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EDITORIAL POLICIES REGARDING MANUSCRIPT SUBMISSION

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NIH Manuscript Submission Request: For more information, go to:

• About the NIH Public Access Policy

If the research described in the submitted manuscript has been funded in whole or in part by the National Institutes of Health (NIH), the following applies:

1. The NIH has adopted a voluntary policy that requests authors of NIH-funded research to submit their accepted manuscripts to the NIH PubMed Central repository.
2. The NIH program is voluntary and authors do not have to participate. NIH officials have given public assurances that there will be no repercussions if authors choose not to participate.
3. The AAI does not support this policy, which it views as a costly, duplicative effort by NIH that diverts federal dollars from biomedical research and threatens the integrity of the scientific record by creating multiple versions of the same article and allowing public dissemination of an unfinalized manuscript. The policy also puts authors at risk of inadvertently violating copyright agreements with the journals that publish their works. For more information on the AAI’s concerns about the NIH policy, go to About the NIH Public Access Policy.
4. Despite The AAI’s serious concerns about this policy, The AAI will accommodate authors who wish to submit their manuscripts to NIH, as described below. The AAI grants the undersigned corresponding author a onetime waiver permitting him or her to submit to NIH PubMed Central this manuscript, if accepted for publication by The JI, provided:

a) that the corresponding author agrees to instruct NIH to release the manuscript to the public no earlier than 12 months after final publication in The JI;

b) that the corresponding author agrees that no changes or modifications will be made to the version of the manuscript that has been accepted by The JI;

c) that this onetime waiver granted by The AAI applies solely to deposition into NIH PubMed Central and does not extend to any other repository, agency, or entity; and

d) that the corresponding author agrees to, and will include in the text of the abstract submitted to PMC, the following disclaimer:

This is an author-produced version of a manuscript accepted for publication in The Journal of Immunology (The JI). The American Association of Immunologists, Inc. (The AAI), publisher of The JI, holds the copyright to this manuscript. This manuscript has not yet been copyedited or subjected to editorial proofreading by The JI; hence, it may differ from the final version published in The JI (online and in print). The AAI (The JI) is not liable for errors or omissions in this author-produced version of the manuscript or in any version derived from it by the National Institutes of Health or any other third party. The final, citable version of record can be found at www.jimmunol.org.

PEER REVIEW INFORMATION

The Process: By submitting a manuscript to The JI, the authors agree to subject it to the confidential peer-review process. Editors and reviewers are informed that the manuscript must be considered confidential. After a manuscript is received, it is assigned by the Science Coordinator to a specific Deputy Editor and a Section Editor, whose expertise is considered to be appropriate. The Section Editor prepares a list of expert reviewers, which may include some suggested by the Science Coordinator. Authors can indicate specific individuals whom they would like to have excluded as reviewers as well as individuals thought to be particularly appropriate, although these suggestions may not always be accepted. Generally, requests to exclude certain potential reviewers will be honored except in fields with a limited number of experts.

All potential reviewers are contacted individually to determine availability. Manuscript files are sent to at least two expert reviewers. Reviewers are asked to complete the review of the manuscript within two weeks and to return a short review form. Based on the reviewers' comments, the Section Editor recommends a course of action and communicates the reviews and recommendations to the Deputy Editor for a final decision.

The Deputy Editor considers the comments made by the reviewers and the recommendation of the Section Editor, selects those comments to be shared with the authors, makes a final decision concerning the manuscript, and prepares the decision letter for signature by the Editor-in-Chief. If revisions of the manuscript are suggested, the Deputy Editor also recommends who should review the revised paper when resubmitted. Authors are informed of the decision by e-mail; appropriate comments from reviewers and editors are appended.

