Official Journal of the American Academy of Allergy, Asthma and Immunology



Editor in Chief DONALD Y. M. LEUNG, MD, PhD
Managing Editor GEORGE WOODWARD
Senior Journal Manager RACHEL SAMPSON

All manuscripts must be submitted online through the JACI's Elsevier Editorial System (EES) Web site at http://ees.elsevier.com/jaci/. Electronic files of the manuscript contents must be uploaded at that Web site, and the onscreen steps should be followed to submit the manuscript to the Editorial Office.

Items pertaining to manuscripts submitted for publication, as well as letters or other forms of communication regarding the editorial management of the Journal should be sent to:

The Journal of Allergy and Clinical Immunology
Editorial Office
National Jewish Health
1400 Jackson St., Suite J324
Denver, CO 80206

Telephone: (303) 398-1963
Fax: (303) 270-2269

This document contains complete guidelines for the preparation of your manuscript. For instructions regarding statistical analyses and reporting and for special instructions regarding (a) submissions having to do with allergen identification or allergen structure and (b) submissions having to do with animal models, see "Special Instructions" (below). For instructions regarding online submission, please see the "Tutorial for Authors" at the EES Web site ( http://ees.elsevier.com/jaci/ ). Technical support is available by e-mail at jacistaff@njhealth.org. In any correspondence, please provide the corresponding author's name, title of the manuscript, manuscript number (if assigned), and a clear description of the problem.

Please note:
(A) To be listed as an author, an individual must meet the requirements approved by the International Committee of Medical Journal Editors (ICMJE). In order to be included in the list of authors, an individual must have done all of the following: (1) made substantial contributions to conception and design, acquisition of data, or analysis and interpretation of data; (2) drafted the article or reviewed it critically for important intellectual content; and (3) given final approval of the version to be published.
(B) The JACI does not allow "ghostwriting," or uncredited authorship. All writers of a manuscript should be identified as authors.
(C) Statements and opinions expressed in the articles and communications in the Journal are those of the author(s) and not necessarily those of the Editor(s) or publisher, and the Editor(s) and publisher disclaim any responsibility or liability for such material. Neither the Editor(s) nor the publisher guarantee, warrant, or endorse any product or service advertised in this publication, nor do they guarantee any claim made by the manufacturer of such product or service.

Article Types

The Journal will consider publication of several types of manuscripts:

A. Original articles. These should describe fully, but as concisely as feasible, the results of original clinical and/or laboratory research. The average Original article fills 7 pages in the printed journal, although manuscripts that exceed this may be occasionally accepted for publication at the Editors' discretion. In general, an Original article should not exceed 3500 words, not including the abstract, figure legends, and references. Abstracts should be 250 words or less. If possible, each figure legend should be held to 60 words or less. Each Original article may be accompanied by no more than 8 graphic presentations (tables and/or figures)— for example, 3 tables + 5 figures. (Additional text, tables, or figures can be designated as "supplemental" material, which will be included in the JACI's Online Repository. For more on this option, please see the "Online Repository Materials" section below.) Please note: Original article manuscripts that are determined to significantly exceed these limits may be returned to the authors for shortening prior to review. The manuscript should be organized in the order listed below. Failure to follow this format may result in the manuscript being returned to the author(s) for revision prior to review.

The title page, abstract, Capsule Summary, key words, abbreviations, text, acknowledgments, references, tables and figure legends should be included in one word-processing file (in .doc or .wpd format). Figures should be loaded as separate files in the format specified below.

1. Title page. The full title should be relevant and concise (no more than 15 words). It should be followed by:

• The list of authors, including their full names, highest academic degrees, and institutional affiliations. Restrict the list of authors to those who have made material contributions to the research and who contributed to the writing and review of the manuscript.
• The name, address, telephone number, fax number, and e-mail address of the author who should be contacted regarding reprint requests or other correspondence received in the Editorial Office regarding the manuscript.
• A declaration of all sources of funding. Authors are required to disclose any financial relationship with a biotechnology and/or pharmaceutical manufacturer that has an interest in the subject matter or materials discussed in the submitted manuscript.
• A total word count, which includes the number of words in the body of the manuscript (Introduction through Discussion only); the abstract should not be included in the count. Figure and table legends are included in the estimation of the overall space required for figures and tables, so they should not be counted here.

2. Abstract. As a general rule, the abstract should be no longer than 250 words. It should summarize the results and conclusions concisely. Tabular data should not be included and acronyms/abbreviations should be avoided or spelled out fully. Abstracts should be structured as follows:

• Background: What is the major problem that prompted the study?
• Objective: What is the purpose of the study?
• Methods: How was the study done?
• Results: What are the most important findings?
• Conclusion: What is the most important conclusion drawn?

3. Clinical Implications or Key Messages. Provide ONE of the following:

either
• a very brief paragraph (consisting of no more than 30 words) summarizing the diagnostic, therapeutic, or management implications of the article. The heading for this paragraph should be Clinical Implications.

or
• (if the article is mechanistic) two or three independent bulleted statements that present the key findings or concepts in the article and perhaps comment on their implications. The heading for this small set of bulleted statements should be Key Messages.

