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Nomenclature: GeneticsGenetics: Discourage use of aliases/nicknames forgenes and proteinsGene symbol Gene descriptionAcceptable expressionTP53The TP53 gene (p53 is the alias;the official term is preferred tothe alias)tumor protein p53 (LiFraumeni syndrome)geneMay be necessary to “dual report” for aliases wellentrenched in use:“ERBB2 (previously HER2/neu)” 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 25

Nomenclature: Genetics (cont)The Human Genome Variation Society recommendsavoiding the terms mutation and polymorphism, preferringinstead the terms sequence variant, sequence variation,alteration, or allelic variant.In view of this recommendation, single-nucleotide variation(SNV) is now more frequently used instead of SNP (singlenucleotide polymorphism) and may become standard.To aid readers’ understanding during this transition, at firstmention SNV may be used, with SNP in parentheses:“ SNV (formerly SNP) ” 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 26

Units of Measure: CurrenciesCurrencies will be updated, including AfricandenominationsEthiopian birr (ብር)Ghana cedi (GH )Malawi kwacha (MK)Nigeria naira ( )Uganda shilling (USh)Zimbabwe dollar ( ) 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 27

Units of Measure: Spacing in TemperaturePer SI convention, we will no longer close updegree symbols in temperature but use a spaceafter the number: temperature of 37.5 C (not 37.5 C or 37.5 C) 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 28

Numbers: CI Not ExpandedIn the list of abbreviations (Section 14.11, page 504in the print), an asterisk was added after CI toindicate that this abbreviation no longer needs to beexpanded. “Low-quality evidence has shown that risedronatereduces the risk of fragility fractures (hazard ratio, 0.27;95% CI, 0.09-0.83; P .02).” “The primary analysis followed a modified intention-totreat principle and used a 1-sided 95% CI fornoninferiority.” 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 29

Statistics: Terms UpdatedThe terms multivariable and multivariate are not synonymous, asthe entries in the current Glossary suggest (Chapter 20.9, page881 in the print). To be accurate, multivariable refers to multipleindependent variables for a single outcome (dependent variable).Multivariate refers to 1 or more independent variables for multipleoutcomes. See the Update on the stylebook site. Most clinical studies use a multivariable approach (a singleoutcome) “Using sex-stratified multivariable-adjusted Cox proportionalhazards models, black women and men were more likely todevelop diabetes than white men and women (black women:HR, 2.86 [95% CI, 2.19-3.72]; black men: HR, 1.67 [95% CI,1.28-2.17]).” Diabetes is the single outcome; sex and raceare independent variables. 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 30

Mathematical Composition: UpdatesUpdate to the chapter to include more examples. To avoid confusion, do not display forms of statisticalanalysis as subscript, such as Pinteraction .001.Better: P .001 for interaction. Thin spaces (a character usually 1 5 or 1 6 the width ofan em dash; the Unicode value for the 1/6 em space is2006) should be used before and after the followingmath symbols used as verbs, conjunctions, or operators: , , , , , , , , , , ·, , , , , Π, Σ, and .When used to describe a quantity, they are closed up:Patient age 30 years. Values were 50 to 25. Whiteblood cell count is expressed as 109/L. 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 31

Typography, Tagging, DisplayAddition of XML (discussion and tagging examples) XML (extensible markup language) provides rules fornaming and defining parts of a document and theirrelationship with each other. XML uses tags in start-end pairs (such as title Title ofthe Article /title and body /body ) to define theelements in that piece of content. For more on JATS tagging, .1d3/chapter/gen-intro.html. 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 32

Electronic Editing WorkflowSoftware programs have text editing functionality that allows usersto view edits and track changes. Some newer software programspermit collaborative writing and editing. How authors and editorsrespond to the editing depends on not only the software programbut also the technologies and workflow involved.For example, JAMA Network manuscript editors send editedmanuscripts to authors showing text insertions and deletions andcomments/questions as a PDF file. Authors can respond by usingediting/commenting tools directly on the PDF; by printing it out,marking up the copy, scanning it, and returning via email; or byoutlining corrections and query answers in an email. Authors arealso provided with proofs that are generated programmatically tolook like a composed proof for initial review before finalcomposition and publication. 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 33

XML-Based Workflow (cont)The JAMA Network journals have created efficiencies by using a“single-source” workflow. In this process, content remains in theoriginal document format (eg, Word) and is stored with the XMLfile and related content (eg, supplemental files, multimedia).Because XML is the basis of this workflow and content, anychanges required (before, during, or even after publication) mustbe made in the source document and new XML generated. If anindividual output is corrected but the source file is not, any currentand future versions of that content will not reflect the change.For example, if a correction is made to the HTML version only,and the source file is not updated, the PDF will not contain theupdated content. 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 34

