Information for authors

The Editorial Board encourages authors to familiarize themselves with the information below to ensure that their submissions are handled efficiently and evaluated fairly in accordance with the JCI's guidelines and policies.

Access our submission site or create a new author account

Revised March 27, 2018 | Revision history

 

 

Submission categories

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Research

Research manuscripts provide substantial new mechanistic insights into biology and disease. They are complete descriptions of studies of scientific importance and broad interest to the JCI readership.

Clinical Medicine

Clinical Medicine submissions report new medical therapies, interventions, diagnostic advances, or observational studies in humans that have the potential to change medical practice. Reports of interest include intervention trials, new procedures, or diagnostic advances that provide an early demonstration of clinically relevant outcomes.

Note: The JCI is no longer considering new Technical Advance submissions. Submissions in this category may be submitted to JCI Insight.

Note: The recommended length for Research and Clinical Medicine submissions is 9,000 words; the maximum allowable length of an accepted manuscript is 12,000 words, including the text of legends, tables, and references.

Concise Communication

Note: The Brief Report category was reconfigured and renamed Concise Communication as of November 2017.

Concise Communication articles are brief but complete highly significant findings reported in a shorter format of 4,000 words or fewer in length; this strictly enforced word limit includes all text (the title page, main text, references, legends, and table). Concise Communications are limited to 4 display items (figures and/or tables). The size of a figure must not exceed three-quarters of a portrait-oriented page. The Study Approval section must be included in the main text Methods section. A complete, detailed description of methods is also required and may appear in the main text, a Supplement, or a combination of both.

 

Manuscript submission

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Manuscripts must be submitted through the JCI’s submission website. An account is required in order to proceed with submission; authors can register for accounts or access their existing accounts by following the instructions at the-jci.org. In brief, during the online submission process, submitters are asked to state adherence to JCI editorial policies; specify funding sources; upload the manuscript and supporting documents; and enter a cover letter, abstract, author list, and keywords. During this process, authors may suggest a member of the Editorial Board with appropriate expertise to handle their submission. In addition, authors may note up to 2 reviewers they wish to exclude and reason(s) for exclusion.

There is no charge for submission to the JCI.

Required documents

First-time submissions

  • PDF file of the entire manuscript, complete with figures, figure legends, and tables, prepared as described in Manuscript preparation. The preferred format for the presentation of figures is to show each figure together with its corresponding legend on the same page.
  • PDF file of any cited reference that is in review or in press at another journal, or is publicly unavailable.

Revised submissions

  • PDF of the complete manuscript (as above) prefaced by a point-by-point response to reviewer comments.
  • In addition, provide a Word or RTF file of the manuscript with text only (no figures); the file should also include tables in Word format.
  • Publication-quality figures in TIFF format will be requested from corresponding authors. See detailed instructions for figure preparation.
  • If the submission includes any cropped gels, upload a separate PDF, PPT, or PPTX file (distinct from any other supplemental material you provide) that displays the entire unedited gel. Clearly indicate which bands were used in the figures.
  • Clinical Medicine submissions ONLY

 

 

Manuscript preparation

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Manuscript content and format

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Research and Clinical Medicine manuscripts include the following sections (see Requirements specific to Clinical Medicine submissions):

Note: The recommended length for Research and Clinical Medicine submissions is 9,000 words; the maximum allowable length of an accepted manuscript is 12,000 words, including the text of legends, tables, and references.

Concise communication manuscripts include the following (see Requirements specific to Concise Communication submissions):

  • Title page
  • Abstract
  • Introduction
  • Combined Results and Discussion
  • Methods
  • Author contributions
  • Acknowledgments
  • References
  • Display items (limit of 4): any combination of figures and tables
  • Supplemental material, if applicable

Note: The maximum allowable length for an accepted Concise Communication manuscript is 4,000 words, including the text of legends, tables, and references.

For all manuscripts, ensure that:

  • Each section starts on a new page.
  • Figure legends appear on the same page as the corresponding figures.
  • The manuscript is double-spaced throughout, including references and tables; however, figure legends may be single spaced if necessary to keep a figure and its legend on the same page.
  • All pages are numbered.

Title page

Title

The manuscript title should be clear, concise, descriptive, and limited to 10 words including conjunctions. Subtitles, colons, and nonstandard abbreviations are unacceptable. For publication, titles may be revised by the JCI to ensure clarity and accessibility to our wide readership, with the final approval of the authors.

Authors and affiliations

First and last names of all authors, as well as their affiliations (departments, institutions, and locations) during the period when the work was performed. Assign affiliation footnotes consecutively using superscript numbers (1, 2, 3, etc.). If any author's affiliation has changed since completion of the work, specify the present affiliation and location below the numbered list. Provide the complete name, address, telephone number (including country code, where applicable), and e-mail address of the corresponding author. If the author list includes a consortium/study group as author (e.g., CARDIoGRAM Consortium) without specifying the individuals’ names, list the members of each consortium named and their affiliations in the Supplemental material; add the following sentence to the Acknowledgments section: “See Supplemental Acknowledgments for consortium details.”

