Abbreviating the Pandemic

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If you’ve followed AMA style for at least the last several years, you may remember this big (welcome) announcement:

The companion abbreviation “AIDS” was given expansion-exempt status even before this with the 2007 publication of the 10th edition. It took some time for HIV to catch up.

Why did we decide that these 2 abbreviations no longer needed expansion? For one, they are ubiquitous, instantly recognizable (at least to English-reading audiences), and are long and cumbersome to write out in full.

After more than a year of publishing coronavirus-related content (JAMA’s first article was published in January 2020 by Fauci and colleagues), the AMA Manual committee has determined that COVID-19 and SARS-CoV-2 meet those same criteria to forgo expansion: ubiquity, familiarity, and cumbersome expansions.

  • Before: Protection against coronavirus disease 2019 (COVID-19) is mediated in large part by an immune response directed against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein.
  • After: Protection against COVID-19 is mediated in large part by an immune response directed against the SARS-CoV-2 spike protein.

While we all hope to soon have this pandemic in our collective rearview mirror, it is not likely that we will forget coronavirus disease 2019 or severe acute respiratory syndrome coronavirus 2.–Stacy Christiansen, Chair, AMA Manual of Style

Citing Online Journal Articles and Data from Repositories

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The new edition of the AMA Manual of Style is here, and it has nearly 200 more pages on everything from reference citations to the ethical and legal issues associated with medical publishing.

If the amount of new content seems overwhelming, may I suggest starting with the basics?

I dove in by reviewing the References chapter.

Online Journal References

According to section 3.11.4, “Online Journal Articles, Preprints, and Manuscripts,” the basic components of an online journal reference haven’t changed: authors’ surnames and initials, the title of the article, abbreviated name of the journal, publication year, pagination, the date the article was accessed, and the DOI or URL.

What has changed it that the date accessed should now be listed before the DOI or URL, and the URL is not followed by a period.

Data Repositories

I’ve also edited a few articles that included an analysis of data sets from a repository. Data repositories serve as archives for isolated data sets that allow data to be mined for secondary use in research. In a situation like this, the data set used and the original source for the data should be cited.

In the example shown below, the information for the original source for the data is listed first, followed by the name of depository, the date of data deposit, and the DOI for the data set.

DeLeon TT, Almquist D, Kipp BR, et al. Data from: Assessment of clinical outcomes with immune checkpoint inhibitor therapy in melanoma patients with CDKN2A and TP53 pathogenic mutations. Dryad Digital Repository. Deposited March 12, 2020. doi:10.5061/dryad.m0cfxpp0g

Accurate references are a critical element of any published article. The updated guidelines on references ensure that readers are directed to additional resources for more information.—Juliet Orellana

Common Mistakes in Submitted Images

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The production graphics team at JAMA Network reimagines author art following AMA style guidelines. Our department is a fantastic resource to assist editors and authors with submission of art and reassure them that, with only a bit of tweaking, images can be not only press ready, but also meet journal style guidelines.

Because there are limited ways to present medical data graphically, we tend to see the same issues with author-provided art occur over and over again. Here is a short list of common submission errors to watch out for as editors before relaying an author’s images to your publication’s graphics department.

  • Plotting odds ratios as arithmetic instead of logarithmic.

Odds ratios need to be graphed on log scales, because plotting odds ratios on a linear scale is misleading.

  • Log scales that use half numbers.

Using half numbers on a log scale does not meet AMA style guidelines.

  • Failure to include tick marks with numbers on the x and/or y axis.

Our department reproduces author-submitted art to conform to style guidelines, and when art is submitted without ticks, it is sometimes difficult to align it with our templates.

  • Not providing vector art for Kaplan-Meier plots, forest plots, dot pots, or other plotted data.
  • Low-resolution images provided for photographic imagery.
  • Providing photographic imagery with text, arrows, A/B designators, or other types of callouts in the image area of the art.
  • Providing dot plots, scatter plots, and other types of images with inappropriate symbols.
  • Plotting mean values as bar graphs.

Bar charts are not an acceptable format for mean values and may only be used for frequency data (counts) only.

