Methods and Materials

Methods and Materials

(Revised, 7/2017)

JARO receives submissions from scientists from a variety of disciplines and backgrounds, who are familiar with past practices with reporting information on how experimental procedures were carried out in their manuscripts. In some cases, the information given is not sufficient for either a reviewer or prospective reader to evaluate the rigor of the procedures, or to be able to reproduce results in their own labs. For this reason, as of July, 2017, JARO is requesting that authors adhere to new reporting guidelines. Manuscripts that do not meet these guidelines may be returned to authors without review, with a request to provide the appropriate information.

Although JARO has word limits on the Abstract, Introduction and Discussion, JARO does not have a page limit or word limits on the Methods and Materials or Results sections. Therefore, the methods and materials should be complete. References to prior methods papers may be made, but only if the original method has been exactly followed, and is completely and clearly described in the prior material. Otherwise, JARO requires that the methods be rewritten (to avoid plagiarism) and be completely described. The purpose of complete methods is to aid in reproducibility and to allow readers to fully understand how the study was done. The following are the guidelines for JARO:

  • Methods include all procedures and instructions, manipulations of subject material, selection of subjects, methods used to compute stimuli, versions of programs used, specific hardware, etc. Materials include samples, animal sources and lineage, special storage of key reagents, identification of antibodies by lot, complete primer sequences, etc. The goal of the methods section is to allow studies to be replicated in a lab that is similarly equipped.

  • For work that relies on antibodies, the methods section should include information about how antibodies were validated either by citing prior work (for example antibodies listed in the JCN database (http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1096-9861/homepage/other_resources.htm) or (preferably) in the Antibody Registry (http://antibodyregistry.org). Alternatively, authors may provide a full blot image (not cropped) for each antibody to demonstrate protein specificity, and should include an evaluation of staining in a knock-out animal if possible.

  • In animal studies, the methods section should also include relevant information as outlined in the ARRIVE Guideline checklist for Methods (http://www.nc3rs.org.uk/arrive-guidelines). A filled-out copy of the checklist may be included as a supplemental file (not to be published) to aid in the review process.

  • The description of data analysis in the methods section should include all processing steps taken to analyze the data (including, but not limited to: additional software filtering, how samples and/or subjects and technical replicates were pooled to determine sample sizes, whether aspects of the experiments were randomized or not, whether the experimenters (and subjects, if relevant) were blinded to subject treatment, and if blinding was used, at what point in the analysis such blinding was unmasked).

  • For studies using analysis of images, the analysis section should also include a description of all steps taken while acquiring images, image processing steps prior to analysis, and any additional steps taken in the preparation of images for figures.

  • Custom software should be publicly available (for example, on GitHub or a similar repository) or a statement regarding the availability of the software from the authors should be made. Key elements of computational models should be deposited in a database such as ModelDB (https://senselab.med.yale.edu/modeldb/). We also encourage authors to share data in a way that suits the data. Such sharing may include placing the data on a public repository, on a lab web site, or offering to provide the primary data upon request. If work in the manuscript relies on computer simulation code, instructions for providing access to the code for review by both reviewers and readers should be provided.

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