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The Past, Present, and Future of
Scholarly Publishing
www.aje.com
About American Journal Experts (AJE)
• Founded in 2004
• High quality English editing for
researchers
• Native English editors from top US
universities
• Match your paper with an editor in our
field
www.aje.com
About American Journal Experts (AJE)
• AJE has supported over 500,000 manuscripts across almost 450
research fields
www.aje.com
Our Partners
www.aje.com
The people of AJE
• Researchers with publication experience who want to help other
researchers.
www.aje.com
State of the industry
• Academic
publishing is a
$12 billion
industry...in flux
University
Libraries
Authors
Funding
Agencies
Mega-Publishers
Journals
copyrights,
fees ($)
Imprimatur
(seal of
approval)
access to
journals
funding ($)
copyrights,
fees ($) software, services,
funding
The Big Deal:
$ Millions
access to
journals
www.aje.com
THE PAST
The beginning and evolution of scholarly publishing
www.aje.com
Key Journal Functions
• Validation – The peer review process determines if the
science/research is valid.
• Dissemination – The journal makes the research available to the
community.
• Registration/Preservation – The date of publication and location
provide a record of who made the discovery and preserve that record.
Priem J and Hemminger BM (2012) Decoupling the scholarly journal.
Front. Comput. Neurosci. 6:19. doi: 10.3389/fncom.2012.00019
www.aje.com
Early discoveries
• 1610 - Galileo’s discovery of the rings
of Saturn
– smaismrmilmepoetaleumibunenugttauir
as
• Altissimum planetam tergeminum
observavi
– “I have observed the most distant
planet to have a triple form.”
www.aje.com
The history of academic publishing
• 1665 - The first journals
– Journal des Sçavans (France)
– Philosophical Transactions of the Royal Society (UK)
• Editorial review only – no peer review
• Even then, journals provided
– Dissemination by sharing discoveries more widely
– Registration through establishing priority (one author)
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The history of academic publishing
• 1731- Peer review
– Medical Essays and Observations (Scotland)
– Philosophical Transactions of the Royal Society (UK)
• Even as late as the early 1900s, true peer review
was rare (validation)
www.aje.com
Academic publishing goes international
• 1930s - English moves to the front
– After WWII, scientific publishing as we know it began to flourish
– Ex: In 1951, 50,675 chemistry papers; In 2001, 606,680 papers
• 1947 - One of the first international journals was launched
– Biochimica et Biophysica Acta
– Fear of “compartmentalizing knowledge”
– In 2014, 57 out of 6,166 journals in the JCR are “Multidisciplinary” (<1%)
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Academic publishing goes online
• 1990 - Postmodern Culture
– Online only, no print version
• 2006 - PLOS ONE
– No weight to “novelty” of results
– Multidisciplinary
– High volume
www.aje.com
THE PRESENT
A snapshot of scholarly publishing today
www.aje.com
Scholarly publishing by the numbers
• The total number of researchers grew by 120% from 2007 - 2013
AJE, The Business of Research, 2018
UNESCO. UNESCO Science Report (2015).
http://en.unesco.org/unesco_science_report.
www.aje.com
STM journals
• Global market
– About 2,000 journal publishers
– Up to 30,000 active, peer-reviewed scholarly journals
• Almost 10,000 open access journals
• English-language journals
– About 680 publishers
– About 11,550 journals
– Annual revenues of $9 - $10 billion
• Growing 7-8% per year
Thomson Reuters; Directory of Open
Access Journals (www.doaj.org), 2013
www.aje.com
Publication trends
• In 2016, the number
of articles published
was more than 2
million
• In 2017, China
published the most
number of scientific
articles of any
country
AJE, AJE Scholarly Publishing Report: 2016, 2018
Scientific American, China Declared World’s Largest
Producer of Scientific Articles, 2018
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Research is international
• Research is collaborative
• In 2016, the top two
collaborating countries in
biomedical research was
China and the US, working
together on 19,162 published
papers
AJE, Collaboration in Science Annual Report: New Data, 2018
Top 8 countries for biomedical
research collaboration in 2016
www.aje.com
Subscription model
Author Publisher Library
copyright access
moneyimprimatur
Monopolies
www.aje.com
Open access - another big shift
www.aje.com
Open access model
Author Publisher Library
copyright
accessmoney
imprimatur
Anyone!
access
access Content → Service
www.aje.com
Open access is here to stay
• Costs shift to the author, but they drive competition among journals
• Mandates by governments and funding agencies are incentivizing OA
– Horizon 2020 by the EU
• More and more researchers are realizing the potential for letting
anyone read their results and build off of them
AJE, Open Access Mandates: The Changing
Landscape of Scholarly Publishing, 2018
www.aje.com
Current journal functions
• Journals provide authors:
– Validation
– Dissemination
– Registration/Preservation
• All functions are performed individually by each and every journal
Priem J and Hemminger BM (2012) Decoupling the scholarly journal.
Front. Comput. Neurosci. 6:19. doi: 10.3389/fncom.2012.00019
Validation
Stamping
Feedback
www.aje.com
Peer review in the past 50 years
• Most common model:
– External reviewers
– Freeform responses
• Quality of results
• Fit for journal
– Final decision by journal editor
– Reviews returned anonymously
• Authors don’t know reviewers
• Double blind peer review
• New experiments are iterating on these principles
www.aje.com
Functions of Peer Review
• Good science?
• Impact and novelty?
• Publish in this journal?
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Problems with Peer Review
• Inefficiency and reviewer fatigue
• Inconsistency (Smith, 2006):
– Reviewer A: I found this paper an extremely muddled paper with a large
number of deficits.
– Reviewer B: It is written in a clear style and would be understood by any
reader.
• Personal and manuscript-related bias
www.aje.com
Peer review statistics
• Kravitz and Baker (2011):
– Average # of reviews before publication: 6.3
– Average # journals submitted to: 2.1
– 1.5 million articles x 80% receiving reviews x 2.3 reviewers per paper =
2.76 million reviews per year
www.rubriq.com
Time Spent on Rejected Reviews Annually:
15.6 Million Hours = 1779 Years
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THE FUTURE
What is to come
www.aje.com
A shifting industry
More research, more publications = new challenges
• Reviewer fatigue
• Discovery of new content
• Unsustainable subscription prices
www.aje.com
Preprints
• Preprints on the rise
– arXiv, bioRxiv, ChemRxiv, PeerJ
• Researchers using preprints to share their work early
– Benefits include exposure for one’s work, collaboration opportunities, and
possibly career advancement
• Preprints are new and still have unknowns
– Concern for getting scooped
– Many authors have not heard of preprints
Science, Are Preprints the Future of Biology?
A Survival Guide for Scientists, 2018
www.aje.com
New media and channels
• Videos to share research
• Sharing research on social media will
continue to grow
– ResearchGate
– Twitter
Research Square, Research Square Videos, 2018
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Sharing and storing data
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The future
• Endless amounts of new knowledge
– Tools for discovery
– Tools for sharing (social media)
– Tools for archiving data
• Changes to the publishing process
– Preprint sharing
– Iterations on peer review including open peer review
• Collaborations among researchers
– More opportunities to collaborate
– Collaborations may offer more funding opportunities
www.aje.comwww.aje.com
Writing a Better
Manuscript
Paul Klenk, PhD, MBA
Author Education
American Journal Experts (AJE)
www.aje.com
Outline
• Tips for Publication Success
• Conventions in Scholarly Writing
• Creating Figures for Scientific Publications
Lunch
• Ethics in Research Publication
• Choosing the Right Journal for your Research
www.aje.com
Scholarly Communication
Communication is hard.
“The single biggest problem in communication is the illusion that it has
taken place.” – George Bernard Shaw
Point of view is important.
“If there is any one secret of success, it lies in the ability to get the other
person's point of view and see things from that person's angle as well as
from your own.” – Henry Ford
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The goal: publish quickly
• Publication – still the primary
goal of researchers in an
academic setting
Investigate
Present
Review
Publish
Read
Teach
Mentor
www.aje.com
The goal: publish quickly
• Every time you get rejected, it can cost
you months of time or more
– Average time from submission to
acceptance: 188 days
– Average time from acceptance to
publication: 175 days
• Find a journal that fits your work
closely. Take your best shot first
AJE, State of Authorship Report: Time and Costs
Involved in Publishing Research, 2016, 2018
www.aje.comwww.aje.com
Tips for Publication
Success
www.aje.com
Manuscript sections
1. Introduction
2. Materials and Methods
3. Results
4. Discussion and Conclusions
5. Title and Abstract
6. References
Journal Cover letters
Responding to reviewers
www.aje.com
Introduction
• Assume no one has read your abstract
• Define all acronyms
• References
– < 5 years old
– Primary literature
– Balanced
General
Specific
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Introduction
• Explain the problems your
research addresses in the
context of recent advances
in the area
• Define the study objective,
and briefly describe the
experimental design
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Materials and Methods
• Common cause of rejection - lack of detail*
• Important questions
– Have I explained my methods sufficiently so they can be reproduced?
– 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?
*See Provenzale, 2007
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Materials and Methods
• Watch for journal requirements
– Animal studies (ARRIVE guidelines, IACUC approval)
– Human subjects (CONSORT guidelines, IRB approval)
– Source of reagents
• Do the results of the methods I chose answer my hypothesis?
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Should the Results and Discussion be combined?
• 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 objectives
• Follow the most logical order (not necessarily chronological)
– Be especially careful of gaps
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Discussion and Conclusions
• Put the most salient results in the first paragraph
Serial position effect
(www.wikipedia.org)
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Discussion and Conclusions
• 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
www.aje.com
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
www.aje.com
Title
• Capture reviewers and readers
– Answer question, “What does this research contribute to the field?”
• Reviewers will expect paper’s content to match the title
– Keep it short
– Consider how readers will search for your paper
• If no one can find it, no one will cite it
Paiva, et al., 2012
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Title
• Include:
– Key terms: Species names, geographical regions, method used
– The most common name used for genes, methods, etc.
