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Instructions for ContributorsThe AJRCMB focuses on papers that use cellular, biochemical, developmental, genetic, immunologic, and molecular approaches to understand structure and function of the respiratory system under physiologic and pathophysiologic conditions. Acceptance of manuscripts is based on scientific excellence, significance, and clarity of presentation. The Journal also publishes Editorials and state-of-the-art Translational Reviews. Editorials are invited by the Editor and offer review and commentary on original papers. Editorials should be submitted to Carl Schutt at the ATS Peer Review Office (cschutt@thoracic.org). Translational Reviews are initiated by submitting authors, but consultation with the Editor (shapiros@dom.pitt.edu) before submission is recommended. All manuscripts are processed as rapidly as possible in an attempt to complete the review process in less than four weeks. If an author believes that a manuscript is of special merit to warrant accelerated publication, this should be noted in the cover letter to the Editor. If the request is approved by the Editor, the manuscript will be preferentially handled as a Rapid Communication as described below. The Journal is published in both print and electronic formats and may be viewed online at http://www.atsjournals.org/ or at http://intl.atsjournals.org/ Manuscript Submission To submit your manuscript, go to Manuscript Central at http://mc.manuscriptcentral.com/atsjournals. Within this site (ScholarOne) you may use the "Create a New Account" icon to create a user account if you do not already have an existing account. The system automatically designates the individual who uploads the manuscript as the "Corresponding Author." To assure the uninterrupted flow of correspondence during the Peer Review process, all users should avoid creating more than one account. If you are not sure if you already have an existing account or forgot your User ID and Password, please e-mail Ms. Fay Ling in Technical Support (fling@thoracic.org). Technical support is available from Monday through Friday, 9:00 am to 5:00 pm, Eastern Standard Time, by e-mail (fling@thoracic.org), or by phone (212) 315-8638. Manuscripts that do not conform to guidelines may not be processed. Authors are strongly encouraged to send the following to our Peer Review Office within 24 hours of completing the online submission (see address below): completed Assignment of Copyright form and the Disclosure of Financial Interest form obtained at or from the Peer Review Office. All correspondence related to manuscripts should be addressed to: All correspondence related to manuscripts should be addressed to: Steven D. Shapiro, M.D., Editor Copyright Form An Assignment of Copyright Form must be signed by all authors and forwarded to forms@thoracic.org. The form may be photocopied and the signatures of authors can be on several different forms. Please be sure to include your manuscript number. NIH Public Access Policy If any of the authors have been supported financially by the NIH to conduct the research that is reported in the article, they should indicate this on the copyright form and provide the grant number and contact name on the title page of the manuscript. The ATS will submit an electronic copy of the final accepted version on the authors' behalf to the NIH National Library of Medicine's (NLM) and PubMed Central (PMC) at a time in compliance with NIH requirements. Cover Letter A cover letter must accompany each manuscript and should be entered in the "Author Comments" box, one of the data entry screens appearing during the online submission process. It should identify the corresponding author, and should state that the material is original and has not been submitted for publication elsewhere. It must also state that no part of the research presented has been funded by tobacco industry sources. The letter must include a statement indicating that all authors have read the manuscript and approve its submission. Requests for rapid publication should be made in the cover letter together with a brief explanation of the rationale ( see Rapid Communications below). Conflict of Interest
The AJRCMB requires that the author(s) must disclose any commercial association that might be perceived as a conflict of interest. The conflict of interest form can be found by accessing the Author Center within the ScholarOne site using the following link: http://mc.manuscriptcentral.com/atsjournals. A conflict of interest form should be uploaded for each author at the time of submission. It is the responsibility of the Corresponding Author to review this policy with all authors and to list this information in the cover letter for the manuscript. At the time of publication, the information will be disclosed in a footnote to the published manuscript. Less direct associations, such as consultancies, stock ownership in an author's or relative's name, patents, etc., which could lead to a real or perceived conflict of interest should be disclosed in a letter to the Editor or entered in the "Authors Comments" section on the website. The extent and means of possible disclosure will then be