Decisions: There are four categories for initial decisions: accept, accept with minor revision, return for revision, and reject. Some manuscripts are accepted provisionally, pending relatively minor revisions. In this case, the Deputy Editor may conduct the rereview. For many manuscripts, authors are invited to resubmit if revision or additional experimentation can address major criticisms. Typically, one or more reviewers will then be asked to consider the adequacy of the revisions. Cutting Edge papers are allowed only minor revisions because of time constraints. All revised manuscripts are carefully reexamined, and ultimate acceptability is not guaranteed. The JI does not provide for an advance determination of the acceptability of a particular manuscript for publication, nor does it promise expedited review of selected manuscripts.

Communication with Authors: To minimize the possibility of misinterpretation or errors in verbal communication, the Editorial Office will provide information, in writing, only to the corresponding author and will not provide extensive details (e.g., exact status of a review or a predicted time to final decision). Deputy Editors do not take calls from authors concerning decisions or other related matters. All such inquiries should be addressed in writing to the Editor-in-Chief, who will discuss concerns with the Deputy Editor. This policy has been established to provide for uniformity and fairness in addressing concerns about the review process.

Rebuttals: If the authors believe that a serious scientific error occurred during the review, a letter of rebuttal may be sent to the Editor-in-Chief, explaining the reasons why the decision should be reconsidered. When appropriate, the matter will be taken up with the initial Deputy Editor, Section Editor, or additional reviewers. Rebuttals that challenge rejections that were based on priority alone are rarely successful, since the assignment of priority is necessarily a matter of opinion. If the authors of a rejected manuscript are able to make new advances that go far beyond the original submission, they will often expedite consideration of their paper through the submission of a completely new manuscript.

The JI Reviewers

Selection: Selection of reviewers is the responsibility of the Section Editor, although the Science Coordinator makes recommendations to the Section Editor from a list of individuals who have reviewed manuscripts previously. This database includes self-identified areas of expertise as well as information about the perceived usefulness and timeliness of past reviews. Individuals who consistently have provided tardy or unhelpful reviews are removed from the database. Every effort is made to avoid both real and apparent conflicts of interest with respect to research activities or collaborative or personal interactions. Reviewers are asked to withdraw from considering any manuscript in which they identify a conflict that has escaped the attention of the Section Editor.

Scientific Integrity: Information contained in manuscripts is considered confidential and should not be shared or distributed. If necessary, a reviewer can consult with others for an adequate evaluation of the research findings if all individuals involved maintain confidentiality, objectivity, and avoid conflict of interest. AAI is not responsible for acts and conduct by reviewers that are not in accordance with accepted professional standards. Reviewers are asked to be objective in their evaluations and to judge primarily the novelty and soundness of the information presented.

Anonymity: Although reviews are anonymous, all comments should be capable of withstanding public scrutiny. Except in very unusual circumstances, the identity of the reviewers and Section and Deputy Editors involved in the review of any given manuscript is kept confidential.

The JI Editorial Board: The AAI Council, upon recommendation of the Publications Committee, appoints the Editor-in-Chief for a term of five years. Deputy Editors, Section Editors, and Associate Editors are nominated by the Editor-in-Chief and appointed by the Publications Committee. Deputy Editors are appointed for variable terms. Section Editors and Associate Editors are appointed for one renewable term of two years in most circumstances. The Editor-in-Chief, the Deputy Editors, and the Section Editors constitute the Editorial Board and as such are required to be members of AAI. The Editor-in-Chief is responsible for the specific editorial conduct of The JI. The AAI Publications Committee is responsible for the management and evaluation of The JI and any other official publications of AAI, subject to the general supervision of the AAI Council.

Manuscripts Submitted from the Institution of an Editor: Manuscripts submitted from the institution of any Section or Deputy Editor or the Editor-in-Chief are reviewed by other editors from outside that institution. The Editorial Office ensures confidentiality and equity in reviewing all manuscripts.

ONLINE SUBMISSION

Submit online at ji.msubmit.net Individual manuscript, figure, and table files must be uploaded to the system. The system then creates a single PDF for review purposes. Authors should save copies for themselves of all the files in their original formats. See Author Instructions for online submission requirements. See the Figures section for help with preparing digital art. The JI's online submission system requires browsers where cookies and Javascript are enabled.