4. Capsule summary. The Table of Contents entry for each Original Article published in the Journal includes a short summary that encapsulates the report's findings for a clinically oriented audience. To create this summary, the authors must compose one or two brief sentences (totaling no more than 35 words) that describe the article's contribution to the literature. These sentences should succinctly state why the article is important and compelling and what relevance it has for the clinician.

5. Key words. A list of up to ten key words should follow the Capsule Summary.

6. Abbreviations. Provide a list of any abbreviations/acronyms (and their definitions) on a separate page following the key words. Only standard abbreviations are to be used. Consult Scientific Style and Format by the Council of Biology Editors or the AMA's Manual of Style. A laboratory or chemical term or the name of a disease process that will be abbreviated must be spelled out at first mention, the acronym or abbreviation following in parentheses.

Please note: Abbreviations in the title and abstract are not acceptable. Even if they are included in the list of abbreviations, they should be spelled out in those locations.

7. Text. The manuscript should be written in clear and concise English. Authors whose primary language is not English should obtain assistance with writing to avoid grammatical problems. The text should be organized in sections as follows: Introduction, Methods, Results, andDiscussion. Each section should begin on a new page. The generic terms for all drugs and chemicals should be used.

In studies involving human subjects, a statement describing approval by the appropriate Institutional Review Board is required. Studies involving experimental animals must include a statement in the Methods section indicating which guidelines were followed for the care and use of the animals (e.g., the "Principles of Laboratory Animal Care" formulated by the National Society for Medical Research or the "Guide for the Care and Use of Laboratory Animals" prepared by the Institute of Laboratory Animal Resources, National Research Council, and published by the National Academy Press [revised 1996]).

8. Acknowledgments. General acknowledgments for consultations, statistical analyses, and the like should be listed at the end of the text, including full names of individuals involved. However, acknowledgment of funding should be listed on the title page.

9. References. It is the Editors' expectation that authors will perform a comprehensive search of the literature to gather the most current articles relative to the subject matter. All references that are five years old or more should be replaced with current literature, unless the referenced publication is a classic work that underscores the core subject.

References should follow "Vancouver style." See http://www.nlm.nih.gov/bsd/uniform_requirements.html for more information. Manuscripts in preparation, personal communications, and other unpublished information should not be cited in the reference list but may be mentioned in the text in parentheses. The references must be identified in the text by superscript Arabic numerals and numbered in consecutive order as they are mentioned in the text. The list of references, in numeric sequence, should be typed at the end of the article. Typing of the references is preferred over the use of your word processing program's footnote or endnote feature (or a program such as EndNote or Reference Manager) to create citations. If you do use EndNote, please remove the links between the reference number and the citations by taking the following steps: (1) Using the "Select Al" feature (Ctrl-A for PCs. Cmd-A for MACs), highlight the entire text of the file, including the references. (2) Use the keystroke command "Ctrl-6" for PCs of "Cmd-6" for MACs. (3) Save. This will remove the links (permanently) without disturbing the reference numbers or the citations. It is recommended that you save one copy of your manuscript with the EndNote links in place (for your reference) and one copy of your manuscript without the EndNote links (for submission purposes).

Please note that inclusive page numbers are required. List all authors' names when there are six or fewer; when there are seven or more, list the first six and add "et al."

Examples of Reference Formatting

Journal article:
Parkin DM, Clayton D, Black RJ, Masuyer E, Friedl HP, Ivanov E, et al. Childhood leukaemia in Europe after Chernyobyl: 5-year follow-up. Br J Cancer 1996;73:1006-12.

Book:
Ringsven MD, Bond D. Gerontology and leadership skills for nurses. 2nd ed. Albany (NY): Delmar Publishers; 1996.

Chapter in a book:
Phillips SJ, Whisnant JP. Hypertension and stroke. In: Laragh JH, Brenner BM, editors. Hypertension: pathophysiology, diagnosis, and management. 2nd ed. New York: Raven Press; 1995. p. 465-78.

Internet resource:
US positions on selected issues at the third negotiating session of the Framework Convention on Tobacco Control. Washington, DC: Committee on Government Reform; 2002. [Cited 2002 March 4.] Available from http://www.house.gov/reform/min/inves_tobacco/index_accord.htm .

B. Rapid publications. Manuscripts summarizing novel experimental results of exceptional importance or urgency will be considered for expedited publication. The average Rapid Publication article fills 6 pages in the printed journal, although manuscripts that exceed this may be occasionally accepted for publication at the Editors' discretion. In general, a Rapid Publication article should not exceed 3000 words, not including the abstract, figure legends, and references. Abstracts should be 250 words or less. If possible, each figure legend should be held to 60 words or less. Each Rapid Publication article may be accompanied by a combination of no more than 8 graphic presentations (tables and/or figures). (Additional text, figures, or tables can be designated as "supplemental" material, which will be included in the JACI's Online Repository. For more on this option, please see the "Online Repository Materials" section below.) Please note: Rapid Publication manuscripts that are determined to significantly exceed these limits may be returned to the authors for shortening prior to review. In a cover letter accompanying the submission, the authors should explain to the Editors why the manuscript is deserving of expedited publication. The formatting and characteristics of a Rapid Publication manuscript should be identical to those of an Original Article manuscript. If a manuscript is accepted as a Rapid Publication manuscript, it will appear earlier (by at least one issue) than it would if accepted as an Original Article manuscript. (Note: The Editors may choose to handle a manuscript submitted for expedited publication as an Original Article manuscript; the authors would be notified accordingly.)