determined by discussion with the Editor. Human and Animal Study Guidelines The AJRCMB endorses recommendations concerning human research described in the Declaration of Helsinki. Manuscripts that do not conform to these standards may be rejected on that basis. Manuscripts reporting human research must state within the text that the institutional review board for human studies approved the protocols and that informed written consent was obtained from the subjects or their surrogates if required by the institutional review board. Animal studies must conform to NIH guidelines (Guide for the Care and Use of Laboratory Animals. NIH publication No. 86-23. Revised 1985. U.S. Government Printing Office, Washington, D.C. 20402-9325). Humane care for animals is required, and details should be provided. For example, paralyzing agents are not an acceptable alternative to anesthesia and should be used only in conjunction with suitable anesthetic agents. Genomics Data in ATS Journals 1. It is the authors’ responsibility to ensure that all data collected and analyzed in their experiments adhere to the Minimal Information About a Microarray Experiment (MIAME) guidelines. The MIAME checklist is available at:
We require that authors submit all primary microarray data to one of the public repositories (ArrayExpress, GEO, or CIBEX), in a format that complies with the MIAME guidelines, by the time of publication. 2. Nucleic acid or protein sequences should be deposited in EMBL or Genbank databases and accession numbers submitted prior to publication of manuscripts. ScholarOne's 20 Author Limit ScholarOne has a limit of up to 20 contributing authors per manuscript submission. If a manuscript is submitted with more than 20 authors, the first 19 available slots should be used to list the first 19 authors (the corresponding author must be included within this list). The 20th slot should designate a group name using the institution of the remaining authors. If the remaining authors are from different institutions, the corresponding author uploading the manuscript may simply choose a group name. The individuals included within this group should then be listed within the cover letter inputted in the author comments section. Note: The final typeset version of the article will contain all author names. Criteria For Authorship Each author should have participated sufficiently in the work, the data analysis, and the preparation of the manuscript, and have reviewed and approve the manuscript as submitted to take public responsibility for it. This would include substantial participation in some or all of the following aspects of the work relating to the manuscript:
Manuscript Preparation All manuscripts should be concisely written and should contain complete documentation of results. References should be selected to document key ideas and observations. Manuscripts must be written in American English. All submissions should include a cover letter, and all original manuscripts should include,in the following order: (a) title page, (b) abstract, (c) keywords, (d) text, (e) acknowledgments, (f) references, (g) footnotes, (h) tables, (i) figure legends, and (j) figures. Title Page
The title page should include a concise and descriptive title (limited to 100 characters, including spaces); the first name, middle initial, and last name of each author; the departmental and institutional affiliation of each author; and the telephone and fax numbers as well as the e-mail address of the corresponding author. (The corresponding author listed on the title page does not have to be the same person listed as the corresponding author for Peer Review in the ScholarOne system.) A running title of no more than 50 characters (including characters and spaces) be included. Please note that the title that appears on the manuscript itself must be identical to the manuscript title entered into the ScholarOne site. Abstract
The abstract summarizing the rationale, methods, results, and conclusions of the study should be limited to 250 words or less. References should be avoided but, if used, must be presented in full rather than by a reference number. The abstract should be written as a single paragraph. Keywords
A list of keywords for inclusion in the published article should be included. These will be published just below the abstract on the first page of the article. Abbreviations
A list of abbreviations is attached at the end of these Instructions. Other terms frequently used should be written out completely at first use, abbreviated in parentheses, and abbreviated thereafter. A separate section listing all abbreviations used in the manuscript, however, is not required. Source of Materials
Generic names of drugs should be used instead of trade names. The location (city, state, country) of a manufacturer listed in the text should be provided after the first reference to the manufacturer. Text The text (including spaces) must have a character count of less than 55,000. The text should include the following sections: Materials and Methods, Results, and Discussion. If a manuscript varies from this format, the rationale for the change should be explained in the cover letter. Subheadings may be used if desired. Acknowledgments
