Manuscript Composition

Contents

  1. Title Page (title, authors, affiliations, running head, address for correspondence)
  2. Abstract
  3. New & Noteworthy
  4. Keywords
  5. Glossary
  6. Main Text (introduction, materials and methods, results, discussion)
  7. Appendix
  8. Footnotes
  9. Acknowledgements (grants, disclosures)
  10. References and unpublished observations
  11. Figure Captions
  12. Tables
  13. Equations 
  14. Mathematical Models and Computer Simulation

Title Page

All submissions must contain a title page however brief the article may be (including, but not limited to, brief items such as editorials). The title page must contain the full 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 corresponding author's name, e-mail, and physical address for correspondence. Only one author may be designated as the corresponding author.

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. Do not include any specific titles (e.g., PhD, MD, and Prof. are not needed). Include a brief itemized list of how each author contributed to the study.

"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.

Authors who publish in APS journals may now present their names in non-Latin characters (in their native writing system) along side the standard English transliteration of their name in the main author line of the published article; for example, "Ta-Ming Wang (王大明)". We will accept any non-Latin languages that have standard Unicode characters designated for the native characters. For authors that choose this option, please only provide the native expression for the original written form of the transliterated name; that is, do not include any associated degree, rank, or title information in the native format. This feature is meant for the person's name only, not for ancillary information regarding academic achievement or institutional affiliation. To take advantage of this new feature, please insert the native expression of your name along side the English transliteration in the main title page of your manuscript submission.

See Authorship Changes for more information.

ORCID

The APS Journals program is now participating in the ORCID Registry. Authors submitting manuscripts to APS journals will now have the option to attach their ORCID identifier to their author profile in the APS Manuscript Submission system, or register for one if they are a new participant. This ORCID identifier will be included in the article metadata, if published, which may facilitate broad-reaching linkages of many pieces of an author’s work across multiple databases (such Pubmed, PMC, and others).

ORCID is "an open, non-profit, community-based effort to create a permanent registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers."

Please see the ORCID website for more information and to register for an ORCID identifier.

FundRef

The APS Journals program is now participating in the FundRef Registry (a CrossRef.org initiative).

Authors submitting manuscripts to APS journals will now be able to indicate the funder(s) associated with their work via an interface in the APS Manuscript Submission system. This FundRef identifier will be included in the article metadata, if published, which may facilitate discovery of the article by anyone who is able to search on that funder name in the FundRef Registry.

FundRef "provides a standard way to report funding sources for published scholarly research. Publishers deposit funding information from articles and other content using a standard taxonomy of funder names. This funding data is then made publicly available through CrossRef's search interfaces and APIs for funders and other interested parties to analyze."

Please see the CrossRef website for more information about the FundRef Registry.

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 Acknowledgments 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 60 characters including spaces between words.

Address for Correspondence

Only one author may be designated as the corresponding author. A full address for correspondence must be included, with a current, valid e-mail address for the corresponding author. The address of the corresponding author will appear on the first page of the article. Please note that a valid e-mail address is essential to participate in the APS electronic proofing service. 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.

Abstract

A one-paragraph abstract of not more than 250 words must accompany each manuscript. Longer abstracts may be subject to editorial truncation, to conform to the conventional perceptions of brevity that characterize an "abstract". The abstract should state 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. Even for short editorial-style articles, a brief "abstract" should be provided, if only to identify the topic (e.g., "This is an editorial summarizing recent new developments in physiology.").

New & Noteworthy

Participating Journals: AJP-Heart (AHeart), Journal of Applied Physiology (JAPPL), Journal of Neurophysiology (JN), AJP-Gastrointestinal (AGI), and Advances (ADV).

New & Noteworthy is a brand of annotation summarizing what is new about an author's original research. Only authors submitting research articles to APS participating journals (see above) should submit their annotation in the online EJPress submission form field, ensuring that the exact statement also appears in their final submitted manuscript after Abstract and Keywords.

Specifications:

WORD LIMIT: 50 words for AHeart; 75 words for JAPPL, JN, AGI, and ADV.

