Effective strategies to monitor clinical risks using biostatistics - Pubrica.pdf
AMWA-MAC 2015 Conference Presention MJSpiering
1. Rules & Tools for Scientific
Editing
AMWA-MAC Conference
Gaithersburg, Maryland
March 13, 2015
Martin J Spiering, PhD, ELS
CSR, Incorporated, Arlington, VA
2. What is Scientific Editing?
• Editing of scientific documents (journal
manuscripts, grant proposals, dissertations,
slides, textbooks, etc.)
• Editing for content, language, and
presentation
3. Scientific Editing Addresses Factors
Important for Manuscript Quality
Survey of 30 journal editors (Hing et al., J
Orthop Surg Res. 6:19, 2011)
Manuscript factors Percentage score
Manuscript is understandable 73%
Manuscript is well written 53%
Thorough literature review 50%
References papers from my
journal
40%
No financial conflict of interest 37%
Key factors for manuscript acceptance
4. Scientific Editors Ensure…
…that a document is
• accurate
• clear
• brief
They help authors use a voice that clearly and
competently speaks to the audience
5. Opportunities for Scientific
Communication Specialists
Time to leave academic writing to
communications experts?
(http://www.ivacheung.com/2015/02/time-to-leave-
academic-writing-to-communications-experts)
7. One Approach: “Analytical Editing”
“In addition to questions about the
language, we can also question the
assumptions, documentation, and
implications of the research.”
Tom Lang, AMWA Journal 28(3):105–109, 2013
8. Analytical Editing
“Question the assumptions,
documentation, and implications of the
research.”
“Investigative” editing — overlaps with/augments
scholarly peer review
9. Assumptions
• Have the authors sufficiently reviewed the
literature/is it relevant to the current study?
10. Probing Literature Review
Some authors start too general:
“In the beginning God created the heaven and
the earth (Genesis 1:1).”
Some start too specific:
“The role of gene X in disease Y affecting
people with condition Z caused by zinc
deficiency remains enigmatic (Smith et al. 2010
& 10 other citations).”
11. Probing Literature Review
Some authors do not lay out the background early
and in one place; leads to disjointed, hurried
writing:
E.g., from Discussion:
“We observed that gene X influences the severity
of disease Y. In this regard, it is noteworthy that
earlier studies have found a possible involvement
of pathway Z in…”
12. Literature Review
Better to say in Introduction:
“Gene X influences the severity of disease Y,
but its precise role is unknown. One possibility
is that gene X is involved in pathway Z.”
And then in Discussion:
“We confirmed that gene X influences the
severity of disease Y and established that gene
X controls disease severity through pathway Z.”
13. Assumptions
• Have the authors sufficiently reviewed the
literature/is it relevant to the current study?
• What is the central research
question/hypothesis?
14. (Mis)stating the Research
Question
A cardinal mistake: not to clearly and briefly say
why the study was done
At the end of an Introduction:
“Many studies recently conducted in the 2000s have
reported that gene X is highly involved in a variety of
diseases such as disease Y, negatively affecting
patients worldwide. In this paper, we set out to
extensively explore the plausible role of the gene X in
disease and disease-associated pathways, such as
pathway Z, and symptoms.”
15. State the Research Question
Say it clearly and succinctly:
“Previous studies have suggested a role for gene X in
disease Y. Here, we tested the hypothesis that gene
X controls the severity of disease Y. We also report
that gene X exerts its control through pathway Z.”
16. (Mis)stating the Research
Question
Do not send mixed/unclear messages:
In Introduction: “We tested the hypothesis that gene X
controls the severity of disease Y.”
In Discussion: “We confirmed our hypothesis that
gene X is involved in pathway Z.”
In Conclusion: “In summary, pathway Z influences the
severity of disease Y, and gene X regulates it.”
17. State the Research Question
Unify the message:
In Introduction: “We tested the hypothesis that gene
X controls the severity of disease Y.”
In Discussion: “Our observations confirmed the
hypothesis that gene X controls the severity of
disease Y.”
In Conclusions: “In summary, gene X controls the
severity of disease Y. Gene X exerts its control
through pathway Z.”
18. Assumptions
• Have the authors sufficiently reviewed the
literature/is it relevant to the current study?
• What is the central research
question/hypothesis?
• Can the authors’ approach address the
hypothesis?
19. Assumptions
Unclear writing obscures the validity of the
approach:
“In this work, we used gene microarray analysis
and real-time PCR to test involvement of tumor
necrosis factor (TNF) in fatty liver disease.”
