Instructions to Authors

(Revised June 2009)

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Scope
The American Journal of Pathology, the official journal of the American Society for Investigative Pathology (ASIP), seeks to publish high-quality original papers on the cellular and molecular biology of disease. The Editors accept manuscripts that advance basic and translational knowledge of the pathogenesis, classification, diagnosis, and mechanisms of disease, without preference for a specific analytic method. High priority is given to studies on human disease and relevant experimental models using cellular, molecular, animal, biological, chemical, and immunological approaches in conjunction with morphology.

Manuscript Categories
Regular Articles are categorized in the Table of Contents according to the following research topics: Biomarkers, Genomics, Proteomics, and Gene Regulation; Cardiovascular, Pulmonary and Renal Pathology; Cell Injury, Repair, Aging and Apoptosis; Epithelial and Mesenchymal Cell Biology; Gastrointestinal, Hepatobiliary and Pancreatic Pathology; Growth Factors, Cytokines, Cell Cycle Molecules; Immunopathology and Infectious Diseases; Matrix Pathobiology; Metabolic, Endocrine and Genitourinary Pathobiology; Molecular Pathogenesis of Genetic and Inherited Diseases; Musculoskeletal Pathology; Neurobiology; Stem Cells, Tissue Engineering and Hematopoietic Elements; Tumorigenesis and Neoplastic Progression; and Vascular Biology, Atherosclerosis and Endothelium Biology. Not all topic areas will appear in each issue, as this is dependent on the content of original research accepted for publication. Upon acceptance, authors will be asked for their preference of topic category assignment; however, the Editors will make the final determination regarding topic category placement.

Short Communications are intended to provide a forum for the rapid publication of timely and significant findings, in brief. Manuscripts in this category should be concise but definitive, and must not exceed 12 double-spaced typed pages (excluding references and legends) and a maximum of three figures.

In addition to original research articles, the Journal publishes articles categorized as Reviews, Mini-Reviews, Biolological Perspectives, and Commentaries. Authors who wish to publish a Review or Mini-Review should send their curriculum vitae along with an outline of the proposed article for prior approval by the Editor-in-Chief. Reviews have a maximum of 6,000 words, 100 references, and four tables or figures (one of which is mechanistic); Mini-Reviews should have a maximum of 4,000 words, 50 references, and two tables or figures (one of which is mechanistic). Biological Perspectives are submitted by invitation only and provide streamlined, mechanistic insight into the current state of research in the discussed topic. Commentaries are submitted by invitation only and relate to a concurrently published manuscript. All invited papers are subject to the same review process as unsolicited articles.

Review Process
The Editors perform an initial evaluation on all submissions to determine whether they believe the manuscript will achieve a sufficient priority score to warrant publication. Priority is determined by the Editors' assessment of the manuscript relative to other papers being considered. The aim is that expeditious treatment will enable authors to submit their manuscript elsewhere as soon as possible without suffering unnecessary delays. For manuscripts accepted for external review, the Editor-in-Chief assigns manuscripts to Associate Editors according to their expertise. The Associate Editor will solicit reviewers (typically, two external reviews are sought). Authors are encouraged to identify up to five potential reviewers. It is the practice of the Journal to conduct a blinded peer-review process. The peer-review process is kept completely confidential; it is considered a violation of this confidentiality for authors to identify or attempt to communicate directly with peer reviewers or Associate Editors regarding their manuscript. The reviewer comments and Associate Editor's recommendation are evaluated by the Editor-in-Chief for disposition and transmittal to the authors. Every effort is made to complete the review process within 45 days of the date received.

Review Decisions
Only a portion of manuscripts will be accepted for publication. A number of worthy manuscripts will be rejected based on priority. The Journal will advise authors whether the manuscript is accepted, acceptable with revisions, or rejected. A manuscript may be returned to the authors without outside review if the Editors find it inappropriate for publication in this Journal.

Journal Scientific Integrity Policy
The Journal has developed principles for defining scientific misconduct as well as procedures for handling such matters. General guidelines are described below; detailed information can be viewed at http://ajp.amjpathol.org/content/integrity. To report suspected misconduct relating to authors, reviewers, or Editors, send written complaint to the Editorial Office at The American Journal of Pathology, 9650 Rockville Pike, Bethesda, Maryland, USA 20814-3993 or ajp{at}asip.org. Issues relating to staff conduct should be directed to the ASIP Executive Officer at American Society for Investigative Pathology, 9650 Rockville Pike, Bethesda, Maryland, USA 20814-3993 or mesobel{at}asip.org.