C. Letters to the Editor. Letters to the Editor are brief reports of clinical or laboratory observations, substantiated by controlled data but limited in scope, and without sufficient depth of investigation to qualify as original articles. These manuscripts are reviewed in the Editorial Office and undergo peer review. Citation research shows that Letters to the Editor are indexed in Medline, accessible to literature searches, and cited like original articles.

A Letter to the Editor must:

(1) Be brief. The average Letter to the Editor fills 2 pages in the printed journal, although manuscripts that exceed this may be occasionally accepted for publication at the Editors' discretion. In general, a Letter to the Editor should not exceed 1000 words, not including the figure legend and references. If possible, the figure legend should be held to 60 words or less. Please note: Letter to the Editor manuscripts that are determined to significantly exceed these limits may be returned to the authors for shortening prior to review.
(2) Have a short, relevant title.
(3) Have a complete title page (see section A1).
(4) Be accompanied by a short summary that encapsulates the report's findings for a clinically oriented audience. To create this summary, the authors must compose one or two brief sentences (totaling no more than 35 words) that describe the report's contribution to the literature. These sentences should succinctly state why the report is important and compelling and what relevance it has for the clinician.
(5) Begin with the salutation "To the Editor:"
(6) Close with the author's name(s), academic degree(s), institutions(s), and location(s).
(7) Have no more than nine references.
(8) List the references as complete bibliographic citations following the closure of the letter (see section A8 above for formatting).
(9) Present lists of Keywords and Abbreviations, as relevant (see sections A4 and A5 above).
(10) Be accompanied by a Transfer of Copyright statement signed by all authors.

Special note regarding case studies: Case studies will only be considered for publication in the Letters to the Editor section of the Journal.

D. Correspondence and Reply. Correspondence concerning recent publications in the Journal or other subjects of unique interest to the readership will be considered for publication and accepted based on their pertinence, their scientific quality, and available space in the Journal. When a particular Journal article is referenced in a correspondence considered acceptable for publication, response from the authors of the article will be requested. Upon review and approval by the Editor, the Correspondence and relevant Reply will both be published.

Both Correspondence and Reply manuscripts must:
(1) Contain no more than 500 words (this count will include any brief tabular data).
(2) Have a short, relevant title, distinct from the title of the referenced article.
(3) Have a complete title page (see section A1).
(4) List the references as complete bibliographic citations at the end of the letter with the journal article being discussed as the first reference (see section A8 for formatting).
(5) Cite references (where appropriate to the subject), but no more than seven.
(6) Have no more than one graphic presentation (table or figure). (See the section on Graphic Presentations below).
(7) Begin with the salutation "To the Editor:" and close with the author's name(s), academic degree(s), institutions(s), and location(s).
(8) Be accompanied by a Transfer of Copyright statement signed by all authors.

E. Review articles. Review articles published in the Journal are invited by the Editors to correlate with features, themes, and highlights. They support the programs of the Postgraduate Education and Continuing Medical Education Committees of the American Academy of Allergy, Asthma and Immunology. Please note: Current space constraints do not allow acceptance of unsolicited review manuscripts.

F. Rostrum articles. Opinion articles about subjects of particular interest and/or debate are accepted for peer review after preliminary review by the Editor.
These articles should have an unstructured abstract, must be accompanied by no more than 25 references, and should otherwise follow the guidelines for Original articles (see section A). The average Rostrum article fills 6 pages in the printed journal, although manuscripts that exceed this may be occasionally accepted for publication at the Editors' discretion. In general, a Rostrum article should not exceed 3000 words, not including the abstract, figure legends, and references. Abstracts should be 200 words or less. If possible, each figure legend should be held to 60 words or less. Each Rostrum manuscript may be accompanied by a combination of no more than 6 graphic presentations (tables and/or figures). (Additional text, tables, or figures can be designated as "supplemental" material, which will be included in the JACI's Online Repository. For more on this option, please see the "Online Repository Materials" section below.) Please note: Rostrum manuscripts that are determined to significantly exceed these limits may be returned to the authors for shortening prior to review. Due to space constraints, we are currently unable to accept unsolicited Rostrum manuscripts.

Formatting of Articles

Basic Formatting
Be sure the entire manuscript (all text, legends, captions, etc.) is in a standard font such as Times New Roman, Arial, or Courier, size 12. All sections, including references, should be double-spaced, with margins of at least one inch on all sides. On each page, the last name of the first author and the page number should appear in the upper right corner. Begin numbering with the title page as page 1. Be sure to display line numbers (1, 2, 3, and so forth) in the left margin of the manuscript. (Line numbering can be added from the Page Setup or Format menu of word processing programs.) The line numbering should be continuous throughout the entire manuscript, from the title page through final page (i.e., do not begin numbering from 1 again at the top of each page).