20. Assumptions
More accurate writing helps clarify whether the
methods can address the hypothesis:
“In this work, we used gene microarray analysis
coupled with real-time PCR to test whether
expression of the gene for tumor necrosis
factor (TNF) is altered in fatty liver disease.”
23. Documentation
Inadequate/incomplete description of methods is
seen as major contributor to the “reproducibility
crisis” in science:
“[…] studies of published trial reports showed that
the poor description of interventions meant that
40–89% were non-replicable”
(http://www.thelancet.com/journals/lancet/article/PIIS0140-
6736%2813%2962228-X/fulltext)
24. Documentation
Do the authors clearly describe the methods they
used?
• The authors have ultimate insight into how they did
their experiments and responsibility for complete
reporting.
• Some journals require authors to follow checklists
developed, e.g., by CONSORT (Consolidated
Standards of Reporting Trials).
• Editors should use these (or a journal’s) checklists
to ensure that methods and the experimental design
are adequately reported.
25. Documentation
• Do the authors clearly describe the methods
they used?
• Are data presented in an appropriate format
(text, tables, or graphs) and have they been
statistically evaluated?
27. Documentation
Rules of thumb for data presentation:
• To report more than three data values, use a table
(or a graph/chart)
• To highlight differences between groups, use bar
graphs
• To show trends, use line graphs
• To visualize correlations, use scatter plots
• To show highly complex (“Big”) data, use heat
maps, Venn diagrams, or interactive graphics
28. Distracting/redundant reporting:
“Patients undergoing surgery for ingrown toenails
were younger (aOR 2.1, 95% CI 1.2–2.6), had a
higher BMI (aOR 1.4, 95% CI 1.3–1.6), and were less
likely to wear sandals (aOR 4.3, 95% CI 3.4–4.8) than
patients treated conservatively (Table 1).” (Table 1
shows all data given in the text.)
Better to say:
“Patients undergoing surgery for ingrown toenails
were younger, had a higher BMI, and were less likely
to wear sandals than patients treated conservatively
(Table 1).”
29. “Univariate linear regressions of preoperative pain and
the change in shoulder pain at 2 years (compared with
preoperative values) was significant (p < 0.0001) with
an r2 = 0.18. The same regression for neck pain was
also significant (p < 0.0001) with an r2 = 0.43.”
Unclear/inaccurate/incomplete description
of stats:
30. First step: ask the authors
“Univariate linear regressions of
preoperative pain and the change in
shoulder pain at 2 years (compared
with preoperative values) was
significant (p < 0.0001) with an r2 =
0.18. The same regression for neck
pain was also significant (p < 0.0001)
with an r2 = 0.43.”
31. Second step: let the authors revise
Authors now state the purpose of the analysis!
32. “To assess the influence of preoperative shoulder and
neck pain severities on the changes in pain from
baseline to the 2-year follow-up, we conducted
univariate linear regression analyses.”
Third step: further revise (if needed) and
ask authors to review the changes
33. Fourth step: revise reporting of results
“These analyses showed that preoperative shoulder
pain and neck pain severities were significant
predictors of the changes in shoulder pain (r2 of 0.18,
p < 0.0001) and neck pain (r2 of 0.43, p < 0.0001),
respectively.”
34. Documentation
• Do the authors clearly describe the methods
they used?
• Are data presented in an appropriate format
(text, tables, or graphs) and have they been
statistically evaluated?
• Are the data consistent between the different
elements (text, tables, figures) and sections
(Methods, Results, Discussion)?
35. Documentation
Common data mismatches:
Between Abstract and Results
Between Discussion and Results
Between text of the Results and data in Tables
Miscalculated totals or percentages in Tables (and
Results)
Allocate significant effort to checking consistency
among sections and elements
36. Documentation
• Does the study require ethical review (e.g.,
that human participants were sufficiently
protected or animals humanely treated)?
37. Implications
• Is the Discussion focused on the results and
informed by previous research?
• Do the results and their discussion support
the authors’ conclusions — what are the
conclusions?
• Do the authors misstate/overstate their
findings?
38. Analytical Editing: Untangling
Meaning
“All substance abuse treatment recruitment sites
employed 12–16 week cognitive-behavioral relapse
prevention treatment models and actively referred clients
to 12-step facilitation for aftercare. As such, the control
group in this study served as a natural standard of care,
consisting of standard aftercare practice.”
