the-aps.org>publications>instructions for preparing your manuscript

#
Instructions for Preparing Your Manuscript

Revised July 2007

This document will take you through all the major steps of preparing your manuscript for submission to the American Physiological Society Journals, from how best to format and organize the paper itself, to how to create digital images suitable for print and web publication, to advice on how to present supplemental data files such as video clips and long tables.

These instructions pertain to all of the American Journal of Physiology sections, as well as the Journal of Applied Physiology, the Journal of Neurophysiology, Advances in Physiology Education, and Physiological Genomics. Physiology and Physiological Reviews (both invited only) have specific instructions that you should review if you are submitting to them.

# Exceptions for the Journal of Neurophysiology

The Journal of Neurophysiology departs from usual Journal style in some areas; specifically regarding keywords, and references. These exceptions are marked below with the "JN" icon: , and bordered to the left with a bold black line.

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> Main Contents
> General Information
> Ethical Policies
> Standards
> Technical Requirements
> Manuscript Sections
> Types of Articles
> Figures
> Tables
> Mathematical Equations and Modeling
> Data Supplements

#
General Information
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The American Physiological Society (APS) Journals seek definitive papers that present the entire contents of a research project. In general, all data from a group of subjects, animals, or samples should be presented together in a single paper. If this cannot be done, then the manuscript should be cross-referenced. Identical subject, animal, and sample numbers should be used in the different manuscripts to identify their commonality.

> Section Contents
> Peer Review Policy
> Copyright and Permissions
> Cost of Publication
> Restrictions on Prepublication
> Authorship Changes
> Use of Previously Published Illustrations
> "Submitted" and "Accepted" Dates
> "Advertisement" Note

# Peer Review Policy
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Manuscripts are refereed critically by two or more reviewers. Acceptance of manuscripts is based on scientific content and presentation of the material; membership in the Society is not a prerequisite for publication. The Editor/Associate Editor selects the reviewers, corresponds with the author, and makes the final decision on the acceptance or rejection of the manuscript. If a manuscript is submitted by an Editor of the Journal, another Editor handles that manuscript. The APS Peer Review office helps ensure confidentiality by blinding user records in the APS Central system to be used for this purpose. See also Peer Review and Revision.

# Copyright and Permissions
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The Mandatory Submission Form serves as the official copyright transfer form. (Forms customized to your manuscript will become available on completion of the submission process; check the Home Page of the journal you are submitting to for blank forms.) The APS Journals are copyrighted for the protection of authors and the Society. The code at the bottom of the first page of an article indicates the copyright owner's consent that copies of that article may be made beyond what is permitted by sections 107 and 108 of the US Copyright Law -- unless the copies are for general distribution, for advertising, for creating new works, or for resale -- provided the per-copy fee is paid through the Copyright Clearance Center, Inc.:

> Copyright Clearance Center, Inc.
> 222 Rosewood Dr.
> Danvers, MA 01923

For information about any of these exceptions or for permission to reproduce previously published illustrations or tables, write to:

> Penny Ripka
> Publications Office
> American Physiological Society
> 9650 Rockville Pike
> Bethesda, MD 20814-3991
> 301-634 7243 (fax)
> pripka@the-aps.org

Include an explicit statement of intended use and detailed specification of the material to be reproduced.

Important Information about the NIH Public Access Policy and Your Manuscript

# Cost of Publication
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Mandatory Submission Fee

- There is a one-time Mandatory Submission Fee of $50 for each article submitted to most of the APS Journals.

- The Mandatory Submission Fee is waived only for invited authors and for those submitting to Advances in Physiology Education.

Page Charges

- To recover part of publication costs, the APS charges authors of research articles $70 per printed page. By signing the Mandatory Submission Form, the author agrees to pay page charges once his/her paper is published. (Forms customized to your manuscript will become available on completion of the submission process; check the Home Page of the journal you are submitting to for blank forms.)

- Excessive changes made in proof will be subject to additional charges.

- The page charges are waived for invited authors and for those publishing in Physiological Reviews, Physiology, and Advances in Physiology Education.

Cost of Color

Among scholarly publishers, the APS offers one of the most favorable terms for color figure publication.

- We publish scientifically necessary color figures free of charge if the first or the last author is an APS member in good standing (this includes student members).

- Nonmembers will be charged the low subsidized rate of $400 per color figure.

- Color is free for authors publishing in Physiological Reviews and Physiology.

- At proof stage, if the author requests a color Iris proof copy of his/her figure(s), a service charge of $75 per figure will be added to the article publication fees.

Reprint Services

The APS provides high quality reprints to its authors.

- Please order reprints when you receive the electronic or mailed proof of your article.

- The Reprint Order Form is enclosed in the electronic proof package. Please fill it out and send within 48 hours to the address indicated on the form. Please note that the articles containing color can ONLY be ordered at proof stage.

- If your article has color figures, there is an additional press charge of $100 per 100 reprints ordered.

- Toll-free link: at your request, the APS can create a link from your online published article to a URL you specify. Readers accessing your article from this URL can do so without a subscription to the journal. The per-article cost is $150 ($250 for articles in Physiological Reviews) and can be noted on the Reprint Order Form. Payment for the link will be added to the invoice for publication fees.

- See the current reprint prices.

Author Choice Program for Open Access

You may now choose to pay a fee ($2000) to make your online article free immediately (for more information on the APS Author Choice program, see http://www.authorchoice.org). The payment form can be found at http://www.the-aps.org/authorchoice/pdf/form.pdf.

# Restrictions on Prepublication
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Except in reviews and invited editorials, the APS Journals will not accept submissions in which, other than in abstracts of less than 400 words, a significant portion of the data in the form of figures and/or tables has been published elsewhere. For the APS guidelines regarding duplicate and/or prior publication, see the APS Ethical Policies and Procedures.