Conflict of interest statement

Provide a statement consistent with the JCI’s conflict of interest policy. If no author has a conflict, include the following: “The authors have declared that no conflict of interest exists.”

Abstract

The abstract may not contain any primary data or references; all nonstandard abbreviations must be defined.

  • Research and Concise Communication submissions: Unstructured abstract of no more than 200 words stating the rationale, objectives, findings, and conclusions of the manuscript.
  • Clinical Medicine submissions: Structured abstract of no more than 250 words providing trial information under the following sections:
    • Background. Provide context or background for the study and state the study’s primary objective or hypothesis in 1–2 sentences.
    • Methods. Describe the basic procedures used during the study, including selection of study subjects and observational and analytical methods. Define the primary outcomes that were measured for each group of subjects.
    • Results. Summarize the main findings, including specific effect sizes and their statistical significance, if possible. Include (if relevant) the number of participants in each group, the primary outcome for each group, and any significant adverse events or side effects.
    • Conclusion. In 1–2 sentences, state the principal conclusions, emphasizing new and important aspects of the study or observations.
    • Trial registration. List the public registry and trial registration number, e.g., ClinicalTrials.gov NCT00950003.
    • Funding. List all sources.

Main text

  • The manuscript includes the following sections: Abstract; Introduction; Results; Discussion (combined Results and Discussion in the case of Concise Communications); Methods; Author contributions; Acknowledgments.
  • Nonstandard abbreviations are defined at first mention, with the abbreviated form appearing in parentheses. Thereafter, they should be used without definition. Standard JCI abbreviations do not need to be defined.
  • Methods of statistical analysis are summarized in a stand-alone paragraph titled Statistics.
  • A specific declaration of approval of human and animal studies by the appropriate institutional review board(s) must be made in a stand-alone paragraph titled “Study approval” at the end Methods; in the case of human studies, this includes a statement indicating that written informed consent was received from participants prior to inclusion in the study. Participants should be identified by number, not by name. Manuscripts without declaration of ethical approval for experiments will not be reviewed.

Author contributions

Provide a paragraph titled “Author contributions” specifying how each author (identified by initials) contributed to the manuscript. Examples include designing research studies, conducting experiments, acquiring data, analyzing data, providing reagents, and writing the manuscript. Multiple contributions may be listed for a single individual, and more than one individual may be associated with a single contribution.

Acknowledgments

An Acknowledgments paragraph states sources of support in the form of grants, equipment, or drugs. Other appropriate acknowledgments (for example, to other scientists for their help or advice) may also be included.

References

  • References are cited in the text by sequential numbers in parentheses (do not use superscript).
  • In the References section, references are numbered in the order in which they appear in the text.
  • JCI reference style follows the AMA Manual of Style (10th edition, pages 39–79), with the following exception: when a publication has more than 6 authors, include only the first author, followed by “, et al.” Journal names are abbreviated according to the NLM catalog. The JCI strongly encourages authors to use EndNote in Microsoft Word to ensure that the format is correct. Reference style examples are provided here.
  • Submitted manuscripts, manuscripts in preparation, unpublished observations, personal communications, and preliminary report citations are cited parenthetically in the text and not in the References section. Obtain and submit written permission (an e-mail is sufficient) when citing a personal communication or unpublished observation.

Figures and figure legends

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Figures
  • Figures are cited sequentially in the text using Arabic numerals (for example, Figure 7).
  • Type appearing within figures (axis labels, for example) is in Helvetica or a similar typeface and is of sufficient size and contrast to retain clarity if reduced in size.
  • Avoid use of bold type in figure labels.
  • Scale bars are defined in the figure legends, not in the figures themselves.
  • Standard abbreviations are used whenever possible.
  • Avoid gratuitous use of color for decorative effect, boxes around graphs and figures, and small type and symbols on large graphs; avoid pairing red and green in graphs to ensure legibility for color-blind readers. Whenever possible, do not place labels over any part of a color figure.
  • Do not include tabular material within figures.
  • For submission to the JCI, compressed figure files should be included in the PDF of the manuscript. Authors will be required to submit high-resolution figures prepared according to the JCI figure instructions.
Figure legends
  • Limited to 300 words each, including a short title and an explanation in brief but sufficient detail to make the figure intelligible without reference to the main text (unless a similar explanation has been given in a preceding figure legend).
  • Include a key to any symbols used.
  • The exact number of samples (n) is included for each figure panel presenting multiple samples.
  • The statistical test used is described in each figure legend.
  • Each figure (including all parts, if applicable) with corresponding legend must be presented on its own page.

Tables

  • Tables are self-contained and self-explanatory.
  • Tables are accompanied by brief titles.
  • Footnotes are assigned as superscript capital letters starting with A and continuing in alphabetical order.
  • Tables with sections (for example, Table 1A, 1B, 1C) are not acceptable.
  • Each table must be presented complete on its own page.

Graphical abstracts

Authors may submit a graphical abstract, a single image that visually represents the primary findings of an article. Published graphical abstracts appear at the top of the online version of the artice. Details are available here.