Keyboarding the electronic manuscript

• All design considerations regarding typefaces, page layout, and artwork will be handled by the publisher after an accepted paper has been transferred from the Editorial Office to the publisher. Please do not input any special typesetting codes.
• Be careful to distinguish between the letter O and the numeral 0 and between the letter I and the numeral1.
• A "hard return" results from pressing the Enter key on the computer keyboard. Use hard returns only at the ends of paragraphs, titles, and headings, to separate items in a bulleted or numbered list, and so forth. Rely on the word-processing program's word wrap ("soft return") feature for all other endings.
• Use the program's Page Break function to begin each section on a new page.
• Use the word-processing program's capabilities for bold, underlining, italic, subscript, and superscript. Text that is to be italicized in published form (genus + species designations) may be keyboarded through use of either italic or underlined text.
• Left-justify all text and headings in the manuscript.
• Use two hyphens for a long dash.

Article Length

Authors must comply with the page limits that have been established for each type of article. Manuscripts that exceed standard limits for length will be returned to the authors to be shortened before peer review can be initiated. Articles of excessive length will not be accepted for publication.

One way to shorten a manuscript is to ask the Editors to consider posting ancillary materials (non-essential tables, figures, appendices, questionnaires, etc.) in an Online Repository (OR) on the JACI Web site. For instructions, see the guidelines for Submission of "Online Repository Materials" below.

Graphic Presentations

The total number of graphic presentations (tables and/or figures) per manuscript should be no greater than 8 (examples: 8 tables + 0 figures; 5 tables + 3 figures; 2 tables + 6 figures; 0 tables + 8 figures).

A. Tables. If tables appear in the manuscript, they must be included in the electronic submission. They may be placed within the manuscript file or loaded as separate files (in .doc or .wpd format). Tables should supplement, not duplicate, the text; they should be on separate pages, one table per page, and should be self-explanatory and numbered with Roman numerals in order of mention. A brief title should be provided directly above each table. Any text within the table should be in Times New Roman font. Any abbreviations should be defined at the bottom of the table. When creating a table, use the word-processing program's table formatting feature; otherwise, use only tabs (not spaces) to align columns. Glossy prints and reduced versions of typewritten tables are unacceptable. The table number should appear in the electronic file. The maximum size for a table is ½ page. The maximum number of graphic presentations (tables and/or figures) per manuscript is 8 (examples: 8 tables + 0 figures; 5 tables + 3 figures; 2 tables + 6 figures; 0 tables + 8 figures).

B. Figure legends. Figure legends should be typewritten, double-spaced, and listed on a separate page after the tables. They should not appear on the figures. The figure legend will be included when sizing the figure and its length must therefore be taken into consideration. The figure title should appear at the beginning of each legend. The legends themselves should be succinct (no more than 60 words), identifying the data or subject being presented, but explaining methods or results. Do not place titles or legends within the figures.

C. Figures. If illustrations appear in the manuscript, they must be submitted in electronic format along with the rest of the manuscript. Each figure should be submitted as a separate electronic file, and should not be inserted into the file containing the text of the manuscript. Complete instructions for online submission are available in the "Tutorial for Authors" at the EES Web site http://ees.elsevier.com/jaci/ ). The maximum number of graphic presentations (tables and/or figures) per manuscript is 8 (examples: 8 figures + 0 tables; 6 figures + 2 tables; 3 figures + 5 tables; 0 figures + 8 tables).

Basic guidelines:

• Use a short filename, and include the extension, i.e., ".tif" or ".eps." Avoid the use of symbols such as # or &. There must be only one period in the filename: the one before the extension. Filenames of excessive length or with certain punctuation will fail to download and/or open.
• Put the figure number beneath the image for identification. Do not put titles or legends within the figure file.
• Text within the figure should be in Times New Roman font. Keep a consistent font size throughout each figure, and for all figures, to provide higher readability and a professional look.
• Images need to be easily readable with good contrast, particularly figures that have multiple parts and/or a lot of different symbols or components. Clarity and consistency should be uniform among the parts of a multi-part figure, and among all the figures in a manuscript.
• In colorizing your figure(s), we ask that you keep in mind that some of our readers are color-blind and are often unable to distinguish different colors in graphically represented data. To accommodate this group, we suggest that you consider some type of aid, such as labeling each column of a bar graph with an identifier or providing a key with symbols identifying each set of data being presented or compared. It is also helpful to use colors of varying intensity so that they are distinguishable as different shades of gray when viewed by the color-blind. We thank you for complying with this request.

Color modes:

• Grayscale isused for black-and-white or 256 shades of gray.
• CMYK (Cyan/Magenta/Yellow/blacK) is a four-color process used by high-end production printers. All color images must be submitted to JACI in CMYK mode.
• RGB (Red/Green/Blue) is excellent for online viewing. It is acceptable for review purposes and the Online Repository but not for the print journal.

Types of figure art:

• Line art is the most common type: graphs, charts, scatterplots, flowcharts, text, and anything else that involves sharply delineated lines.

•May be in black-and-white or color.

• Best created and saved in EPS (Encapsulated PostScript).

• Must be created in high resolution, 1000 dpi (dots per inch) minimum, whether black-and-white or color, to provide sharp, clear lines.

• Continuous-tone art includes immunoblots, microphotographs, photographs, and anything else that involves soft edges gradually shading from one tone to another.

• May be in black-and-white or color. Has no text in the image (other than the labels A, B, etc.)