AHeart, JAPPL, JN, AGI

  • Annotations apply only to Original Research Articles, Innovative Methodologies, and Rapid Reports.
  • Annotations appear in final published articles and the journal table of contents.
  • Branded "New & Noteworthy"

ADV

  • Annotations apply to all articles in the journal.
  • Snapshot statement is solely posted on the journal's Facebook page with a link back to the published article.

Keywords

Include three to five words or short phrases relevant to the article.

Glossary

A glossary may be included (and is often helpful) in equation-laden articles with many different symbols (such as mathematical modeling or computational papers), specifying the units (and/or dimensions) as well as each definition. The glossary will usually precede the Methods section. See this article for an example.

Main Text

Introduction

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

Materials and Methods

Describe techniques, cell/animal models used (including species, strain, and sex), and lists of reagents, chemicals, and equipment, as well as the names of manufacturers and suppliers, including URLS for those supplies obtained online, so that your study can be most easily replicated by others. For studies involving humans, the sex and/or gender of participants must be reported. Also in this section, describe the statistical methods that were used to evaluate the 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 Guiding Principles for Research Involving Animals and Human Beings). All animal or human studies must contain an explicit statement that the protocols were submitted to, and approved by, an institutional review board or committee or that the protocols were performed under a license obtained from such a committee, board, or governing office.

See Experimental Details to Report in Your Manuscript for more information.

See Abbreviations, Symbols, and Terminology for style information.

Results

Provide the experimental data and results as well as the particular statistical significance of the data. See Promoting Transparent Reporting of Results for more information.

APS has published an editorial on the use of statistics, and authors are encouraged to consult it.

Discussion

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.

Appendix

An Appendix may be included (and is often helpful) in mathematical modeling or computational papers, e.g., to provide details of a solution strategy.

Acknowledgements

The acknowledgements section is where you may wish to thank people indirectly involved with the research (e.g., technical assistance; gifts of samples, reagents, or cell lines; loans of equipment or laboratory space; comments or suggestions during the creation of the manuscript). However, it is important that anyone listed here know in advance of your acknowledgement of their contribution, as documented during the submission process.

Current addresses of authors (which may differ from those in the affiliation line) may 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 (e.g., to persons living or deceased). Dedications of articles are not permitted.

Grants

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

Disclosures

Authors are required at the time of submission to disclose any perceived or potential conflict of interest, financial or otherwise. See Author Conflict of Interest. If the article is accepted for publication, information on the perceived or potential conflict of interest, or lack thereof, must be noted in the Disclosures section.

Footnotes

The footnotes section is the place to list any additional items pertinent to your article, including but not limited to links to non-peer-reviewed data that may be available to readers from your institutional web site.

Footnotes should be numbered consecutively throughout. They should be assembled on a separate page at the end of the article.

References

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.

Reference lists should be arranged alphabetically by author and numbered serially. The reference number should be placed in parentheses at the appropriate place in the text.

The style of citation should be as follows, with journal name abbreviated as in Medline, PubMed, and Index Medicus. Appropriate templates for your citation management software are available from the respective company websites (e.g., EndNoteReference Manager).

The examples given below are shown with numbers because that is the style for most APS Journals, except for the Journal of Neurophysiology (see note, below, after these examples). The first is a standard book reference; the second is a standard reference to an "early view" or "prepress" reference, such as the APS "Articles in PresS" (note the use of the “digital object identifier”—doi—in this citation); the third is a standard journal reference.

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

2. 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.

3. 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.

MORE Example References

References for the Journal of Neurophysiology should be 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 (this is ONLY for the Journal of Neurophysiology, NOT for other APS Journals):

  • one author (Brown 1982)
  • two authors (Brown and Smith 1982)
  • three or more authors (Brown et al. 1982).

For the in text citations in the Journal of Neurophysiology, here are some other important details. 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). Note the use of commas between two consecutive years or nonconsecutive years. Do not use dashes for ranges (Brown et al. 1982, 1983, 1986, 1987, 1988). If more than two references with the same year and author(s) are cited, use lowercase letters after the year (Brown 1982a, 1982b). Lowercase letters should be inserted in same-year references in the reference list.

