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Scholarly journals: present and future

Scholarly journals: present and future

Lecture to the students-reviewers of the Aresty Rutgers Undergraduate Research Journal, November 2022.

Matteo Cavalleri

November 21, 2022
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  1. ENABLING DISCOVERY | POWERING EDUCATION | SHAPING WORKFORCES
    Scholarly
    journals:
    present and
    future
    Emma Van Burns, PhD
    Matteo Cavalleri, PhD
    Patricia Johnson, PhD

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  2. 2
    What is the purpose of a scholarly journal?
    Dissemination
    Spreading the word
    through publishing
    platforms
    But also indexing and
    generally organizing
    knowledge
    Registration
    Precedence of
    discovery can be
    established based on a
    paper’s submission
    date to a journal
    Archival
    Safeguarding and
    preserving knowledge
    Publishers play an
    important role
    preserving the scientific
    record
    Certification
    Peer-review is still
    the gold standard for
    certifying articles
    This is not the same
    as quality-control!

    Peer-review management, Curation, Infrastructure, Ethics, & much, much more. Here’s a list of 96 things publishers do: https://bit.ly/2UW3rKX

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  3. 3
    < 1600s
    Scientists share their results by writing letters (and sometimes books) and
    mailing them to each other
    mid-1600s Small groups begin to meet in person, becoming the first scholarly societies
    1665
    The first scientific journal, Philosophical Transactions of the Royal Society, publishes
    its first issue
    1730s
    The Royal Society of Edinburgh begins publishing Medical Essays and Observations,
    probably the first fully peer-reviewed journal
    1800s
    Modern publishing companies Wiley (1807), Springer Nature, Taylor & Francis,
    and Elsevier are founded
    mid-1900s
    Peer review by external reviewers becomes a standard component of the
    publication process
    1975 Journal Impact Factors are first released
    The origins of scholarly publishing

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  4. 4
    1987 The first open access journal, Flora Online, begins publishing on the internet
    1990 Postmodern Culture becomes the first online journal to publish with no printed version
    1991 arXiv, the first online preprint database, is launched
    2008
    Predatory journals are identified in the first edition of Beall’s List of Predatory Journals
    and Publishers
    2012
    ORCID (Open Researcher and Contributor ID) issued its first alphanumeric codes to
    uniquely identify researchers
    2018
    A consortium of European funding agencies launches the Plan S initiative requiring
    research funded by them to be published in open access journals
    2019 Wiley and German institutions sign the first Projekt DEAL transformative agreement
    Recent developments in scholarly publishing

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  5. 5
    Author(s)
    The peer review process
    Write
    manuscript
    (Prescreening)
    Initial
    assessment
    Peer review
    time
    First
    decision
    Revise manuscript +
    respond to reviewers
    Reject
    (Final)
    Decision
    Reject
    Initial
    submission
    Editor
    assignment
    Reviewers
    invited Feedback
    submitted Reviewers
    invited
    Revised
    manuscript
    submission
    Revision
    request
    Copy editing,
    typesetting, etc.
    Accept
    Review +
    edit proofs
    Proofs sent
    Proofs approved
    (payment sent)
    Online and/or
    print publication
    Journal staff
    Journal editor
    Reviewers

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  6. 6
    What are the differences between editors and reviewers?
    Reviewers
    Editors
    −Are formally affiliated with the journal
    −Have general expertise covering the
    overall scope of the journal
    −Make final decisions on whether to
    publish submitted manuscripts
    −Represent the journal to the scientific
    community and to the public
    −Have no formal affiliation with the
    journal
    −Have specific expertise on the exact
    topic of the manuscript
    −Provide specific feedback on submitted
    manuscripts, including suggestions for
    improvement, and recommendations
    on whether to publish them

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  7. 7
    Who are the editors?
    External / academic
    Internal / “in-house”
    − Employed full-time by the publisher
    − Have a background in the field
    − More general expertise
    − Employed part-time by the
    publisher and full-time by a
    university (or other institution)
    − Are active researchers, authors, and
    experts in the field
    − More specific expertise

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  8. 8
    How are manuscripts assigned to a specific Editor?
    Automatically
    Manually
    − Papers selected individually by each
    editor
    − Editor chosen by the author upon
    submission
    − Individual assignment by the Editor-in-
    Chief or other lead Editor
    − Random assignment
    − Sequential (round robin) assignment
    − Assignment based on sections/subject
    areas selected by the authors
    − Assignment based on manuscript type
    (article, review, editorial, etc.)
    …or a combination of both
    Initial assignment to a Deputy Editor based on subject area,
    then the Deputy Editor manually assigns to an Associate Editor