Our team’s goal is to work with editorial staff to produce images that support an article, are visually appealing, and produce the best possible results at press. Hopefully this information can aid authors and editors in submitting art to obtain these goals!–Carolyn Hall

Transformation and Promoting Trust in the Peer Review Process

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Today is the start of Peer Review Week, an annual global event celebrating the essential role that peer review plays in maintaining scientific quality. This year’s focus is on trust in peer review, and this post addresses the evolving transformation of the peer review in scientific publication.

Peer review continues to develop, albeit slowly, in terms of models and methods, with increasing calls for openness and transparency. There are 3 common forms of peer review:

  • Double-blind review: Authors’ and reviewers’ identities are hidden from each other in an attempt to minimize bias.
  • Single-blind review: Authors identities are revealed to all, but reviewer identities are not revealed to authors (also known as anonymous review)
  • Open review: Author and reviewers are identified are revealed and various levels of the process and outputs may or may not be made public

Types of open review, with increasing levels of openness, include the following:

  • Level 1: Reviewer and author identities are revealed to each other during the peer review process
  • Level 2: Indication of editor and/or reviewer names on the article
  • Level 3: Posting of peer review comments with the article, signed or anonymous
  • Level 4: Publication of peer review comments (signed or anonymous) with authors’ and editors’ responses, decision letters, and submitted and revised manuscripts
  • Level 5: Publication of the submitted manuscript after a quality check and inviting public discussion from the community

A recent look at the types of peer review used by some top-ranked general medical and science journals shows that most journals use single-blind review, with some allowing reviewers to choose to sign their reviews. For example, JAMA has a single-blind review process and offers reviewers the option to sign their reviews that are shared with authors, and copies of reviews are shared with other reviewers.

JAMA also has an editorial collaborative process, called editorial review before revision, during which senior editors, a manuscript editor, and an editor with expertise in data display collaborate to provide guidance to the authors on all that is needed during revision to reach a favorable final decision.

However, these processes are not public. A short video that explains an inside view of the editorial and peer review process at JAMA is available.

JAMA Network

The BMJ has a fully open review process with the following published with all research articles: all versions of the manuscript, the report from the  manuscript committee meeting, reviewers’ signed comments, and authors’ responses to all comments from editors and reviewers. Nature publishes reviewer names and comments and author rebuttal letters; however, authors and reviewers can opt out of the open review process. And eLife has a mixed model with reviewers’ names revealed to each other during the review process; decision letters, anonymous reviewer comments, and author response letters published with the article; and an option for reviewers to sign their reviews.

One of the earliest demonstrations of open and collaborative peer review was launched in 2001 by Copernicus Publications, an open-access publisher of scientific journals. These journals use a 2-stage process:

“In the first stage, manuscripts that pass a streamlined access review are immediately posted as preprint in the respective discussion forum. They then undergo an interactive public discussion, during which the referees’ comments (anonymous or attributed), additional community comments by other members of the scientific community (attributed), and the authors’ replies are posted. In the second stage, the peer-review process is completed and, if accepted, the final revised papers are published in the journal.”1

Many studies have compared the quality of single-blind, double-blind, and open review. Early randomized trials2,3 found no differences in the quality of double-blind, single-blind, or open review. But some studies have found differences, such has higher quality for blinded review,4 higher quality for signed reviews,5 and higher quality for open review.6 And some studies7,8 have identified biases that may be better managed with double-blind review (eg, bias toward gender, geography, institutions, and celebrity authors).  However, no study has yet compared the quality of published articles that have undergone these different types of peer review.

Drummond Rennie, the founder of the International Congress on Peer Review and Scientific Publication, has been a vocal proponent of open peer review. Writing about freedom and responsibility in publication in 1998, Rennie commented,

“The predominant system of editorial review, where the names of the reviewers are unknown to the authors, is a perfect example of privilege and power (that of the reviewer over the fate of the author’s manuscript) being dislocated from accountability….to the fellow scientist who wrote the manuscript. For that reason alone, we must change our practices. ….The arguments for open peer review are both ethical and practical, and they are overwhelming.”9

There have also been numerous studies demonstrating the feasibility of each type of peer review. However, some studies have found that double-blind review is not always successful and have reported rates of failure to ensure blinding ranging from 10% to 40%. Other studies have found that reviewers who are asked to sign their reviews may be more courteous or positive in their recommendation, may take longer to complete their reviews, and may be more likely to decline invitations to review.