Author Conduct
Authorship is defined as 1) substantial contributions to conception and design, or acquisition of data, or analysis and interpretation of data; 2) drafting the manuscript or revising it critically for important intellectual content; and 3) final approval of the version to be published. Authors should meet conditions 1, 2, and 3. When submitting a manuscript to the Journal, the corresponding author takes responsibility on behalf of all authors for the authorship, authenticity and integrity of the research being reported. Authors should take special care that manuscripts submitted to the Journal are prepared in accordance with the Uniform Requirements for Manuscripts Submitted to Biomedical Journals (see http://www.icmje.org); in particular the ethical considerations regarding authorship, conflicts of interest, redundant publication and treatment and confidentiality of research subjects should be carefully adhered to. Additionally, the Journal takes great care to secure the confidentiality and integrity of the peer-review process; it is considered a violation of this confidentiality for authors to identify or attempt to communicate directly with peer reviewers or Associate Editors regarding their manuscript. The Editors will consider any deliberate ethical violation in either the reported research or the manuscript preparation and review to be actionable misconduct, the potential results of which may be manuscript rejection or public article retraction, reporting of conduct to the authors’ governing institutions, and/or the denial to consider any future submissions to the Journal. Willful misconduct does not include incidents of honest misjudgment or inadvertent error. Detailed information regarding possible misconduct can be found in the Journal Scientific Integrity Policy at http://ajp.amjpathol.org/content/integrity.

Manuscript Submission
Manuscripts should be submitted online via the Rapid Review system (http://www.rapidreview.com/ASIP2/CALogon.jsp). Detailed instructions on preparing and submitting files can be found on the author submission website at the above URL. Authors having difficulty submitting files online should complete the online submission form on Rapid Review to receive the assigned manuscript number, and mail one electronic (disk) copy of the manuscript and figures. These items should be clearly marked with the assigned manuscript number and sent to: Michael P. Lisanti, M.D., Ph.D., Editor-in-Chief, The American Journal of Pathology, 9650 Rockville Pike, Bethesda, Maryland, USA 20814-3993. The cover letter must state any conflicts of interest (both financial and personal), affirm that the manuscript has not been published previously and is not being considered concurrently by another publication, and affirm that all authors and acknowledged contributors have read and approved the manuscript. Submissions will be ineligible for review if previously published in any form (print or online) other than as an abstract. This includes any public posting of raw manuscripts or pre-reviewed material.

A non-refundable manuscript processing fee of U.S. $50 is required with submission. This fee may be paid electronically at the time of submission. Manuscripts arising from research in developing countries may be eligible for waiver of the submission fee only if all authors are located in a qualifying country (waiver must be applied for at time of submission; for a list of eligible countries, see http://ajp.amjpathol.org/webfiles/images/journals/AJPA/waivernations.pdf). Otherwise, manuscript submission fees will not be waived.

Manuscript Preparation
Manuscripts should be prepared in the style of the Journal and in accordance with The Uniform Requirements for Manuscripts Submitted to Biomedical Journals (see http://www.icmje.org). Standard abbreviations can be found in the CSE Style Manual (7th ed., 2006). All pages of the manuscript should be double-spaced and numbered (including references, tables and figure legends). Other formatting specifications (eg, font size and type, margin settings, etc.) are left to the authors’ discretion, as papers accepted for publication will be reformatted according to the print specifications of the Journal. Manuscripts not prepared in accordance with the submission guidelines detailed below may be returned to the authors. Authors are encouraged to include a list of nonstandard abbreviations to aid reviewers. In addition, authors should be ready to comply with Editors’ requests for copies of any similar works in preparation, copies of cited manuscripts that are submitted or in press, and/or supporting manuscript data (eg, data not shown but summarized in the manuscript) that may aid the review process.

Title Page
The title page must include a concise title accurately reflecting the findings of the work; names (not initials) of all authors; department, institution and address where the research was performed; number of text pages, tables and figures; a short running head (40 characters or less); grant numbers and sources of support; and name, address, phone, fax, and email of the corresponding author; name and address of author who should receive reprint requests. If an author changes employment after the study was performed, the new affiliation information for that author should be included as a footnote. Any affiliations (eg, employment, consultancies, stock ownership, honoraria, expert testimony) with any organization or entity having a direct financial or personal interest in the subject matter or materials discussed in the article should also be clearly stated.

Abstract
An abstract of 220 words or less should be prepared on a separate sheet and should be intelligible to the general reader without reference to the text. The abstract should clearly summarize the background, methodology, results, and significance of the study. Abbreviations and citations should be avoided.