# Authorship Changes
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Changes to authorship are handled differently depending on when the error is noticed, i.e., on the stage of publication of the paper.

1. After submission but before acceptance

   If you realize that changes to authorship (e.g., altering the order of authorship or adding/removing a name) are needed, please follow these steps:

   - Download the Change of Authorship Form.
   - Have ALL authors sign it.
   - Fax, mail, or e-mail the signed form to the APS Peer Review office (301-634-7243)
2. After publication in Articles in PresS

   If you have realized that an author's name was misspelled in such way as to affect finding the article in PubMed or through other searches, notify the Peer Review office so that the article can be fixed by amending the Article in PresS edition. Please note: this is the ONLY case when Articles in PresS edition will be corrected. Follow the steps above when submitting the correction. Other authorship corrections can still be made for the final print and online editions (see point 3 below).

3. During production of the final print and online editions

   Changes to authorship (e.g., altering the order of authorship; adding/removing a name; adding or changing an initial) can still be made during production. You will need to follow these steps:

   - Download the Change of Authorship Form.
   - Have ALL authors sign it.
   - Fax, mail, or e-mail the signed form to the Journal Editorial Office (301-634-7243).
4. After the final edition has been published in print and online

   Any changes to authorship can only be made through a corrigendum to the print edition. The online version will have a permanent link to the corrigendum. Follow the steps in point 3 when submitting the changes.

# Use of Previously Published Illustrations
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APS Journals do not allow the use of previously published illustrations in regular research papers. If scientifically appropriate, previously published illustrations may be included only in reviews, invited editorials, or other invited papers, and only if permission is obtained from both the author and the original publisher. Authors are responsible for obtaining permission letters and must include them with their accepted manuscript in advance of publication. Authors are also responsible for providing publication-quality electronic files or laser prints of the previously published illustrations. These are best obtained from the original publisher or original author. Previously published images downloaded from the Internet are not acceptable for publication. See also Special Considerations for Invited Authors.

# "Submitted" and "Accepted" Dates
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The "submitted" date for a manuscript is the date when the manuscript was submitted to APS Central online peer review system. The "accepted" date is the date when the official letter of acceptance is sent out (usually via e-mail) from the review Editor.

# "Advertisement" Note
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The APS is required by US Postal regulations to affix the following note on the title page of all articles for which page charges are assessed: "The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked 'advertisement' in accordance with 18 U.S.C. Section 1734 solely to indicate this fact."

# Ethical Policies
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  Section Contents
  Ethical Policies and Procedures
  Use of Humans and/or Animals in Experiments
  Fetal Tissue Research Policy
  Conflict of Interest
  see also: Cell Lines and Reagents

# Ethical Policies and Procedures
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Authorship

The Editors of the journals of the American Physiological Society (APS) expect each author to have made an important scientific contribution to the study and to be thoroughly familiar with the original data. The Editors also expect each author to have read the complete manuscript and to take responsibility for the content and completeness of the manuscript and to understand that if the paper, or part of the paper, is found to be faulty or fraudulent, that he/she shares responsibility with his/her coauthors. The Mandatory Submission Form, which is published in the journals, should be signed by each author. In cases in which obtaining a signature from each author would delay publication, the corresponding author’s signature is sufficient provided that the corresponding author understands that he or she signs on behalf of the other authors who have not signed the form. An author’s name can be removed only at his/her request, but all coauthors must sign a change of authorship agreement for any change in authorship (additions, removals, or change of order) to be made.

Author Conflict of Interest

Authors of research and other articles are required at the time of submission to disclose to the APS Publications Office any potential conflict of interest (e.g., consultancies, stock ownership, equity interests, patent-licensing arrangements) and that they accept full responsibility for the conduct of the study, had full access to all the data, and controlled the decision to publish. Failure to do so may jeopardize eventual publication. If disclosures are to be made, the author(s) will be asked to fill out a Conflict of Interest Disclosure form. The information provided in the form, unless already disclosed in the submitted article, will be held in confidence while the paper is under review. If the article is accepted for publication, information on the potential conflict of interest -- including a lack of control of the decision to publish -- will be included in the Disclosures section, following the Acknowledgments section.

Editor and Reviewer Conflict of Interest

Editors and Reviewers should avoid making decisions on papers for which they may have a personal or financial conflict of interest. Reviewers who are collaborating with the author, or who are working on very similar research, should recuse themselves from reviewing a paper for which they have a conflict. An Editor in Chief should have a Consulting Editor or Associate Editor make a decision on a paper for which he or she has a conflict. When an Editor in Chief submits a paper to his or her journal, the paper is automatically assigned to a Guest Editor, a Consulting Editor, or an Associate Editor, who will handle all aspects of the peer review of the paper. The reviews are handled outside the web-based peer review system, so that the Editor in Chief will not have access to them.

Duplicate Publication, Plagiarism, Falsification

The journals of the APS accept only papers that are original work, no part of which has been submitted for publication elsewhere except as brief abstracts. When submitting a paper, the corresponding author should include copies of related manuscripts submitted or in press elsewhere. Taking material from another’s work and submitting it as one’s own is considered plagiarism. Taking material (including tables, figures, and data; or extended text passages), from the author’s own prior publications is considered redundant publication or self-plagiarism, and is not permitted. Fabricating a report of research or suppressing or altering data to agree with one’s conclusions is considered fraud. This includes altering figures in such a way as to obscure, move, remove, or introduce information or features.

Prior Publication

Material published by the author before submission in the following categories is considered prior publication: 1) articles published in any journal; 2) articles, book chapters, and long abstracts containing original data in figures and tables, especially in proceedings publications; 3) widely circulated, copyrighted, or archival reports, such as the technical reports of IBM, the preliminary reports of MIT, the institute reports of the US Army, or the internal reports of NASA.