Support for open review, with options, continues to evolve. In a 2016 OpenAire survey of 3062 academic editors, publishers, and authors,10 60% indicated that open peer review (“including making reviewer and author identities open, publishing review reports and enabling greater participation in the peer review process”) should be common in scholarly practice, but they had some concerns. For example, 74% responded that reviewers should be able to choose to participate in open review, and 67% reported being less likely to review if open review was required.

The Nature journals have been experimenting with various models of peer review, and in 2016, Nature Communications announced that about 60% of its authors agreed to have their reviews published.11  In 2019 and 2020, Nature journals began offering “transparent peer review” with options for authors and reviewers to opt out.12

Elsevier conducted a pilot of open review from 2014 to 2017 in 5 journals, with reviews published.13 During this pilot, younger and nonacademic scholars were more willing to review and provided more positive and objective recommendations. There was no change in reviewer willingness to review, their recommendations, or turn-around times. But, only 8% of reviewers agreed to reveal their identities with the published reviews.

Thus, the key to successful transformation to open peer review and maintaining trust in the process may be offering options to authors and reviewers. Whichever model is used, journals should clearly and publicly describe their processes (eg, in Instructions for Authors) and continue to evaluate and test ways to improve the peer review process for authors, reviewers, and editors.–Annette Flanagin, Executive Managing Editor and Vice President, Editorial Operations, for JAMA and the JAMA Network, and Executive Director of the International Congress on Peer Review and Scientific Publication

*Note: Portions of this post have been presented at several meetings.

References:

  1. Copernicus Publications. Interactive peer review. Accessed August 23, 2020. https://publications.copernicus.org/services/public_peer_review.html
  2. Justice AC, Cho MK, Winker MA, Berlin JA, Rennie D; PEER Investigators. Does masking author identity improve peer review quality? a randomized controlled trial. JAMA. 1998;280(3):240–242. doi:10.1001/jama.280.3.240 https://jamanetwork.com/journals/jama/fullarticle/187758
  3. van Rooyen S, Godlee F, Evans S, Smith R, Black N. Effect of blinding and unmasking on the quality of peer review: a randomized trial. JAMA. 1998;280(3):234–237. doi:10.1001/jama.280.3.234 https://jamanetwork.com/journals/jama/fullarticle/187750
  4. McNutt RA, Evans AT, Fletcher RH, Fletcher SW. The effects of blinding on the quality of peer review: a randomized trial. JAMA. 1990;263(10):1371–1376. doi:10.1001/jama.1990.03440100079012 https://jamanetwork.com/journals/jama/fullarticle/380957
  5. Walsh E, Rooney M, Appleby L, Wilkinson G. Open peer review: a randomised controlled trial. Br J Psychiatry. 2000;176(1):47-51. doi:10.1192/bjp.176.1.47
  6. Bruce R, Chauvin A, Trinquart L, et al. Impact of interventions to improve the quality of peer review of biomedical journals: a systematic review and meta-analysis. BMC Medicine. 2016;14(85). https://doi.org/10.1186/s12916-016-0631-5
  7. Lerback J, Hanson B. Journals invite too few women to referee. Nature. 2017;541(7638):455–457. doi:10.1038/541455a
  8. McGillivray B, De Ranieri E. Uptake and outcome of manuscripts in Nature journals by review model and author characteristics. Res Integr Peer Rev. 2018; 3(5). https://doi.org/10.1186/s41073-018-0049-z
  9. Rennie D. Freedom and responsibility in medical publication: setting the balance right. JAMA. 1998;280(3):300–302. doi:10.1001/jama.280.3.300
  10. Ross-Hellauer T, Deppe A, Schmidt B. Survey on open peer review: attitudes and experience amongst editors, authors and reviewers. PLOS One. 2017;12(12): e0189311. https://doi.org/10.1371/journal.pone.0189311
  11. Transparent peer review one year on. Nat Commun. 2016; 7(13626). https://doi.org/10.1038/ncomms13626
  12. Peer review policy. Nature Journals. Accessed August 23, 2020. https://www.nature.com/nature-research/editorial-policies/peer-review#transparent-peer-review
  13. Bravo G, Grimaldo F, López-Iñesta E, et al. The effect of publishing peer review reports on referee behavior in five scholarly journals. Nat Commun. Published online Junary 18, 2019. https://doi.org/10.1038/s41467-018-08250-2

Preprints in the Time of COVID

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Fans of the 1985 Gabriel García Márquez novel Love in the Time of Cholera are all too familiar with the concept of pining over something long desired, but luckily for medical editors, the 11th edition of the AMA Manual of Style has been quick to provide necessary and accessible updates for editors to use during the time of coronavirus disease 2019 (COVID-19).