– A descriptive answer
• Avoid:
– Abbreviations
– Filler terms: “Effect of,” “Comparison of,” “A study of,” or “Observations on”
– “Novel” / “First time”
– A question
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Abstract
• Your abstract may be all someone can read easily
– Convince readers to read the entire paper
• Determine what the journal requires
– Unstructured abstract
– Structured abstract (headings)
– Plain-language summary
www.aje.com
Abstract
• Watch the word count
– Use strong verbs (analyze vs. perform an analysis)
– Avoid filler phrases (“It is currently known that…” “We found that…”
• Make sure that each piece of information is critical to the reader and
relates to your main conclusions
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Abstract
• Include:
– Importance of the research
– Critical background
– Clear hypothesis
– Methods summary
– Key results
– Succinct conclusion
• Avoid:
– Excessive abbreviations
– Citations
– References to text/figures
– Statistics
– Bringing up topics that your
research doesn’t address
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References
• Important questions:
– Do I cite all the studies that I need to?
– Are all citations relevant to my study?
– Are all citations as recent as possible?
• Reference formats change according to journal
– Keep the complete citation; “et al.” is not always acceptable
www.aje.com
Journal Cover Letter
• Opportunity to make your case to the Journal Editor
• Suggest reviewers – at least two regions in the world
• “all authors have reviewed this paper and have approved it for
publication”
• This work has not been submitted to other journals even in another
language
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Responding to Reviewers
• Take a deep breath!
• Professional and respectful –
“esteemed colleague”
• Thank the reviewers for their
helpful comments
• Respond to every comment
• Challenge based on the science
where appropriate
• Help the editor communicate with
the reviewer
You
Journal
Editor
Peer
Reviewer
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Conventions of Scholarly Writing
www.aje.com
“Attention to detail of the language will avoid
severe misunderstandings which might lead
to rejection of the paper.”
-- Cell & Molecular Biology Letters instructions
for authors
www.aje.com
Key topics
• Verb tense
• Formal tone
• Journal specific conventions
www.aje.com
Verb tense
• Present
– Action is occurring now
– Action started in the past but continues now
• Past
– Action already occurred
• Future
– Action will occur later
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Verb tense
• Perfect
– Action is defined relative to another action
– Uses helping verb ‘have’ (have/has/had)
• He has worked here for seven years.
• She had eaten all the cake when her friend arrived.
• Progressive
– Emphasizes the continuance of an action
– Formed using helping verb ‘be’ (is/are/was/were) and the present
participle of a verb (-ing)
• I don’t know why she is running in the rain.
• He was writing his thesis when the computer broke.
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How to choose verb tense
• Widely accepted fact: present
– DNA is composed of four nucleotides.
– Trypanosomes exhibit global trans-splicing of RNA.
• Ideas no longer accepted: past
– Bacteria were believed to lack introns.
– Physicists once thought electrons traveled in defined orbits.
• Describing a figure, result, or paper: present
– The results indicate…
– Their landmark paper describes…
– Figure 1 shows…
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How to choose verb tense
• Past tense
– We tested independently derived cultures.
– Cells were transfected, irradiated, and assayed.
– The dehydration process comprised five steps.
• Present tense
– Use for characteristics that are relevant facts
• The Mississippi River Delta occupies almost 12,000 km2 in the
state of Louisiana.
– Use when referring to aspects of the paper itself
• In this study, we report a new frog species.
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Verb tense for previous studies
• Results that are still relevant: present perfect
– Johnson et al. have shown that gene X is in an operon.
– Unusual glycosylation events have been observed in these cells.
• Methods: past
– Smith and Anderson sampled 96 swamps.
• Specific historical events: past
– Gene X was first cloned into a vector in 1996.
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Verb tense combinations for previous studies
• Past perfect and past: one occurred earlier than another
– Cells that had been irradiated were assayed for DNA damage.
– Patients who had elected surgery completed surveys.
• Past progressive and past: one occurred while the other was
ongoing
– While the cells were incubating, the temperature was raised 1
degree per hour.
– While patients were preparing for surgery, nurses collected
baseline parameters.
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Formal Tone
• Word choice
• Pronoun usage
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Formal tone - word choice
• 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
www.aje.com
– Addresses
– Approximately
– Large
– Currently
– Performed/conducted
– Such as
– Observed
Formal synonym Informal term
– Deals with
– About/around
– Big
– Nowadays
– Done
– Like
– Seen/saw
Formal tone - word choice
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Formal tone - word choice
• 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… OR
– One unique function of this protein is…
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Formal tone - word choice
• 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
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Formal tone - word choice
• Human emotions or behaviors projected onto other animals or to
inanimate objects
– It is unclear why cows in the US only eat when facing north.
– NOT: It is unclear why cows in the US choose to face north when they
eat.
– Bacteria in rich soil frequently secrete compounds that kill neighboring
bacteria.
– NOT: Bacteria in rich soil regularly attack each other.
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Formal tone - pronouns
• Avoid ambiguity with demonstrative pronouns
– This, that, these, those
– This analyzes the effects…
– This research analyzes the effects…
– 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+.
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“Please be attentive to the
requirements of APA style, as
indicated on submission guidelines.
Failure to do so can erode the
impression your manuscript makes on
reviewers.”
-- Innovative Higher Education instructions
for authors
www.aje.com
Journal-specific conventions - voice
• Active = subject is performing action
• Passive = subject is being acted on
– We inspected the burners regularly (active)
– The burners were inspected regularly (passive)
– Others have explained these differences… (active)
– These differences have been explained… (passive)
– I removed the coating with alcohol (active)
– The coating was removed with alcohol (passive)
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Journal-specific conventions - voice
• Active voice
– Shorter
– Identifies agent
• Passive voice
– Once considered more objective
– Useful if the agent is unknown
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Journal-specific conventions - person
• First person = subject/object is speaking
– I prefer to eat the vegetables from my garden.
– We will decide what is best for the company.
• Second person = subject/object is being spoken to
– You prefer to eat vegetables from the nearby market.
– You are doing a great job!
– Children, please wash your hands before dinner.
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Journal-specific conventions - person
• Third person = subject/object is being spoken about
– He prefers to eat as few vegetables as possible
– Doctors renew their licenses periodically.
– I am standing where she stood yesterday.
• Which is best?
– First person is increasingly common and helps keep writing more
concise
– Defer to journal guidelines
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Journal-specific conventions - formatting
• Serial comma
– “A, B, and C” vs. “A, B and C”
• Spacing
– Between sentences
– “p = 0.05” vs. “p=0.05”
• Abbreviations
– (sec vs. s; m/s vs. m·s-1)
– Spell out when defining
– Use abbreviation consistently
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Journal-specific conventions - formatting
• Words vs. numerals
– “A total of ten species” vs. “A total of 10 species”
• Number style
– 1,000 vs. 1000 vs. 1 000
– 0.05 vs. .05
– 17.3 vs. 17,3 (rare in English-language publications)
• Manuscript elements
– Figure 1 vs. Fig. 1
– Figure 1 vs. figure 1
– Capitalization/parallelism in section headings
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Journal-specific conventions – split infinitives
• Ban against splitting infinitives
– To confirm empirically these data
– NOT: To empirically confirm these data
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It’s Not All Bad…
[A]uthors can submit
manuscripts formatted in a
variety of reference styles,
including Harvard,
Vancouver, and Chicago.
www.aje.comwww.aje.com
Creating Figures for Scientific
Publications
www.aje.com
Figure quality is a paper’s “Suit and Tie”
• Before a journal reviewer or colleague even begins reading your
paper, they have formed an opinion about the quality of your
work.
• Your figures reflect your overall effort in experimental design,
technical execution, and attention to detail.
• “A picture is worth a thousand words”
www.aje.com
The power of figures
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Types of figures
1. Primary Data
2. Secondary Data
3. Illustrative Diagrams
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Primary Data Figures: Where to start
• High-quality figures start in the lab
• Think in figures
– Controls
– Use your muse, use your nemesis
Every day, every experiment
www.aje.com
Primary Data Figures: Save your work
• Protect the original files
• Toggle the “Read-only” option
on the data files
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Pixel-based files
• Two sub-types of Pixel-based files
– Lossy
– Lossless
Dr. Jan Michels, Nikon Small World Competition
www.aje.com
Lossy file formats
• Example: JPG
• Highly simplified explanation:
– The image is divided into tiles
– The number of colors in each tile is
simplified
– How simplified depends on the
“Quality” setting chosen
– These protocols are re-applied every
time the file is saved
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OriginalQuality 4(/12)
Lossy file formats (compression)
• Compression leads to a
greatly reduced file size
• Fine for everyday use, not
for primary data
• Once a compression is
applied, it cannot be
reversed
Quality 2 (/12)Quality 0 (/12)
www.aje.com
Lossless files
• Example: Tiff
• Color of each pixel is
recorded.
• The color of each pixel
will not change simply by
saving.
• The price of fidelity: file
size.