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  9. 9
    Author(s)
    Journal staff
    Journal editor
    Reviewers
    The peer review process
    Write
    manuscript
    (Prescreening)
    Initial
    assessment
    Peer review
    First
    decision
    Revise manuscript +
    respond to reviewers
    Reject
    (Final)
    Decision
    Reject
    Initial
    submission
    Editor
    assignment
    Reviewers
    invited Feedback
    submitted Reviewers
    invited
    Revised
    manuscript
    submission
    Revision
    request
    Copy editing,
    typesetting, etc.
    Accept
    Review +
    edit proofs
    Proofs sent
    Proofs approved
    (payment sent)
    Online and/or
    print publication
    *
    time

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  10. 10
    What happens during pre-screening?
    Staff and/or editors check for:
    − Plagiarism
    − Duplicate submissions
    − Journal-specific requirements (word count, figure formatting,
    supplementary files, ethical approval for animal experiments, etc.)
    Editors check for:
    − Scope
    − Legibility
    − Technical/presentation quality
    − Soundness
    − Novelty (most journals)

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  11. 11
    The pre-screening plagiarism check
    Inevitable and harmless Tolerable
    Some overlap in the experimental
    section can be tolerated. Many
    papers use the same standard
    experimental methods.
    Questionable
    The red overlap is harmless
    (hundreds of papers have already
    been published on this topic) but the
    purple overlap is highly questionable.
    The text was probably lifted
    intentionally from the source paper
    and only minimally modified.

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  12. 12
    The pre-screening plagiarism check
    Plagiarism Outrageous plagiarism

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  13. 13
    Rejection before peer review (desk/editorial rejection)
    Out of scope
    Failure to meet specific
    journal requirements
    Ethical concerns
    (plagiarism, data/image
    manipulation,
    authorship issues)
    Results are not
    supported
    Results are presented
    too poorly for reviewers
    to evaluate
    Flawed methodology
    Lack of originality,
    novelty, impact, or
    significance
    Authors can avoid many editorial rejections by carefully reviewing the journal’s scope,
    requirements, ethical guidelines, and previously published papers before submission.
    Insufficient results
    presented

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  14. 14
    Author(s)
    Journal staff
    Journal editor
    Reviewers
    The peer review process
    Write
    manuscript
    (Prescreening)
    Initial
    assessment
    Peer review
    First
    decision
    Revise manuscript +
    respond to reviewers
    Reject
    (Final)
    Decision
    Reject
    Initial
    submission
    Editor
    assignment
    Reviewers
    invited Feedback
    submitted Reviewers
    invited
    Revised
    manuscript
    submission
    Revision
    request
    Copy editing,
    typesetting, etc.
    Accept
    Review +
    edit proofs
    Proofs sent
    Proofs approved
    (payment sent)
    Online and/or
    print publication
    *
    time

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  15. 15
    Who are the reviewers?
    It’s called peer review
    for a reason!

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  16. 16
    Who are the reviewers?
    Recently published on
    the topic
    Experts in the field Diverse
    representation

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  17. 17
    How do editors find reviewers?
    − Author suggestions
    − Reviewer suggestions
    − Cited papers, especially relevant reviews
    − Keywords
    − Web of Science
    − Scifinder
    − Online/public search engines
    − Publisher databases

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  18. 18
    How do editors choose reviewers?
    − Relevant recent publication record indicating expertise in the field
    − No obvious conflicts of interest (recent coauthorship, joint grants awarded)
    − Not affiliated with the same institution or city
    − Not currently occupied with other review assignments
    − Diversity of multiple reviewers (geographical, career level, etc.)

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  19. 19
    Author(s)
    Journal staff
    Journal editor
    Reviewers
    The peer review process
    Write
    manuscript
    (Prescreening)
    Initial
    assessment
    Peer review
    First
    decision
    Revise manuscript +
    respond to reviewers
    Reject
    (Final)
    Decision
    Reject
    Initial
    submission
    Editor
    assignment
    Reviewers
    invited Feedback
    submitted Reviewers
    invited
    Revised
    manuscript
    submission
    Revision
    request
    Copy editing,
    typesetting, etc.
    Accept
    Review +
    edit proofs
    Proofs sent
    Proofs approved
    (payment sent)
    Online and/or
    print publication
    *
    time

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  20. 20
    Common reasons for rejection after review (for most journals)
    Lack of originality,
    novelty, impact, or
    significance
    Unclear motivation/
    not valuable to the field
    Ethical concerns
    (plagiarism, data/image
    manipulation,
    authorship issues)
    Claims/conclusions are
    not supported
    Unclear/illogical
    presentation
    Concerns that the
    conclusions are
    incorrect
    Too preliminary
    Flawed/improper
    methodology or
    statistical unsoundness
    Generally, the editor will request revisions if they believe the paper can be improved
    enough to meet the journal’s publication standards, and will reject the paper if they don’t.