Acknowledgments to individuals and research support should be placed in a single paragraph after the Discussion. Grant and funding information, however, should be acknowledged as a footnote on the title page of the manuscript, rather than in this section. References and Supplemental Information
References should be limited to 50; exceeding this limit may delay manuscript processing. References should be typed double-spaced beginning on a separate sheet and numbered in the order that they appear in the text. All authors' names (do not use "et al."), complete article titles, and inclusive page numbers should be cited. The titles of journals should be abbreviated according to the style used in Index Medicus. If an article cited in the References is in press, one copy must be attached at the end of the manuscript submitted online. Unpublished observations and personal communications should be referred to as such in the text and not be referred to in the reference list. Submit written permission when citing a personal communication. Manuscripts "submitted for publication" are considered unpublished work and should not be included in the reference list. They should be cited in parentheses in the text as "unpublished data" or "unpublished observations." If overlapping work or supplemental information is discussed within the manuscript text, a labeled copy of the overlapping article or supplemental information should be attached at the end of the submitted manuscript file. Examples of References
Journal Articles
(This follows the general NCBI/PubMed style.) Articles in Press Kimelman D, Kirschner M. Synergistic induction of mesoderm by FGF and TGF-B and the identification of an mRNA coding for FGF in the early Xenopus embryo. Cell (In press) Complete Books Weibel ER. Stereological Methods. London: Academic Press; 1979. Articles in Books Burgess JK, McParland BE. Analysis of gene expression. In: Conn MP, editor. Laser capture microscopy. San Diego: Academic Press; 2002. p. 259-270. Abstracts Carré PC, King TE Jr., Mortenson RL, Riches DWH. Overexpression of the interleukin 8 and fibronectin genes by alveolar macrophages in bronchiolitis obliterans with organizing pneumonia [abstract]. Am Rev Respir Dis 1993;147:A479. Government or Association Reports U.S. Public Health Service. Smoking and Health. A Report of the Surgeon General. Washington DC: U.S. Government Printing Office; 1979. DHEW Publication No. (PHS)79-50066. Journal Article in Electronic Format Manoloff ES, Francioli P, Taffé P, van Melle G, Bille J, Hauser PM. Risk for Pneumonocytis carinii transmission among patients with pneumonia: a molecular epidemiology study. Emerg Infect Dis [serial online] 2003 Jan [cited 2003 Feb 14] Vol. 9(1). Available from http://www.cdc.gov/ncidod/EID/vol9no1/02-0141.htm Risk for Pneumonocytis carinii transmission among patients with pneumonia: a molecular epidemiology study. Emerg Infect Dis [serial online] Jan [cited Feb. 14, 2003] Vol. 9(1). Available from http://www.cdc.gov/ncidod/EID/vol9no1/02-0141.htmCitation Managers If you use use a citation manager to organize and style your references, you must make sure that you have downloaded the corrected style. For EndNotes you may go directly to http://www.endnote.com/support/enstyledetail.asp; for Reference Manager, go to http://www.refman.com/ and select “Get the Latest Styles and Filters” in the yellow box on the left. Permissions
Authors are responsible for obtaining proper written permission to reprint materials from any other copyrighted sources. This permission must be obtained prior to submission and included with the manuscript upon submission. Credit should be given within the manuscript for use of reprinted materials. Footnotes
Footnotes should be numbered consecutively. Designate footnotes to tables by these superscript symbols and in this order: *, † , ‡ , §, ||, , **, , etc. Tables
Tables should be typed double-spaced on separate sheets. Tables should be numbered consecutively with Arabic numbers and should have a short title. Use superscript symbols for footnotes (see Footnotes). Each table should be self-explanatory and should not appear as part of a figure or be included within the figure legend. All tables should appear directly before the figure legend section and must be submitted as a word processing file, not as art. Figures
Figures should be limited to a total number of 7 and no more than two journal pages, including legends. Figures should be numbered with Arabic numbers, and composite figures should be labeled with uppercase letters (e.g., Figure 3B) and should correctly correspond to their citations within the text. Each figure should appear on its own separate page. The labels and text within a figure should not be larger than the type used in the text of the published article: no larger than 10 point (2.5 mm in height) and no smaller than 6 point (1.5 mm in height). The size of the symbols must also be in scale with the figure, and all figures within an article should be the same point size. To further save space, all figure titles and explanations of symbols should appear only in the figure legend , not in the actual figure. Labels should be placed within the