Guidelines Added to Resources SectionSection on Guidelines added to Resources chapter Committee on Publication Ethics(COPE). https://www.publicationethics.org EQUATOR Network. https://www.equator-network.org International Committee of Medical Journal Editors (ICMJE)Uniform Requirements. https://www.icmje.org World Association of Medical Editors (WAME) policystatements. http://www.wame.org/policies-and-resources 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 35

Publishing Glossary: UpdatesMany additions and deletions, especially to reflecttechnological updates to publishing, documentcreation and retrieval, and communication Removal of CD-ROM, CPU, DOS, elite type, fax, harddisk, internet, keyboard, LAN, mainframe, mouse, pageproof, password, PC, program, RTF, storage Addition of cloud, ghost writer, IP address, JATS,landscape, NISO, open access, scholar’s margin,stylesheet, STEM, thin space, Unicode 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 36

Editorial Assessment: Corrections Corrections are important to theintegrity of the publishedliterature Errors range from relativelyminor and inconsequential errorsto major errors that invalidate theresults and the underlyingscience Christiansen S, Flanagin A. Correcting themedical literature: “to err is human, to correctdivine.” JAMA. 2017;318(9):804-805.doi:10.1001/jama.2017.11833 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 37

Editorial Assessment: CorrectionsMinor ErrorSubstantive ErrorsInconsequential error (eg, atypographical error that couldresult in misunderstanding)Errors requiring a Correction notice(eg, author name misspelled,incorrect numbers, important missinginformation)Article corrected onlineCorrection notice publishedAn indication of correction anddate of correction are added tothe article information (HTMLand PDF versions)The article is corrected online withindication of correction and date ofcorrection added to the articleinformation (HTML and PDFversions)No Correction noticeThe Correction notice and correctedarticle are reciprocally linked 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 38

Pervasive errorsInadvertent errors that result in the need to correct importantor numerous data and information in the abstract, text, tables,and figures (eg, a coding error)No major changesChange and validChange andinvalidIf none of theconclusions orinterpretations areaffected and there areno statistically significantchanges in the resultsIf the direction orsignificance of theresults, interpretations,and conclusionschange—and thescience is still validIf the results,interpretations, andconclusionschange—and thescience is no longervalidLetter of explanationand CorrectionRetraction andReplacementRetraction 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 39

New Option: Retraction and Replacement Why? – 21% of retractions are due to error, not misconduct This mechanism allows authors to do the right thing without thestigma or penalties associated with retractions When? - Used judiciously – for cases of inadvertent pervasiveerrors that when corrected change the findings, interpretations,and/or conclusions And after review – the science is still considered valid How? - Requires a Letter of explanation from all authors An itemization of all errors and corrections Replacement article retains the original article DOI and anyusage and citation metrics No “retraction” or do not use watermark 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 40

Retraction and ReplacementArticle InformationRetraction and Replacement: This article was retracted and replaced on August 23, 2018, to fix errorsthroughout the article and tables (see Supplement 2 or the retracted article with errors highlighted andSupplement 3 for the replacement article with corrections highlighted). 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 41

Retraction and Replacement 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 42

Ethical and Legal Updates: Authorship Contributor: anyone – an author, a collaborator, writer,assistant, etc Author: meets all 4 ICJME criteria and completes an authorshipform.– Byline author: Author name in byline– Nonbyline author: author name not in byline – listed at theend of article Collaborator: nonauthor member of a formal group whocontributes significantly Group author: a group of individuals, usually involvingmulticenter study investigators, members of working groups, andofficial or self-appointed expert boards, panels, or committees,who wish to display a group name to indicate authorship. 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 43

Ethical and Legal Updates: AuthorshipAuthors et al – who is who? 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 44

Shared Authorship Positions It has become increasingly common for authors to request“co-first authorship,” “co-senior authorship,” or some otherindication of equal contribution. Journals accept indication of co-first authorship – butsomeone’s name will need to go first in the byline or authorlist. Requests for “co-first authorship” beyond 3 or 4 namedauthors may not be justifiable. This information can be displayed in the Acknowledgmentjust before the list of author contributions, such as “Drs Brown and Jones served as co-first authors andcontributed equally to the work.” 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 45