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  21. 21
    What’s the difference between “major” and “minor” revisions?
    Major revisions
    Minor revisions
    − May involve changes to the manuscript itself,
    such as clarifying the arguments, updating
    figures, etc.
    − Authors expected to complete the revision
    fairly quickly
    − Generally not sent back to reviewers before the
    editor’s decision
    − May involve additional experiments and/or
    analysis in addition to changes to the
    manuscript itself
    − Authors may be given more time to complete
    the revision
    − Generally sent back to reviewers before the
    editor’s decision

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  22. 22
    Rejection letters come in different forms
    Simple rejection
    The paper will not be
    published in this journal.
    Suggestion to resubmit
    “Soft rejection”
    The editor would be willing
    to consider a new, revised
    submission in the future.
    Transfer offer
    The submission could
    be considered by a
    different journal.

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  23. 23
    Author(s)
    Journal staff
    Journal editor
    Reviewers
    The peer review process
    Write
    manuscript
    (Prescreening)
    Initial
    assessment
    Peer review
    First
    decision
    Revise manuscript +
    respond to reviewers
    Reject
    (Final)
    Decision
    Reject
    Initial
    submission
    Editor
    assignment
    Reviewers
    invited Feedback
    submitted Reviewers
    invited
    Revised
    manuscript
    submission
    Revision
    request
    Copy editing,
    typesetting, etc.
    Accept
    Review +
    edit proofs
    Proofs sent
    Proofs approved
    (payment sent)
    Online and/or
    print publication
    *
    time

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  24. 24
    Accept as-is
    Once accepted, the manuscript enters the production process
    and is published online and/or in print.

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  25. 25
    Author
    Corrections
    Early View
    Online
    Publication
    Issue Build
    and checking
    Issue
    Publishing
    and
    Distribution
    Typesetting
    Submission Peer review Copy-editing
    Peer Review Article Publishing (Early View) Issue Publishing
    What happens after acceptance?

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  26. 26
    What happens during post-acceptance editing?
    − Figure formatting/standardization
    − Formatting
    − Typesetting
    − Copy editing (minor spelling/grammar)
    − Author gets to approve final version
    abcdefg

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  27. ENABLING DISCOVERY | POWERING EDUCATION | SHAPING WORKFORCES
    Trends in
    scholarly
    publishing

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  28. 28
    How are journals evaluated and compared?

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  29. 29
    What is a transfer offer?
    A rejected manuscript is recommended as suitable
    for a different journal (from the same publisher)
    If the author accepts the offer, the submission is
    moved to the new journal
    All files submitted to the original journal – including any
    reviewers’ reports – are shared with the new journal
    The author may also update or revise the
    manuscript between submissions
    An editor of the new journal begins evaluation
    of the manuscript
    If necessary, the manuscript will be re-
    evaluated by external reviewers

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  30. 30
    Why should authors accept the transfer offer?
    Benefits to authors Benefits to reviewers
    − Minimizes redundant reviews
    − Fewer total reviews are needed,
    lessening the load on the peer review
    community
    − Up to three times more likely to be
    accepted
    − Faster publication times
    − No need to re-enter submission
    information

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  31. 31
    The many models for peer review: reviewer anonymity
    “Single-blind”
    Editor
    Author
    Reviewers




    Editor
    Author
    Reviewers



    “Double-blind”
    Editor
    Author
    Reviewers



    “Triple-blind”
    Editor
    Author
    Reviewers



    Open

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  32. 32
    The many models for peer review: reviewer comments
    Transparent
    Reports are published
    along with the paper
    Confidential
    Reviewer reports are
    not published
    Open
    Readers may post
    additional reports
    after publication
    Independent
    Reader feedback
    published elsewhere
    (PubPeer, etc.)
    None
    Post-publication
    reader evaluation
    only
    ?