After the manuscript has been checked by journal staff, the Corresponding Author will receive an email acknowledging receipt of the manuscript. The email contains links to the Submission Form and Color Charges Form (if applicable). The Corresponding Author must download, sign and fax these forms to 301-634-7831 to complete the submission. The manuscript will not be sent for review until The JI Editorial Office receives these forms signed by the Corresponding Author. Please contact infoji{at}aai.org if you do not receive the acknowledgment e-mail. Please do NOT use the old hard copy forms found in old copies of the printed journal.

All publication fees are payable in U.S. dollars. Accepted manuscripts are published only upon commitment by the author(s) or institutional financial officer to pay these charges.

Submission Fee: If the corresponding author is not an AAI* member, a fee of $50 per manuscript must be paid by credit card (American Express, MasterCard, or Visa) during the submission process. If payment by credit card is impossible, please contact infoji{at}aai.org to arrange payment by check (drawn on a U.S. bank). We do not accept cash or purchase orders. *There is no processing fee for regular, emeritus or honorary AAI members in good standing.

Page Charges:

• $60 per page for up to 8 printed pages in the article

• $150 for each additional page from 9 to 12 pages

• $210 for each additional page over 12 pages

Color Charges: Color figures may include multiple color panels. Authors will be notified of the cost of color reproduction on the Reprint Form received with their electronic page proofs and must confirm acceptance of the charges in writing. Authors should expect that color figures in the accepted paper will be reproduced in color and will incur color charges.

Note that AAI members receive a significant discount on color charges.

• Non-AAI Members: $850 for each color page, and $300 for each additional color figure on the same color page for corresponding authors who are not AAI members (i.e., first figure on first page: $850; second figure on the first page: $300; first figure on second page: $850, etc.).

• AAI Members: $650 for each color page and $300 for each additional color figure on the same page for corresponding authors who are regular, emeritus, or honorary AAI members in good standing on the date of manuscript acceptance (i.e., first figure on first page: $650; second figure on the first page: $300; first figure on the second page: $650, etc.).

Online Posting Fee: $150 per published article.

Reprints: Reprints must be ordered in advance of publication. A Reprint Form showing the cost of reprints, together with an order slip, is sent with the electronic page proofs. The invoice for reprints will also include page charges and color figure charges. Reprint orders from noncontributors must be directed to the Editorial Office (Reprint Order Form).

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MANUSCRIPT PREPARATION

General Guidelines: A 12-point serif font, preferably Times New Roman, is required. Do not use compressed type format. Double-space entire manuscript. The average length of full-length articles is eight printed pages. Instructions for estimating the printed length of a manuscript are included below.

Each of the following components should begin on a separate page:

1. The Title Page must include the full title; a running title (not to exceed 60 characters); each author's full name (first name, middle initial, last name); the affiliations of all authors and their institutions, departments, or organizations (use the following symbols in this order: *, †, ‡, §, ¶, ||, #, **, ††, ‡‡, §§, ¶¶, || ||, ##); and three to five keywords, selected from the Keywords List, that describe the topic of the manuscript. (Keywords are used in editor and reviewer assignments and are not published with the manuscript. Please note that the list of keywords does not represent an exhaustive view of what The JI considers important topics, but it has been found useful for reviewer assignment purposes.)

2. The Abstract must be 250 words or less for full-length manuscripts; 150 words or less for Cutting Edge. Reference citations should not be included in the Abstract. The species of animals or species of origin of cells used in the manuscript must be clearly stated in the Abstract.

3. The Introduction, Materials and Methods, Results, and Discussion sections should begin on separate pages. Do not combine the Results and Discussion sections for full-length papers.

4. If the manuscript contains human or animal studies, the Materials and Methods section must state that the studies have been reviewed and approved by an appropriate institutional review committee.