Corresponding Authors Requests for having up to 2 individuals listed as correspondingauthors on a published article will be considered if justified. In such cases, 1 author must be designated as the primary pointof contact who will serve the primary corresponding author For all communications with the journal Will review an edited manuscript/proof Make decisions regarding release of information to the newsmedia Handle any postpublication inquires, errors/corrections, etc Two can be listed in the Corresponding Author section of thepublished article, but the primary corresponding author will belisted first. 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 46

Formatting 2 Corresponding AuthorsFrom same institutionCorresponding Authors: Jie Qiao, MD, PhD (jie.qiao@263.net), andTianpei Hong, MD, PhD (tpho66@bjmu.edu.cn), Peking University ThirdHospital, 49 N Garden Rd, Beijing 100191, China.From same institution, different departmentsCorresponding Authors: Jie Qiao, MD, PhD, Center of ReproductiveMedicine (jie.qiao@263.net), and Tianpei Hong, MD, PhD, Department ofEndocrinology and Metabolism (tpho66@bjmu.edu.cn), Peking UniversityThird Hospital, 49 N Garden Rd, Beijing 100191, China.From different institutionsCorresponding Authors: Linhong Wang, PhD, Chinese Center for DiseaseControl and Prevention, Beijing 100050, China (linhong@chinawch.org.cn);Yonghua Hu, MD, Department of Epidemiology and Biostatistics, School ofPublic Health, Peking University, Beijing 100191, China(yhhu@bjmu.edu.cn). 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 47

Intellectual Property Updates: Data Sharing Many research sponsors and government agencies havepolicies to encourage data transparency and sharing. In 2017, the International Committee of Medical JournalEditors (ICMJE) issued a statement on sharing clinical trialdata that indicates new requirements for sharing of dataunderlying the results presented in published clinical trials.(JAMA. 2017;317[24]:2491–2492. doi:10.1001/jama.2017.6514) Beginning in July 2018, data sharing statements arerequired for reports of RCTs; optional for other study types Statements are required, but actual sharing is not yetrequired 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 48

Data Sharing Statement – Questions for Authors Will data be shared? Yes or no (with optional explanation If yes, what types of data– Deidentified participant data– Participant data with identifiers– Data dictionary How shared and where to access? When will data be shared? Will supporting documents be shared– Trial protocol and statistical analysis plan– Statistical/analytic code– Informed consent document Who can access? For what types of analyses? By whichmechanisms (eg, with investigator support or a signedagreement)? Any restrictions on access or use? 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 49

Data Sharing Statement: JAMA ExampleData Sharing Statement: See Supplement 4. (This is a PDF) 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 50

Data Sharing Statement – Other Examples New England Journal of Medicine: Links to a PDF– A data sharing statement provided by the authors isavailable with the full text of this article at NEJM.org. Annals of Internal Medicine: Included in ArticleInformation section– Reproducible Research Statement: Studyprotocol: Available from Dr. Miller(email, dmiller@wakehealth.edu). Statistical code and dataset: Available to approved persons through agreement withthe authors (email, dmiller@wakehealth.edu). 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 51

Public access and open access Public access: free access to content, permitting users toread, download, print, search, and link to content, but withcopyright restrictions and limitations on sharing and reuse. Many journals make research articles free public access at6, 12, or 24 months after publication; required for USfunded research since 2013 Many journals deposit research articles in publicrepositories (eg, PMC) for free public access at 6,12, or 24months after publication; some permit posting beforepublication in preprint servers or repositories 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 52

Open access Open access: Users have unrestricted access withouttypical copyright restrictions and can freely read,download, copy, distribute, print, search, or link to fulltext of articles, and reuse and modify the content in partor whole, without permission, for any lawful purposeprovided that authors are properly acknowledged andcited. Typically requires an author processing charge (APC)– Range: 1200 to 5000– Clinical medicine journal average: 2093– Multidisciplinary journal average: 3464– Data from Pay It Forward report for the year 2013 UC-Pay-It-Forward-Final-Report.rev .7.18.16.pdf 2018 American Medical Association. Confidential and Privileged.AMWA session 2018 Slide 53

Differences between public and open accessPublic AccessFree to readOpen AccessFree to read, reuse, modifywithout permissionNo author feeAuthor processing charge(APC)Delayed access (6, 12, 24Immediate access withmonths after publication)publicationTransfer of copyright orUse of CC license; authorpublication license to journal retains copyrightRequired by NIHRequired by some funders,eg, Gates, Wellcome Trust 2018

Grammar Update Singular “they” AMA Manual will join other resources, such as The Chicago Manual of Style and AP Stylebook, in permitting use of they as a singular pronoun when rewriting the sentence as plural would be awkward or unclear. [Note: the other manuals say that