Dr. Gregory Rouse,
Nikon Small World Competition
Jpeg: 15.2 KB
Tiff: 790 KB
www.aje.com
Lossless versus Lossy files
Lossy file compression is even worse for line drawings
and graphs.
www.aje.com
LZW lossless file compression
• Efficient storage, not information loss
• Highly simplified explanation:
– Replaces a pixel color with a short code throughout the whole image file
Image
Pure White, Pure White, Pure Black, Medium Blue
Pure White, Pure White, Pure Black, Pure Black
Pure White, Pure White, Pure White, Pure White
Pure White, Pure White, Pure White, Pure White
Without LZW Compression
1, 1, 2, 3
1, 1, 2, 2
1, 1, 1, 1
1, 1, 1, 1
With LZW
Compression
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LZW lossless file compression
• Effective on images with a large
number of colors
– 82 mm wide, 300 dpi (typical journal
requirements)
– Uncompressed Tiff: 2,710 KB
– LZW Compressed Tiff: 1,550 KB
Cameron Johnson, Nikon Small World
Competition
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LZW lossless file compression
• Very powerful on images with a
limited number of colors
– 82 mm wide, 1200 dpi (typical
journal requirements)
– Uncompressed Tiff: 25,200 KB
(25.2 MB)
– LZW Compressed Tiff: 256 KB
– Jpeg (with a high quality
setting): 586 KB
www.aje.com
Saving figures - types of formats
• Pixel-based
– Industry standard: Tiff
– Uneditable with a set resolution
– General guidelines:
• Photos: 300 dpi
• Photos with lettering or line-art: 600 dpi
• Line-art (graphs or diagrams): 1200 dpi
• Vector-based
– Industry standard: Eps (& pdf)
– Editable with “infinite resolution”
www.aje.com
Saving figures from programs
• Microsoft Office (PowerPoint)
– Download extra add-ins from Microsoft
– Common method:
• Save as pdf
• Convert pdf to proper file in Adobe Acrobat or Photoshop
• Adobe Illustrator
– Save As (vector) or Export (pixel)
– Open the Ai file in Photoshop
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Moving graphs between programs
• Graphs are vector objects
• Copy and Paste often works
• Save (or Export) as a vector file
– Postscript file (Eps)
– Pdf file
• Pixel-based file = a picture of a graph
www.aje.com
Figure creation rule #1
• Work at actual publication size
– Journal guidelines
– Print and measure
– General guidelines
• Single column: 85 mm
• 1.5 columns: 135 mm
• Double column: 175 mm
• Keep a sense of scale
www.aje.com
Figure creation rule #2
• Use the correct size and type of font
– Journal guidelines
– General guidelines
• 8 point Arial (with symbol)
• Avoid bolding and italics
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Crafting effective graphs
• Consider the purpose of your graph
http://chemlab.truman.edu/DataAnalysis/PreparingGraphs
_files/PreparingGraphs.asp
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Crafting effective graphs
• Visualization aid or research tool?
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Crafting effective graphs
• Question everything
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Crafting effective graphs
Simplify Legends
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Crafting effective graphs
Don’t Hesitate to Try Something “New”
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Crafting effective graphs
Be Careful with Patterns
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How to use color effectively
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Illustrative diagrams
• Use diagrams to reduce reviewer (and general reader) confusion
(Cejka & Plank et al., 2004)
www.aje.com
Illustrative diagrams
• Marketing for scientists
(Could be You et al., 2014)
www.aje.com
Outline
• Tips for Publication Success
• Conventions in Scholarly Writing
• Creating Figures for Scientific Publications
Lunch
• Ethics in Research Publication
• Choosing the Right Journal for your Research
www.aje.com
Questions?
Contact support@aje.com for information about
our services
Universidade de Sᾶo Paulo
Group Code: SIBIUSP10
Flavia Jaszczak
flavia@aje.com
Paul Klenk
paul.klenk@aje.com
www.aje.com
Lunch
www.aje.comwww.aje.com
Ethics in Research Publication
www.aje.com
Key Topics
1. Plagiarism and self-plagiarism
2. Authorship and ghost authorship
3. Ethics in author services
www.aje.com
What is plagiarism?
• The misrepresentation of someone else’s original thought as your own
• The U.S. Office of Research Integrity defines plagiarism as “the
appropriation of another person’s ideas, processes, results, or words
without giving appropriate credit”
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Types of plagiarism
• Verbatim plagiarism
• Plagiarism of ideas
• Loose paraphrasing
• Plagiarizing alternative sources
• Self-plagiarism
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Verbatim plagiarism
• Copying text word-for-word from someone else’s work
– Original text: Salmonella typhimurium and Clostridium
perfringens bacteria were present in over 75% of the chickens processed.
– Verbatim plagiarism: Salmonella typhimurium and Clostridium
perfringens bacteria were present in over 75% of the chickens processed.
– Proper citation of a direct quotation: Other researchers found that
“Salmonella typhimurium and Clostridium perfringens bacteria were
present in over 75% of the chickens processed” (Wu et al. 2015).
• If content from several sources is duplicated, this form of plagiarism is
known as mosaic or patchwork
www.aje.com
Plagiarism of ideas
• Mentioning someone else’s unique idea, whether in the form of a
theory, an interpretation, data, a method, an opinion, or new
terminology, without citing your source, even if explained in your own
words
– Original text: Salmonella typhimurium and Clostridium
perfringens bacteria were present in over 75% of the chickens processed.
– Plagiarized idea: Other researchers found that Salmonella typhimurium
and Clostridium perfringens bacteria occurred in the majority of the
processed chickens.
– Proper citation of a paraphrase: Other researchers found that
Salmonella typhimurium and Clostridium perfringens bacteria occurred in
the majority of the processed chickens (Wu et al 2015).
www.aje.com
Loose paraphrasing
• Paraphrasing someone else’s work with only slight changes, effectively
maintaining the other author’s logic while mentioning most or all of the
same ideas. Please note that the flow of an argument is indeed an
original idea
– Original text: Cross-contamination experiments showed that Clostridium
perfringens and Salmonella spp. were easily transferred from
raw chicken products to consumers.
– Loose paraphrase: Clostridium perfringens and Salmonella spp.
transferred easily from raw chicken products to consumers because of
handling practices. Cross-contamination experiments demonstrated that
these practices were the cause of the contamination. (2 sentences)
www.aje.com
Plagiarizing alternative sources
• Failing to cite the source of publicly available knowledge that is not in
the scholarly literature
• As with journal articles, sources such as books, webpages, and blogs
should be referenced if they contributed unique information to your
manuscript
• Personal communications and lectures (including descriptions of
unpublished ideas, with permission) should also be referenced
www.aje.com
Self-plagiarism
• Any attempt to take any of your own previously published text, papers,
or research results and make it appear brand new
• When your manuscript contains uncited recycled information, you are
countering the unspoken assumption that you are presenting entirely
new discoveries
• It is best practice to cite your previous work thoroughly, even if you are
simply revisiting an old idea or a previously published observation
www.aje.com
Self-plagiarism and publishing
• Although self-plagiarism is not theft of ideas, it can create issues in the
scholarly publishing world
– After publication, the journal generally owns the copyright
– While you own the ideas, reuse of the text without citation would require
the permission of the journal
• Submitting the same article to two journal is duplicate plagiarism
www.aje.com
“1 in 3 Scholarly Journals has access to iThenticate to check for
plagiarism before publication”
Check articles “against 49,000,000 Scholarly articles, books, and
conferences proceedings” from scientific, technical, and medical journals
www.ithenticate.com
www.aje.com
Authorship
• “Clearly conveying who is responsible for published work is integral to
scientific integrity” (Panter).
• The top four International Committee of Medical Journal
Editors (ICMJE) guidelines:
1. Significant involvement in study conception/design, data collection, or
data analysis/interpretation
2. Involvement in drafting or revising a manuscript
3. Approval of the final version of a manuscript for publication
4. Responsibility for the accuracy and integrity of all aspects of research
www.aje.com
Authorship responsibility, order, and guidelines
• Some journals require a public guarantor for each article, or an author
who takes responsibility for the entire research project
• Author names may be listed:
– Alphabetically
– By magnitude of contribution
• Professional guidelines
– Coalition for Responsible Publication Resources (CRPR)
– World Association of Medical Editors (WAME)
www.aje.com
Honorary authorship
• Gift
– The study is gifted to someone who did not contribute
– Better to reference the person in the acknowledgment section
• Guest
– Often added to the list to use the credibility of another researcher’s name,
even if they did not contribute to the study
• Coercive
– When someone in authority over the author requests that another person
be added as an author, even though they did not contribute to the study
www.aje.com
Problems with honorary authorship
• Elevating the study beyond its potential impact
– Using someone else’s good name to elevate the work
• Attributing without permission
www.aje.com
Ghost authorship
• The opposite of honorary authorship, entailing a significant contribution
to a manuscript without acknowledgment of that contribution
• Includes any content contributed to the study that is not acknowledged
(drafting, data collection and analysis, etc.)
• “Such ghost authorship was present in approximately one-tenth of
papers published in six medical journals in 2008” (Wislar et al. 2011).
• It is not having somebody edit your language or formatting
www.aje.com
Problems with ghost authorship
• Masking industry ties to a paper
– Ex: Author does the work but gets no credit
• Hiring a writer to overcome poor language skills, lack of expertise, or
time constraints
– Using someone else’s good name to elevate the work
• Acquiring data, performing analysis, etc. may be hired out to a ghost
researcher
www.aje.com
Avoiding ghost authorship
• Authors should sign a formal declaration about their contributions
• Authors should publish a comprehensive list of contributions and a
detailed acknowledgments section
www.aje.com
Ethics in author services
• Author services companies are increasing
– What help is appropriate?
– How can unethical behavior be identified?
• Language editing should entail clarifying language without adding or
subtracting information
• Formatting a manuscript should consist of changing layout elements
and references to conform to a journal’s specifications but not adding
or subtracting content
www.aje.com
Ethics in author services
• Appropriate author services will:
– Will have clear ethical limits on what they will and will not provide
– Will deny a client’s request that crosses an ethical boundary
– Will not help a client plagiarize or commit other ethical violations
– Will not help fabricate or manipulate figures
– Will improve a manuscript’s form without changing the manuscript’s
content
– May be accredited by an outside agency or be a member of a society
such as the Committee on Publication Ethics (COPE)
www.aje.com
References - sources from AJE
• Plagiarism
• Self plagiarism
• Authorship
• Ghost authorship
• Ethics
www.aje.com
References - other sources
• “Ghost Writing Initiated by Commercial Companies” World Association
of Medical Editors. June 20, 2005. http://www.wame.org/about/policy-
statements#Ghost%20Writing (accessed October 23, 2017).