5. Acknowledgments appear immediately after the Discussion and before References.

6. Grant support must not be included in the Acknowledgments but should be cited as a footnote to the title.

7. Disclosures contain conflict of interest disclaimers (details).

8. References must be numbered as they appear in the text. All authors must be listed for each reference. If citations are included in tables or in figure legends, they must be numbered according to the position of citation of the table or figure in the text. Only published papers and papers in press may be included in the References. In press articles, i.e., papers not yet published, must be submitted as online attachments in PDF format at the time of article submission. NOTE: Do NOT submit as attachment papers that are already published, e.g., manuscripts published ahead of print. Such papers must be incorporated into the References and cited with their DOI numbers and the publication dates. Citations of "manuscripts in preparation," "unpublished observations," and "personal communications" must appear parenthetically in the text. Manuscripts "submitted for publication" (i.e., not yet accepted) also are mentioned parenthetically in the text. Written approval by the persons cited in personal communications must accompany the manuscript unless they are also authors of the manuscript submitted to The JI.

Format for references:

Periodicals: Wells, A. D., M. C. Walsh, D. Sankaran, and L. A. Turka. 2000. T cell effector function and anergy avoidance are quantitatively linked to cell division. J. Immunol. 165: 2432–2443.

Books: McIntyre, T. M., and W. Strober. 1999. Gut-associated lymphoid tissue: regulation of IgA B-cell development. In Mucosal Immunology, 2nd ed. P. L. Ogra, J. Mestecky, E. Lamm, W. Strober, J. Bienenstock, and J. R. McGhee, eds. Academic Press, San Diego, CA. 319–356.

9. Footnotes should be used to designate the source of support, new or special abbreviations used, correspondence address, current address, manuscripts submitted for publication, etc. Footnotes should be numbered consecutively and will appear on the title page, but for submission are grouped together and placed on a separate page between the References and the Figure Legends.

10. Abbreviations that may be used without definition are provided in the Standard Abbreviations list. Spell out nonstandard abbreviations used less than three times. Nonstandard abbreviations used three or more times must be defined in a footnote. Abbreviations and their definitions must be consistent throughout the text.

11. Figure legends must be numbered with Arabic numerals in order of appearance in the text and should include a short title after the figure number. Where possible, symbols and patterns used to distinguish data should be defined in a key placed within the graphic rather than in the figure legend.

12. Tables must be numbered with Roman numerals in order of appearance in the text. Table legends are prepared as footnotes to the table and are included with the table. Tables must be in DOC file format. Each table should be submitted as a separate file.

13. Figures

    As of October 1, 2007, The Journal of Immunology requires that color figures be submitted in the RGB color space. For more information see RGB Workflow.

    At initial submission, please submit low resolution files of the smallest possible size that will convey the needed information. Smaller files can be downloaded more quickly by reviewers and will hasten the review process.

    At submission of a revised manuscript, high-resolution figures that meet the following specifications must be submitted. For more information, see TIPS.

    • File Sizes: Figure files should not exceed 10 MB (average size is about 2 MB).

    • Image Sizes: Figures should be submitted in final size (printed 1:1). Figures may be printed in one of two formats: single-column (width from 3.37 to 8.23 cm or 20 picas) or double-column (width from 12.65 to 17.1 cm or 42 picas). The single-column format is preferred. Unless the file is too large, multi-piece figures should be submitted as a single file.

    • Text and Lines: Text in figures must be 6-8 points in size, except for single letter markers, which may be 12 points. Helvetica should be used for all figure text (except for the use of symbols). If Helvetica is not available to authors, Times Roman may be used. Line widths must be greater than one point thick or they will not appear on the PDF version of the article.

    • Numbering: Figures must be numbered as they appear in the text.

    • File Format: Figures should be in TIFF (better for halftone art e.g., blots, photographs) or EPS (better for line art or monochrome art, i.e., anything that involves sharply delineated lines) format. PowerPoint files are not suitable quality, as their resolution is too low for print.