Text
The remaining sections of the text, which should include Introduction, Materials and Methods, Results, Discussion, and Acknowledgments (in this order), need not begin on new pages. Commonly-abbreviated terms should be spelled out in their first occurrence and then may be referenced in abbreviation through the remainder of the manuscript. Consult the Human Genome Organisation Gene Nomenclature Committee website (http://www.genenames.org/) for gene names and symbols. For a complete list of other approved nomenclature organizations (eg, bacteria, viruses, mice), please contact the Editorial Office.

For Materials and Methods, authors should describe experimental and statistical methods in enough detail that other researchers can replicate results and evaluate claims. In general, inclusion of method or reagent details as supplementary material is not acceptable. The sequences of oligonucleotides, if not previously published, should be provided. Novel DNA or protein sequences should be deposited to an appropriate database (eg, Genbank, EMBL, SWISS-PROT), with the accession numbers included in the manuscript. When providing supplier information for materials sources, company name and location (city and state, or city and country) should be provided. Website references to company information are not permitted. All novel materials and the procedures to prepare them should be described in sufficient detail to allow their reproduction (eg, DNA constructs, analytical software). Materials that are approved for investigational-use only should be clearly indicated. Publication in the Journal implies that the authors agree, upon reasonable request, to share any materials or data that are integral to the results presented in the article, including whatever would be necessary for a skilled investigator to verify or replicate the claims. Authors must disclose upon submission any restrictions on the availability of materials or information, such as for patented or dual-purpose materials.

Reporting guidelines for specific study designs (eg, randomized controlled trials) can be found in the Uniform Requirements for Manuscripts Submitted to Biomedical Journals (see http://www.icmje.org). Authors must affirm that the research protocol was approved by the appropriate institutional review boards or ethics committees for human (including use of human cells or tissues) or animal experiments and that all human subjects provided appropriate informed consent and/or that regulations concerning the use of animals in research were adhered to. If race/ethnicity is reported, authors should state who determined race/ethnicity, how the options were defined, and why race/ethnicity was important in the study. Authors should be prepared to provide study protocol number(s) if requested.

Authors should obtain permission from all individuals named in the Acknowledgments who contributed substantially to the work reported (eg, data collection, analysis, or writing/editing assistance) but did not fulfill the authorship criteria. Likewise, authors should receive permission from all individuals named as sources for personal communication or unpublished data. Such permissions should be affirmed by the corresponding author in the cover letter.

References
References should begin on a new page, be double-spaced and numbered in order of citation in the text, including citations in tables and figure legends. Complete author citation is required (use of "et al" is not acceptable). References should conform to the style of the Journal. Examples follow:
Journals: Cecena G, Wen F, Cardiff RD, Oshima RG: Differential sensitivity of mouse epithelial tissues to the polyomavirus middle T oncogene. Am J Pathol 2006, 168:310-320
Books: Fishman AP: Pulmonary Hypertension and Cor Pulmonale. Pulmonary Diseases and Disorders. Edited by Fishman AP. New York, McGraw-Hill, 1988, pp. 999-1048
Web sites: See Data Supplements section below for proper use of web site references. Cite in text only. Use the digital object identifier when available. Include the name of the institution sponsoring the web site, URL address with direct linkage to the referenced information, and date of access.
In press: To be used only for papers accepted for publication. Cite as for journal with (in press) in place of volume and page numbers.
Submitted papers/unpublished data: Cite in text only.

Tables
Tables should be typed double-spaced and submitted on separate pages, as part of the manuscript. Tables should be black and white text only and should not include figures or other non-typeset images.

FiguresAuthors should give considerable care in preparing figures. Figures may consist of multiple related panels (labeled A, B, C, etc.) described under one figure legend. Each figure (with all of its related panels) should be arranged on a single page as it should appear in final publication. Figure panels submitted on separate pages will be arranged at the publisher's discretion. If figures are to be published in black and white, they should be submitted for review in black and white. Digital figure files are required, but authors may provide production-quality hardcopies for review purposes. Hardcopies should not differ from the output of digital figure files. When preparing composite figures, the front side of individual parts should be clearly and properly labeled. Figures should be sized to fit one column (8 cm) or two columns (17 cm). Maximum page length is 22.5 cm. Figures deviating from these dimensions will be sized at the publisher's discretion. Unwanted background material should be excluded, and edges should be straight. Figure legends should be submitted as part of the manuscript and should state the staining method and degree of magnification. If the exact scale is critical, scale bars should be used on the photograph and specified in the legend.