• Wislar, Joseph S., et al. “Honorary and ghost authorship in high impact
biomedical journals: a cross sectional survey.” BMJ (October
2011) 343. https://doi.org/10.1136/bmj.d6128 (accessed October 23,
2017).
www.aje.comwww.aje.com
Choosing the Right Journal for
Your Research
www.aje.com
The goal: publish quickly
• Every time you get rejected, it can
cost you months of time or more
– Average time from submission to
acceptance: 188 days
– Average time from acceptance to
publication: 175 days
• Find a journal that fits your work
closely. Take your best shot first
AJE, State of Authorship Report: Time and
Costs Involved in Publishing Research, 2018.
www.aje.com
Outline
• Search tips
• Journal information/metrics
• Final decisions
www.aje.com
SEARCH TIPS
Create and curate your own list of target journals
www.aje.com
Search tips and basic strategy
• Start a list of journals publishing articles that inform your work
• Find articles similar to the one you want to publish
• Collect a list of journals that publish those articles
• Research those journals
• Make a prioritized list of targets
www.aje.com
Options
www.aje.com
Search!
• Use your draft title and abstract (finding a journal)
• Use keywords (more general searches)
www.aje.com
Pros and Cons
• PubMed
– All peer-reviewed
– Advanced search capabilities
– Restricted to certain biomedical
journals
• JANE
– Easy interfaces
– Layered over PubMed, so no
extra coverage
• Google Scholar
– Good at finding free versions
– Expansive
– Includes gray literature and junk
• JournalGuide
– Compares data across all fields
– Indicates presence of journal in
major international index
– Relies on third parties, so some
information unavailable
www.aje.com
Pros and Cons
• SciELO
– All open access full text
– Brazilian Portuguese journals
– Limited set of journals
• Web of Science
– Thomson Reuters Impact Factor
– Cited reference searching
– Requires library subscription
www.aje.com
Collect “hits” into journal list
www.aje.com
Advanced search strategies
• Limit your search to recent articles (last 5 years)
– expand to earlier articles only if needed
• Note the name of the publisher to investigate later
– Introduce you to new options
– Avoid questionable publishers
www.aje.com
Dealing with the results
• Make a list of your top journal choices
• Find out more about them!
• Explore journal metrics and online information
www.aje.com
JOURNAL INFORMATION / METRICS
What can you find out about the journals that might be a good fit?
www.aje.com
Information to gather
• Find the journal’s website, and grab key info:
– Publisher/affiliated societies
– Contact information (in case of questions)
– Aims and scope
– Publication frequency
– Look at recent papers from the journal
www.aje.com
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?
www.aje.com
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
www.aje.com
Researchers’ experience in general
• Online resources:
– University/program listservs
– Other academic websites
– Google search!
academia.stackexchange.com
www.reddit.com/r/academia
authoraid.info
www.aje.com
Identifying “predatory” journals
• Take care to avoid journals that are only out to turn a profit
• Questionable publishers are springing up frequently, but they can be
hard to distinguish from legitimate new journals
www.aje.com
Identifying “predatory” journals
• Look for some warning signs:
– A single publisher has launched a huge number of journals at one time,
with little content
– Issues are late or skipped
– The journal claims affiliation with a country or region that is different from
the actual location of the publisher or editor
– There are fundamental errors in the titles or abstracts
– Editorial board is “coming soon”
www.aje.com
Journal metrics and types
• Some established metrics can help you discern the strength of a
specific journal – but take each one with a grain of salt
– Journal Impact Factor (Clarivate Analytics): average measure of
citations/published article
– SNIP (Scopus/Elsevier): citation metric normalized for citation habits in the
journal’s field
– Eigenfactor: measures total impact of articles in a journal (estimating how
frequently the journal is accessed)
– h-index: assesses overall productivity combined with impact
www.aje.com
Journal metrics and types
Issue: All citations are NOT the same! No
metrics currently evaluate whether a citation
was positive and essential, just filler, or negative
(to refute prior errors)
www.aje.com
Beware of “predatory” metrics
• Some questionable journals invent new metrics to make the
journal appear more credible
• Watch for metrics that
– Are not transparent
– Are not used outside of one publisher
– Intentionally piggy back on established metrics (e.g., “Global Impact
Factor”)
www.aje.com
Verify journal indexing
• Don’t take a journal’s word for it. Visit the index website:
- Clarivate Analytics Journal Master List (http://ip-
science.thomsonreuters.com/mjl/)
- SCOPUS journal title list (download at
http://www.elsevier.com/online-tools/scopus/content-overview)
- PubMed/MEDLINE (search at
http://www.ncbi.nlm.nih.gov/nlmcatalog with filter ‘Currently
indexed in MEDLINE’)
www.aje.com
FINAL DECISIONS
The last steps
www.aje.com
Benefits and risks - high impact factor journal
• High impact factor = stronger
“stamp of approval”
• High risk of rejection and lost
time
www.aje.com
Questions to consider - high impact factor journal
• Is it more important to get this research out quickly or to
maximize the prestige of the journal?
• Is this paper from a project that is a primary focus of your
lab’s efforts, or is it a side project that might be nice to
wrap up?
www.aje.com
Benefits and risks - multidisciplinary journal
• Multidisciplinary journal = more
readers, broader impact
• Need to rewrite paper to
appeal
www.aje.com
Questions to consider - multidisciplinary journal
• Is your work relevant to a broad audience, or will its most
interested readers be within your field?
• Can you easily frame your research to a multidisciplinary
audience?
www.aje.com
Benefits and risks - specialized journal
• Specialized journal with fewer
submissions = higher chance of
acceptance
• Risk of “walling off” your
research within your field
www.aje.com
Questions to consider - specialized journal
• Is getting the research accepted quickly an important
consideration?
• Will a specialized journal be visible enough to researchers
in other fields? (Most researchers search at the article
level now anyway.)
www.aje.com
Benefits and risks - open access journal
• Open access journal = greater
exposure and (perhaps) more
citations
• Chance of running into
questionable publishers
www.aje.com
Questions to consider - open access journal
• Is open access an important motivation for you?
• Will you be concerned if only researchers with
subscriptions can see your work?
www.aje.com
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
www.aje.com
Benefits and risks - megajournal
• Increasing number of journals
focusing on rigor of research, not
perceived interested/novelty
• Fast and easy 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”
www.aje.com
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
www.aje.com
For more resources on choosing the
right journal, visit the
AJE Author Resource Center
www.aje.com/br/arc
www.aje.com
Outline
• Tips for Publication Success
• Conventions in Scholarly Writing
• Creating Figures for Scientific Publications
Lunch
• Ethics in Research Publication
• Choosing the Right Journal for your Research
www.aje.com
Scholarly Communication
The best communication starts with the needs of the person you’re
communicating with rather than your own.
• Reader – Tell story of main point rather than chronologically
• Journal Editor – Help editors in their negotiation with reviewers
• Reviewer – Thank volunteer reviewers for improving your work
• Co-Authors – Address difficult ethical questions by explaining facts
• Potential Reader – Use clear figures to spread your main point
www.aje.com
AJE Services
All services are provided by our team with PhDs and advanced degrees
www.aje.com
AJE Editing Certificate
• Informs all journals that the
English language in your
manuscript meets the
required standards
• Each certificate includes a
code and website link for
journal editors to verify it was
edited by AJE
www.aje.com
Questions?
Contact support@aje.com for information about
our services
Universidade de Sᾶo Paulo
Group Code: SIBIUSP10
Flavia Jaszczak
flavia@aje.com
Paul Klenk
paul.klenk@aje.com
www.aje.com
Author Education
• Access to 300+ free resources
• Articles, reports and white
papers
• Educational webinars
• Helpful videos
• Topics range from how to write
a manuscript to choosing a
journal to sharing your research
www.aje.com
English Editing
• English editing by a Native English expert in your field
• Corrects errors in spelling, grammar, and word choice
• Includes an AJE Editing Certificate
Sertraline and rapid eye movement sleep without atonia: an 8-week, open-label study in depressed patients, AJE Sample Standard Editing, https://www.aje.com/services/editing/, 2018
www.aje.com
Manuscript Formatting
• Our formatting experts will modify your
page layout, text formatting, headings, title
page, image placement, and
citations/references to meet the guidelines
of your target journal.
• We will also check the accuracy of your
references and will indicate if you need to
revise the paper so your title, running head,
abstract, main text, and figure legends
comply with the journal’s word count
restriction.
www.aje.com
Figure Formatting
• Service entails generating publication-ready figures from your files
that meet your chosen journal’s specifications
• Changes may include file type, resolution, color space, font, scale,
line weights, and layout (to improve readability and professional
appearance)
www.aje.com
Poster Preparation
AJE’s Poster Preparation service helps authors save time on creating
posters so they can spend more time on their research. The service entails:
• Editing to ensure text is clear and error-free
• Turning figures, tables, and images into high-resolution, journal-quality
panels
• Design of a professional poster to bring all the elements together
• A round of revision
www.aje.com
Poster Examples
Meax, S. The Interaction of UFP1 with the Stem-loop Binding Protein is Critical for Initiation of Histone mRNA Degradation at the end of S-phase, Program in Molecular Biology and Biotechnology, https://www.aje.com/services/posters/, 2018
Andersen, T. and Shepherd, J.M, A Climatological Analysis of Drought and Tornadic Activity and in the Southeastern United States, The University of Georgia, https://www.aje.com/services/posters/, 2018
www.aje.com
Journal Recommendation
• This new service from AJE helps save time in the publication process
• Recommendation of 3 - 5 journals that are well-matched to your article’s
findings
Your individual report will include information for each journal, including:
Your report will also include links to the journal websites, rationale for
including journal in the report, and how well the journal adheres to your
requirements
Impact
Factor
Journal
Scope
Article
Types
Similar
Published
Articles
Journal
Guidelines
Geographic
Focus
www.aje.com
Questions?