The worldwide effort to provide research on COVID-19 has led to a substantial emerging literature, and many study results and manuscripts have been posted on preprint servers prior to peer-reviewed publication. Thus, medical editors who are working with COVID-19 articles may find that more authors are citing sources from preprint servers, leading to references that are, just like Florentino Ariza’s love life, a bit…complicated.

However, medical editors will not need to inhabit a world of magical realism to solve this dilemma. They only have to refer to the recent update to chapter 3.11.4.1, Preprint and Publication of Unedited Manuscripts. In it, they’ll find that many of the things that made citing these sources cumbersome, such as duplicative ID numbers, have been removed and that the order of elements is similar to other, perhaps more familiar, references.

This update hopefully makes life easier for medical editors during a high-volume time. It may even leave more time for reading for pleasure! I can make a great book suggestion 😉–Amanda Ehrhardt

An Interview With AMA Manual of Style Committee Member Connie Manno

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With the recent release of the 11th edition of the AMA Manual of Style, I was curious to learn more about the members of the style committee, their background, and their experience working on the manual update. After all, these editorial masterminds spent countless hours debating every detail of AMA style to make our jobs as editors easier.

The first person with whom I chose to chat was Connie Manno, Director of the Freelance Editing Unit at JAMA Network and coauthor of chapter 4, Tables, Figures, and Multimedia. (Full disclosure—she’s my manager.)

Background

Connie started working as a coordinator in the freelance unit at the JAMA Network in 1998 after getting started with the organization as a freelance proofreader. In 2017, she was promoted to the director of the unit.

The freelance team currently consists of 5 in-house coordinators, 12 freelance editors, and 4 freelance copyreaders and is constantly growing. The team has doubled since Connie started in the unit to keep up with the increasing number of manuscripts and the greater amount of content published by the JAMA Network.

Expectations for Freelance Editors

When asked about the expectations of the freelance editors, Connie stated that the preference is for each to edit at least 3 major manuscript per week and to handle the initial set of author revisions. The editors are expected to take a substantive editing approach, with strict adherence to the AMA Manual of Style.

They are contacted at least monthly with updates to or reminders about journal style and policy. The coordinators review the work of the freelance editors and provide feedback as necessary. Furthermore, every spring, the freelance editors are invited to a day-long conference to experience a deeper dive into style and policy.

Over the years, Connie has discovered her aptitude and joy in training new freelancers and coordinators. She attributes her knowledge of AMA style to this aspect of her job. She finds that it’s more effective to provide the exact sections of the manual to new editors on their reviewed manuscripts so that they can see why changes were made and know where to look for those items in the future. Like many of your manuals, Connie’s is meticulously organized with tabs, highlights, and underlines.

On Editing Figures

One section of scientific manuscripts that can be particularly challenging to edit is figures. Because of her eye for visual representation of data, Connie was asked to take over development of chapter 4 from Stacy Christiansen, Chair of the AMA Manual of Style and Managing Editor of JAMA. Connie worked on the chapter for the last 3 years of development. Basic editing had been done, but Connie was responsible for finding good examples and, of course, making sure that those examples were edited according to AMA style.

In the process and by working with figure and statistical experts on JAMA for about a year, she gained more in-depth knowledge about which type of figures are best for representing different types of statistics and the data needed for completeness of presentation. You can see Connie’s recent AMA Style Insider post for a summary of updates to the chapter–she hopes that you find it informative and helpful!

Questions?

Please feel free to send your questions about figures and tables style to stylemanual@jamanetwork.org or @AMAManual on Twitter.–Sara Billings

Updates to Reporting Black and White as Racial Categories

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Everyone in the business of communication has a responsibility to use and promote the use of clear and accurate language, with words that reflect the world around us. As evidenced by perpetual updates to style manuals, dictionaries, and other resources, nomenclature is never a static enterprise.