No specific feature within an image may be enhanced, obscured, moved, removed, or introduced. The grouping of images from different parts of the same gel or blot, or from different gels or blots, fields, or exposures must be made explicit by the arrangement of the figure (eg, using dividing lines) and in the figure legend. Adjustments of brightness, contrast, or color balance are acceptable only if they are applied to the whole image, whether experimental or control image, and as long as they do not obscure or eliminate any information present in the original (Adapted with permission from the JCB). Any evidence of inappropriate manipulation may prompt the Editors to request an explanation and access to original data, which the authors must make available. Information can be found in the Journal Scientific Integrity Policy at http://ajp.amjpathol.org/content/integrity.

Digital Art
Beginning July 1, The American Journal of Pathology’s requirement for color images, which has traditionally been CMYK, is changing to RGB (Red, Green, Blue) color mode. Images submitted in RGB will retain the vivid reds, greens, and blues of the original digital files for online publication. Authors should therefore submit all figures (for both new and revised manuscripts) in the RGB color mode. The preferred formats for digital figures are PDF, TIFF, and EPS. For detailed instruction on preparing digital art for submission or production, visit http://cpc.cadmus.com/da/ or contact the Editorial Office (ajp{at}asip.org).

Data Supplements and Non-Traditional Media
Figures and tables that are critical to the evaluation and understanding of the research presented, but which cannot be accommodated via the print medium (eg, video), will be considered part of the manuscript submission and will be published on the Journal website if the manuscript is accepted. Supplemental material published on the Journal website is subject to the same copyright as applies to the printed article. Online data will remain associated with its article and is not subject to any modifications or updates after publication. Authors of accepted manuscripts will be charged $50 per supplemental data file to be published on the Journal website (up to 1MB; files over 1MB will be charged an additional $50 per megabyte). Beginning with the January 2010 issue, supplemental data files published on the Journal website will be charged $95 per file (up to 1MB; files over 1MB will be subject to an additional $95 per megabyte).

Complex data sets such as microarray data and gene sequences should be deposited in a reliable public archive. Microarray repositories should comply with the Minimum Information About a Microarray Experiment (MIAME) guidelines (http://www.mged.org/Workgroups/MIAME/miame_1.1.html). Examples include Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) and Array Express (http://www.ebi.ac.uk/arrayexpress/). Tissue microarray data exchange specifications can be found at http://www.biomedcentral.com/1472-6947/3/5. Otherwise, the data may be published as supplemental data on the Journal's website (http://ajp.amjpathol.org/content/integrity).

Other materials that are not required to understand and evaluate the article may be stored on an institutional website and referenced as a URL within the manuscript text. In this case, the authors must assume responsibility for maintaining a live, unrestricted link to the material from the URL published within the article, in perpetuity. Failure to maintain a live, unrestricted link may result in retraction of the article by the Editors. Material that has been published previously (print or online) is not acceptable for posting as supplementary data. Instead, the appropriate reference(s) to the original publication should be made in the text and references.

The Editors will make the final determination as to whether a given data set is essential to the manuscript and whether they will require publication of the material on the Journal website. Failure to relinquish required materials for online publication can result in the reversal of a manuscript’s acceptance.

Copyright
Copyright of published manuscripts is held by the American Society for Investigative Pathology, which must receive the assignment of copyright from the authors of accepted manuscripts. For US government employees, the above assignment applies only to the extent allowable by law. For detail, see http://www.asip.org/pubs/ajprights.pdf.

Through The American Journal of Pathology’s affiliation with PubMed Central (PMC), the Journal deposits all final published articles in PMC, to be made available to the public twelve months after final print publication. Publishing in the AJP automatically places authors in compliance with the NIH Public Access Policy (see http://publicaccess.nih.gov/submit_process.htm, Submission Method A). Authors therefore should NOT complete a separate deposit of their material but will be contacted by PubMed Central for grant verification once the article has been received by the PMC article system. For information on how to cite your articles in NIH grant applications, please visit http://www.asip.org/pubs/AuthorNotice.htm.

Contact the Editorial Office regarding permission to deposit manuscripts in other government-sponsored repositories in cases where The American Journal of Pathology does not have a system in place to automatically deposit materials on behalf of their authors. Deposit of accepted or published manuscripts in any non-AJP repository without prior permission by the Journal is a violation of copyright.

Embargo Policy
All information regarding the content of submitted or accepted manuscripts is strictly confidential. Information contained in or about accepted articles cannot appear in print, audio, video, or digital form or be released by the news media until the Journal embargo date has passed, not to exceed the publication date of the article. For detailed information on embargo release dates or for news media requests for preprint copies of specific articles, contact the Editorial Office at 301-634-7959 or ajp{at}asip.org.