Supplemental data

Authors of accepted manuscripts may provide related supplemental data to be posted online along with the published manuscript. This may include figures, tables, videos, or appendices but excludes large datasets. All Supplemental Data information (except videos) should be combined into a single PDF file. Before submission, carefully review all files; they will not be checked by a copy editor. The JCI is not responsible for any errors contained in data supplements.

Accepted file formats

  • PDF files should be used for any submission of the complete manuscript; supplemental data (except for long tables in Excel format or videos); and, if applicable, unpublished references, ICMJE uniform disclosure forms, and reporting checklists.
  • PDF, PPT, or PPTX files showing the full, unedited versions of any gels that are cropped in the figures.
  • For revised submissions, the manuscript should be submitted in Word or RTF, along with the PDF.
  • If a manuscript is accepted, figure files should be in TIFF format (see figure instructions).

Nomenclature

Specific reporting guidelines

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Conflicts of interest

A detailed conflict of interest policy is available here. All authors are expected to disclose financial relationships, consultancies, stock or equity interests, patent-licensing arrangements, or any other interest of a financial nature, whether or not directly related to the subject material of the study, since it could undermine the objectivity, integrity, or perceived value of the publication.

Experimental design

Randomization

If samples have been randomly assigned to experimental groups or processing order, a statement specifying the randomization procedure should be included in Methods.

Blinding

If investigators have been blinded to the sample group allocation during the experiment or analysis of the experimental outcome, a statement describing the level of blinding should be included in Methods.

Number of replicates (experimental unit)

Authors must provide sufficient details about the sample collection to distinguish between independent biological replicates and technical replicates. Biological replicates represent samples from different sources, while technical replicates represent an assay of a sample from the same source multiple times. The exact number of samples (n) for each figure panel representing multiple experiments must be included in the figure or its legend. For representative experiments, authors must state the number of times this experiment was repeated.

Methods/experimental procedures

The Methods section should include an adequate description of the experimental procedures to allow researchers in the field to reproduce the work. Authors may include additional methods in the supplemental materials as needed.

Statistics

Authors must fully describe all statistical tests used during the analysis in the methods, and the statistical test used must also be reported in the relevant figure legend. We encourage authors to describe methods used to assess whether the data met the assumptions of the statistical test utilized (e.g., normal distribution). Authors must specify whether statistical tests are one-sided or two-sided. When making multiple comparisons on a single data set, authors should choose statistical tests that account for multiple groups (such as ANOVA rather than a series of t tests). The statistical analysis should also correct for repeated measures when comparing multiple measurements within subjects. A statement describing inclusion/exclusion criteria must be included in Methods if any samples were excluded from the analysis. Error bars must be defined, either in Methods or in the legends themselves; e.g., “Data represent mean ± SEM.” Variance around the mean and statistical analysis should not be presented if fewer than 3 independent samples are included.

Graphs and images

  • It is strongly encouraged that data be displayed in their raw form and not in a way that conceals their distribution. We recommend that individual data be presented as dot plots next to the average for the group with appropriate error bars. Presenting data as columns with error bars (dynamite plunger plots) is discouraged.
  • No specific feature within an image may be enhanced, obscured, moved, removed, or introduced. The groupings of images from different parts of the same gel or from different gels or fields or exposures must be made explicit by the arrangement of the figure (e.g., using dividing lines) and in the text of the figure legend. Adjustments of brightness, contrast, or color balance are acceptable if and as long as they do not obscure or eliminate any information present in the original. Nonlinear adjustments (e.g., changes to gamma settings, curves, or input levels) must be disclosed in the figure legend. The Editors reserve the right to consult the Office of Research Integrity or the appointed official at the authors’ home institution if the figures appear to have been manipulated.
  • Images and datasets should generally only be presented once in a manuscript. Any instances in which images or datasets, including control data, are presented in multiple figure panels in the manuscript or supplement must be explicitly described in the figure legend.
  • Authors of new submissions that contain cropped gels/blots are encouraged, but not required, to submit a file that contains the entire unedited gel for all representative cropped gels in the submission. Each gel should be annotated as “Full unedited gel for Figure X,” and the authors should highlight which lanes of the unedited gel correspond to those shown in the cropped images within the manuscript. This file should be separate from the primary submission PDF and distinct from any other supplemental data provided. For authors of revised submissions, this file is required. Authors may choose whether to publish full uncut blot data if their submission is ultimately accepted.

Human subjects

All clinical investigation must have been conducted according to Declaration of Helsinki principles. All human studies must have been approved by the appropriate institutional review board(s), and a specific declaration of such approval must be made in a stand-alone paragraph at the end of the Methods section, including a statement indicating that written informed consent was received from participants prior to inclusion in the study. Participants should be identified by number, not by name. Manuscripts without declaration of ethical approval for experiments will not be reviewed. For manuscripts that include patient photographs, a separate statement must be included, in the Study Approval section of Methods, that written informed consent was provided for pictures appearing in the manuscript.