Specifying the race or ethnicity of an individual can provide information about the generalizability of the results of a specific study. Because many individuals may have mixed heritage, a racial or ethnic distinction should not be considered absolute, and ideally it should be based on a person’s self-designation.

In the JAMA Network journals, we ask authors to provide an explanation of who classified individuals’ race, ethnicity, or both, the classifications used, and whether the options were defined by the investigator or the participant. In addition, the reasons that race/ethnicity were assessed in the study also should be described (eg, in the Methods section and/or in table footnotes).1

We have received a number of queries about the presentation of racial and ethnic terms in the AMA Manual of Style, in particular the manual’s style current preference for using lowercase for the term black. The 11th edition specifies capitalizing racial and ethnic terms that derive from geographic nouns such as Asian, Alaska Native, and Latina (chapter 10.3.2, Capitalization, Proper Nouns, Sociocultural Designations), but the terms black and white have been lowercased as racial designators (because they are not derived from proper nouns).

However, ongoing and recent events spurred us to reconsider this style recommendation. The manual’s committee met several times, conducted research, and sought input on this issue from multiple sources. We deem this issue too important to wait for change.

In weighing the options (keep black and white lowercase, capitalize just Black, or capitalize both Black and White), we reviewed usage recommendations in a variety of sources, including other style manuals (Chicago Manual of Style,2APA style,3 and the AP Stylebook4), writing by an array of scholars, and guidance on diversity from academic and government sources, such as the US National Institutes of Health.5

The committee has concluded that we will now capitalize both Black and White, which aligns with the capitalization preference applied to other racial/ethnic categories. We acknowledge that there may be instances in which a particular context may merit exception to this guidance, for example, in cases for which capitalization could be perceived as inflammatory or otherwise inappropriate.

The online style manual will be updated to reflect this change, including the section on race/ethnicity in the Usage chapter  (chapter 11.12.3, Usage, Inclusive Language, Race/Ethnicity) and the aforementioned entry in the Capitalization chapter.

There are additional language issues to consider, including use of “other” as a category and abbreviating racial and ethnic terms. The nonspecific “other” is sometimes used for comparison in data analysis but may also be a “convenience” grouping/label that should be avoided, unless it was a prespecified formal category in a database or research instrument.

In such case, the categories included in “other” should be defined and reported. Authors and researchers are advised to be as specific as possible when reporting on racial/ethnic categories (even if these comprise a small percentage of participants).

Example (not recommended): “The study included 200 White individuals, 100 Black individuals, and 100 of other race/ethnicity.”

In this situation, an editor should ask the author for further explanation, considering that the racial/ethnic background of a quarter of the study is not provided.

Example (preferred): “The study included 200 White individuals, 100 Black individuals, and 100 of other race/ethnicity, which included Chinese, Japanese, Korean, and Native Hawaiian/Pacific Islander and those who reported multiple categories.”

Racial and ethnic terms also should not be abbreviated unless necessary for space constraints (eg, in tables and figures with clear expansion in explanatory footnotes or legends).

The manual’s committee will continue to explore changing trends in usage of other racial and ethnic terms as well, such as Latinx. As with all changes to the style manual, we welcome input from readers. The update to the manual online will be implemented as soon as possible, and the JAMA Network journals will begin to use Black and White as we edit new content.–Stacy Christiansen and Tracy Frey, for the AMA Manual of Style committee

References:

1. Instructions for Authors. JAMA. Updated April 13, 2020. Accessed June 19, 2020.  https://jamanetwork.com/journals/jama/pages/instructions-for-authors#SecReportingRace/Ethnicity

2. Black and White: a matter of capitalization. CMOS Shop Talk. Posted June 22, 2020. Accessed June 22, 2020. https://cmosshoptalk.com/2020/06/22/black-and-white-a-matter-of-capitalization/

3. APA Style. Racial and ethnic identity. Accessed June 20, 2020. https://apastyle.apa.org/style-grammar-guidelines/bias-free-language/racial-ethnic-minorities

4. AP Stylebook. Race-related coverage. Accessed June 22, 2020. https://www.apstylebook.com/race-related-coverage

5. Racial and ethnic categories and definitions for NIH diversity programs and for other reporting purposes. National Institutes of Health. Released April 8, 2015. Accessed June 20, 2020. https://grants.nih.gov/grants/guide/notice-files/not-od-15-089.html

Nephrology Nuance

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When you’re in quarantine, you have to look for little things to spark joy in your life. I’ve found myself getting excited when I edit an article for which new AMA style guide updates come into play. Recently, while editing an article focusing on patients with end-stage kidney disease, I had the chance to refresh my knowledge on the new guidelines in the 11th edition of the AMA Manual of Style regarding nephrology nomenclature (14.18).