Doctoral dissertations that are made available by UMI/Proquest or institutional repositories are not considered prior publication. Data portions of submitted papers that have appeared on an author’s web site will be permitted, with the proviso that the author inform the Editor at the time of the submission that such material exists so that the Editor can determine the suitability of such material for publication. Failure to do so will result in an automatic rejection of the manuscript. Examples of such work include, but are not limited to, immunofluorescence micrographs and/or animated gif/video files posted on a web site, or NIH-mandated posting of DNA microarray data. After the article is published in a journal of the American Physiological Society, the data should be removed from the author’s web site.

Authors with concerns about possible prior publication that does not fall clearly into one of these categories should contact the Director of Publications and forward the material for examination.

Experiments Involving Animals or Humans

Authors using humans, animals, or fetal tissue in their experiments should refer to APS’s policies on those subjects. Links to these policies can be found at http://www.the-aps.org/publications/i4a/policies.htm.

Ethical Procedure

APS reviewers have a responsibility to report suspected duplicate publication, fraud, plagiarism, or concerns about animal or human experimentation to the Editor. A reviewer may recognize and report that he/she is refereeing, or has recently refereed, a similar or identical paper for another journal by the same author(s). Readers may report that they have seen the same article elsewhere, or authors may see their own published work being plagiarized. In all cases the first action of the journal Editor is to inform the Publications Committee Chair through the Director of Publications by supplying copies of 1) the relevant material and 2) a draft letter to the corresponding author asking for an explanation in a nonjudgmental manner. The Publications Committee Chair must approve any correspondence with the author before it is sent to the author. If the author’s explanation is unacceptable and it seems that serious unethical conduct has taken place, the matter is referred to the Publications Committee. After deliberation, a decision is made whether the case is serious enough to warrant a ban on future submissions and/or if the offending author’s institution should be informed. The decision has to be approved by the Executive Cabinet of the APS Council, and the author has the right to appeal a sanction, with the opportunity to present his/her position, to the Publications Committee and the full APS Council.

If the infraction is less severe, the Editor, upon the advice of the Publications Chair, sends the author a letter of reprimand and reminds the author of APS publication policies; if the manuscript has been published, the Editor may require the author to publish an apology in the journal to correct the record. If, through the author’s actions, APS has violated the copyright of another journal, the Publications Chair writes a letter of apology to the other journal.

In serious cases of fraud that result in retraction of the article, a retraction notice will be published in the journal and will be linked to the article in the online version. The online version will also be marked “retracted” with the retraction date.

# Use of Humans and/or Animals in Experiments
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The research described in papers submitted to any of the APS publications that involve the use of human beings, including healthy volunteers, must adhere to the principles of the Declaration of Helsinki as well as to Title 45, U.S. Code of Federal Regulations, Part 46, Protection of Human Subjects, Revised November 13, 2001, effective December 13, 2001. Research involving animals must adhere to APS’s Guiding Principles in the Care and Use of Animals. APS insists that all investigations involving humans or animals reported in its publications be conducted in conformity with these principles, and that a statement of protocol approval from an IRB or IACUC or equivalent is included in the methods section of the paper. In describing surgical procedures, the type and dosage of the anesthetic agent should be specified. Curarizing agents are not anesthetics; if these were used, evidence must be provided that anesthesia of suitable grade and duration was employed. Manuscripts reporting the results of experiments on human subjects, including healthy volunteers, must include a statement that informed consent was obtained. Editors/Associate Editors are expected to refuse papers in which evidence of the adherence to these principles is not apparent. They reserve the right to judge the appropriateness of the use of animals and humans in experiments published in the journals. Differences of opinion will be adjudicated by the Publications Committee.

Registering of clinical trials is a requirement for peer review and publication for any study that uses clinical trials. There must be a statement in the Methods section that states where the clinical trial was registered (for example, see the registration site sponsored by the United States National Library of Medicine).

# Fetal Tissue Research Policy
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The American Physiological Society publications require all papers submitted to any of the APS Journals and involving the use of human fetuses, fetal tissue, embryos, and embryonic cells to adhere to the US Public Law 103-41, effective December 13, 2001. Please read the APS Policy Regarding Publication of Research on Human Fetuses, Fetal Tissue, Embryos, and Embryonic Cells and the criteria that must be met by all researchers submitting their work to the APS Journals.

# Conflict of Interest
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Authors of research and other articles are required at the time of submission to disclose to the APS Publications Office any potential conflict of interest (e.g., consultancies, stock ownership, equity interests, patent-licensing arrangements, lack of access to data, or lack of control of the decision to publish). In such cases, the author(s) will be asked to fill out a Conflict of Interest Disclosure form. The information provided in the form, unless already disclosed in the submitted article, will be held in confidence while the paper is under review. If the article is accepted for publication, information on the potential conflict of interest -- including a lack of control of the decision to publish -- will be included in the Disclosures section, following the Acknowledgments section.

# Standards
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All authors of articles submitted to APS journals should submit their relevant data to all appropriate data repositories, such as the National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI).

  Section Contents
  MIAME Standard for Microarray Data
  HUGO Gene Nomenclature

# MIAME Standard for Microarray Data
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The American Physiological Society has adopted the microarray data standard developed by the Microarray Gene Expression Data society (MGED) and requests that all authors using microarray data analysis in their research submit a complete data set to one of three databases prior to manuscripts submission: the NCBI Gene Expression Omnibus (GEO); the EMBL-EBI ArrayExpress repository; or the Center for Information Biology Gene Expression (CIBEX) database.