Animals

Authors are encouraged to follow the ARRIVE (Animal Research: Reporting of In Vivo Experiments) guidelines for reporting on animal studies. For animal models, the precise genotype, strain, source, number of backcrosses, sex, and age of animals studied must be provided in the manuscript. All animal studies must have been approved by the appropriate institutional review board(s), and a specific declaration of such approval must be made in a stand-alone paragraph at the end of the Methods section.

Cell lines

Authors must describe the source of all cell lines utilized. Authors are also encouraged to include information regarding authentication of cell lines and testing for mycoplasma contamination.

Antibodies

A description of all antibodies used is included in Methods, providing the source and catalog/clone number for commercial antibodies or a description/reference to a description of the generation of custom antibodies.

Large datasets

Large datasets for gene expression microarrays, SNP arrays, and high-throughput sequencing studies must be deposited in a public repository. Microarray data must be deposited in a MIAME-compliant public database. High-throughput sequencing data must be deposited in a MINSEQE-compliant public database. Provide the relevant accession numbers in the text of the main manuscript. Deposition of other types of large datasets in a public repository is strongly encouraged. Other supporting datasets must be made available to any interested reader on the publication date from the authors directly. Researchers who encounter a persistent refusal by an author of a paper to comply with these guidelines should contact the Editors’ office by e-mail at editors@the-jci.org.

Original nucleotide or amino acid sequences

Authors must submit original nucleotide or amino acid sequence data to GenBank, the EMBL-EBI database, DNA Databank of Japan (DDBJ), or another appropriate publicly available database in general use in the field that gives free access to researchers from the date of publication.

Chemical compounds

For any new chemical compound described, the chemical structure must be reported. Authors must also provide adequate data to support assignment of identity and purity of the compounds. For most compounds, chemical identity should be established through spectroscopic analysis. Authors should include adequate experimental and characterization data in Methods or Supplemental Methods. Methods describing the synthesis of new compounds must also be included.

T cell assays

For authors reporting T cell assays and NK cell assays, we recommend including Minimal Information About T cell Assays (MIATA) in Methods, figure legends, or elsewhere as appropriate.

Software

Authors describing new software that they have developed are encouraged to report the source code for software in the Supplemental Methods or include a statement regarding how the software can be obtained.

Requirements specific to Clinical Medicine submissions

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In accordance with the requirements set forth in the Uniform Requirements for Manuscripts Submitted to Biomedical Journals issued by the International Committee for Medical Journal Editors (ICMJE), we ask that authors provide specific information regarding the ethical treatment of research participants, patient consent, patient privacy, protocols, authorship, and competing interests. A Clinical Medicine submission must include:

Supporting materials required for the submission of specific study types

The JCI recommends that authors check the Equator Network for a list of reporting guidelines for each study type.

Clinical trials
  • A structured abstract
  • Conflict of interest documentation (an ICMJE uniform disclosure form should be uploaded as supplemental data)
  • Clinical trial registration information
  • Appropriate reporting checklists and flow diagram (see below)
  • Declaration of institutional review board approval and informed patient consent
  • Trial registration number
  • Reporting guidelines: The appropriate flow diagram should be included in the manuscript, and the corresponding checklist should be included in the supplemental materials.
  • Clinical study protocols: The JCI encourages (but does not require) authors to submit a copy of the protocols associated with their studies in the supplemental materials. Indicate where study protocols can be accessed in the Methods section (e.g., URL).
Systematic reviews and meta-analyses

A systematic review is a literature review that follows an explicit protocol to systematically identify, appraise, and synthesize the findings of studies that address a similar question. A meta-analysis is a quantitative synthesis of the results of a systematic review.

  • Registration of systematic reviews. The JCI supports, but does not require, the prospective registration of systematic reviews. Authors whose systematic review was prospectively registered (for example, in a registry such as PROSPERO) should also provide the registry number in the abstract.
  • Reporting guidelines. Authors of systematic reviews and meta-analyses must provide a completed PRISMA checklist and flow diagram. Additionally, authors must state in the Methods section whether a protocol exists for their systematic review and, if so, indicate where this protocol can be accessed (e.g., URL).
Observational studies

The JCI defines observational studies as those in which the assignment of the medical intervention is not at the discretion of the investigator.

  • Trial registration. While registration is not required for all observational studies under ICMJE guidelines, the JCI encourages authors to register. Observational studies may be registered with any of the trial registries approved by the WHO, which can be viewed here.
  • Reporting guidelines. Trial authors must adhere to STROBE statement reporting guidelines. Check the STROBE statement website for information concerning specific study types, including observational studies in epidemiology, genetic association studies, cohort studies, case-control studies, and cross-sectional studies.
Diagnostic accuracy studies
  • The JCI defines a diagnostic accuracy study as a study that compares the performance of two or more diagnostic tests. Submissions must include the STARD checklist and STARD Flowchart of Diagnostic Test Results. The Methods section should provide a clear description that is sufficient for the reproduction of the study’s findings. Include a description of all measures used and any statistical measures employed. If applicable, provide details about samples, randomization, methods for blinding of observations, and number of observations. Additionally, indicate where study protocols can be accessed (e.g., URL).