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  33. 33
    Different journal access/fee structures
    Gold Open Access
    Articles are freely accessible online, but authors
    must pay an Article Processing Charge (APC)
    Subscription
    Usually free to publish, but only
    subscribers can access the papers
    Copyright belongs to the publisher Authors retain copyright of their work

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  34. 34
    Transformative agreements between publishers and institutions
    A Transformative Agreement is a contract between
    an institution/consortium and a publisher allowing
    researchers to access subscription content as well as
    publish their work in Open Access journals.
    Gold Open Access
    Articles are freely accessible online, but authors
    must pay an Article Processing Charge (APC)
    Subscription
    Usually free to publish, but only
    subscribers can access the papers

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  35. 35
    The Open Science / Open Research movement
    … broad term, covering the many exciting developments in
    how science is becoming more open, accessible, efficient,
    democratic, and transparent. This Open Science revolution
    is being driven by new, digital tools for scientific
    collaboration, experiments and analysis and which make
    scientific knowledge more easily accessible by professionals
    and the general public, anywhere, at any time …
    - European Commission

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  36. 36
    Open Research
    Increasing accessibility of
    publicly funded research
    OPEN ACCESS
    Enabling reproducibility and verification of
    research data, methodology, and reporting
    standards
    OPEN DATA
    Embracing greater transparency
    throughout the research process
    OPEN PRACTICES
    Supporting inclusive and networked
    research practices
    OPEN COLLABORATION
    Helping to integrate researcher
    identification and evaluation tools
    OPEN RECOGNITION &
    REWARD

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  37. 37
    Impact & Integrity Through Open Research
    Make research more open,
    transparent & accessible
    More Open
    Create a more efficient
    landscape for conducting,
    funding & supporting research
    More Reproducible
    Protect the integrity & overall
    reputation of research
    More Accountable

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  38. 38
    The Open Researcher and Contributor ID (ORCID)
    − It is impossible to accurately distinguish researchers based on
    their full names.
    • Names are not always unique
    • Names are not always written the same way
    • Names may change throughout a person’s lifetime
    − Researchers are not always properly credited for their work, and
    Editors struggle to identify and invite reviewers.
    − ORCID issues researchers a unique alphanumeric code that
    resolves this name ambiguity problem.
    − Many journals now require authors to include their ORCID codes
    upon submission and publish them with the papers.

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  39. 39
    Advancements beyond simple pdf files
    Supplementary files
    Embedded video
    HTML article format Executable code

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  40. ENABLING DISCOVERY | POWERING EDUCATION | SHAPING WORKFORCES
    Predatory
    journals

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  41. 41
    What is a predatory journal?
    Predatory journals profit by exploiting authors’ desire to publish their work.
    − Use the Open Access publication model and charge fees to publish and/or submit
    (but most Open Access journals are legitimate)
    − Do not provide legitimate peer-review and publishing services
    − May use names of real researchers without their consent
    − May falsely imitate well-known legitimate journals or publishers
    − May post false claims of being indexed or fake journal metrics, such as Impact Factors

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  42. 42
    How can we defend ourselves from predatory journals?
    Check lists of known/suspected predatory journals as well as indexing services for legitimate journals:
    − Beall’s List of Predatory Journals and Publishers: https://beallslist.net/
    − Cabells’ Journal Blacklist: https://www2.cabells.com/about-predatory ($)
    − Useful appraisal tool: https://thinkchecksubmit.org/
    − Directory of legitimate Open Access journals: https://doaj.org/
    − Clarivate’s Master Journal list: https://mjl.clarivate.com/home
    Watch for warning signs that a journal may be predatory:
    − Has a low-quality/unprofessional website
    − Promises unreasonably fast publication times and/or high acceptance rates
    − Lacks transparent editorial and peer review policies
    − Lacks a well-defined scope or publishes papers far outside its stated scope
    − Accepts manuscript submissions by email
    − Sends frequent spam emails asking for submissions
    − Unfamiliar to you and your colleagues

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  43. ENABLING DISCOVERY | POWERING EDUCATION | SHAPING WORKFORCES
    Tips & best
    practices for
    manuscript
    writing

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  44. 44
    Common types of ethical misconduct in publishing
    − Plagiarism
    − Others' data + words
    − Your own data + words
    − Reuse of images – get publisher's permission to reuse!
    − Falsifying/fabricating:
    − Data
    − Images
    − Reviewer reports
    − Citations
    − Dual/duplicate submission
    − Fractured publication: “salami slicing”