Contact support@aje.com for information about
our services
Universidade de Sᾶo Paulo
Group Code: SIBIUSP10
Flavia Jaszczak
flavia@aje.com
Paul Klenk
paul.klenk@aje.com

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Apresentação - Slides do Workshop AJE na USP

  • 1. www.aje.comwww.aje.com The Past, Present, and Future of Scholarly Publishing
  • 2. www.aje.com About American Journal Experts (AJE) • Founded in 2004 • High quality English editing for researchers • Native English editors from top US universities • Match your paper with an editor in our field
  • 3. www.aje.com About American Journal Experts (AJE) • AJE has supported over 500,000 manuscripts across almost 450 research fields
  • 5. www.aje.com The people of AJE • Researchers with publication experience who want to help other researchers.
  • 6. www.aje.com State of the industry • Academic publishing is a $12 billion industry...in flux University Libraries Authors Funding Agencies Mega-Publishers Journals copyrights, fees ($) Imprimatur (seal of approval) access to journals funding ($) copyrights, fees ($) software, services, funding The Big Deal: $ Millions access to journals
  • 7. www.aje.com THE PAST The beginning and evolution of scholarly publishing
  • 8. www.aje.com Key Journal Functions • Validation – The peer review process determines if the science/research is valid. • Dissemination – The journal makes the research available to the community. • Registration/Preservation – The date of publication and location provide a record of who made the discovery and preserve that record. Priem J and Hemminger BM (2012) Decoupling the scholarly journal. Front. Comput. Neurosci. 6:19. doi: 10.3389/fncom.2012.00019
  • 9. www.aje.com Early discoveries • 1610 - Galileo’s discovery of the rings of Saturn – smaismrmilmepoetaleumibunenugttauir as • Altissimum planetam tergeminum observavi – “I have observed the most distant planet to have a triple form.”
  • 10. www.aje.com The history of academic publishing • 1665 - The first journals – Journal des Sçavans (France) – Philosophical Transactions of the Royal Society (UK) • Editorial review only – no peer review • Even then, journals provided – Dissemination by sharing discoveries more widely – Registration through establishing priority (one author)
  • 11. www.aje.com The history of academic publishing • 1731- Peer review – Medical Essays and Observations (Scotland) – Philosophical Transactions of the Royal Society (UK) • Even as late as the early 1900s, true peer review was rare (validation)
  • 12. www.aje.com Academic publishing goes international • 1930s - English moves to the front – After WWII, scientific publishing as we know it began to flourish – Ex: In 1951, 50,675 chemistry papers; In 2001, 606,680 papers • 1947 - One of the first international journals was launched – Biochimica et Biophysica Acta – Fear of “compartmentalizing knowledge” – In 2014, 57 out of 6,166 journals in the JCR are “Multidisciplinary” (<1%)
  • 13. www.aje.com Academic publishing goes online • 1990 - Postmodern Culture – Online only, no print version • 2006 - PLOS ONE – No weight to “novelty” of results – Multidisciplinary – High volume
  • 14. www.aje.com THE PRESENT A snapshot of scholarly publishing today
  • 15. www.aje.com Scholarly publishing by the numbers • The total number of researchers grew by 120% from 2007 - 2013 AJE, The Business of Research, 2018 UNESCO. UNESCO Science Report (2015). http://en.unesco.org/unesco_science_report.
  • 16. www.aje.com STM journals • Global market – About 2,000 journal publishers – Up to 30,000 active, peer-reviewed scholarly journals • Almost 10,000 open access journals • English-language journals – About 680 publishers – About 11,550 journals – Annual revenues of $9 - $10 billion • Growing 7-8% per year Thomson Reuters; Directory of Open Access Journals (www.doaj.org), 2013
  • 17. www.aje.com Publication trends • In 2016, the number of articles published was more than 2 million • In 2017, China published the most number of scientific articles of any country AJE, AJE Scholarly Publishing Report: 2016, 2018 Scientific American, China Declared World’s Largest Producer of Scientific Articles, 2018
  • 18. www.aje.com Research is international • Research is collaborative • In 2016, the top two collaborating countries in biomedical research was China and the US, working together on 19,162 published papers AJE, Collaboration in Science Annual Report: New Data, 2018 Top 8 countries for biomedical research collaboration in 2016
  • 19. www.aje.com Subscription model Author Publisher Library copyright access moneyimprimatur Monopolies
  • 20. www.aje.com Open access - another big shift
  • 21. www.aje.com Open access model Author Publisher Library copyright accessmoney imprimatur Anyone! access access Content → Service
  • 22. www.aje.com Open access is here to stay • Costs shift to the author, but they drive competition among journals • Mandates by governments and funding agencies are incentivizing OA – Horizon 2020 by the EU • More and more researchers are realizing the potential for letting anyone read their results and build off of them AJE, Open Access Mandates: The Changing Landscape of Scholarly Publishing, 2018
  • 23. www.aje.com Current journal functions • Journals provide authors: – Validation – Dissemination – Registration/Preservation • All functions are performed individually by each and every journal Priem J and Hemminger BM (2012) Decoupling the scholarly journal. Front. Comput. Neurosci. 6:19. doi: 10.3389/fncom.2012.00019 Validation Stamping Feedback
  • 24. www.aje.com Peer review in the past 50 years • Most common model: – External reviewers – Freeform responses • Quality of results • Fit for journal – Final decision by journal editor – Reviews returned anonymously • Authors don’t know reviewers • Double blind peer review • New experiments are iterating on these principles
  • 25. www.aje.com Functions of Peer Review • Good science? • Impact and novelty? • Publish in this journal?
  • 26. www.aje.com Problems with Peer Review • Inefficiency and reviewer fatigue • Inconsistency (Smith, 2006): – Reviewer A: I found this paper an extremely muddled paper with a large number of deficits. – Reviewer B: It is written in a clear style and would be understood by any reader. • Personal and manuscript-related bias
  • 27. www.aje.com Peer review statistics • Kravitz and Baker (2011): – Average # of reviews before publication: 6.3 – Average # journals submitted to: 2.1 – 1.5 million articles x 80% receiving reviews x 2.3 reviewers per paper = 2.76 million reviews per year www.rubriq.com Time Spent on Rejected Reviews Annually: 15.6 Million Hours = 1779 Years
  • 29. www.aje.com A shifting industry More research, more publications = new challenges • Reviewer fatigue • Discovery of new content • Unsustainable subscription prices
  • 30. www.aje.com Preprints • Preprints on the rise – arXiv, bioRxiv, ChemRxiv, PeerJ • Researchers using preprints to share their work early – Benefits include exposure for one’s work, collaboration opportunities, and possibly career advancement • Preprints are new and still have unknowns – Concern for getting scooped – Many authors have not heard of preprints Science, Are Preprints the Future of Biology? A Survival Guide for Scientists, 2018
  • 31. www.aje.com New media and channels • Videos to share research • Sharing research on social media will continue to grow – ResearchGate – Twitter Research Square, Research Square Videos, 2018
  • 33. www.aje.com The future • Endless amounts of new knowledge – Tools for discovery – Tools for sharing (social media) – Tools for archiving data • Changes to the publishing process – Preprint sharing – Iterations on peer review including open peer review • Collaborations among researchers – More opportunities to collaborate – Collaborations may offer more funding opportunities
  • 34. www.aje.comwww.aje.com Writing a Better Manuscript Paul Klenk, PhD, MBA Author Education American Journal Experts (AJE)
  • 35. www.aje.com Outline • Tips for Publication Success • Conventions in Scholarly Writing • Creating Figures for Scientific Publications Lunch • Ethics in Research Publication • Choosing the Right Journal for your Research
  • 36. www.aje.com Scholarly Communication Communication is hard. “The single biggest problem in communication is the illusion that it has taken place.” – George Bernard Shaw Point of view is important. “If there is any one secret of success, it lies in the ability to get the other person's point of view and see things from that person's angle as well as from your own.” – Henry Ford
  • 37. www.aje.com The goal: publish quickly • Publication – still the primary goal of researchers in an academic setting Investigate Present Review Publish Read Teach Mentor
  • 38. www.aje.com The goal: publish quickly • Every time you get rejected, it can cost you months of time or more – Average time from submission to acceptance: 188 days – Average time from acceptance to publication: 175 days • Find a journal that fits your work closely. Take your best shot first AJE, State of Authorship Report: Time and Costs Involved in Publishing Research, 2016, 2018
  • 40. www.aje.com Manuscript sections 1. Introduction 2. Materials and Methods 3. Results 4. Discussion and Conclusions 5. Title and Abstract 6. References Journal Cover letters Responding to reviewers
  • 41. www.aje.com Introduction • Assume no one has read your abstract • Define all acronyms • References – < 5 years old – Primary literature – Balanced General Specific
  • 42. www.aje.com Introduction • Explain the problems your research addresses in the context of recent advances in the area • Define the study objective, and briefly describe the experimental design
  • 43. www.aje.com Materials and Methods • Common cause of rejection - lack of detail* • Important questions – Have I explained my methods sufficiently so they can be reproduced? – 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? *See Provenzale, 2007
  • 44. www.aje.com Materials and Methods • Watch for journal requirements – Animal studies (ARRIVE guidelines, IACUC approval) – Human subjects (CONSORT guidelines, IRB approval) – Source of reagents • Do the results of the methods I chose answer my hypothesis?