Rationale

Within a short time span, microarrays have become an important, commonly used tool in molecular genetics and physiology research. For microarray analysis of gene expression to have any long-term impact, it is crucial that the issue of reproducibility be adequately addressed. In addition, since microarray analytic standards are certain to change, it is crucial that authors identify the nature of the experimental conditions prevalent at the time of their research. If today’s research is to be relevant tomorrow, the core elements that are immune to obsolescence must be made clear. The APS Journals are adopting the MIAME standards to ensure that what is cutting edge today is not obsolete few years later.

The outline below indicates the general nature of the information we expect you to provide, but we request that you follow the specific guidelines provided at the MGED web site.

Summary of requested information

- Experimental design detailing the parameters of the microarray hybridization experiment including the number of hybridizations, whether dye switching was utilized, and the use of any reference samples.

- Details of the samples including the tissue from which nucleic acids were extracted, the materials and methods used for extraction, and the labeling protocol.

- Hybridization procedures.

- Measurement data and specifications in the form of tab-delimited tables or Excel spreadsheets. As summarized in the published guidelines to the format, “The first could contain the ‘raw’ output of the image analysis software (spot quantitation matrix), the second could contain the ‘processed’ data following normalization and transformation (gene expression data matrix), and if one is produced, the final table could contain ‘summary’ data that was ultimately used in the analysis, such as the subset of differentially expressed genes identified or gene clusters.”

- Array design including complete details of the location and identification of each feature on the array, whether commercial or noncommercial, information on the design of the array, and the spotting protocols.

How to ensure compliance with the MIAME standard

- On the MGED website, read the pertinent information and follow the guidelines provided before preparing your microarray information for deposit.

- Deposit your microarray data in the GEO data base, following the required guidelines.

- Provide the accession numbers for your GEO-deposited data in the Methods section of your paper to make it available during the peer review of your submitted paper.

- Also, provide the set of login credentials (username and password) that will let referees access the data set during review, if it is set up as a private resource.

# HUGO Gene Nomenclature
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In accordance with the HUGO Gene Nomenclature Committee (HGNC), the APS requests that authors obtain approval for new human and mouse gene symbols by contacting either the HGNC for human genes (e-mail: hgnc@genenames.org) or Mouse Genomic Nomenclature Committee (MGNC) for mouse genes (e-mail:
nomen@informatics.jax.org). Additional information on gene nomenclature guidelines is available from the HGNC website.

# Technical Requirements
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> Section Contents
> File Formats for Online Submission and Print
> Organization of the Manuscript
> Abbreviations, Symbols and Terminology
> Special Symbols
> Spelling and Compounding
> Citing Unpublished Observations and Personal Communications
> Drugs, Chemicals and Trade Names
> Cell Lines and Reagents
> Unique Material and Data Banks

# File Formats for Online Submission and Print
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Please submit a Microsoft Word (.doc) file or a Rich Text Format (.rtf) file to APS Central. Separate files must be submitted for all discrete elements of the manuscript [e.g., separate files for each figure and table, a separate file for the complete text of the manuscript (including abstract, all main text, bibliography, figure legends and table legends, etc.)].

The APS Central system will concatenate the various files into a single document for review. If the paper is accepted, the separate files will be moved forward into the final print production process.

# Organization of the Manuscript
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APS no longer requires a hard copy printout of the article text. However, to ensure uniformity, please follow the checklist below.

- The manuscript must be double-spaced with wide margins in an 8.5 x 11-in. document.

- The pages should be numbered in the upper right-hand corner (beginning with the first page of text). All sections should begin on separate pages, arranged as follows:

  1. title page

  2. abstract and keywords

  3. main text (introduction; Materials and/or Methods, or Experimental Procedures; Results; Discussion, with conclusions)

  4. text footnotes

  5. acknowledgments

  6. references

  7. figure legends

  8. tables

- Be sure the text is clear and concise, conforming to accepted standards of American English style and usage. Avoid jargon, clichés, and laboratory slang.

- See Manuscript Sections for further description.

# Abbreviations, Symbols, and Terminology
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All abbreviations must be explicitly defined at first usage. However, internationally accepted biochemical abbreviations such as ADP, NADH, and Pi do not need to be defined; please consult the list of accepted abbreviations. Other abbreviations need only be defined at first mention. For word usage, symbols, etc., authors are referred to Scientific Style and Format: The CBE Manual for Authors, Editors, and Publishers (6th ed., 1994). For chemical and biochemical terms and abbreviations, consult the recommendations of the IUPAC-IUB Combined Commission on Biochemical Nomenclature. Isotope specification must conform to the IUPAC system. Authors are referred to the following articles for style in specialized fields: "Glossary on respiration and gas exchange" (J Appl Physiol 34: 549-558, 1973); and "Glossary of terms for thermal physiology" (J Appl Physiol 35: 941-961, 1973).

# Special Symbols
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For special characters not available on the standard 104-key keyboard (e.g., Greek characters, mathematical symbols, figure symbols), use the Symbol font or use the "Insert Symbol" function in Microsoft Word; do not use Math font or image files (e.g., GIF) within the text for special characters or text constructions. Please also note that we cannot process files prepared in LaTex.

# Spelling and Compounding
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Authors should consult Webster's Third New International Dictionary or Merriam Webster's Collegiate Dictionary, 11th edition, for spelling and compounding. The APS Journals follow American English rules for spelling.

# Citing Unpublished Observations and Personal Communications
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Citations of submitted papers still in preparation, in peer review, or of other unpublished materials cannot be included in the reference list, which may only contain published work. Such citations can, however, be provided in parentheses in text as unpublished observations (e.g., "J. M. K. Smith, unpublished observation").

The APS Journals discourage the use of personal communications. However, if they are used, the author(s) must have in their file a letter granting permission from the communicant and stating that the person whose opinion is cited has seen and approved the actual wording of the citation. If requested, the author will send the letter to the APS Publications office.