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  45. 45
    Ethical misconduct: authorship misrepresentation
    Inclusion of non-
    contributing authors
    Exclusion of
    contributing authors
    Unexplained author
    addition or removal
    during revision
    Criteria for authorship:
    1. planning and contribution to some component of the work or
    interpreting at least a portion of the results
    2. writing a draft of the article or revising it for intellectual content
    3. final approval of the version to be published

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  46. 46
    Search Engine Optimization (SEO) begins with keywords
    − Search engines typically focus on paper titles, abstracts, and section headings
    − Include 1-2 different keywords or phrases in the title, 2-3 in the abstract, 5-7 in
    keyword fields, and in section headings as needed
    − Use the keywords consistent with your field – if unsure, review the keywords used in
    recent publications
    − Test potential keywords on trends.google.com, Google Scholar, Web of Science, etc.
    − Avoid excessive keyword repetition, known as “keyword stuffing,” which will cause
    search engines to suppress or even un-index a web page
    − Post links to your paper across your social media, networking, and institutional sites

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  47. 47
    Further resources for Search Engine Optimization
    Search engine optimization: What is it and why should we care? - Cushman - 2018 -
    Research and Practice in Thrombosis and Haemostasis - Wiley Online Library
    The impact of metadata implementation on webpage visibility in search engine results
    (Part II) – ScienceDirect
    Academic Search Engine Optimization (ASEO) | Optimizing Scholarly Literature for
    Google Scholar & Co. (utpjournals.press)

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  48. 48
    Writing an effective, optimized title
    − An effective title accurately indicates the paper’s scope in ~15 words or less
    (consider moving longer phrases to the start of the abstract)
    − It states what was found, not what was done
    − It contains 1-2 related keywords, ideally at the beginning of the title
    − It encourages readers’ interest in clicking on and reading the entire paper
    − It does not include “Study on,” “Research on,” “Effect of,” “Investigation of,”
    “Characterization of,” etc…
    − It does not include unfamiliar jargon or acronyms

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  49. 49
    Improving a suboptimal title
    Effect of Metal Catalyst on
    the Outcome of Coupling
    Reactions with Aryl Alcohols
    X What effect?
    X Which metal(s)?
    X What type of coupling reaction(s)?
    X Which aryl alcohols?
    Ruthenium Trichloride:
    a High-Yield Catalyst for C–H
    Activation with 2,4-
    Disubstituted Aryl Alcohols
    ü Specific
    ü Concise
    ü Contains many keywords

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  50. 50
    Writing a good abstract (max. 250 words!)
    − Hypothesis
    − Explain keywords
    − Main findings
    − Main conclusions
    − Importance/impact
    − Unanswered questions
    7-10 sentences
    No citations
    No abbreviations
    Findings first

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  51. 51
    A general procedure for designing successful charts:
    1. Choose the appropriate chart type and plot the data.
    2. Sequentially adjust every parameter of the chart —
    anything that can be changed from the defaults!
    (Fonts, colors, line widths, grid lines, axis increments, tick
    marks, key format/location…)
    3. At each stage, consider: what setting communicates the
    most effectively to the audience?
    Consider the chart’s intended setting and audience.
    4. Eliminate clutter and do not introduce new clutter.
    5. Use consistent design for all figures in the same
    document.
    AaBb
    Data 1
    Data 2
    Data 3

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  53. 53
    Journal Impact Factors: a simple but flawed metric
    − Used as a measure of journal prestige… unfortunately?
    − Field-dependent
    − Skewed by popular (or infamous) articles and reviews
    − Volatile
    − Doesn’t predict future citations
    − Not transparent
    arXiv:1906.02660
    arXiv:1906.02660
    @DuttonChemistry, Jason Dutton, Assoc. Prof. Latrobe University
    IF(2022) =
    # citations in 2022 to citable papers published in 2020 and 2021
    # of citable papers published in 2020 and 2021

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  54. 54
    Different journal access/fee structures
    Green Open Access
    A subscription journal
    that allows authors to
    self-archive their papers
    Gold Open Access
    Articles are freely accessible online, but authors
    must pay an Article Processing Charge (APC)
    Hybrid
    A subscription journal that allows
    authors to make their papers
    Open Access by paying an APC
    Diamond Open Access
    Articles are freely accessible online with
    no charges to authors; costs are covered
    by a university or other institution
    Subscription
    Usually free to publish, but only
    subscribers can access the papers
    Copyright belongs to the publisher Authors retain copyright of their work

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