    • Guidelines: For general guidelines for creating digital art go to Cadmus Digital Art or the Cadmus FAQ page. Topics included are:

      Resolution (dots per inch) | Color requirements | Cropping and sizing | Font usage | Scanned Images | Supported Applications (The JI does not support PowerPoint.)

    • Graphic Art Preflight: To avoid production delays due to unacceptable digital art formats, authors of revised papers must check in advance whether figures meet the standards required for final print and online production. It is mandatory to use Rapid Inspector, a tool that walks authors through the process to make needed corrections.

14. Cover art changes with each issue of The JI. Authors are encouraged to submit color figures with their manuscripts for possible use as cover illustrations.

15. Estimation of Printed Pages: One printed page in The JI contains approximately 8,000 characters, including spaces. Thus, an 8 page, full-length article would contain approximately 64,000 characters. Each line in a table occupies about 60 characters for a single-column table (120 characters for a double-column table). Figures occupy about 180 characters per centimeter height for single-column figures (360 characters for double-column figures). Determine the total character count for the text of your manuscript and add the character-equivalents for the tables and figures. This will provide a reasonable estimate for the printed length of a manuscript.

CUTTING EDGE MANUSCRIPT PREPARATION

Submit online at ji.msubmit.net.

Individual manuscript, figure, and table must be uploaded to the system. The system then creates a single PDF for review purposes. Authors should save copies for themselves of all the files in their original formats. If a paper is accepted, authors will be asked to submit the high-resolution figure files separately. See the Figures section for help with preparing digital art. Manuscripts submitted to the Cutting Edge section should conform to the Information for Authors for full-length manuscripts presented above as well as the additional guidelines below:

1. Cutting Edge articles, including figures and references, must fit within 4 journal pages. Authors should estimate the size of figures and tables and limit the text accordingly. One printed page in The JI contains approximately 8,000 characters, including spaces. Thus, a 4-page Cutting Edge article would contain approximately 32,000 characters. The formula for estimating the number of pages is provided in Manuscript Preparation.

2. List the phone number, fax number, and e-mail address of the corresponding author on the title page.

3. The Abstract is limited to 150 words.

4. The Materials and Methods section may be sharply limited but should be sufficient to allow the evaluation of results and conclusions.

5. Authors may combine the Results and Discussion sections.

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PREPARATION OF THE REVISED MANUSCRIPT

Submit the revised manuscript online at ji.msubmit.net

Follow The JI Editorial Office instructions contained in the previous decision letter carefully and thoroughly. A revised manuscript not returned within nine months of the date of the decision letter will be considered a new manuscript and subject to a new, complete review.

Individual manuscript files, files for each figure and table (even if they are unchanged from the previous submission), and a point-by-point reply to all referee comments, must be uploaded to the system. The revised manuscript text must be marked to show changes, using highlighting or a colored font (Microsoft Word files preferred). High-resolution figure files should be submitted. Figures must be in TIFF or EPS format. Instructions for figures are available at the Cadmus Digital Art Website. Authors should retain for themselves copies of all the files in their original formats.

After the manuscript has been checked by journal staff, the Corresponding Author will receive an email acknowledging receipt of the revised manuscript. The email contains links to the Submission Form and Color Charges Form (if applicable). The Corresponding Author must download, sign and fax these forms to 301-634-7831 to complete the submission of the revised manuscript. Your manuscript will not be sent for review until The JI Editorial Office receives these forms signed by the Corresponding Author. Please contact infoji{at}aai.org if you do not receive the acknowledgment e-mail. Please do NOT use the old hard copy forms found in old copies of the printed journal.

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SUPPLEMENTAL DATA AND DEPOSITION OF MATERIALS

Supplemental Data: All supplemental material accompanying an article must be submitted with the original paper for peer review. When submitting online, upload the file when requested. Supplemental material should be limited to short videos (must be no longer than 30 seconds and under 10 MB, with no sound or voice-over) or large tables, large sequence alignments, or large data sets such as those obtained with microarray hybridization experiments. Such supplemental data must be larger than two printed journal pages; smaller pieces of data should be incorporated into the manuscript as regular figures/tables.