For both unpublished observations and personal communications provide the cited person's last name and all initials.

# Drugs, Chemicals, and Trade Names
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Proprietary (trademarked) names should be capitalized, with the spelling carefully checked. The chemical or generic name should be lowercase and precede the trade name or abbreviation of a drug the first time it appears.

# Cell Lines and Reagents
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The source of cells utilized (species, sex, strain, race, age of donor, whether primary or established) should be clearly indicated. The source of reagents should be stated (name, city, and state within parentheses) when first cited. If tests to rule out the presence of mycoplasmal contamination were not performed, this fact should be clearly stated. Other data relating to unique biological, biochemical, and/or immunological markers should also be included if available, with their source identified. Publication of results is based on the principle that results must be independently verifiable. Authors are expected to make unique reagents available to qualified investigators either directly or through a recognized distributor. See also Unique Materials and Data Banks and Ethical Policies and Standards for other requirements.

# Unique Materials and Data Banks
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Work published in the APS Journals must necessarily be independently verifiable. Authors describing results derived from the use of antibodies, recombinant plasmids and cloned DNAs, mutant cell lines or viruses, and other similarly unique materials are expected to make such materials available to qualified investigators on request. Authors should also submit published nucleic acid/amino acid sequences to a widely accessible data bank. Sequence data for the United Protein Database (UniProt) should be submitted directly to UniProt using SPIN, a new web-based tool for submitting protein sequences. Also, for other special types of submissions (e.g., genomes, bulk submissions), additional submission protocols are available from the following organizations:

- DDBJ: Center for Information Biology and DNA Data Bank of Japan.
  National Institute of Genetics
  1111 Yata
  Mishima, Shizuoka 411-8540
  Japan
  Tel: +81 559 81 6853
  Fax: +81 559 81 6849
  ddbj@ddbj.nig.ac.jp
- EMBL: EMBL Nucleotide Sequence Submissions, European Bioinformatics Institute
  Wellcome Trust Genome Campus
  Hinxton, Cambridge CB10 1SD
  UK
  Tel: +44 1223 494444
  Fax: +44 1223 494468
  datasubs@ebi.ac.uk
- GenBank: National Center for Biotechnology Information
  National Library of Medicine
  Bldg. 38A, Rm. 8N-803
  Bethesda, MD 20894
  Tel: 301-496-2475
  Fax 301-480-9241
  info@ncbi.nlm.nih.gov

See also MIAME Standards for Microarray Data and Data Supplements.

# Manuscript Sections
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> Section Contents
> Title Page
> Abstract
> Keywords
> Introduction
> Materials and Methods
> Results
> Discussion
> Acknowledgements
> Grants
> Disclosures
> References
> Footnotes

# Title Page
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All submissions must contain a title page, however brief the article may be. The title page must contain the title of the article; author(s) name(s); all departments and institutions in which the work was done; an abbreviated title for the running head; and the name, e-mail, and address for correspondence.

Title

Make the title succinct and informative. Avoid unnecessary words like "Studies in....". The title must not exceed 160 characters, including spaces between words.

Authors

List all authors' names and their first names or initials exactly as they should be known, in the order of importance of their contribution to the study. Do not include any specific titles (e.g., PhD, MD, and Prof. are not needed). "Group authorship" is allowed, with the name of a group (such as a consortium or program) to be listed as an author, with members of the group listed in the Acknowledgements section; however, the Program Director of the named group must be the one who signs for the group when the group's "author" signature is needed, i.e., on a Mandatory Submission form or a Change of Authorship form.

See Authorship Changes for more information.

Affiliation

List all departments and institutions in which the work was done, with city and state or country. Identify each author's affiliation by superscript numbers matched to the appropriate institution. Affiliation must reflect the organization(s) supporting the author(s) while the research was done. This may differ from the current affiliations of the author(s), which will be listed in such cases in the Acknowledgment section as the present address(es) of the author(s).

Running head

The running head is an abbreviated version of the title, which will appear at the top of every page subsequent to the first page. Running heads must not exceed 55 characters including spaces between words.

Contact information

A full address for correspondence must be included, with a current, valid e-mail address for the corresponding author. This address will be published on the title page. Please note that a valid e-mail address is essential to participate in the APS electronic proofing service called "Rapid Proof." Also, provide your phone and fax numbers for use while your article is in production. If the contact information to be used during production differs from that to be included in the final article, indicate this explicitly. To contact APS during the submission and peer review and/or during production after acceptance, go to the APS website (www.the-aps.org) and choose the appropriate Journal's web page.

# Abstract
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An informative one-paragraph abstract of not more than 250 words must accompany each manuscript. Note that longer abstracts are usually cut off at the end when displayed on Medline. It must state concisely what was done and why (including species and state of anesthesia), what was found (in terms of data, if space allows), and what was concluded.

# Keywords
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Include three to five words or short phrases, relevant to the article, that do not appear in the title or running head. These should be included on the same page as the abstract.

> Authors submitting to the Journal of Neurophysiology are not required to provide keywords.

# Introduction
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Provide a brief overview of the scope and relevance of the study, especially with regard to previous advancements in related fields.

# Materials and Methods
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(Sometimes called "Experimental Procedures"). Describe techniques, cell/animal models used, and lists of reagents, chemicals, and equipment, as well as the names of manufacturers and suppliers, so that your study can be most easily replicated by others. Also in this section, describe the statistical methods that were used to evaluate the data. If your research involved the use of microarrays, see MIAME Standard for Microarray Data and insert in this section the URL pointing to your microarray data. If clinical trials were used, a statement of registration is required; also, for all investigations involving humans or animals, a statement of protocol approval from an IRB or IACUC, or an equivalent statement, must be included (see Use of Humans and/or Animals in Experiments).