• Best created and saved in TIFF (Tagged-Image File Format).

• Must be created in a relatively high resolution, 300 dpi minimum, to provide a clear image.

• Combination art puts line art and continuous-tone art together, either as separate parts (e.g., A is an immunoblot and B is a graph) or as a continuous-tone image in combination with text.

• May be in black-and-white or color.

• Best created and saved in EPS (Encapsulated PostScript).

• Must be created in relatively high resolution, 600-1000 dpi minimum.

Resolution:

Perhaps the most important attribute of a figure file is its resolution, which determines how clearly a figure will appear. It is important to create each figure in the correct resolution for its type (see above). If a figure is created in too low a resolution, the resolution cannot be increased later; the figure will have to be recreated from scratch. Readers are drawn to professional-style images that are clear, crisp, legible, and eye-catching.

The Artwork Quality Check (Artwork QC) feature in EES is designed to inform authors whether an uploaded figure file is acceptable for review and for production. (For more information, see the "Tutorial for Authors" at the EES Web site ( http://ees.elsevier.com/jaci/ ).

Figure files must address two sets of needs: (1) those of the Editor and Reviewers and (2) those of the publisher. While the Journal can be somewhat lenient in the variety of formats used for review purposes, the final figures in a revised manuscript must comply with the publisher's specifications. For the Editors and Reviewers, it is important that the figures get their message across. For that they need to be clear and legible.

Sizing of figures:

It is important that you submit all figures in the dimensionsin which they are to be published in the journal. They must be sized to the smallest dimensions that allow legibility and clarity without undue use of space.

Illustrations should fit within one or two columns. The legend is added to the figure during production, and space for it must be allowed in calculating figure size. Dimensions are to be no more than:

• 1 column width: 3" wide by 4" high for ¼ page
• 1 column width: 3" wide by 8" high for ½ page
• 2 column width: 6" wide by 1.5" high for ¼ page
• 2 column width: 6" wide by 2.5" high for 1/3 page
• 2 column width: 6" wide by 4" high for ½ page

Online Repository Materials

The Journal will consider posting ancillary materials (non-essential tables, figures, appendices, questionnaires, etc.) in an Online Repository (OR) on the JACI Web site ( http://www.jacionline.org). The OR is for peer-reviewed material that cannot be included in the print version of an article due to space considerations. The Editor and reviewers are able to review material proposed for the OR. Readers of the Journal's print version will be directed to the OR for reference. Note: OR material consisting of 15 pages or less is built directly into the downloadable PDF of the manuscript.

On an individual basis, the Editors will determine whether ancillary material submitted in support of a manuscript is warranted. In some instances, an Editor may suggest when requesting a revision that part of the data be presented for the OR and removed from the manuscript, perhaps at the request of the reviewers. In both cases, authors should include a cover letter to the Editor, indicating the material to be considered for the OR and justifying its inclusion.

The ancillary material must be submitted in EES simultaneously with the rest of the manuscript. The OR material should be loaded as separate files, and should follow the end of the regular manuscript. For revisions that will include newly designated OR material, the Marked Manuscript should show where materials were removed from the original version, and include appropriate statements directing readers of the article in the print journal to the OR. The Unmarked Manuscript will reflect the latter changes. For more complete instructions, see the "Tutorial for Authors" at the EES Web site ( http://ees.elsevier.com/jaci/ ).

Online Repository materials must be accompanied by a separate title page that includes the heading "Online Repository," all author names and their affiliations, and contact information for the corresponding author. All text files for the OR should be formatted per directions for regular manuscript materials (see section A). Figures for the OR do not need to conform to the print specifications for resolution, but they do need to appear clear and crisp when viewed electronically. PowerPoint files may be used. Figures and Tables must be labeled with unique designations as Figure E1, Table E1, etc. Similarly, if citations are made within the ancillary material, a list of references, separate from the manuscript's references, must be included and labeled E1, E2, etc. Authors may repeat sentences or references in the OR that are included in the manuscript, if necessary for reader comprehension. In the manuscript text, materials that are housed in the Online Repository must be referenced specifically ("see Figure E1 in the Online Repository"). It is important to remember that material for the OR is independent from the manuscript and will appear online only.

US National Institutes of Health (NIH) voluntary posting/"Public Access Policy

Elsevier facilitates author posting in connection with the voluntary posting request of the NIH (referred to as the NIH "Public Access Policy"; see http://www.nih.gov/about/publicaccess/index.htm ). Any article accepted for publication in an Elsevier journal from authors who have indicated that the underlying research reported in their article was supported by an NIH grant will be sent by Elsevier to PubMed Central (PMC) for public access posting 12 months after final publication. The version of the article provided by Elsevier will include peer-review comments incorporated by the author into the article. Because the NIH "Public Access Policy" is voluntary, authors may elect not to deposit such articles to PMC. If you wish to "opt out" and not deposit to PMC, you may indicate this by sending an e-mail message to NIHauthorrequest@elsevier.com.

Required Documents

The signed Transfer of Copyright documents, Conflict of Interest declarations, and permissions forms (when applicable) must be received in the Editorial Office before an accepted manuscript can be sent to the publisher. These forms can be faxed to 303-270-2269 or uploaded electronically in to your submission. Templates of these forms are available for downloading from the EES Web site ( http://ees.elsevier.com/jaci/ ). (If you are submitting your Transfer of Copyright and Conflict of Interest disclosure forms to us as part of your electronic submission in EES, please be sure to include all of these forms with each subsequent version of your manuscript.)