Requirements specific to Concise Communication submissions

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  • The strictly enforced word limit of 4,000 words or fewer includes all text (the title page, main text, references, legends, and table [if applicable]).
  • Limit of 4 display items, including any combination of figures and tables
  • Each display item may be up to 3/4 page and must fit on a single page with its legend.
  • Combined Results and Discussion section.
  • The Study Approval section must be included in the main text Methods section. A complete, detailed description of methods is also required and may appear in the main text, a Supplement, or a combination of both.
 

In-Press Previews

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The JCI provides the option to publish a PDF of the accepted research paper as an In-Press Preview prior to copyediting and layout. Following provisional acceptance of the manuscript, the corresponding author may select the In-Press Preview option when resubmitting via our submission site. If the author chooses this option, the PDF will be published on the JCI website soon after acceptance, and the paper will be indexed by PubMed. This version will be replaced upon finalization of copyediting, layout, and author proofing according to the journal’s regular publication schedule.

  • Corresponding authors choosing the In-Press Preview option will be asked to provide a clean PDF of the paper, omitting any editorial comments/responses or redlining.
  • JCI staff will confirm basic identifying information (e.g., title, author names, affiliations) with the corresponding author prior to publication of the In-Press Preview.
  • NOTE: No changes may be made once the In-Press Preview version is published on the JCI website; any edits must be included in the author proof.
 

After acceptance

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Copyright

All authors associated with the submission are sent an e-mail requesting assignment of copyright to the American Society for Clinical Investigation (ASC)I prior to publication. Authors with Wellcome Trust or related funding should request a CC-BY license, and the ASCI will ensure that these articles are published according to the funding agency's policy.

Please see the JCI’s Licensing information for copyright information.

Publication costs

All JCI research articles are freely available online at the journal's website immediately upon publication. Charges (in US$) assessed to authors help support publication of the JCI. Authors will receive an invoice with the publication proofs. For publication of Research and Clinical Medicine articles, authors will be assessed $4500. For Concise Communications, the publication fee is $3000.

Title and abstract edits

For publication, titles and abstracts may be revised by the JCI to ensure clarity and accessibility to our wide readership, with the final approval of the authors.

Publication proofs

Proofs will be sent to the corresponding author, who will be asked to answer copy editor queries and make any necessary corrections; substantive changes to the text are not permitted. If the corresponding author will be unavailable, JCI staff must be informed of another author responsible for the proof. The proof must be returned within 2 days; late proofs could lead to a delay in publication.

Depositing in PubMed Central

Authors of articles published in the JCI do not need to submit their accepted articles separately to PubMed Central. The JCI deposits all articles in PubMed Central, and all research typically becomes available in Pubmed Central three months after publication. This satisfies the NIH Public Access Policy and other similar funder requirements. For authors of research articles whose funders require it, the JCI will deposit research articles in PubMed Central with a CC-BY license and without an embargo.

Indexing information

The JCI is indexed in the following resources:

Press embargoes

The Editorial Board recognizes that some authors may wish to publicize their work in the lay press. An embargo date and time is established for each article to be published in the JCI, and violation of the embargo by authors is considered grounds for withdrawal of the manuscript from publication and/or other measures that the Editors may choose to take. Any specific questions about the JCI embargo policy should be addressed to the Science Editors at press_releases@the-jci.org.

 

 

Editorial policies and practices

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Prior publication

The JCI considers the following to be prior publication and therefore unacceptable:

  • any printed or online material describing the findings, methods, or results of a submitted/in-press manuscript in excess of 400 words
  • any published tables or illustrations that in any way duplicate the content of another manuscript
  • videotapes of professional meetings distributed to the public or the press describing data included in a manuscript submitted for publication or in press
  • any interview given to members of the scientific or lay press describing data included in a manuscript submitted for publication or in press

The JCI does not consider doctoral theses or dissertations to be prior publications. The JCI will consider manuscripts that have been posted to a community preprint server; authors must disclose the preprint server and the accession number or DOI in their cover letter. At the time of publication, authors should ensure that preprint server updates the preprint with a link to the published article, including the DOI link.

Review of manuscripts

The Science Editors assign manuscripts to appropriate Associate Editors. Papers may be rejected without external review if the Associate Editor, together with a Science Editor or the Editor-in Chief, determines that the study does not significantly advance the field or the subject material is inappropriate for the JCI’s readership. When papers are sent for external review, the choice of reviewers is made by the Associate Editor and may include reviewers suggested by the authors. Requests by authors to exclude a specific potential reviewer will be honored to the greatest extent possible if a compelling reason is provided. At least two, and generally three, expert referees are asked to review the manuscript in a timely manner and to assign a priority based on content, originality, quality, relevance, and interest. Authors are informed of the final decision by e-mail, with applicable comments from reviewers and Editors included.