body of the figure, not outside of it. Figures should not exceed the page dimensions of 17.4 x 21.3 cm (6 7/ 8 x 8 3/ 8 inches); single-column figures should not exceed 8.4 x 21.3 cm (3 5/ 16 x 8 3/ 8 inches); and doublecolumn figures should not exceed 17.4 x 21.3 cm (6 7/ 8 x 8 3/ 8 inches). It is preferred that figures be submitted at final size. Light and electron micrographs should be composed to fill the width of either a single or double column. Photographs (micrographs and gels) should be submitted on glossy paper, carefully cropped, and of sufficient magnification to illustrate important observations. Micrographs should include internal scales; legends should not contain the magnification. If needed, figures may be reduced for better layout. For computer-generated figures, avoid using screens and light dot-pattern shading because they do not reproduce well. Instead, differentiate bars in a graph by using hatch marks or other large patterns. Photocopies will not be accepted as original art. Revisions
The submission of the Revised Manuscript starts from the Corresponding Author's "Author Center"; the process is initiated by clicking on the manuscript title in the "Manuscripts to be Revised" field. The revised Manuscript ID number is set automatically by the ScholarOne system (the character R1, R2, or R3 is appended to the previous manuscript ID). You will see a confirmation appear on the screen once your revision is fully submitted and an emailed confirmation will also be sent to you. Please note that the author is required to input "Responses to Reviewers" and "Responses to the Associate Editor" before the revision is submitted. If you have any questions, please contact Ms. Fay Ling in Technical Support at fling@thoracic.org or call (212) 315-8638. When revised manuscripts are submitted online, two high-quality hard copies must be sent to the Peer Review Office along with any missing Assignment of Copyright signatures and a copy of any in press article or supplemental data. Unmounted illustrations must be lightly labeled on the back with the author's name, figure number, and an arrow to indicate the top of the figure. Labels should be 3 to 4 mm in height. Paperclips should not be used on illustrations. Legends should present a short title and sufficient explanation to be intelligible without reference to the text. Color
The cost of publishing color art in the Journal is partially subsidized by the ATS, with a portion of the costs billed to authors according to the following prices: $600 for the first color page and $350 for each additional page that contains color. Corresponding authors of manuscripts accepted for publication will be asked to confirm in writing their acceptance and responsibility for payment of this color art billing. Submitting Figures on Disk
Figures may now be submitted as digital files on disk. However, because of the great variety of graphics software and formats available, the digital art file may not be usable. For this reason, as well as to provide a double check of the proper image, authors must include a high quality "hard copy" produced from the digital files. The Journal reserves the right at any time to use this hard copy as camera-ready copy rather than using the digital file. Digital figures must be submitted as TIFF or EPS files; color art may only be submitted in the RGB format. Fonts in EPS files should be converted to "create outlines" or "convert to paths," as this will eliminate the need to download the fonts for outputting. Black and white line art must be processed at a minimum of 900 dpi (data per inch), halftones at 300 dpi, combos (color image + type, or black and white image + type) at 500 dpi, and color at 300 dpi. Images and text should be submitted on separate disks. If the submitted figures are too large to fit on a 3.5 inch disk, they may be submitted on a CD-ROM (not 1/2, or MO, size) or Zip disk. Please submit figures on a separate disk. Please download the Guidelines for Submitting Digital Image Files from the ATS Website or call the Journal Editorial Office (212-315-8648) for detailed information on resolution, file format, and other important details about digital art submission. IMAGE MANIPULATION
Electronically submitted figures must be accurate representations of actual research images. Specific features within an image should not be enhanced, obscured, moved, deleted, or added. The grouping of images from different parts of the same gel, or from different gels, fields, or exposures must be made explicit by using dividing lines (or other graphic means of demarcation) and must also be stated in the figure legend. Adjustments of brightness, contrast, or color balance are acceptable if applied to the entire image, as long as these techniques do not obscure, eliminate, or misrepresent any information present in the original, including backgrounds (backgrounds should not be faded out to the extent that they are undetectable). Nonlinear adjustments (e.g., changes to gamma settings) as well as other manipulations such as pseudo-coloring must be disclosed in the figure legend. Authors should always have access to their original unprocessed images to provide to the Editor upon request.