1. Transfer of Copyright. Items are accepted for publication on the understanding that they are contributed solely to the Journal of Allergy and Clinical Immunology and have not been or will not be published elsewhere except in abstract form. Each author must sign a Transfer of Copyright statement, using the exact wording provided the downloadable form that is available at the EES Web site ( http://ees.elsevier.com/jaci/ ).

Elsevier, the publisher of JACI, has a long tradition of liberal copyright policies and for many years has permitted both the posting of preprints on public servers and the posting of final papers as accepted on secure internal servers. Now authors of papers published in an Elsevier journal may also post their final version, as accepted by the journal, publicly on their personal Web site or their institutions' Web sites (including their institutional repository). The "final version" is the author's Word (or Text or similar word processing) file, which can be updated by the author to incorporate changes made during the peer-review and editing processes.

Authors do not need to ask Elsevier's permission to do this. They do need to include the full citation of the published article (once known) and a link to the homepage of the journal or, better, the DOI of the published article.

The posting cannot be for commercial purposes (such as systematic distribution or creating links for customers to articles) and it is not permitted to post to Web site outside of their institution (other than their own personal web page). Similarly, posting of the Journal's PDF or HTML files is not permitted and any exception would require permission from Elsevier. We believe it is important to preserve the integrity of the official record of publication at the publisher. Therefore, the final published version as it appears in the journal (PDF or HTML) will continue to be available only on an Elsevier site.

2. Conflict of Interest Declaration. The Journal requires all authors to acknowledge, on the title page of the manuscript, all funding sources that supported their work as well as all institutional or corporate affiliations of the authors. Authors are also required to disclose to the Editor, in separate signed documents sent by each author at the time of the manuscript's submission, any commercial associations that might pose a conflict of interest. These include consultant arrangements, speakers' bureau participation, stock or other equity ownership, patent licensing arrangements, support or financial or materials grants for research, employment, or expert witness testimony. The disclosure will be held in strict confidence during the review process and will not influence any editorial decisions. However, if the paper is accepted for publication, disclosure of any such associations will be published as a footnote to the article. No article can be published in the Journal unless a signed and completed Conflict of Interest statement has been received from each author.

The form should use the exact statement provided in the downloadable form that is available at the EES Web site ( http://ees.elsevier.com/jaci/ ). The statement may be printed on the author(s)' letterhead and should be followed by a signature line and the date; the author's name should be typed below the signature line. The document(s) should be faxed to the Editorial Office at 303-270-2269.

3. Permission to Reuse Previously Published Material/Informed Consent Releases. Authors of manuscripts submitted to JACI must provide the Editorial Office with proof of permission to reuse previously published material for any figure or table that has appeared in another publication. Because articles appear in both the print and online versions of the journal, wording in the permission should specify "permission to publish in all forms and media." To request permission, please contact the appropriate journal or publisher and provide the following information:

• Your name, institutional affiliation, mailing address, telephone and fax numbers, and email address
• Source of previously published material: Full title of journal or book, article title, authors, volume, year, and page numbers
• Amount of the material to be used: Please specify particular pages, tables, or figures (specify table/figure numbers)
• Intended use of the published material: State that you are seeking publication in the Journal of Allergy and Clinical Immunology, and provide the article title, first author, JACI year and volume (or state "In press"), and the number of the table or figure in the JACI submission where the material will appear.

Upon obtaining written permission to reuse the specified material, forward the documentation to the Editorial Office, or fax a copy to 303-270-2269. Acceptance of a manuscript is conditional upon receipt of permission.
Please note: It sometimes takes up to 6-8 weeks to obtain permissions from a publisher, so be sure to allow plenty of time. Photographs of identifiable persons must be accompanied by signed releases showing informed consent.

4. Other Documentation

• Nucleotide Sequence Data. When manuscripts include or describe original sequence data, authors must submit these data to GenBank. A footnote must include the accession number under which the data were submitted. Instructions are available from http://www.ncbi.nlm.nih.gov/Genbank or http:// www.ebi.ac.uk/embl/Submission .
• Protein Sequence Data. When manuscripts include or describe original protein sequence data, authors must submit these data to Protein Identification Resource (PIR). A footnote must include the accession number under which the data were submitted. Instructions are available from http://pir.georgetown.edu .
• New Allergen Data. When manuscripts include or describe a hitherto-unnamed allergen, authors must contact the WHO/IUIS Allergen Nomenclature Sub-Committee for approval of a new name. A footnote should indicate that the data have been submitted. A questionnaire is available from Allergen Nomenclature Sub-Committee, Bøge Allé 10-12, DK-2970 Hørsholm, Denmark; telephone 45-45-76-7777 #5116; FAX 45-45-76-5152; Internet: anonymous FTP to biobase.dk:pub/who-iuis/newallergen. nomenclature and pub/who-iuis/newallergen.form .