ASCI members. Any current ASCI member who is a corresponding author of a first-round submission to the JCI may designate one submission per calendar year to be guaranteed for external peer review. Submissions must fit within the scope of the journal and will be held to the same standard as other manuscripts considered by the Editorial Board. Please note previously submitted manuscripts are not eligible for guaranteed external review. Upon submission of a manuscript, eligible ASCI members who have not yet used this option for the calendar year will receive an e-mail notification that the option is available and must respond within 2 days to elect this option.

Confidentiality

The peer-review process rests on the assumption that an assigned reviewer will treat all manuscripts as privileged information. A reviewer may request advice from another party, subject to the general principle of confidentiality and notification of the JCI.

Revisions, rejections, and rebuttals

Manuscripts may be accepted with no changes, provisionally accepted pending minor revisions, or rejected. For a rejected manuscript, if the reviewers and the Board believe that the paper, if appropriately revised, will merit a high enough priority to be published in the JCI, the authors are invited to submit a revision. All revised manuscripts are carefully reexamined. While acceptance cannot be guaranteed, the Board will make every effort to ensure that revised manuscripts are accepted presuming that the authors are able to address all reviewer criticisms and that no new studies published in the interim have compromised the paper’s novelty. If the authors of a rejected manuscript believe that a serious scientific error occurred during the review process, they may send a rebuttal explaining why the Board should reconsider the decision (see Contacting the JCI). While few rebuttals are successful in reversing the original decision, they are taken seriously, and their handling can take several weeks; we receive a large number of manuscripts each week to which we must give first priority.

If authors of rejected manuscripts are subsequently able to make new advances that go far beyond the original submission, they may consider submitting a substantially revised manuscript for de novo review. The authors should refer to the prior version in their cover letter, particularly to indicate how the present version differs. The Editors will make a determination of whether the work is substantially advanced beyond the original submission. Note that de novo submissions are considered as new papers and may be sent to the same or independent referees.

Contacting the JCI

Questions regarding manuscript handling and status should be addressed to staff@the-jci.org. To avoid the possibility of misinterpretation and/or errors in communication, information will be given only to the corresponding author.

Questions concerning editorial policies or decisions should be addressed to the Science Editors at editors@the-jci.org. Other members of the Editorial Board do not take calls or written inquiries from authors concerning decisions or other editorial matters. In general, responses are sent after evaluation of the written material and subsequent discussion by the Editorial Board.

Authors may submit inquiries to the JCI regarding manuscripts of potential suitability. Inquiries must include the manuscript abstract and a statement detailing the reasons why the manuscript might be of interest to the journal’s readership. Decisions on such inquiries are not a substitute for peer review but are intended to provide informal guidance to authors in determining where to submit their research for full peer review.

Legal status of manuscripts

By submitting a manuscript to the JCI, the authors agree to subject it to the confidential peer-review process outlined above. However, all manuscripts remain the property of the submitting author(s) unless a decision to accept the manuscript is made and the authors officially assign copyright to the ASCI.

Reagent sharing

As of the date of publication, authors will be required to make materials and methods used available to academic researchers for their own use. No exceptions will be made to this policy. This requirement includes antibodies, cell lines, and any newly created mutant animals. Animals can be made available through the authors' institution or via a publicly available repository. Other reagents, methods, etc., must be made available to the academic community. Failure to adhere to these guidelines will be considered a violation of the authorship agreement and could result in retraction of the published article.

Datasets

Large datasets for gene expression microarrays, SNP arrays, and high-throughput sequencing studies must be deposited in a public repository. Microarray data must be deposited in a MIAME-compliant public database. High-throughput sequencing data must be deposited in a MINSEQE-compliant public database. The relevant accession numbers must appear in the main text of the manuscript. Deposition of other types of large datasets in a public repository is strongly encouraged. Other supporting datasets must be made available to any interested reader on the publication date from the authors directly. Researchers who encounter a persistent refusal by an author of a paper to comply with these guidelines should contact the Editors’ office by e-mail at editors@the-jci.org.

Scientific integrity

In general, the JCI adheres to guidelines established by the US Department of Health and Human Services’ Office of Research Integrity. For further information, refer to the Office’s website at http://ori.hhs.gov/.

Duplicate publication and scientific fraud are rare events that have a very serious impact on the integrity of the scientific community. If the Board discovers or is presented with evidence of such problems, the Board will contact the appropriate official(s) at the institution(s) from which the manuscript originated. It is then left to the institution(s) in question to pursue the matter appropriately. Depending upon the circumstances, the journal may choose to publish errata, corrigenda, or expressions of concern, or to retract the manuscript in its entirety. If we detect any manipulation of images or figures prior to publication, we will automatically request all primary data for all figures for verification purposes.

When a member of the scientific community disagrees strongly with the methodology and/or conclusions of an article the JCI has published, but does not allege fraud, the JCI encourages the concerned individual to contact the authors of the article directly or to allow the natural corrective mechanisms of science to settle the issue with time.

Conflicts of interest

The Journal of Clinical Investigation and American Society for Clinical Investigation (ASCI) are dedicated to upholding the highest standards of integrity and ethical conduct in research, and in its evaluation and related communication. It is important that the editors, authors, and referees conduct themselves in accordance with stringent standards and transparent policies for addressing potential conflicts of interest. Herein, we delineate what constitutes a potential conflict of interest for the JCI as it relates to editors, authors, and referees. Those found in violation of these policies may be subject to sanctions as determined by the JCI editors.