Videos must be 320 x 480 pixels or smaller for best viewing within a browser. Submit videos in MPG or QuickTime. Change QuickTime file extensions to ".mov" so that Web browsers will recognize the file type and play the movie. Compress videos as much as possible to help control file size. Name videos by order of citation appearance (e.g., video1.mov). Authors will be notified if problems exist with videos as submitted and will be asked to take responsibility for modifications. No editing will be done to videos at the Editorial Office. Legends or short explanations of the material must accompany all supplemental material. Links to the material will appear in two places in the online journal, in the Table of Contents and in the information box associated with the first page of the full-text article. There will not be any links in the body of the article. In the printed paper, supplemental material will be footnoted the first time mentioned: "The online version of this article contains supplemental material."

Distribution and Depositing of Materials:

Unique materials: It is required that unique materials described in manuscripts published in The JI will be made available, within reason, to qualified investigators for their own noncommercial use. A reasonable amount may be charged by authors to cover preparation and shipping of the requested material. An agreement to this effect is included in the Manuscript Submission Form.

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STYLE GUIDE

General style conventions: In general, The JI follows Scientific Style and Format: The CSE Manual for Authors, Editors, and Publishers, seventh edition, published by the Council of Science Editors, Inc., in instances where style issues are not directly addressed.

Abbreviations for references: BIOSIS is the primary source for journal name abbreviations; Index Medicus is the secondary source.

Nomenclature:

Allergen nomenclature: Nomenclature for allergens should be assigned in cooperation with the IUIS Allergen Sub-Committee. Authors of accepted manuscripts that describe novel allergens will be requested to complete a brief standard form available at IUIS Allergen Nomenclature.

CD nomenclature: For the purpose of consistency, The JI will follow CD nomenclature. For murine molecules, The JI will follow the nomenclature previously published (J. Immunol. 160: 3861-3868, 1998). For human molecules, standard CD nomenclature will be followed as updated (J. Immunol. 168: 2083-2086, 2002).

Chemical names: The JI uses The Merck Index and the IUPAC-IUB Commission on Biochemical Nomenclature-Chemical Abstracts as the primary references for proper spelling and style of chemical names.

Chemokine/chemokine receptor nomenclature: The systematic name for chemokines and chemokine receptors should be used. The original name may be given in parenthesis if desired. See Cytokine 21:48-9, 2003.

Enzyme Nomenclature is The JI source for style and spelling of enzyme names.

Gene nomenclature: The HUGO guidelines for gene nomenclature may be used for naming human genes. Mouse Genome Informatics is a reference source for naming mouse genes.

Genetic nomenclature for mice: The JI uses the revisions for standardized genetic nomenclature for mice published periodically in Mouse Genome. A current listing of inbred strains of mice and rats is available at Mouse Genome Informatics. Authors are encouraged to deposit their mapping data with the Mouse Genome Database (MGD) before publication and to include the assigned MGD accession numbers in their manuscripts. Data may be submitted electronically by e-mail. Information about electronic submission of datasets can be obtained at the Data and Nomenclature Submissions page. Gene symbols should be reserved with MGD in advance of publication. An electronic nomenclature submission form is available from the MGD Website.

HLA nomenclature: HLA nomenclature is updated periodically by the WHO Nomenclature Committee for Factors of the HLA System. A recent reference is Hum. Immunol. 64: 919-20, 2003. Annual comprehensive revisions are published in Human Immunology, usually in the spring.

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STANDARD ABBREVIATIONS

The abbreviations listed here are used without definition in articles published in The JI. The form may be used for both singular and plural, or made plural with "s" at the author's option. The list of standard abbreviations is published in the first issue of each volume.

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KEYWORDS