  • 45. www.aje.com Should the Results and Discussion be combined? • 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 objectives • Follow the most logical order (not necessarily chronological) – Be especially careful of gaps
  • 46. www.aje.com Discussion and Conclusions • Put the most salient results in the first paragraph Serial position effect (www.wikipedia.org)
  • 47. www.aje.com Discussion and Conclusions • 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
  • 48. www.aje.com 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
  • 49. www.aje.com Title • Capture reviewers and readers – Answer question, “What does this research contribute to the field?” • Reviewers will expect paper’s content to match the title – Keep it short – Consider how readers will search for your paper • If no one can find it, no one will cite it Paiva, et al., 2012
  • 50. www.aje.com Title • Include: – Key terms: Species names, geographical regions, method used – The most common name used for genes, methods, etc. – A descriptive answer • Avoid: – Abbreviations – Filler terms: “Effect of,” “Comparison of,” “A study of,” or “Observations on” – “Novel” / “First time” – A question
  • 51. www.aje.com Abstract • Your abstract may be all someone can read easily – Convince readers to read the entire paper • Determine what the journal requires – Unstructured abstract – Structured abstract (headings) – Plain-language summary
  • 52. www.aje.com Abstract • Watch the word count – Use strong verbs (analyze vs. perform an analysis) – Avoid filler phrases (“It is currently known that…” “We found that…” • Make sure that each piece of information is critical to the reader and relates to your main conclusions
  • 53. www.aje.com Abstract • Include: – Importance of the research – Critical background – Clear hypothesis – Methods summary – Key results – Succinct conclusion • Avoid: – Excessive abbreviations – Citations – References to text/figures – Statistics – Bringing up topics that your research doesn’t address
  • 54. www.aje.com References • Important questions: – Do I cite all the studies that I need to? – Are all citations relevant to my study? – Are all citations as recent as possible? • Reference formats change according to journal – Keep the complete citation; “et al.” is not always acceptable
  • 55. www.aje.com Journal Cover Letter • Opportunity to make your case to the Journal Editor • Suggest reviewers – at least two regions in the world • “all authors have reviewed this paper and have approved it for publication” • This work has not been submitted to other journals even in another language
  • 56. www.aje.com Responding to Reviewers • Take a deep breath! • Professional and respectful – “esteemed colleague” • Thank the reviewers for their helpful comments • Respond to every comment • Challenge based on the science where appropriate • Help the editor communicate with the reviewer You Journal Editor Peer Reviewer
  • 58. www.aje.com “Attention to detail of the language will avoid severe misunderstandings which might lead to rejection of the paper.” -- Cell & Molecular Biology Letters instructions for authors
  • 59. www.aje.com Key topics • Verb tense • Formal tone • Journal specific conventions
  • 60. www.aje.com Verb tense • Present – Action is occurring now – Action started in the past but continues now • Past – Action already occurred • Future – Action will occur later
  • 61. www.aje.com Verb tense • Perfect – Action is defined relative to another action – Uses helping verb ‘have’ (have/has/had) • He has worked here for seven years. • She had eaten all the cake when her friend arrived. • Progressive – Emphasizes the continuance of an action – Formed using helping verb ‘be’ (is/are/was/were) and the present participle of a verb (-ing) • I don’t know why she is running in the rain. • He was writing his thesis when the computer broke.
  • 62. www.aje.com How to choose verb tense • Widely accepted fact: present – DNA is composed of four nucleotides. – Trypanosomes exhibit global trans-splicing of RNA. • Ideas no longer accepted: past – Bacteria were believed to lack introns. – Physicists once thought electrons traveled in defined orbits. • Describing a figure, result, or paper: present – The results indicate… – Their landmark paper describes… – Figure 1 shows…
  • 63. www.aje.com How to choose verb tense • Past tense – We tested independently derived cultures. – Cells were transfected, irradiated, and assayed. – The dehydration process comprised five steps. • Present tense – Use for characteristics that are relevant facts • The Mississippi River Delta occupies almost 12,000 km2 in the state of Louisiana. – Use when referring to aspects of the paper itself • In this study, we report a new frog species.
  • 64. www.aje.com Verb tense for previous studies • Results that are still relevant: present perfect – Johnson et al. have shown that gene X is in an operon. – Unusual glycosylation events have been observed in these cells. • Methods: past – Smith and Anderson sampled 96 swamps. • Specific historical events: past – Gene X was first cloned into a vector in 1996.
  • 65. www.aje.com Verb tense combinations for previous studies • Past perfect and past: one occurred earlier than another – Cells that had been irradiated were assayed for DNA damage. – Patients who had elected surgery completed surveys. • Past progressive and past: one occurred while the other was ongoing – While the cells were incubating, the temperature was raised 1 degree per hour. – While patients were preparing for surgery, nurses collected baseline parameters.
  • 66. www.aje.com Formal Tone • Word choice • Pronoun usage
  • 67. www.aje.com Formal tone - word choice • 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
  • 68. www.aje.com – Addresses – Approximately – Large – Currently – Performed/conducted – Such as – Observed Formal synonym Informal term – Deals with – About/around – Big – Nowadays – Done – Like – Seen/saw Formal tone - word choice
  • 69. www.aje.com Formal tone - word choice • 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… OR – One unique function of this protein is…
  • 70. www.aje.com Formal tone - word choice • 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
  • 71. www.aje.com Formal tone - word choice • Human emotions or behaviors projected onto other animals or to inanimate objects – It is unclear why cows in the US only eat when facing north. – NOT: It is unclear why cows in the US choose to face north when they eat. – Bacteria in rich soil frequently secrete compounds that kill neighboring bacteria. – NOT: Bacteria in rich soil regularly attack each other.
  • 72. www.aje.com Formal tone - pronouns • Avoid ambiguity with demonstrative pronouns – This, that, these, those – This analyzes the effects… – This research analyzes the effects… – 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+.
  • 73. www.aje.com “Please be attentive to the requirements of APA style, as indicated on submission guidelines. Failure to do so can erode the impression your manuscript makes on reviewers.” -- Innovative Higher Education instructions for authors
  • 74. www.aje.com Journal-specific conventions - voice • Active = subject is performing action • Passive = subject is being acted on – We inspected the burners regularly (active) – The burners were inspected regularly (passive) – Others have explained these differences… (active) – These differences have been explained… (passive) – I removed the coating with alcohol (active) – The coating was removed with alcohol (passive)
  • 75. www.aje.com Journal-specific conventions - voice • Active voice – Shorter – Identifies agent • Passive voice – Once considered more objective – Useful if the agent is unknown
  • 76. www.aje.com Journal-specific conventions - person • First person = subject/object is speaking – I prefer to eat the vegetables from my garden. – We will decide what is best for the company. • Second person = subject/object is being spoken to – You prefer to eat vegetables from the nearby market. – You are doing a great job! – Children, please wash your hands before dinner.
  • 77. www.aje.com Journal-specific conventions - person • Third person = subject/object is being spoken about – He prefers to eat as few vegetables as possible – Doctors renew their licenses periodically. – I am standing where she stood yesterday. • Which is best? – First person is increasingly common and helps keep writing more concise – Defer to journal guidelines
  • 78. www.aje.com Journal-specific conventions - formatting • Serial comma – “A, B, and C” vs. “A, B and C” • Spacing – Between sentences – “p = 0.05” vs. “p=0.05” • Abbreviations – (sec vs. s; m/s vs. m·s-1) – Spell out when defining – Use abbreviation consistently
  • 79. www.aje.com Journal-specific conventions - formatting • Words vs. numerals – “A total of ten species” vs. “A total of 10 species” • Number style – 1,000 vs. 1000 vs. 1 000 – 0.05 vs. .05 – 17.3 vs. 17,3 (rare in English-language publications) • Manuscript elements – Figure 1 vs. Fig. 1 – Figure 1 vs. figure 1 – Capitalization/parallelism in section headings
  • 80. www.aje.com Journal-specific conventions – split infinitives • Ban against splitting infinitives – To confirm empirically these data – NOT: To empirically confirm these data
  • 81. www.aje.com It’s Not All Bad… [A]uthors can submit manuscripts formatted in a variety of reference styles, including Harvard, Vancouver, and Chicago.
  • 83. www.aje.com Figure quality is a paper’s “Suit and Tie” • Before a journal reviewer or colleague even begins reading your paper, they have formed an opinion about the quality of your work. • Your figures reflect your overall effort in experimental design, technical execution, and attention to detail. • “A picture is worth a thousand words”
  • 85. www.aje.com Types of figures 1. Primary Data 2. Secondary Data 3. Illustrative Diagrams
  • 86. www.aje.com Primary Data Figures: Where to start • High-quality figures start in the lab • Think in figures – Controls – Use your muse, use your nemesis Every day, every experiment
  • 87. www.aje.com Primary Data Figures: Save your work • Protect the original files • Toggle the “Read-only” option on the data files
  • 88. www.aje.com Pixel-based files • Two sub-types of Pixel-based files – Lossy – Lossless Dr. Jan Michels, Nikon Small World Competition
  • 89. www.aje.com Lossy file formats • Example: JPG • Highly simplified explanation: – The image is divided into tiles – The number of colors in each tile is simplified – How simplified depends on the “Quality” setting chosen – These protocols are re-applied every time the file is saved
  • 90. www.aje.com OriginalQuality 4(/12) Lossy file formats (compression) • Compression leads to a greatly reduced file size • Fine for everyday use, not for primary data • Once a compression is applied, it cannot be reversed Quality 2 (/12)Quality 0 (/12)
  • 91. www.aje.com Lossless files • Example: Tiff • Color of each pixel is recorded. • The color of each pixel will not change simply by saving. • The price of fidelity: file size. Dr. Gregory Rouse, Nikon Small World Competition Jpeg: 15.2 KB Tiff: 790 KB
  • 92. www.aje.com Lossless versus Lossy files Lossy file compression is even worse for line drawings and graphs.