Revision of Manuscripts

As with new submissions, revisions must be submitted electronically through EES ( http://ees.elsevier.com/jaci/ ). Ensure that the revised manuscript is prepared in accordance with the Journal's format and style for the type of article being revised. Please refer to the "Tutorial for Authors" at the EES Web site ( http://ees.elsevier.com/jaci/ ). Adherence to these guidelines is important to prevent a delay in processing the revised manuscript.

Revisions must include the following:
(1) A Responses to Comments document that includes point-by-point responses to the comments made by the Reviewers, Editor, and Editorial Office. In your Responses to Comments document, reproduce each comment verbatim and in its entirety and follow the comment with your detailed response. Each of the comments should be preceded by the word "COMMENT," and the font style for each comment should be bold. Each of your responses should be preceded by the word "RESPONSE," and the font style for each response should be regular (not bold). In each response, indicate where relevant changes have been made in the manuscript or explain why no changes would be appropriate. If any alterations have been made to your figures or if any figures have been removed or replaced, describe the changes.
(2) ) A Marked Manuscript. The Marked Manuscript should be a version of your revised manuscript in which all of the ways in which it is different from the original manuscript are indicated for the sake of the Editor. To any text that was not part of the original manuscript but has now been added, underline formatting should be applied; to any text that was part of the original manuscript but has now been deleted, strikethrough formatting should be applied. Any table that was part of your original submission should be either embedded within the Marked Manuscript or provided as a separate file (e.g., "Table II - Marked"); if changes have been made to the table, they should be indicated. Likewise, any figure that was part of your original submission should be either embedded within the Marked Manuscript or provided as a separate file (e.g., "Figure 1 - Marked"); if changes have been made to the figure, they should be described in your Responses to Comments document. Line numbering (continuous) should be used throughout the Marked Manuscript.
(3) An Unmarked Manuscript. The Unmarked Manuscript should be your revised manuscript just as you intend it for publication (if it is accepted). Any table that is to be part of your revised manuscript should be either embedded within the Unmarked Manuscript or provided as a separate file (e.g., "Table II - Unmarked"). Any figure that is to be part of your revised manuscript must be provided as a separate file (e.g., "Figure 1-Unmarked"). Line numbering need not be used in the Unmarked Manuscript.
(4) Signed Transfer of Copyright and Conflict of Interest disclosure forms. If you are submitting your Transfer of Copyright and Conflict of Interest disclosure forms to us as parts of your electronic submission in EES, please be sure to include all of these forms with each subsequent revision of your manuscript.

Special Instructions

A. The following are special instructions regarding submissions on allergen identification/structure:
(1) The allergen nomenclature must comply with the requirements of the WHO/IUIS Sub-Committee on Allergen Nomenclature, and the allergen must have been assigned a name by the Committee. Application forms are available at http://www.allergen.org.
(2) For protein allergens: Information must be included on the protein family (where possible) to which the allergen belongs (Pfam designations, http://pfam.sanger.ac.uk ), the allergen function (if known), and protein identifiers (accession number[s] and/or Protein Database code[s]).
Any carbohydrate determinant that may be involved in IgE responses, has functional activity, or is of biological or clinical significance in allergic disease should be identified.
(3) Priority for publication will be given to studies that increase the understanding of the mechanisms of allergic sensitization and/or improve the ability to properly diagnose or treat allergic diseases.
(4) Priority will also be given if the submission provides evidence of biological activity beyond IgE binding in vitro — for example, mechanistic or functional assays, cellular assays, basophil histamine release, environmental exposure assays, and, where possible, in vivo studies of allergenicity.

Reference:
Chapman MD, Pomes A, Breiteneder H, Ferreira F. Nomenclature and structural biology of allergens. J Allergy Clin Immunol 2007:119:414-420.

B. The following are special instructions regarding submissions using animal models:
(1) Animal model studies of interest to the JACI. The Editors would be interested in an animal-model study only if it highlights a new conceptual advance using an experimental approach that would be very difficult, impractical, or unethical to do in human beings. The authors should clearly indicate in their cover letter how their animal-model study meets these criteria.
(2) Mouse pulmonary function tests. The JACI's policy is that measurement of airway responsiveness by unrestrained, single-chamber barometric plethysmography (the Penh method) must be confirmed by invasive techniques. For further explanation of this policy, please see Finkelman FD. J Allergy Clin Immunol 2008;121:334-5.

The following are instructions regarding statistical analyses and reporting for JACI manuscripts:
Although referees with statistical expertise typically review manuscripts submitted to the JACI, the Editorial Board decided that the quality of the manuscripts could be improved by providing authors some guidance on statistical analyses and reporting. Therefore, the JACI Statistical Editor has constructed the following guidelines, which incorporate many comments from Editorial Board members and statistical referees.

1. METHODS: Reporting on Statistical Methods The Consolidated Standards of Reporting Trials (CONSORT) statement is a set of guidelines for reporting on the methods and results of randomized and nonrandomized medical research studies. It is available at the following Web site: http://www.consort-statement.org.