In accordance with the international efforts put forth by KDIGO (Kidney Disease: Improving Global Outcomes), which focus on making terminology more patient-friendly, precise, and universal, the 11th edition has updated the nomenclature used to describe kidney function and disease.

Updates on language choice include:

Kidney vs renal: Select the more patient-friendly term (ie, kidney). Also, avoid using both terms in parallel, as this could lead to confusion over different abbreviations for the same condition (eg, RRT [renal replacement therapy] and KRT [kidney replacement therapy]).

Kidney failure vs end-stage renal disease: Kidney failure is the preferred term except when referring to eligibility for medical care under US legislation or other regulations. Patients with kidney failure should be further described by the presence or absence of therapy by dialysis, transplant, or conservative care and by symptom severity.

Decreased glomerular filtration rate: Use this instead of decreased kidney function. Kidneys execute various functions, not just glomerular filtration, so precision in terminology is preferred.

The final recommendations and a complete glossary of related terms will be available in the near future and used to inform an update to this chapter in the manual online. –Suzanne Walker

Where in the World Is the Publisher’s Location?

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If you’re into vintage video games or, like me, came of age watching copious amounts of PBS programming, you may be familiar with a certain raven-haired, scarlet-bedecked, UNESCO World Heritage Site–stealing woman of mystery.

bustle.com

Where was the elusive Carmen headed, and what thrills were in store on the journey to find her and thwart her devious plans?

In the 10th edition of the AMA Manual of Style, reference citations for books and edited books included the publisher’s location, which at times could be as hard to pinpoint as Ms Sandiego herself. However, the journey to find this information lacked the glamor of international espionage and instead featured fruitless online searches and squinting at the minuscule copyright page of a volume from the 70s that Google allowed for preview.

Particularly perplexing were the occasions when a publisher with multiple offices was listed but no indication was given as to which one produced the book in question. So where in the world was the publisher’s location? Boston? London? Berlin? Hoboken?

Luckily, the 11th edition of the AMA Manual of Style recognizes that this struggle was indeed real, and the publisher’s location is no longer required for reference citations for books and edited books (3.12.8). Now the publisher appears directly after the italicized book title and is followed by the publication year. For example: Tinker R. Who in the World is Carmen Sandiego? HMH IP Company Unlimited Company; 2019.

Hopefully eliminating the publisher’s location from references will save you time during your editing process, time that can be better spent spanning the globe in pursuit of a jet-setting villainess…if you can find her.–Amanda Ehrhardt

The Temperature on Spacing for Degrees

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Tucked deep within the weighty 10th edition of the AMA Manual of Style were brief entries providing guidelines for reporting measures of temperature. In sum: writers and editors reporting Celsius or Fahrenheit should (1) close up spaces between numerals, degree symbols, and temperature units and (2) repeat the degree symbol and the unit when reporting temperature ranges. For example: 37.5°C-37.9°C.

Simple? Yes—with the possible exception of closing up the space between numerals and degree symbols, as many non-AMA publications include a space between temperature values and degree symbols, and the degree symbol was 1 of only 3 exceptions to the usual AMA style rule to add a full space between an Arabic measure of quantity and the unit of measure. (The other exceptions being the percent sign and the symbols for normal and molar solutions, often closed up in other publications.)

To separate or not to separate? That was the question.

The new (and even more comprehensive) 11th edition aims to ease any resulting separation anxiety, now calling for a full space between temperature values and degree symbols. Moreover, units no longer need be repeated when a hyphen is used. For example: 37.5-37.9 °C.

The 11th edition also makes more explicit that the degree symbol is not used with Kelvin values and highlights that relative temperatures should be expressed as higher and lower rather than warmer or colder.–Phil Sefton