39. Analytical Editing: Untangling
Meaning
“All substance abuse treatment recruitment sites
employed 12–16 week cognitive-behavioral relapse
prevention treatment models and actively referred clients
to 12-step facilitation for aftercare. As such, the control
group in this study served as a natural standard of care,
consisting of standard aftercare practice.”
Did aftercare involve both cognitive-behavioral
treatment to prevent relapse and referral to 12-step
facilitation?
40. Analytical Editing: Untangling
Meaning
“For aftercare, all sites recruiting patients to treat their
substance abuse offered 12–16-week cognitive-behavioral
therapy to prevent relapses and referred clients to 12-step
meetings.”
Or
“All sites recruiting patients to treat their substance abuse
offered 12–16-week cognitive-behavioral therapy to
prevent relapses; for aftercare, they referred clients to 12-
step meetings.”
43. • Go to “File” “Info”
• To keep accurate time, either
close the working document when
done or have a second document
open and select it whenever you
stop work on the first document
Tracking Time
Let Word Do the Work
44. Let Word Do the Work
Checking consistent comma use in a series
45. Comma use in a series
• Go to “File” “Options”
“Proofing”
• Under “When correcting
spelling and grammar in
Word” go to “Settings” and
choose “always” (or “never”)
after “Comma required
before last item.”
Let Word Do the Work
51. • Highlight word/section where you want to
place query
• Hit “Record Macro” and name your macro
(e.g., “ClarityQuery”)
• Insert comment and write query
• Stop recording
Let Word Do the Work
52. • To run your new macro,
highlight text where you want
to insert query and go to
“View Macros.”
• In “Macros” panel select and
run “ClarityQuery.”
Let Word Do the Work
53. Let Word Do the Work
Time for placing comment and typing query: 15 sec
Time for using macro: 1 sec!
54. Example 2: using a (prewritten) macro that
changes hyphens to em dashes in tables
Let Word Do the Work
55. Let Word Do the Work
Time for manually changing hyphens to dashes: 20 sec
Time for using macro: 1 sec!
69. Rules & Tools for Scientific Editing
• Analytical (investigative) editing adds value to
scientific communication; fills gap between peer
review and standard editing.
• Does not require specialized knowledge — only
critical thinking skills and an eye for detail.
• Word’s functions and tools and add-on software
help expedite many editing tasks and free up
time and energy for analytical tasks.
70. Thank you!
Comments/questions? E-mail me at
mspiering@csrincorporated.com or
spieringmj2002@yahoo.com 4250 Fairfax Dr. Suite 500
Arlington, VA 22203
71. Resources for Scientific Editing
Books:
General scientific writing and editing:
Essentials of Writing Biomedical Research Papers. Mimi Zeiger, 2nd
Ed. McGraw-Hill.
Writing Science in Plain English. Anne E. Greene. University Of
Chicago Press
The Copy Editor’s Handbook─A Guide for Book Publishing and
Corporate Communications. Amy Einsohn, 3rd Ed. University of
California Press.
Style and usage manuals:
AMA Manual of Style. JAMA Archives and Journals, 10th Ed. Oxford
University Press.
Scientific Style And Format: The CSE Manual for Authors, Editors,
And Publishers. Council of Science Editors, 7th Ed. (8th edition is in
press.)
The Chicago Manual of Style. University of Chicago Press Staff, 16th
Ed. University of Chicago Press.
Garner’s Modern American Usage. Bryan A. Garner, 3rd Ed. Oxford
University Press.
72. Resources contd.
Books:
Freelance business and speeding up editorial tasks:
The Business of Editing. Richard H. Adin. Waking Lion Press.
Dictionaries:
The American Heritage Dictionary, 5th Ed. Houghton Mifflin
Harcourt.
Merriam Webster’s Collegiate Dictionary, 11th Ed. Merriam-Webster,
Inc.
Oxford Dictionary of English, 3rd revised ed. Oxford University
Press.
Dorland’s Illustrated Medical Dictionary, 32nd Ed. Saunders.
Stedman’s Medical Dictionary, 28th Ed. Lippincott Williams &
Wilkins.
73. Resources contd.
Books:
Biomedical research:
Molecular Biology of the Cell. Alberts et al., 5th Ed.
Garland Science. (Good for use as a reference and as a
way to read up on fundamental principles and topics of
cell biology, molecular biology and genetics, and
biochemistry.)