The first CONSORT statement provides a checklist of items that should be included in a manuscript that reports the results of a randomized clinical trial (RCT). Items 7 through 12 of the checklist are relevant to the statistical methods section for a manuscript submitted to the JACI based on a RCT. Thus:

CONSORT TOPIC	ITEM NUMBER	SPECIFIC ISSUES
Sample size	7	How sample size was determined and, when applicable, explanation of any interim analyses and stopping rules.
Randomization-sequence generation	8	Method used to generate the random allocation sequence, including details of any restrictions (e.g., blocking, stratification)
Randomization-allocation concealment	9	Method used to implement the random allocation sequence (e.g., numbered containers or central telephone), clarifying whether the sequence was concealed until interventions were assigned.
Randomization -- Implementation	10	Who generated the allocation sequence, who enrolled participants, and who assigned participants to their groups.
Blinding (masking)	11	Whether or not participants, those administering the interventions, and those assessing the outcomes were blinded to group assignment. If done, how the success of blinding was evaluated.
Statistical methods	12	Statistical methods used to compare groups for primary outcome(s); methods for additional analyses, such as subgroup analyses and adjusted analyses.

With respect to item 12, the statistical methods and commercial software should be cited.

Item 7 and item 12 of the checklist are relevant to the Statistical Methods section of a manuscript submitted to the JACI based on a nonrandomized study. Thus:

CONSORT TOPIC	ITEM NUMBER	SPECIFIC ISSUES
Sample size	7	How sample size was determined.
Statistical methods	12	Statistical methods used to compare groups for primary outcome(s); Methods for additional analyses, such as subgroup analyses and adjusted analyses.

2. Results
Items 13 through 19 of the CONSORT checklist describe items that are important to the Results section for a manuscript submitted to the JACI based on a RCT (some of the items might not be relevant if the study is nonrandomized). Thus:

CONSORT TOPIC	ITEM NUMBER	SPECIFIC ISSUES
Participant flow	13	Flow of participants through each stage (a diagram is strongly recommended). Specifically, for each group report the numbers of participants randomly assigned, receiving intended treatment, completing the study protocol, and analyzed for the primary outcome. Describe protocol deviations from study as planned, together with reasons
Recruitment	14	Dates defining the periods of recruitment and follow-up.
Baseline data	15	Baseline demographic and clinical characteristics of each group.
Numbers analyzed	16	Number of participants (denominator) in each group included in each analysis and whether the analysis was by "intention-to-treat". State the results in absolute numbers when feasible (e.g., 10/20, not 50%).
Outcomes and estimation	17	For each primary and secondary outcome, a summary of results for each group, and the estimated effect size and its precision (e.g., 95% confidence interval).
Ancillary analyses	18	Address multiplicity by reporting any other analyses performed, including subgroup analyses and adjusted analyses, indicating those pre-specified and those exploratory.
Adverse events	19	All important adverse events or side effects in each intervention group.

2A. Results: Descriptive Statistics at Baseline
If the distribution for a continuous variable is approximately normally distributed, then report either• the sample mean and the sample standard deviation
or
• the sample mean and the 95% confidence interval for the population mean.

If the distribution for a continuous variable is known (or suspected) to be non-normal, then report either• the sample median and the sample interquartile range
or
• the sample median and the sample first and third quartiles.

Many blood and urine measurements are log-normally distributed-i.e., the log-transformed variable is approximately normally distributed. If the distribution for a continuous variable is known (or suspected) to be lognormal, then an alternative to sample medians and quartiles is to report either
• the sample geometric mean (calculate as the exponentiation of the sample mean of the natural log-transformed data) and the sample coefficient of variation
or
• the sample geometric mean and the 95% confidence interval.

If the distribution of the variable is categorical, then report the raw numbers and the percentages for the categories. Do not use more than three digits for the percentages-i.e., 79% or 79.3% are fine, but 79.32% is not.

Statistical tests, along with reported P values, for comparing groups at baseline are not necessary unless there is a strong reason to include them.

2B. Results: Outcomes
Every P value should be reported using two digits after the decimal point. If each of the first two digits after the decimal point is zero, then a third digit can be used. If each of the first three digits after the decimal point is zero, then simply report P < .001.

If the P value is close to the level to be used for claiming a statistical significance or if each of the first two digits after the decimal point is zero, then a third digit can be used. For example, if the significance level is 0.05, then P = .046 or P = .054 can be reported. Nonsignificant results (e.g., where the P value is >0.05) should be accompanied by P values; it should not simply be stated that they are nonsignificant (NS).

P values alone are not sufficient to report the results of statistical tests. The JACI'S readers need to see the magnitude of the effects via point estimates and 95% confidence intervals for the group comparisons.

An estimate of odds ratios and relative risks (and their corresponding confidence interval estimates) should not exceed two digits beyond the decimal point.

The following is an excellent article that discusses many of the statistical errors that arise in immunologic research:
Murphy JR. Statistical errors in immunologic research. J Allergy Clin Immunol 2004;114:1259-63.

The following is an excellent article that discusses the reporting of subgroup analyses in clinical research: Wang R, Lagakos SW, Ware JH, Hunter DJ, Drazen JM. Statistics in medicine-reporting of subgroup analyses in clinical trials. NEJM 2007;357:2189-2194.

Finally, if authors desire more detailed guidance on appropriate methods for analyzing study outcomes, then they can visit the Web sites of other biomedical journals. An excellent example is the Web site of Annals of Internal Medicine ( http://www.annals.org/shared/author_info.html ).



Updated August 2009