Editorial conflicts of interest

The JCI editors (Editor in Chief, Deputy Editors, Associate Editors, Executive Editor, and Science Editors) are responsible for maintaining the highest possible standards in evaluating contributions to the JCI as well as for maintaining the integrity of the Journal. In the interest of establishing full transparency, editors are obliged to disclose any and all potential conflicts of interest to the JCI. We have determined two tiers of potential conflict and corresponding actions to be taken. The editors will report changes to their potential conflicts as they occur. An annual formal review of all disclosures will be performed in the evaluation of compliance.

First tier of potential conflicts for editors

  1. Ownership. If an editor currently has direct ownership of equity in a private or public company in the health care field of $10,000 or more (including restricted stock; the market price of all options, vested or unvested; and warrants), a first-tier potential conflict must be declared. Interests held by immediate family members (spouse or children) of the editor are included. This does not apply to ownership of mutual funds, where the editor does not directly control the purchase and sale of stocks.
  2. Income. If an editor has received $10,000 or more per annum of income from any single private or public company in the health care field in the preceding calendar year, a first-tier potential conflict must be declared. This includes any and all sources of financial benefit, including, but not limited to, consultancy, speaking fees, royalties, licensing fees, retainers, salary (including deferred compensation), honoraria, service on advisory boards, and providing testimony as an expert witness. Income generated by immediate family members (spouse or children) of the editor is included.
  3. Research support. If an editor’s research was funded by $50,000 or more per annum from a private or public company in the health care field in the preceding fiscal year, including funding for personnel working within the laboratory, a first-tier potential conflict must be declared.

If an editor declares a first-tier potential conflict relating to 1, 2, or 3, this information will be published on the JCI website and the editor will be recused from editorial discussion and decisions related to the manuscript. An editor will be considered to be in conflict if a manuscript is funded solely by an organization with which the editor has a potential conflict, regardless of whether a research institution employs the authors.

Second tier of potential conflicts for editors

  1. Relationship with a company. If an editor had a relationship with a private or public company in the health care field wherein the editor received some compensation for services, but the total amount of income was between $1,000 and $9,999 for the preceding calendar year, a second-tier potential conflict must be disclosed. This includes, but is not limited to, any compensation as detailed above in item 2.
  2. Relatives. If an editor has a close relative other than a spouse or child (sibling or parent) employed by or with a significant financial interest in a private or public company in the health care field, a second-tier potential conflict must be declared.
  3. Prospective employment. If an Editor is negotiating with, has arranged prospective employment with, or is expected to initiate a significant financial relationship as defined in 1, 2, or 3 with a private or public company in the health care field, a second-tier potential conflict must be declared.
  4. Personal. Editors will be required to declare a second-tier potential conflict if a manuscript is submitted by a close personal contact (former student, fellow or mentor, for example) or a recent collaborator (over the last 3 years). Relevant collaborations may include co-authoring a research article or serving as co-investigators on a grant.
  5. Competition. Editors will be required to declare a second-tier potential conflict if a submitted manuscript presents data that are highly relevant to a manuscript the editor has under review or in press elsewhere. Editors are prohibited from using unpublished information from the manuscripts under consideration by the JCI to further their own research, nor can they use new information gained from unpublished manuscripts for financial gain.
  6. Personal benefit. The editor must recuse himself/herself from discussion of a manuscript if he or she could benefit personally from its disposition. For example, if a manuscript is submitted describing the off-label use of a compound produced by a company for which an editor has a potential conflict, the editor must recuse himself/herself.
  7. Intellectual property. The editor must recuse himself/herself from discussion of a manuscript if he or she has a planned, pending, or awarded patent that could be positively or negatively impacted by the publication of a manuscript under consideration.

The second tier of potential conflicts will necessitate only internal disclosure to the Editorial Board and the JCI staff. The editor in potential conflict will also be recused from editorial discussion and decisions related to the manuscript.

The Science Editors or other editorial staff member designated by the Editor in Chief will be responsible for recording and updating all potential conflicts. The Editor in Chief of the JCI will review any JCI editorial staff potential conflicts.

We are aware that other potential issues may arise, and these will be evaluated by the Editor in Chief on a case-by-case basis.

JCI editors are discouraged from serving as editors for other primary research journals for which they would make final decisions on manuscripts. All such editorial duties for other journals must be approved by the Editor in Chief.

In order to avoid even the appearance of potential favoritism to institutional colleagues, manuscripts from Johns Hopkins University will not be handled by the Editorial Board at large, but instead in a separate process. In these circumstances, a Science Editor will be the only editor privy to the manuscript and, if the manuscript is sent for review, will work with an outside consultant to formulate a decision.

Author conflicts of interest

All authors are expected to disclose all financial relationships that could undermine the objectivity, integrity, or perceived value of a publication. The editors will keep the potential conflicts in mind while evaluating the manuscripts.