Citing Unpublished Observations, Personal Communications, and "In Press" Manuscripts

Submitted papers still in preparation or in peer review and/or any other unpublished materials, observations, or personal communications cannot be included in the reference list, which may only list published work. However, such material can be cited in the text, but at submission, authors will be required to confirm that all individuals acknowledged in the manuscript are aware that they are being acknowledged and approve of the manner and the context of the acknowledgement. This includes, but is not limited to the following circumstances:

  • to publish information disclosed in a personal communication or unpublished observation;
  • to recognize additional individuals who helped in preparation of the manuscript;
  • for permission from a copyright holder to discuss information that has been accepted for publication but is "in press" and not yet available, online or otherwise.

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

Figure Captions

Every figure must have a descriptive figure caption, to describe to the reader in sentence form the relevant details of the figure, to place it in the proper context of the manuscript. magnifying glass Information reported in figures and legends should describe each individual experiment presented, including the number of samples or animals used per treatment. The statistics performed for each experiment should be reported as well. These textual figure captions must be listed in order in the manuscript, following the reference list.

Tables

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 that cannot be presented in a suitable manner, according to APS standards of print publication, may be extracted and set as a supplement to the online article. These supplements remain an integral part of the article for the reader, as text referring to these tables will remain in the article, and links directly to the supplements will be embedded and prominently indicated at all points of entry to the online article (see Data Supplements).

Submitted tables should adhere to the following guidelines:

  • 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 have a brief title; explanatory notes should be in the legend, not in the title.
  • 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 superscript lowercase letters should be used (e.g., a, b, c, etc.).

Equations

Manuscripts with many mathematical characters and equations should be prepared using MathType version 6.0 or higher (available from Design Science, Inc.). Manuscripts with a minimal amount of math may be prepared using word-processing tools such as Microsoft Word Equation Editor, or with features such as bold, italics, superscript and subscript together with characters in the Symbol or Greek fonts. Do not use the Wingdings or Webdings fonts. Please do not submit equations as images. Inline math text that can be regular text (e.g., x2[n − 2]) should be provided as such. Please do not set these as MathType.

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 to simplify the equations.
  • Please use notation that is consistent with the standard nomenclature in applied mathematics. As an aid to the reader, please state the convention that you are following, especially if it is uncommon.
  • Symbols should be defined as they first appear in the text. A glossary may be included (and is often helpful) 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

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.

Articles based on original computer simulation software and code

1.       Upon submission of a paper reporting computer simulation using original, author-generated code, and unless authors have already deposited their software in a publicly accessible repository, authors are required to submit a working version of their software and associated computer code for access by the reviewers. It will be kept confidential during review, and in case of a negative decision (i.e., rejection).

a.       Software and code can be transmitted in a variety of ways, such as deposit via

§  a Dropbox (or similar web-based, file sharing application) link,  without  login requirements (to retain reviewer anonymity) (https://www.dropbox.com/en/help/20)

§   a public repository, such as Git Hub 

§  The link to the software deposit must be included in the cover letter and supporting data for reviewers

b.      Authors must include Terms of Use

c.       Upon manuscript submission, author must choose “computer simulation” category and also check the box marked “computer simulation” to indicate that the submission contains a computer simulation, and that software code has been deposited in one of the above-mentioned ways

2.       Upon manuscript R1 revision  (assuming authors are invited by the journal to revise their manuscript), authors will be required to deposit a full working version of their software and associated computer code on a public website/repository, one that retains original and updated versions of the model and code – if not already deposited publicly.

a.       Authors must include the link to the deposited software in the Methods section.

b.      Authors must state Terms of Use included with the deposited software.  Authors should consult the Intellectual Property owner (usually the author’s institution) regarding requirements, if any, for active user compliance agreement to Terms of Use. 

3.       Original software and code must remain available indefinitely

a.       Updates to the model and code must be reported on the repository site, with comments as to why particular changes were made with the dates of original deposit and each change identified.  In this way, published material remains available in its published form, but improvements are also available from the same immediately accessible web-based location.

b.      Corrections to the model and code must be reported to the current Editor in Chief of the journal and to APS (pubsedit@the-aps.org) in case a correction must be made to the published article.



Resources

Example References

Example reference styles from various sources, including web articles, proceedings, translations, etc.

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