  • 93. www.aje.com LZW lossless file compression • Efficient storage, not information loss • Highly simplified explanation: – Replaces a pixel color with a short code throughout the whole image file Image Pure White, Pure White, Pure Black, Medium Blue Pure White, Pure White, Pure Black, Pure Black Pure White, Pure White, Pure White, Pure White Pure White, Pure White, Pure White, Pure White Without LZW Compression 1, 1, 2, 3 1, 1, 2, 2 1, 1, 1, 1 1, 1, 1, 1 With LZW Compression
  • 94. www.aje.com LZW lossless file compression • Effective on images with a large number of colors – 82 mm wide, 300 dpi (typical journal requirements) – Uncompressed Tiff: 2,710 KB – LZW Compressed Tiff: 1,550 KB Cameron Johnson, Nikon Small World Competition
  • 95. www.aje.com LZW lossless file compression • Very powerful on images with a limited number of colors – 82 mm wide, 1200 dpi (typical journal requirements) – Uncompressed Tiff: 25,200 KB (25.2 MB) – LZW Compressed Tiff: 256 KB – Jpeg (with a high quality setting): 586 KB
  • 96. www.aje.com Saving figures - types of formats • Pixel-based – Industry standard: Tiff – Uneditable with a set resolution – General guidelines: • Photos: 300 dpi • Photos with lettering or line-art: 600 dpi • Line-art (graphs or diagrams): 1200 dpi • Vector-based – Industry standard: Eps (& pdf) – Editable with “infinite resolution”
  • 97. www.aje.com Saving figures from programs • Microsoft Office (PowerPoint) – Download extra add-ins from Microsoft – Common method: • Save as pdf • Convert pdf to proper file in Adobe Acrobat or Photoshop • Adobe Illustrator – Save As (vector) or Export (pixel) – Open the Ai file in Photoshop
  • 98. www.aje.com Moving graphs between programs • Graphs are vector objects • Copy and Paste often works • Save (or Export) as a vector file – Postscript file (Eps) – Pdf file • Pixel-based file = a picture of a graph
  • 99. www.aje.com Figure creation rule #1 • Work at actual publication size – Journal guidelines – Print and measure – General guidelines • Single column: 85 mm • 1.5 columns: 135 mm • Double column: 175 mm • Keep a sense of scale
  • 100. www.aje.com Figure creation rule #2 • Use the correct size and type of font – Journal guidelines – General guidelines • 8 point Arial (with symbol) • Avoid bolding and italics
  • 101. www.aje.com Crafting effective graphs • Consider the purpose of your graph http://chemlab.truman.edu/DataAnalysis/PreparingGraphs _files/PreparingGraphs.asp
  • 102. www.aje.com Crafting effective graphs • Visualization aid or research tool?
  • 105. www.aje.com Crafting effective graphs Don’t Hesitate to Try Something “New”
  • 107. www.aje.com How to use color effectively
  • 108. www.aje.com Illustrative diagrams • Use diagrams to reduce reviewer (and general reader) confusion (Cejka & Plank et al., 2004)
  • 109. www.aje.com Illustrative diagrams • Marketing for scientists (Could be You et al., 2014)
  • 110. www.aje.com Outline • Tips for Publication Success • Conventions in Scholarly Writing • Creating Figures for Scientific Publications Lunch • Ethics in Research Publication • Choosing the Right Journal for your Research
  • 111. www.aje.com Questions? Contact support@aje.com for information about our services Universidade de Sᾶo Paulo Group Code: SIBIUSP10 Flavia Jaszczak flavia@aje.com Paul Klenk paul.klenk@aje.com
  • 114. www.aje.com Key Topics 1. Plagiarism and self-plagiarism 2. Authorship and ghost authorship 3. Ethics in author services
  • 115. www.aje.com What is plagiarism? • The misrepresentation of someone else’s original thought as your own • The U.S. Office of Research Integrity defines plagiarism as “the appropriation of another person’s ideas, processes, results, or words without giving appropriate credit”
  • 116. www.aje.com Types of plagiarism • Verbatim plagiarism • Plagiarism of ideas • Loose paraphrasing • Plagiarizing alternative sources • Self-plagiarism
  • 117. www.aje.com Verbatim plagiarism • Copying text word-for-word from someone else’s work – Original text: Salmonella typhimurium and Clostridium perfringens bacteria were present in over 75% of the chickens processed. – Verbatim plagiarism: Salmonella typhimurium and Clostridium perfringens bacteria were present in over 75% of the chickens processed. – Proper citation of a direct quotation: Other researchers found that “Salmonella typhimurium and Clostridium perfringens bacteria were present in over 75% of the chickens processed” (Wu et al. 2015). • If content from several sources is duplicated, this form of plagiarism is known as mosaic or patchwork
  • 118. www.aje.com Plagiarism of ideas • Mentioning someone else’s unique idea, whether in the form of a theory, an interpretation, data, a method, an opinion, or new terminology, without citing your source, even if explained in your own words – Original text: Salmonella typhimurium and Clostridium perfringens bacteria were present in over 75% of the chickens processed. – Plagiarized idea: Other researchers found that Salmonella typhimurium and Clostridium perfringens bacteria occurred in the majority of the processed chickens. – Proper citation of a paraphrase: Other researchers found that Salmonella typhimurium and Clostridium perfringens bacteria occurred in the majority of the processed chickens (Wu et al 2015).
  • 119. www.aje.com Loose paraphrasing • Paraphrasing someone else’s work with only slight changes, effectively maintaining the other author’s logic while mentioning most or all of the same ideas. Please note that the flow of an argument is indeed an original idea – Original text: Cross-contamination experiments showed that Clostridium perfringens and Salmonella spp. were easily transferred from raw chicken products to consumers. – Loose paraphrase: Clostridium perfringens and Salmonella spp. transferred easily from raw chicken products to consumers because of handling practices. Cross-contamination experiments demonstrated that these practices were the cause of the contamination. (2 sentences)
  • 120. www.aje.com Plagiarizing alternative sources • Failing to cite the source of publicly available knowledge that is not in the scholarly literature • As with journal articles, sources such as books, webpages, and blogs should be referenced if they contributed unique information to your manuscript • Personal communications and lectures (including descriptions of unpublished ideas, with permission) should also be referenced
  • 121. www.aje.com Self-plagiarism • Any attempt to take any of your own previously published text, papers, or research results and make it appear brand new • When your manuscript contains uncited recycled information, you are countering the unspoken assumption that you are presenting entirely new discoveries • It is best practice to cite your previous work thoroughly, even if you are simply revisiting an old idea or a previously published observation
  • 122. www.aje.com Self-plagiarism and publishing • Although self-plagiarism is not theft of ideas, it can create issues in the scholarly publishing world – After publication, the journal generally owns the copyright – While you own the ideas, reuse of the text without citation would require the permission of the journal • Submitting the same article to two journal is duplicate plagiarism
  • 123. www.aje.com “1 in 3 Scholarly Journals has access to iThenticate to check for plagiarism before publication” Check articles “against 49,000,000 Scholarly articles, books, and conferences proceedings” from scientific, technical, and medical journals www.ithenticate.com
  • 124. www.aje.com Authorship • “Clearly conveying who is responsible for published work is integral to scientific integrity” (Panter). • The top four International Committee of Medical Journal Editors (ICMJE) guidelines: 1. Significant involvement in study conception/design, data collection, or data analysis/interpretation 2. Involvement in drafting or revising a manuscript 3. Approval of the final version of a manuscript for publication 4. Responsibility for the accuracy and integrity of all aspects of research
  • 125. www.aje.com Authorship responsibility, order, and guidelines • Some journals require a public guarantor for each article, or an author who takes responsibility for the entire research project • Author names may be listed: – Alphabetically – By magnitude of contribution • Professional guidelines – Coalition for Responsible Publication Resources (CRPR) – World Association of Medical Editors (WAME)
  • 126. www.aje.com Honorary authorship • Gift – The study is gifted to someone who did not contribute – Better to reference the person in the acknowledgment section • Guest – Often added to the list to use the credibility of another researcher’s name, even if they did not contribute to the study • Coercive – When someone in authority over the author requests that another person be added as an author, even though they did not contribute to the study
  • 127. www.aje.com Problems with honorary authorship • Elevating the study beyond its potential impact – Using someone else’s good name to elevate the work • Attributing without permission
  • 128. www.aje.com Ghost authorship • The opposite of honorary authorship, entailing a significant contribution to a manuscript without acknowledgment of that contribution • Includes any content contributed to the study that is not acknowledged (drafting, data collection and analysis, etc.) • “Such ghost authorship was present in approximately one-tenth of papers published in six medical journals in 2008” (Wislar et al. 2011). • It is not having somebody edit your language or formatting
  • 129. www.aje.com Problems with ghost authorship • Masking industry ties to a paper – Ex: Author does the work but gets no credit • Hiring a writer to overcome poor language skills, lack of expertise, or time constraints – Using someone else’s good name to elevate the work • Acquiring data, performing analysis, etc. may be hired out to a ghost researcher
  • 130. www.aje.com Avoiding ghost authorship • Authors should sign a formal declaration about their contributions • Authors should publish a comprehensive list of contributions and a detailed acknowledgments section
  • 131. www.aje.com Ethics in author services • Author services companies are increasing – What help is appropriate? – How can unethical behavior be identified? • Language editing should entail clarifying language without adding or subtracting information • Formatting a manuscript should consist of changing layout elements and references to conform to a journal’s specifications but not adding or subtracting content
  • 132. www.aje.com Ethics in author services • Appropriate author services will: – Will have clear ethical limits on what they will and will not provide – Will deny a client’s request that crosses an ethical boundary – Will not help a client plagiarize or commit other ethical violations – Will not help fabricate or manipulate figures – Will improve a manuscript’s form without changing the manuscript’s content – May be accredited by an outside agency or be a member of a society such as the Committee on Publication Ethics (COPE)
  • 133. www.aje.com References - sources from AJE • Plagiarism • Self plagiarism • Authorship • Ghost authorship • Ethics
  • 134. www.aje.com References - other sources • “Ghost Writing Initiated by Commercial Companies” World Association of Medical Editors. June 20, 2005. http://www.wame.org/about/policy- statements#Ghost%20Writing (accessed October 23, 2017). • Wislar, Joseph S., et al. “Honorary and ghost authorship in high impact biomedical journals: a cross sectional survey.” BMJ (October 2011) 343. https://doi.org/10.1136/bmj.d6128 (accessed October 23, 2017).
