several subjects completed…
Copper, which is one of the most harmful heavy metals,
Copper, one of the most harmful heavy metals,
X
X

CHECKLIST – TITLE AND ABSTRACT

SAMPLE ABSTRACT
Original:
At this time, very little is known about the family of
proteins called editins.
More concise version:
Little is known about the editin family of proteins.
14 words
9 words

SAMPLE ABSTRACT
Original:
While it has previously been shown that editins can
promote the progression of the cell cycle in various cell
types, the exact role that this family of proteins plays is
not clear.
While editins promote cell cycle progression in various
cell types, the exact role they play is unknown.
33 words
17 words

SAMPLE ABSTRACT
Original:
In this study, we isolated two editin proteins, EDT1 and
EDT2, from the yeast Saccharomyces cerevisiae and
characterized some basic biochemical properties, such as
molecular weight, isoelectric point, and multimerization
status.
Here, we isolated two editins, EDT1 and EDT2, from the
yeast Saccharomyces cerevisiae and characterized several
basic biochemical properties…
32 words
28 words

SAMPLE ABSTRACT
Original:
It was found that both editins were present as
dimers.
Both editins were found as dimers.
10 words
6 words

SAMPLE ABSTRACT
Original:
EDT1 as a monomer is 52 kDa with a pI of 5.4, and
EDT2 as a monomer is 54 kDa with a pI of 5.7.
Monomeric EDT1 is 52 kDa with a pI of 5.4, and
monomeric EDT2 is 54 kDa with a pI of 5.7.
25 words
21 words

SAMPLE ABSTRACT
Original:
Epitope tagging studies further demonstrated that
heterodimers of EDT1 and EDT2 could also be isolated, but
it is unknown whether or not heterodimers are functionally
equivalent to homodimers of EDT1 or EDT2.
Epitope tagging demonstrated that heterodimers of EDT1
and EDT2 also exist, but it is unknown whether heterodimers
are functionally equivalent to EDT1 or EDT2 homodimers.
32 words
21 words

SAMPLE ABSTRACT
Original:
Here, we describe the basic properties of two editins
from Saccharomyces cerevisiae as well as a protocol
for their purification.
We report the basic properties of two yeast editins and
a protocol for their purification.
21 words
15 words

SAMPLE ABSTRACT
Original:
Additional future studies will be needed to determine
how these editins contribute to cell cycle progression.
Future studies will be needed to determine how these
editins contribute to cell cycle progression.
16 words
15 words

CHOOSING THE BEST JOURNAL
FOR YOUR PAPER

THE GOAL: PUBLISH QUICKLY
Publication – still the
primary goal of most
researchers in an
academic setting
Investigate
Present
Review
Publish
Read
Teach
Mentor

THE GOAL: PUBLISH QUICKLY
Every time you get rejected, it can cost you
months of time or more
Find a journal that fits your work closely – take
your best shot first

SCHOLARLY JOURNALS
Global market:
2,000 journal publishers
Over 30,000 active, peer-reviewed scholarly journals
At least 10,000 open access journals
English-language journals:
680 publishers
11,550 journals
Annual revenues of $9 to $10 billion
Growing 7-8% per year
Thomson Reuters; Directory of Open Access Journals (www.doaj.org)

PUBLICATION TRENDS
• Over 1.5 million articles a year are published
– Growing at 3% annually (for 200 years!)
• Many more are submitted to journals each year

IDENTIFYING YOUR TARGET JOURNALS
1) Find articles similar to the one you want to publish
2) Collect a list of journals that publish those articles
3) Research those journals
4) Make a prioritized list of target journals

EXAMPLE SEARCH ENGINES
jane.biosemantics.orgwww.ncbi.nlm.nih.gov/pubmed
scholar.google.com www.journalguide.com

SEARCH
Use your draft title and abstract (finding a journal)
Use keywords (more general searches)

PROS AND CONS
• PubMed
– All peer-reviewed
– Advanced search
capabilities
– Restricted to certain
biomedical journals
• Google Scholar
– Good at finding free versions
– Expansive
– Includes gray literature and
junk
• JANE
Easy interface
– Layered over Medline, so no
extra coverage
• JournalGuide
– Standardized layout for
finding and comparing
journals
– Coverage beyond PubMed
while still restricted to peer-
reviewed literature
– Still growing and expanding
functions

ADVANCED SEARCH STRATEGIES
Use “advanced search” options if available
Limit your search to the years 2011-2016
(expand to earlier articles only if needed)
Include recent articles or articles in press
Note the name of the publisher to investigate later

SAVE YOUR SEARCHES TO RUN LATER!