The author will automatically receive a confirmed Manuscript ID number once a manuscript has been uploaded onto the ScholarOne website. Dates of submission of original and revised manuscripts will be published. Submission of a manuscript to the AJRCMB is interpreted as indicating that the data are original and have not been submitted or published elsewhere (including websites) except as an abstract. Disk Submission After a manuscript that has been submitted as hard copy has been reviewed and the final revisions are accepted, authors are required to submit the final version on disk within 7 days, accompanied by a hardcopy printout including the tables. Manuscripts may be submitted on a 3.5 inch disk, CD-ROM (not 1/2, or MO, size), or zip disk. On the disk's label, specify the file name, MS-DOS or Macintosh, and the word processing software used. WordPerfect or Microsoft Word files are preferred, but all files are acceptable. Tables should not be saved as objects or supplied as figures; rather, they should be included as text within the article, and they should not be on a separate disk. Any material submitted on disk must be accompanied by a hard-copy printout. Rapid Communications Concise reports of original observations of sufficient importance that their rapid publication would substantially enhance research in the field will be considered for rapid editorial review and publication. These reports should be definitive studies, fully documented and referenced. Editors will provide decisions within 3 weeks of receipt, and accepted manuscripts that require limited revision will be published 3 to 4 months after receipt. Editorial decisions may not be accompanied by the usual detailed reviewer comments. Request for and justification of rapid publication should be made in the author's cover letter. In addition, the author should choose the "RC" designation for manuscript type when the manuscript is first uploaded. The entire publication, including figures, tables, acknowledgments, footnotes, and references, must fit within four journal pages. This is equivalent to 16 to 18 typed pages using lines no more than 72 elite or 60 pica characters including spaces, and with double-spaced pages containing no more than 25 typed lines. Micrographs are counted as one page and each graph is counted as one-half page. Page Charges All original manuscripts are subject to page charges at a rate of $75 per printed page. Authors will be billed for the charges. Cover Color cover illustrations will be chosen each month from an article appearing in the Journal. The choice of cover art illustration will be made by the Editor. Authors are also encouraged to submit suitable high-quality color figures that do not appear in the actual article. These figures should be related to the topic of their article and be accompanied by a short explanatory legend. Color figures will be published on the cover without additional charge; normal plate charges will continue to apply for color figures used within an article. The dimensions of cover illustrations should be 7-1/2 X 10 inches (width X height). These figures should be submitted according to the Submission of Digital Art Guidelines. Editorials Please send Editorials to Carl Schutt in the ATS Peer Review Office via email cschutt@thoracic.org. The goal of an Editorial is to summarize and translate important topics of research in respiratory biology. These short commentaries will review the historic development of information on the topic, the current understanding of the topic, and its relevance to basic lung biology and disease. Areas of importance for future studies may be identified as well. Topics for Editorials will be selected to highlight an interesting research publication in AJRCMB and will be published in the same issue. Editorials should not exceed three Journal pages (~ 2,200 words of text, plus one/two figures or tables and accompanying references). Inclusion of a summary figure or table is strongly encouraged. The Editor and/or invited experts in the field of interest will review the Editorials manuscripts. Translational Reviews The goal of Translational Reviews is to highlight an important scientific topic in respiratory cell or molecular biology and to provide a perspective on this topic for normal and abnormal function of the respiratory system. These reviews therefore aim to translate state-of-the-art