  • 135. www.aje.comwww.aje.com Choosing the Right Journal for Your Research
  • 136. www.aje.com The goal: publish quickly • Every time you get rejected, it can cost you months of time or more – Average time from submission to acceptance: 188 days – Average time from acceptance to publication: 175 days • Find a journal that fits your work closely. Take your best shot first AJE, State of Authorship Report: Time and Costs Involved in Publishing Research, 2018.
  • 137. www.aje.com Outline • Search tips • Journal information/metrics • Final decisions
  • 138. www.aje.com SEARCH TIPS Create and curate your own list of target journals
  • 139. www.aje.com Search tips and basic strategy • Start a list of journals publishing articles that inform your work • Find articles similar to the one you want to publish • Collect a list of journals that publish those articles • Research those journals • Make a prioritized list of targets
  • 141. www.aje.com Search! • Use your draft title and abstract (finding a journal) • Use keywords (more general searches)
  • 142. www.aje.com Pros and Cons • PubMed – All peer-reviewed – Advanced search capabilities – Restricted to certain biomedical journals • JANE – Easy interfaces – Layered over PubMed, so no extra coverage • Google Scholar – Good at finding free versions – Expansive – Includes gray literature and junk • JournalGuide – Compares data across all fields – Indicates presence of journal in major international index – Relies on third parties, so some information unavailable
  • 143. www.aje.com Pros and Cons • SciELO – All open access full text – Brazilian Portuguese journals – Limited set of journals • Web of Science – Thomson Reuters Impact Factor – Cited reference searching – Requires library subscription
  • 145. www.aje.com Advanced search strategies • Limit your search to recent articles (last 5 years) – expand to earlier articles only if needed • Note the name of the publisher to investigate later – Introduce you to new options – Avoid questionable publishers
  • 146. www.aje.com Dealing with the results • Make a list of your top journal choices • Find out more about them! • Explore journal metrics and online information
  • 147. www.aje.com JOURNAL INFORMATION / METRICS What can you find out about the journals that might be a good fit?
  • 148. www.aje.com Information to gather • Find the journal’s website, and grab key info: – Publisher/affiliated societies – Contact information (in case of questions) – Aims and scope – Publication frequency – Look at recent papers from the journal
  • 149. www.aje.com 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?
  • 150. www.aje.com 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
  • 151. www.aje.com Researchers’ experience in general • Online resources: – University/program listservs – Other academic websites – Google search! academia.stackexchange.com www.reddit.com/r/academia authoraid.info
  • 152. www.aje.com Identifying “predatory” journals • Take care to avoid journals that are only out to turn a profit • Questionable publishers are springing up frequently, but they can be hard to distinguish from legitimate new journals
  • 153. www.aje.com Identifying “predatory” journals • Look for some warning signs: – A single publisher has launched a huge number of journals at one time, with little content – Issues are late or skipped – The journal claims affiliation with a country or region that is different from the actual location of the publisher or editor – There are fundamental errors in the titles or abstracts – Editorial board is “coming soon”
  • 154. www.aje.com Journal metrics and types • Some established metrics can help you discern the strength of a specific journal – but take each one with a grain of salt – Journal Impact Factor (Clarivate Analytics): average measure of citations/published article – SNIP (Scopus/Elsevier): citation metric normalized for citation habits in the journal’s field – Eigenfactor: measures total impact of articles in a journal (estimating how frequently the journal is accessed) – h-index: assesses overall productivity combined with impact
  • 155. www.aje.com Journal metrics and types Issue: All citations are NOT the same! No metrics currently evaluate whether a citation was positive and essential, just filler, or negative (to refute prior errors)
  • 156. www.aje.com Beware of “predatory” metrics • Some questionable journals invent new metrics to make the journal appear more credible • Watch for metrics that – Are not transparent – Are not used outside of one publisher – Intentionally piggy back on established metrics (e.g., “Global Impact Factor”)
  • 157. www.aje.com Verify journal indexing • Don’t take a journal’s word for it. Visit the index website: - Clarivate Analytics Journal Master List (http://ip- science.thomsonreuters.com/mjl/) - SCOPUS journal title list (download at http://www.elsevier.com/online-tools/scopus/content-overview) - PubMed/MEDLINE (search at http://www.ncbi.nlm.nih.gov/nlmcatalog with filter ‘Currently indexed in MEDLINE’)
  • 159. www.aje.com Benefits and risks - high impact factor journal • High impact factor = stronger “stamp of approval” • High risk of rejection and lost time
  • 160. www.aje.com Questions to consider - high impact factor journal • Is it more important to get this research out quickly or to maximize the prestige of the journal? • Is this paper from a project that is a primary focus of your lab’s efforts, or is it a side project that might be nice to wrap up?
  • 161. www.aje.com Benefits and risks - multidisciplinary journal • Multidisciplinary journal = more readers, broader impact • Need to rewrite paper to appeal
  • 162. www.aje.com Questions to consider - multidisciplinary journal • Is your work relevant to a broad audience, or will its most interested readers be within your field? • Can you easily frame your research to a multidisciplinary audience?
  • 163. www.aje.com Benefits and risks - specialized journal • Specialized journal with fewer submissions = higher chance of acceptance • Risk of “walling off” your research within your field
  • 164. www.aje.com Questions to consider - specialized journal • Is getting the research accepted quickly an important consideration? • Will a specialized journal be visible enough to researchers in other fields? (Most researchers search at the article level now anyway.)
  • 165. www.aje.com Benefits and risks - open access journal • Open access journal = greater exposure and (perhaps) more citations • Chance of running into questionable publishers
  • 166. www.aje.com Questions to consider - open access journal • Is open access an important motivation for you? • Will you be concerned if only researchers with subscriptions can see your work?
  • 167. www.aje.com 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
  • 168. www.aje.com Benefits and risks - megajournal • Increasing number of journals focusing on rigor of research, not perceived interested/novelty • Fast and easy 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”
  • 169. www.aje.com 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
  • 170. www.aje.com For more resources on choosing the right journal, visit the AJE Author Resource Center www.aje.com/br/arc
  • 171. www.aje.com Outline • Tips for Publication Success • Conventions in Scholarly Writing • Creating Figures for Scientific Publications Lunch • Ethics in Research Publication • Choosing the Right Journal for your Research
  • 172. www.aje.com Scholarly Communication The best communication starts with the needs of the person you’re communicating with rather than your own. • Reader – Tell story of main point rather than chronologically • Journal Editor – Help editors in their negotiation with reviewers • Reviewer – Thank volunteer reviewers for improving your work • Co-Authors – Address difficult ethical questions by explaining facts • Potential Reader – Use clear figures to spread your main point
  • 173. www.aje.com AJE Services All services are provided by our team with PhDs and advanced degrees
  • 174. www.aje.com AJE Editing Certificate • Informs all journals that the English language in your manuscript meets the required standards • Each certificate includes a code and website link for journal editors to verify it was edited by AJE
  • 175. www.aje.com Questions? Contact support@aje.com for information about our services Universidade de Sᾶo Paulo Group Code: SIBIUSP10 Flavia Jaszczak flavia@aje.com Paul Klenk paul.klenk@aje.com
  • 176. www.aje.com Author Education • Access to 300+ free resources • Articles, reports and white papers • Educational webinars • Helpful videos • Topics range from how to write a manuscript to choosing a journal to sharing your research
  • 177. www.aje.com English Editing • English editing by a Native English expert in your field • Corrects errors in spelling, grammar, and word choice • Includes an AJE Editing Certificate Sertraline and rapid eye movement sleep without atonia: an 8-week, open-label study in depressed patients, AJE Sample Standard Editing, https://www.aje.com/services/editing/, 2018
  • 178. www.aje.com Manuscript Formatting • Our formatting experts will modify your page layout, text formatting, headings, title page, image placement, and citations/references to meet the guidelines of your target journal. • We will also check the accuracy of your references and will indicate if you need to revise the paper so your title, running head, abstract, main text, and figure legends comply with the journal’s word count restriction.
  • 179. www.aje.com Figure Formatting • Service entails generating publication-ready figures from your files that meet your chosen journal’s specifications • Changes may include file type, resolution, color space, font, scale, line weights, and layout (to improve readability and professional appearance)
  • 180. www.aje.com Poster Preparation AJE’s Poster Preparation service helps authors save time on creating posters so they can spend more time on their research. The service entails: • Editing to ensure text is clear and error-free • Turning figures, tables, and images into high-resolution, journal-quality panels • Design of a professional poster to bring all the elements together • A round of revision
  • 181. www.aje.com Poster Examples Meax, S. The Interaction of UFP1 with the Stem-loop Binding Protein is Critical for Initiation of Histone mRNA Degradation at the end of S-phase, Program in Molecular Biology and Biotechnology, https://www.aje.com/services/posters/, 2018 Andersen, T. and Shepherd, J.M, A Climatological Analysis of Drought and Tornadic Activity and in the Southeastern United States, The University of Georgia, https://www.aje.com/services/posters/, 2018
  • 182. www.aje.com Journal Recommendation • This new service from AJE helps save time in the publication process • Recommendation of 3 - 5 journals that are well-matched to your article’s findings Your individual report will include information for each journal, including: Your report will also include links to the journal websites, rationale for including journal in the report, and how well the journal adheres to your requirements Impact Factor Journal Scope Article Types Similar Published Articles Journal Guidelines Geographic Focus
  • 183. www.aje.com Questions? Contact support@aje.com for information about our services Universidade de Sᾶo Paulo Group Code: SIBIUSP10 Flavia Jaszczak flavia@aje.com Paul Klenk paul.klenk@aje.com