74. Resources contd.
Online:
Copyeditors' knowledge base @ KOK Edit─Katharine
O’Moore Klopf’s website (http://www.kokedit.com/ckb.php)
An American Editor ─ Richard Adin’s blog about (medical)
editing as a business (http://americaneditor.wordpress.com)
AMWA Online Forums/Listserves
(http://www.amwa.org/forum.asp?startpage=/forum/default
.asp)
Beall’s List of Predatory Publishers ─ a regularly
updated list of publishers suspected to be engaged in
unethical publication and business practices
(http://scholarlyoa.com/2014/01/02/list-of-predatory-
publishers-2014/#more-2846)
The Scholarly Kitchen ─ provides valuable views and
discussion of current topics in scholarly publishing
(http://scholarlykitchen.sspnet.org)
75. Resources contd.
Online:
International Committee of Medical Journal Editors ─
provides recommendations on the editing, ethics, and conduct
of medical journals (http://www.icmje.org)
Equator Network ─ an international resource hub for
authors, editors, educators, etc. to improve reporting in health
research (http://www.equator-network.org)
CONSORT ─ provides a checklist developed by medical
investigators and editors for transparent reporting of
randomized clinical trials (http://www.consort-statement.org)
2014 article series in The Lancet on increasing the value
of research ─ discusses ways how authors and editors can
improve reporting in studies
(http://www.thelancet.com/series/research)
Retraction Watch ─ useful resource to follow up on
misconduct cases and trends in scholarly publishing, such as
plagiarism, authorship disputes, and data fabrication
(http://retractionwatch.com)
76. Resources contd.
Online writing/editing courses:
Writing in the Sciences ─ free 8-week online course
taught by Dr. Kristin Sainani at Stanford
(http://online.stanford.edu/course/writing-in-the-sciences)
Course catalogue of the Editorial Freelancers
Association ─ on-site and online classes on various topics
(freelance business, editing and proofreading, website
design, etc.); fees vary from ~$50 for a seminar to ~$150
for a 5-week online course (for members; discounts are
available for taking classes in combos) (http://www.the-
efa.org/eve/catalog.php)
77. Resources contd.
Associations:
Council of Science Editors (www.councilscienceeditors.org)
Editorial Freelancers Association (www.the-efa.org)
Board of Editors in the Life Sciences (www.bels.org)
(BELS exam study guide is at
http://www.bels.org/becomeeditor/BELSStudyGuide0724121.pdf)
American Association for the Advancement of Science
(http://www.aaas.org)
78. Online articles on scientific editing and
publishing
Tom Lang’s article on analytical editing, AMWA Journal
28(3):105–109, 2013
(http://www.amwa.org/Files/Journal/2013v28n3_online.pdf;
requires AMWA membership)
Nature article on the emergence of scientific editing companies
catering to academic ESL authors
(http://www.nature.com/naturejobs/science/articles/10.1038/nj
7324-721a)
A 2002 article on scientific editing as a career choice
(http://sciencecareers.sciencemag.org/career_magazine/previou
s_issues/articles/2002_02_01/nodoi.12721417129988179760)
Reflections on scientific editing from a journal editor (requires
subscription)
(http://link.springer.com/article/10.1007%2Fs40596-013-0028-
0)
Exposé of “predatory” online publishers
(http://www.sciencemag.org/content/342/6154/60.full)
79. Tools
Paul Beverley’s (free) collection of >400 useful Word macros—
require basic knowledge of how to insert macro scripts into
Word’s VBA editor (http://www.archivepub.co.uk/book.html)
An American Editor Blogs covering Word macros and additional
editing software
(https://americaneditor.wordpress.com/category/editorial-
matters/editing-tools-editorial-matters)
PerfectIt Website (http://www.intelligentediting.com) & link to
Editor's Toolkit Ultimate (PerfectIt, Editor’s Toolkit, & EditTools)
(http://www.intelligentediting.com/buy-now/editors-toolkit)
Editorium Website (http://www.editorium.com)
EditTools Website (http://www.wordsnsync.com/edittools.php)
Edifix (software to edit references in bibliographies) Website
(https://edifix.com) & an editor’s appraisal here (http://editor-
mom.blogspot.co.uk/2014/08/edifix-subscription-cloud-based-
service.html)
80. Tools contd.
Statistics for Biologists—a Web collection of useful guides and
articles hosted by Nature
(http://www.nature.com/collections/qghhqm)