basic research in the respiratory sciences into a form that is relevant to respiratory function and/or disease. The reviews should define why a topic is of importance, should present the current understanding of this topic, and should indicate the future directions of research in the area. Authors are encouraged to use their own work to illustrate general concepts in the field. Translational Reviews should be 3,000 or 4,000 words of text (including references). Illustrative material, especially summary diagrams, is strongly encouraged. References should be representative rather than exhaustive. The review should also include an abstract limited to 250 words. Online Data Supplement Authors may submit supplemental material for posting on the online data supplement, including additional text, tables and figures (and supporting information), as well as video and soundtrack files. In addition, Excel spreadsheets may also be submitted if it is necessary to include large datasets that would not easily convert to a PDF Format. The supplemental material must be appended to the main manuscript in one file (except for videos and other media that would not convert to PDF format). The cover sheet should identify the material as "online data supplement" and indicate the manuscript title and authors. This material will also be peer reviewed. One important use of the online supplements might be to include an extended Materials and Methods section for which there is not sufficient room in the print verison. Supplemental material must have an independent reference section, sequentially numbered as "E1, E2." Figures and tables should be labeled "Figure E1", "Table E1," etc. If supplementary material is included with an original submission, it must be included again when the revised manuscript is submitted. In addition, the Peer Review Office must receive a hard copy of the supplemental material, a 3.5 inch high-density diskette, and one set of publication-quality figures (laser-printed hard copy is acceptable) with electronic files of the figures on disk or CD-ROM. The staff will create the hypertext link between the Online Data Supplement and the online version of the article. Articles in Press Upon acceptance for publication, articles are posted online within days of acceptance as Articles in Press ( http://ajrcmb.atsjournals.org/articlesinpress.html). Please note that these articles have not yet been copyedited or proofread. Final online and print publication of a manuscript will differ slightly from Articles in Press as a result of copyediting; there may be differences in the quality and position of the graphics. The Articles in Press are citable, searchable, and establish publication priority. The official publication date appears below the title followed by the Digital Object Identifier (DOI), an automatically generated unique identifier for intellectual property in the digital environment. E-Proofing The AJRCMB no longer mails hardcopy galley proofs to the Corresponding Author. Instead, once the article has been typeset, the Corresponding Author will receive an e-mail containing a live URL link to a PDF file of the typeset article. The e-mail also contains detailed instructions on making corrections. Embargo Policy An article published in the AJRCMB may not be discussed by journalists or presented in other public media, such as websites, prior to posting on the Journal's website. It is permissible to present the article's content at a scientific meeting. The ATS, however, may refuse to publish a manuscript, despite acceptance for publication by an editor, if information has been disseminated prematurely in the media. For more information, contact Brian Kell, Director of Communications, (212) 315-6442, Fax: (212) 315-8651, bkell@thoracic.org (Reprints of these Instructions may be obtained from the Peer Review or Editorial Office or from the ATS website). Last Update: March 2007 AbbreviationsA, ampere BCG, Calmette-Guerin bacillus C, complement D, dalton EBV, Epstein-Barr virus °F, degree Fahrenheit g, gram h, hour IFN, interferon K d, dissociation constant liter(s), liter(s) m, meter N, normal (concentration of ionizable groups) OD, optical density P, probability r, correlation coefficient s, second(s) t test, Student's t test U, unit V, volt W, watt yr, year | |||||||||||||||||||||||||||||
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