The JCI requires that all authors issue a statement disclosing all financial holdings, professional affiliations, advisory positions, board memberships, and patent holdings, as described below, even if they believe their conflict is not germane to the content of the submitted paper (these correspond to the first tier of potential conflicts defined for editors). Such potential conflicts will be published in a footnote if the manuscript is ultimately accepted. It is the responsibility of the corresponding author to gather the list of potential conflicts from each author and to communicate the list of all potential conflicts to the editors with the submission.

Potential conflicts to be disclosed by authors
  1. Ownership. If an author currently has direct ownership of equity in a private or public company in the health care field of $10,000 or more (including restricted stock; the market price of all options, vested or unvested; and warrants), a first-tier potential conflict must be declared. Interests held by immediate family members (spouse or children) of the author are included. This does not apply to ownership of mutual funds, where the author does not directly control the purchase and sale of stocks.
  2. Income. If an author has received $10,000 or more of income per annum from any single private or public company in the health care field in the calendar year preceding the date of the original submission, a potential conflict must be declared. This includes any and all sources of financial benefit, including, but not limited to, consultancy, speaking fees, royalties, licensing fees, retainers, salary (including deferred compensation), honoraria, service on advisory boards, and providing testimony as an expert witness. Income generated by immediate family members (spouse or children) of the author are included.
  3. Research support. If an author’s research was funded by $50,000 or more per annum from a private or public company in the health care field in the fiscal year preceding the date of the original submission, including funding for personnel working within the laboratory, a potential conflict must be declared.
  4. Intellectual property. If an author is an inventor on a planned, pending, or awarded patent, a potential conflict must be declared.

Any questions concerning these potential conflicts should be addressed to editors@the-jci.org.

Referee conflicts of interest

Referees should exclude themselves in cases where there is a material potential conflict of interest, financial or otherwise. We ask that referees inform the editors of any potential conflicts that might be perceived as relevant as early as possible following invitation to participate in the review, and we will determine how to proceed. Disclosing a potential conflict does not invalidate the comments of a referee, it simply provides the editors with additional information relevant to the review.

We ask referees to use their judgment in responding to our request for full disclosure, basing their response to the editors on the same financial criteria applied to authors and editors, as described above.

 

Revision history

  • March 27, 2018: Added to Publication proofs section that substantive changes are not acceptable.
  • February 22: Added Graphical abstracts (online).
  • January 15, 2018: Added new policy: consideration of preprints.
  • January 1, 2018: Added In-Press Preview description.
  • November 1, 2017: Replaced Brief Reports with new category: Concise Communications.
  • July 1, 2017: Revised to replace Duke with Johns Hopkins.
  • June 21, 2017: Revised to omit requirement for submission PDFs that figure and corresponding legend appear on same page.
  • March 2, 2017: Reivsed Required documents/First time submissions and /Revised submissions to specify that in the PDF, legends should appear on same page as figures.
  • February 1, 2017: Clarified application of CC-BY copyright licenses for authors of research articles whose funders require it.
  • January 7, 2017: Brief report publication fee changed from $2900 to $3000.
  • December 21, 2016: Added notice that submission fee is discontinued January 1, 2017.
  • October 7, 2016: Added Indexing information.
  • July 26, 2016: Figure instructions page revised to specify 600 ppi for all figures.
  • May 25 2016: Changed figure submission from acceptance to provisional acceptance; added text prohibiting reuse of data within article.
  • April 15, 2016: Updated link to new License information page.
  • April 6, 2016: Added recommendation to use EndNote for references.
  • January 20, 2016: Added link to Figures at top of page; in Figure Instructions, changed requirement from CMYK to RGB.
  • November 24, 2015: Added Executive Editor position.
  • October 9, 2015: Added link to JCI's Terms of Use under After acceptance > Copyright section
  • August 18, 2015: Revised "Authors and affiliations" to include instructions for group/consortium authors.
  • July 2, 2015: Added "Author contributions" requirement.
  • June 17, 2015: Changed manuscript designation "Regular" to "Research."
  • May 18, 2015: Figure legend word limit changed from 250 to 300.
  • May 6, 2015: Revised description of Clinical Medicine category.
  • March 17, 2015: Added description of guaranteed review for ASCI members.
  • December 4, 2014: Added word limit and flat publication fee to begin with April 2015 issue.
  • November 7, 2014: Combined the following pages: Research categories, Submitting your work to the JCI, Clinical medicine submission guidelines, Editorial policies and practices, and Conflict of interest policies. Added Intellectual property text to Conflict of interest policy.
  • March 25, 2014: Added requirement to deposit ChIP-Seq and RNA-Seq data.
  • December 3, 2012: Added Clinical Medicine category.
  • August 23, 2012: Added clarification that full uncut gels/blots be highlighted to demonstrate which lanes apply to the submitted manuscript.
  • August 6, 2012: Posting of "Gene nomenclature and style" document.
  • April 8, 2012: Upload of full uncut gels/blots for first-time submissions no longer required.
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