Financial Disclosure and Conflicts of Interest
All authors must disclose any current or former affiliations (eg, employment, consultancies, stock ownership, honoraria, expert testimony) with any organization or entity having a direct financial or personal interest in the subject matter or materials discussed in the article. Authors should err on the side of full disclosure and should contact the Editorial Office if they have questions or concerns. This information should be provided at the time of submission and reiterated as part of copyright assignment. Failure to do so may result in manuscript rejection or editorial retraction of the article. Further information can be found in the Journal Scientific Integrity Policy at http://ajp.amjpathol.org/content/integrity. Upon manuscript acceptance, all coauthors will be instructed to formally disclose all potential conflicts.

Color Figures
Authors will be charged $750 per color figure per printed page (figures necessitating more than one printed page will incur an additional charge). A summary of color figures charges will be presented to the corresponding author of accepted manuscripts for approval prior to publication. Color figure charges will not be waived, but color figures may be published in black and white, pending editorial approval. Requests for black and white publication must be made prior to production to avoid color charges.

Page Charges
Authors will be charged $65 per printed page. Corresponding authors of published manuscripts who are current, dues-paying members of ASIP at the time of submission will receive free page charges as a benefit of membership. Manuscripts arising from research in developing countries may be eligible for waiver of publication charges only if all authors are located in a qualifying country (for details, see http://ajp.amjpathol.org/webfiles/images/journals/AJPA/waivernations.pdf). Otherwise, page charges will not be waived, except for solicited editorials.

Beginning with articles accepted for the January 2010 issue, the following changes to Publications Charges will apply:Authors will be charged $550 per color figure, $50 per black & white or grayscale figure, and $50 per composed table, per printed page (figures or tables necessitating more than one printed page will incur an additional charge). Authors will be charged $95 per printed page. Corresponding authors of published manuscripts who are current, dues-paying members of ASIP at the time of submission will receive one free color figure as a benefit of membership; page charges will not be waived for ASIP members. Supplemental data files published on the Journal website will be charged $95 per file (up to 1MB; files over 1MB will be subject to an additional $95 per megabyte). A summary of publications charges will be presented to the corresponding author of accepted manuscripts for approval prior to publication.

Open Choice
In addition to publication charges outlined above, authors may elect to participate in the Journal’s Open Choice program. Articles published under Open Choice will become immediately accessible on the Journal website upon publication, without the twelve-month subscriber-only access delay. Authors wishing to participate should contact the Editorial Office following manuscript acceptance. All copyright restrictions regarding reuse still apply. Cost to participate is $1500, which must be received before article restriction is lifted.

Reprints
Reprints should be ordered when page proofs are returned; an order form is included with the proofs. Late reprint orders may result in additional fees. There is no extra charge for color reprints. Author reprints will be supplied in CMYK color mode because it is a printed medium, but electronic reprints will be supplied in RGB color mode for visualization on screen. Each coauthor will receive one complimentary electronic (secure PDF) reprint. Additional electronic reprints can be ordered at the time page proofs are returned, or at a later date. No hardcopy complimentary reprints are provided by the publisher.

Proofs
The corresponding author will be contacted by email once proofs are ready, and will be directed to download electronic proofs from a secure website. Electronic page proofs will be provided in RGB, thus reflecting the online quality. Image files will be converted to CMYK for the printed journal; all images published online will be in RGB. Full instructions on completing proof corrections will be provided at that time. The author should check the proofs carefully, mark any printer's errors, and answer queries as requested. Author changes should be kept to a minimum. Proof corrections and replacement figures (if any) must be returned within 48 hours to avoid any delay in publication.

Cover Figure
The cover figure is selected by the Editors from illustrations appearing in the issue. Authors are encouraged to suggest a figure for consideration or include an additional cover figure submission along with their manuscript submission. Cover figures are published at no charge; cover reprints are available (no complimentary reprints are provided by the publisher).

Editorial CommunicationsAll correspondence concerning editorial matters should be addressed to the Editor-in-Chief at The American Journal of Pathology, 9650 Rockville Pike, Bethesda, Maryland, USA 20814-3993, faxed to 301-634-7961, or emailed to ajp{at}asip.org. Letters to the Editor will be printed at the Editors' discretion in the Correspondence section.

Corrections are published upon request and after editorial review. Retractions are published upon request of authors or their institutions and may also be published by the Journal following a determination of scientific misconduct. Notes of Concern are published in response to editorial concerns relating to scientific or publishing misconduct by authors or reviewers or to alert the scientific community of an ongoing investigation.

[Revised: June 2009]