See Abbreviations, Symbols, and Terminology for style information.

# Results
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Provide the experimental data and results as well as the particular statistical significance of the data.

Regarding the use of statistics, including reporting standard error (SE) and standard deviation (SD) values, an Editorial ("Guidelines for reporting statistics in journals published by the American Physiological Society") was published in all August 2004 issues of the APS Journals. The Editorial is freely available (see, for example, http://physiolgenomics.physiology.org/cgi/content/full/18/3/249), and the authors are encouraged to consult it.

# Discussion
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(Sometimes combined with the results in a section called "Results and Discussion"). Explain your interpretation of the data, especially compared with previously published material cited in the References.

# Acknowledgements
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List the people indirectly involved with the research to whom you may wish to give thanks. Also, current addresses of authors (if they differ from those in the affiliation line) should be included here.

Do not include "promissory notes." APS Journal policy is against inclusion of implicit or explicit promises that future work will be published.

Do not include dedications. Dedications of articles are not permitted.

# Grants
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List the grants, fellowships, and donations that funded (partially or completely) the research. However, industry-sponsored grants should be listed under Disclosures.

# Disclosures
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Authors of research articles are required at the time of submission to disclose to the APS Publications Office any potential conflict of interest (e.g., consultancies, stock ownership, equity interests, patent-licensing arrangements, lack of access to data, or lack of control of the decision to publish). In such cases, the author(s) will be asked to fill out a Conflict of Interest Disclosure form. The information provided in the form, unless already disclosed in the submitted article, will be held in confidence while the paper is under review. If the article is accepted for publication, information on the potential conflict of interest—including a lack of control of the decision to publish—will be included in the Disclosures section, following the Acknowledgments section. The Disclosures section will also include acknowledgments of industry-sponsored grants that supported the research.

# References
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Authors are responsible for accuracy of citations. References must be limited to directly pertinent published works or papers that have been accepted for publication. An abstract, properly identified as "Abstract", may be cited only when it is the sole source.

References should be double-spaced, arranged alphabetically by author, and numbered serially. The reference number should be placed in parentheses at the appropriate place in the text.

Important Note: The reference list should not include citations of submitted papers still in preparation, in peer review, or other unpublished materials. Such information may be provided in parentheses in the text as "personal communication" or "unpublished observations" (e.g., "J. M. K. Smith, unpublished observation").

The APS Journals discourage the use of "personal communications." However, if they are used, the author(s) must have in their file a letter granting permission from the communicant and send it to the APS Publications Office if requested.

For both unpublished observations and personal communications, provide the cited person's last name and all initials.

> References for the Journal of Neurophysiology should be double-spaced and arranged alphabetically by author. The appropriate author name and year for each reference should be included in parentheses at the proper point in the text using the following style:

> - one author (Brown 1982)

> - two authors (Brown and Smith 1982)

> - three or more authors (Brown et al. 1982).

> If more than two references are cited by different authors, separate entries with a semicolon (Brown 1982; Smith 1983). If more than two references are cited by the same first author (or single author), use "et al." where appropriate plus the date, even if the subsequent authors are not the same in all the references (Brown et al. 1982, 1983, 1986-1988). Note the use of commas between two consecutive years or nonconsecutive years and dashes for ranges (Brown et al. 1982, 1983, 1986-1988). If more than two references with the same year and author(s) are cited, use lowercase letters after the year (Brown 1982a,b). Lowercase letters will be inserted in same-year references in the reference list.

> Although the Journal of Neurophysiology does not require that the reference list be numbered, the examples given below are shown with numbers because that is the style for most APS Journals. In all other respects, the reference style used in the example below is the same across all journals.

The style of citation should be as follows, with journal name abbreviated as in Medline, PubMed, and Index Medicus. APS offers a selection of output styles available for a variety of citation management software.

> Examples
> Journal Articles
> Book References
> APS Handbook of Physiology Series
> Articles Published on the Web
> DOIs and Early Publication in Articles in PresS
> Technical Documents, Congress Proceedings, etc.
> Corrigenda/Errata
> Translations
> Many Authors
> Unpublished Observations or Personal Communications

Journal Articles
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1. Villalobos AR, Parmelee JT, Renfro JL. Choline uptake across the ventricular membrane of neonate rat choroid plexus. Am J Physiol Cell Physiol 276: C1288-C1296, 1999.

Book References
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1. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K. Current Protocols in Molecular Biology. New York: Wiley, 1995, p. 25-26.

2. Pollock DM. Endothelin receptor subtypes and tissue distribution. In: Endothelin Molecular Biology, Physiology, and Pathology, edited by Highsmith RF. Totowa, NJ: Humana, 1998.

APS Handbook of Physiology Series
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Large text books require very specific citation information. For example, the APS Handbooks series contains a huge amount of information, and the inclusion in the citation of the section, volume, part, and chapter is essential to aid the reader in finding the information quickly (please note that the APS chooses not to list editors for the APS Handbooks).

1. Kaufman MP, Forster HV. Reflexes controlling circulatory, ventilatory, and airway responses to exercise. In: Handbook of Physiology. Exercise: Regulation and Integration of Multiple Systems. Control of Respiratory and Cardiovascular Systems. Bethesda, MD: Am. Physiol. Soc., 1996, sect. 12, pt. II, chapt. 10, p. 381-447.

Articles Published on the Web
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Many more reports than in past years are being published primarily, if not exclusively, on the World Wide Web. Such articles should be cited in the "online" style as shown below.

Format:
Author/editor (if known). (Revision or copyright date, if available). Title of page [Publication medium]. Page publisher. URL (Protocol://Site/Path/File) [Access date].

