Workshop de Publicação Científica – AJE-USP – 10 de Maio de 2018
O objetivo do Workshop foi apresentar aos participantes informações que tornem o processo de produção do artigo científico, assim como a submissão do mesmo, mais rápido, eficiente e eficaz.
== PROGRAMAÇÃO ==
9h00 – 9h30 | RECEPÇÃO
Registro dos participantes
9h30 – 9h40 | ABERTURA
Dra. Maria Crestana – Chefe Técnica do SIBiUSP (a confirmar)
Paul Klenk – Principal Financial Analyst Research Square / AJE
9h40 – 10h00 | AJE 2018 Scholarly Publishing Landscape
Esta sessão foi uma introdução às demais sessões do workshop. Inicia com um Panorama de Publicações Científicas, passado, presente e futuro. Destaca a comunicação científica e como o Inglês se transformou no idioma da pesquisa.
10h00 – 12h00 | Writing a Better Manuscript
a) Tips for Publication Success
b) Scientific Figures
c) Conventions of Scholarly Publishing
d) AJE Author Resource Center
Nesta sessão foram dadas dicas sobre estrutura, redação, edição e formatação de elementos do artigo científico, com destaque para a introdução, materiais e métodos, bem como a apresentação de resultados por meio de figuras e tabelas. O Centro de Recursos para Autores da AJE também provê diversas informações para os autores.
12h00 – 13h30 | ALMOÇO
13h30 – 14h00 | Ethics in Research Publication
Nesta sessão foram apresentadas orientações sobre a importância do respeito aos princípios éticos e os cuidados que os autores devem ter para evitar casos de retratação e má conduta científica..
14h00 – 15h00 | Choosing the Best Journal to your Research
a) How to avoid predatory journals
b) Journal scope and impact factor
c) How well your paper adheres to the journal guidelines
Esta sessão foi dedicada à apresentação de critérios para a escolha da melhor revista para publicar seu artigo e dicas para evitar revistas predatórias.
15h00 – 15h30 | Encerramento, perguntas e observações finais
[As apresentações serão em inglês e não haverá tradução simultânea]
Palestrante: Paul Klenk – Square Research – AJE
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
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
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
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
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
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
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
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
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
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.
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”
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
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
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
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
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)
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).
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.
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
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
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
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
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
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