COLLECT “HITS” INTO JOURNAL LIST
Report
ranking IF J. title Website
Print
ISSN E-ISSN issues/year
acceptance
rate
JCR
category/rank Keywords used Title of published articules
title:glucose AND preterm
AND mortality (or issn:XXXX-
XXXX AND "gestational
outcome")
The impact of glycemic control on neonatal outcome in singleton pregnancies
complicated by gestational diabetes. (2007) )
Ethnic differences in perinatal outcome of gestational diabetes mellitus. (2006
Maternal metabolic control and perinatal outcome in women with gestational diabetes
mellitus treated with lispro or aspart insulin: comparison with regular insulin. (2007)
1 7.14
Diabetes
Care
http://care.diabetesjourn
als.org/
0149-59921935-5548 12 20
Endocrinology &
Metabolism
(9/116= 7.8%)

DEALING WITH THE RESULTS
• A good number of results is 100 – 300
If you recover < 30 or > 300 results, expand or restrict your search
• Make a list of your top journal choices
• Find out more about these journals

INFORMATION TO GATHER
Find the journal’s website, and pull out key pieces of information:
• ISSN (unique identifier for every journal)
• Publisher/affiliated societies
• Contact information (in case of questions)
• Aims and scope
• Publication frequency

INFORMATION TO GATHER
Look for additional information that can help you make a more informed
decision:
• Acceptance rate
• Speed
Time to first decision, time to publication online
• Costs
Page fees, publication fees, color image fees
• Open access policies
Is self-archiving allowed?
Is full open access available?

JOURNALGUIDE.COM
Find most of the information you need in one place with a standardized
layout:
• ISSN
• Publisher/affiliated
societies
• Aims and scope
• Types of submissions
accepted
• Indexing
• Acceptance rate
• Publication
frequency
• Contact info

JOURNALGUIDE.COM
Find most of the information you need in one place with a standardized
layout:
• Time to
publication/first
response
• Submission/page
fees
• Color image fees
• Open Access
policy

COLLEAGUES’ EXPERIENCE
One of the most valuable pieces of data about a journal is the
experience of real researchers. Ask around!
Advisor/committee
Labmates (past and present)
Collaborators

BENEFITS AND RISKS
• High impact factor = stronger
“stamp of approval”
• High risk of rejection and lost
time
Is it more important to get this research out quickly or to
maximize the prestige of the journal?
Is this project a primary focus of your lab’s efforts or is it a side
project that might be nice to wrap up?

BENEFITS AND RISKS
• Multidisciplinary journal = more
readers, broader impact
• Need to rewrite paper to
appeal to readers with less
context and background
Is your work relevant to a broad audience or will its most interested
readers be within your field?
Can you easily contextualize your research for a multidisciplinary
audience?

BENEFITS AND RISKS
• Specialized journal with fewer
submissions = higher chance
of acceptance
• Risk of “walling off” your
research within your field
Is getting the research accepted quickly an important consideration?
Will a specialized journal be visible enough to researchers in other fields?

BENEFITS AND RISKS
• Open access journal = greater
exposure and (perhaps) more
citations
• May not be the most
prestigious journal in your field
• Chance of running into
questionable publishers
Is open access an important motivation for you?
Will you be concerned if only researchers with subscriptions can see
your work?

SOUND RESEARCH “MEGAJOURNALS”
What is a megajournal?
Review for soundness of
research results and
interpretation, not perceived
importance/impact
Broad subject scope
Publishes any and all
articles that meet criteria
PLOS ONE
2007 2013Binfield, 2013
All megajournals

MEGAJOURNALS
• Increasing number of journals focusing on rigor of research, not
perceived interested/novelty
• Usually include broad subject areas
• Fast and often simpler route to publication
• More effort on your part in other areas:
– Polishing the language
– Sharing the paper post-publication
– Demonstrating the value of the paper without relying on the
journal “brand”

THE FINAL DECISION
Weigh the pros and cons for each journal, then make an ordered list
Start with journal #1 and move down the list only if needed
Remember that the best fit is not the only thing that affects your paper’s
chances:
• Edit your paper carefully
• Spend time creating strong figures
• Write an effective cover letter

WRITING A
COMPELLING
COVER LETTER
Make your case to the journal editor

TAKE CARE WITH THE COVER LETTER
• The cover letter is your opportunity to convince the journal editor to
send your manuscript out for peer review
• It highlights your most important findings
• It explains why your manuscript is a good fit for the journal

COVER LETTER: INTRO
1) Address the journal editor formally by name, if possible
1) Include your contact information
This information may also appear in the journal’s online submission
system, but it is appropriate to include in the letter

COVER LETTER: OPENING PARAGRAPHS
1) State the manuscript title and author names
1) Mention what type of article it is: research article, review, case
study, etc.
1) Describe your study’s rationale and major findings

COVER LETTER: MIDDLE PARAGRAPH
1) Briefly explain how your manuscript fits the journal’s Aims & Scope
1) Don’t simply state the the findings are “novel” or “of interest to the
field – include specific aspects relevant to the journal

COVER LETTER: FINAL PARAGRAPH
Close with a brief paragraph indicating the following:
1) The manuscript is original work
2) No part of the manuscript has been published before
3) The manuscript is not under consideration at any other journal
4) There are no conflicts of interest to disclose
5) A list of potential reviewers – only if journal requests this
6) Any researchers who should not review your manuscript due to
potential conflicts / bias

COVER LETTER: CLOSING THOUGHTS
A well-written cover letter assures the journal editor that
• your manuscript should be considered
• it is a good fit for the journal
Good research may be reviewed regardless of the cover letter’s quality,
but a great cover letter can help your manuscript stand out

EXPERT ROUNDTABLE
Questions & answers with AJE’s team of experts in the United States

AJE Best Practices Workshop USP

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