1. Dudoit S, Yang YH, Callow MJ, Speed TJ. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments [Online]. Dept. of Statistics, Univ. of California at Berkeley. http://www.stat.berkeley.edu/users/terry/zarray/Html/matt.html [3 Sept. 2000].

2. Friedman N, Linial M, Nachman I, Pe’er D. Using Bayesian networks to analyze expression data [Online]. Stanford University. http://robotics.stanford.edu/people/nir/Abstracts/FLNP1Full.html [2000].

Note that the date may be general or specific, to the day.

Some citations may have portions published in print and other relevant portions deposited online. However, if directions to the online portions are available in the printed work, this sort of citation should be avoided.

1. Joachims T. Making large-scale SVM learning practical. In: Advances in Kernel Methods: Support Vector Learning, edited by Schölkopf B, Burges C, and Smola A. MIT Press, 1999. [The software is available at http://www-ai.cs.uni-dortmund.de/SOFTWARE/SVM_LIGHT/svm_light.eng.html]

2. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9: 3273–3297, 1998. [The data are available at http://cellcycle-www.stanford.edu]

DOIs and Early Publication in Articles in PresS
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Current technology allows publication of an article in several editions. For example, the final, citable draft of an accepted article may be posted to a web site, pending final copyediting and page layout/design. This initial post to the web qualifies as publication, but eventually the article will reach the readership in a final, polished form.

The APS publishes peer-reviewed articles upon acceptance as Articles in PresS. These articles may be cited and establish publication's priority before they appear in final print and online forms. (Please note the required use of a "digital object identifier" -- DOI -- in this citation.)

1. Scarafia LE, Winter A, Swinney DC. Quantitative expression analysis of the cellular specificity of HECT-domain ubiquitin E3 ligases. Physiol Genomics (April 26, 2001). doi:10.1152/physiolgenomics.00075.2001.

However, once this article has reached its final stage of publication, it will be cited with is new publication data, as follows:

1. Scarafia LE, Winter A, Swinney DC. Quantitative expression analysis of the cellular specificity of HECT-domain ubiquitin E3 ligases. Physiol Genomics 4: 147-153, 2001. First published April 26, 2001; doi:10.1152/physiolgenomics.00075.2001.

Technical Documents, Congress Proceedings, etc.
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Technical documents, congress proceedings, and some other sorts of material may often be published by the specific institution that sponsored the research.

1. Efron R, Tibshirani B, Goss V, Chu G. Microarrays and Their Use in a Comparative Experiment (Technical Report). Palo Alto, CA: Department of Statistics, Stanford University, 2000.

Corrigenda/Errata
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If an article required a correction, after first publication, this should be noted in the citation of the original article.

1. Hallows KR, Packman CH, Knauf PA. Acute cell volume changes in anisotonic media affect F-actin content of HL-60 cells. Am J Physiol Cell Physiol 261: C1154--C1161, 1991. (Corrigendum. Am J Physiol Cell Physiol 268: March 1995, following table of contents)

2. Steenman M, Chen YW, Le Cunff M, Lamirault G, Varró A, Hoffman E, Léger JJ. Transcriptomal analysis of failing and nonfailing human hearts. Physiol Genomics 12: 97--112, 2003. First published November 12, 2002; doi:10.1152/physiolgenomics.00148.2002. (Corrigendum. Physiol Genomics 18:128, 2004)

Translations
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1. Gavrilov KA, Perel TS. Earthworms and other invertebrates in the soil under...[in Russian]. Pochovedenia 8: 133-140, 1958.

2. Gavrilov KA, Perel TS. Earthworms and other invertebrates in the soil under...[in Russian, English summary]. Pochovedenia 8: 133-140, 1958.

3. Fritsch G, Hitzig E. Uber die Elektrische. In: Some Papers on the Cerebral Cortex, translated and edited by von Bomin G. Springfield, IL: Thomas, 1960, p. 73-96.

4. Vol'Kensktein MV. Molecules and Life: An Introduction to Molecular Biology. New York: Plenum, 1970. [Transl. from the Russian.]

Many Authors
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It is APS Publications policy to list all authors in a research group. That is, the use of only the first author's name, followed by "et al." is unacceptable.

1. Lander ES et al. Initial sequencing and analysis of the human genome. Nature 409: 860–921, 2001.

should read:

1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blocker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, Szustakowki J, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ. Initial sequencing and analysis of the human genome. Nature 409: 860–921, 2001.

However, if there is an inclusive name for the research group as a whole (as in the case above, the " International Human Genome Sequencing Consortium"), it should be used rather than listing hundreds of authors.

So, for example, it is correct to cite:

1. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409: 860–921, 2001.

Unpublished Observations or Personal Communications
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Do NOT include such citations in the Reference list (see Important Note above for more information). Place instead in parentheses in the body of the article where it logically belongs, following the format below. Make sure to include all initials and, for personal communications, obtain a signed letter of permission from the person(s) cited.

> (ABC Jones and Z Smith, personal communication)

> (J Jones, unpublished observations)

> Consult recent issues of the APS Journals for more examples.

# Footnotes
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Text footnotes should be numbered consecutively throughout. They should be printed double-spaced and assembled on a separate page of the manuscript printout.

# Types of Articles
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The APS Journals publish a variety of article types in addition to the regular research papers. For descriptions of the types of articles published in a particular journal, go to that journal's home page. A full list of article types is also available on the Mandatory Submission Form, which is made available at APS Central during submission to the Journal of your interest.

If your research paper is submitted in response to a Call for Papers, please make sure to mark it as such during submission to APS Central.

# Figures
[more info] [back to top]

# Tables
[back to top]

Whenever possible, authors are encouraged to submit figures rather than tables. Statistical summary tables should be submitted when possible, rather than tables with many lines of individual values. Lengthy tables of data, on the Editor's recommendation and with the approval of the author, will be deposited by the APS Publications (see Data Supplements).

- Examples of one- and two-column tables.

Submitted tables should adhere to the following guidelines:

- Each table should appear on a separate page of the manuscript.

- Tables must not duplicate material in text or figures.

- Tables should be numbered consecutively with Arabic numerals and prepared with the size of the journal page in mind: 3.5 in. wide, single column; 7 in. wide, double column.

- Each table should be double-spaced.

- Each table should have a brief title; explanatory notes should be in the legend, not in the title.

- Horizontal and vertical rules should be omitted.

- Nonsignificant decimal places in tabular data should be omitted.

- Short or abbreviated column heads should be used and explained if necessary in the legend.

- Statistical measures of variations, SD, SE, etc., must be identified. (Example: "Values are means ± SE.")

- Table footnotes should be listed in order of their appearance and identified by standard symbols: *, †, ‡, § for four or fewer; for five or more, consecutive superior lowercase letters should be used.

# Mathematical Equations and Modeling

Mathematical aspects of articles normally should be addressed to the many readers of the Journal who are not mathematicians. The presentation should include the mathematical strategy, the assumptions on which the mathematics are based, and a summary of the meaning of the final mathematical statement and its limitations.

> Section Contents
> Equations
> Mathematical Models

# Equations
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Mathematical equations should be simplified as much as possible and carefully checked.

- Use the slant line (/) for simple fractions (a + b)/(x + y) in the text rather than the built-up fraction a + b[over]x + y, which should only be used if the equation is offset from the text.

- Use subscripts or superscripts wherever feasible and appropriate, because they often simplify the equations by eliminating the need for extraneous operations: RA/RD instead of RA•RD or (RA)(RD).

- Use circles for pools in compartmental or flow-type models and whole arrows for interconnections or flows (not arrows with half-heads, as in reversible chemical equations).

- Do not use nonstandard mathematical notations; e.g., do not use computer symbols in equations (* for multiplication or ** for exponentiation).

- Use lowercase letters for time-varying symbols in compartmental model equations, preferably q(t) for masses, c(t) for concentrations, with subscripts as needed.

- Our convention for numerical subscripts for rate constants (k21) is the same as that used in most life sciences but opposite to that currently used in pharmacokinetics; i.e., our kij is the fractional rate of transfer from compartment j to compartment i (or to compartment i from compartment j, if you prefer). Our notation is consistent with standard nomenclature in applied mathematics for matrices and matrix manipulation algorithms in commercial software packages for scientific/mathematical computations involving matrices. However, the author(s) may use a different convention if it is clearly defined in the manuscript.

- Symbols should be defined as they first appear in the text, and a Glossary should also be included in articles with many different symbols, specifying the units (dimensions) as well as each definition. The Glossary will usually precede the Methods section.

- APS style allows punctuation in displayed equations.

# Mathematical Models
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Presentation of the model(s) must be sufficiently clear to allow physiologists with limited experience in modeling to follow the model development, limitations, and physiological relevance. Assumptions concerning the importance of physiological processes included in the model should be clearly stated.

- If the model equation(s) require solution, the method of solution should be described in sufficient detail to permit readers to duplicate the solution in their own laboratories. Algorithms from commercial software libraries should be so identified. Details of the solution strategy may be summarized in an Appendix.

- For simulations, sources or estimation methods for all parameter values should be presented and the numerical values given in the text or a table. A sensitivity analysis must be performed for important parameters (covering ranges of values relevant to the manuscript) to determine how the model predictions are affected by numerical parameter values.

- If the model is used to estimate parameter values, measures of the uncertainties associated with the estimated parameter values should be presented.

- For models intended for use in a predictive setting, validation of the model with a data set not used for model parameter estimation (i.e., cross-validation) is recommended. Sensitivity analysis or parameter uncertainty determination is an important component of modern modeling practice that allows assessment of the validity of a model.

- Results obtained with the model(s) should be compared with appropriate physiological data, either from literature or from new experiments. Simulation results may be examined for prediction of changes or trends in physiological variables similar to those reported for in vitro or in vivo studies. The discussion should include information on the physiological significance of the model study, limitations of the model, and suggestions for new modeling and/or experimental studies.

# Data Supplements
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Video files, extensive tables of data, and other supplemental material that cannot be feasibly published in the printed journal may be submitted for inclusion in the online journal (without charge to the author). Such material must be submitted for peer review along with the finished manuscript and must meet the approval of the journal Editor.

Questions regarding data supplements may be directed to the Web Copy Editor. For microarray data deposits, see MIAME Standard for Microarray Data.

> Section Contents
> Video
> Long Data Tables
> Microfiche

# Video
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Authors are responsible for compiling their own digital video. Files should be in MPEG or Quicktime format and should be no more than 10 megs in size. Authors should include a written caption with each video file, explaining what is happening in the video.

There are many different factors that can affect the file size of a video. Authors are advised to keep the following general guidelines in mind:

- Length of videos should be no more than 30 seconds.

- Frame size should be no more than 320 x 240 pixels.

- Do not include sound unless scientifically necessary. Do not use voice-over narration to explain what is happening in the video; this information should be written in the caption, which will be displayed on the web page that contains the video.

Contact the Web Copy Editor for further assistance or questions.

# Long Data Tables
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Long data tables should be submitted in Microsoft Excel or in Microsoft Word table format. Each table should include a title explaining what the table shows. Tables published online may look different than how they were originally submitted due to the limits of the HTML format.

# Microfiche
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At the author's request, supplemental material may be submitted for deposition at:

> National Auxiliary Publications Service (NAPS)
> c/o Microfiche Publications
> P. O. Box 3513, Grand Central Station
> New York, NY 10017

A footnote will be inserted noting the availability of the material on microfiche and giving the NAPS Document Number.

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