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Author interviews / Institutional case studies

Policies & Procedures

Open, ethical, and adherance to discipline-specific best practices.

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All PeerJ articles are published under a Creative Commons Attribution License (see each article for the exact CC-BY version used). With this license, Authors retain copyright, but allow any user to share, copy, distribute, transmit, adapt and make commercial use of the work without needing to provide additional permission, provided appropriate attribution is made to the original author or source.
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By using this license, all PeerJ articles meet or exceed all funder and institutional requirements for being considered Open Access.
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Authors cannot use copyrighted material within their article unless that material has also been made available under a similarly liberal license.

Publishing plan Policies

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All named authors must have either a free or paid PeerJ publishing plan at the time of submission.
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All named authors must have a paid publishing plan after receiving a final decision of "Accept" and before the manuscript will move into production. Different publishing plans allow different numbers of publications per year - therefore each author’s publishing plan must be high enough to permit this publication.
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If a manuscript has more than twelve authors, then only twelve need to have paid publishing plans. The remaining authors must have at least a free publishing plan.
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Waiver Policy: Authors from countries classified as low income can request a full waiver for a single publication, one per submitting author, per year. In addition, any co-author who was an undergraduate at the time of the research may also request a waiver (provided the paper has senior co-author(s) who have a paid publishing plan, and provided the article passes peer review as normal). Neither circumstance is a waiver for a full publishing plan. Authors should indicate their desire for a waiver in the "Confidential Notes to Staff" field upon submission, and Academic Editors and reviewers are not made aware of the waiver request.
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Publishing plan status is not a determining factor in peer review or editorial decisions.

Author Policies

The Corresponding Author’s Role and Responsibilities are to:

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Inform all co-authors of the submission of the manuscript to the journal (note: each co-author will receive a confirmation email upon submission and will need to confirm their authorship).
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Manage all correspondence between the journal and all co-authors, keeping the full co-author group apprised of the manuscript progress.
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Designate a substitute correspondent for times of unavailability.
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Ensure that by the point of Editorial Acceptance all co-authors have paid publishing plans or assume responsibility for their publication charges (note: authors can pay for a publishing plan at any point up to, and including, Editorial Acceptance. At time of submission is the most cost effective).
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Ensure that the manuscript is in full adherence with all PeerJ policies (including such items as publication ethics, data deposition, materials deposition, etc).
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Post Publication: Respond to all queries pertaining to the published manuscript, provide data and materials as requested.

PeerJ adheres to the ICMJE uniform requirements of authorship: All authors on an article must meet these requirements, which are extracted below:
  • "Authorship credit should be based on 1) substantial contributions to conception and design, acquisition of data, or analysis and interpretation of data; 2) drafting the article or revising it critically for important intellectual content; and 3) final approval of the version to be published. Authors should meet conditions 1, 2, and 3.
  • When a large, multicenter group has conducted the work, the group should identify the individuals who accept direct responsibility for the manuscript (3). These individuals should fully meet the criteria for authorship/contributorship defined above, and editors will ask these individuals to complete journal-specific author and conflict-of-interest disclosure forms. When submitting a manuscript authored by a group, the corresponding author should clearly indicate the preferred citation and identify all individual authors as well as the group name. Journals generally list other members of the group in the Acknowledgments. The NLM indexes the group name and the names of individuals the group has identified as being directly responsible for the manuscript; it also lists the names of collaborators if they are listed in Acknowledgments.
  • Acquisition of funding, collection of data, or general supervision of the research group alone does not constitute authorship.
  • All persons designated as authors should qualify for authorship, and all those who qualify should be listed.
  • Each author should have participated sufficiently in the work to take public responsibility for appropriate portions of the content."

Confidentiality

PeerJ keeps all details about a submitted manuscript confidential, does not publicly comment about submitted or rejected manuscripts and maintains reviewer confidentiality unless given permission to reveal identities. Authors, reviewers and editors must also treat correspondence as confidential unless explicitly stated otherwise.

Open Peer Review

PeerJ is a formally peer-reviewed journal. All publications in the journal undergo a single-blind peer review process where reviewers know the identity of the authors but authors do not, by default, know the identity of the reviewers.

However, PeerJ encourages full transparency in the peer review process via a process sometimes known as ‘open peer review’. This takes two forms:
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Peer reviewers are encouraged (but not required) to provide their names to the authors when submitting their peer review. If they agree to provide their name, then their personal profile page will reflect a public acknowledgement that they performed a review (even if the article is rejected). If the article is accepted, then reviewers who provided their name will be associated with the article itself.
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Authors are given the option to reproduce the complete peer review history of their article alongside the final publication of the article. If they choose this option then all submitted manuscript files, peer review comments, author rebuttals and revised materials are provided as a downloadable package. This is an all-or-nothing option; no text is edited or removed. Therefore, if the reviewers agreed to provide their name to the authors then their name will become part of this published record as well.

Publication Ethics

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PeerJ adheres to the prevailing industry standards and procedures for investigating publication ethics.
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Specifically, PeerJ does not tolerate plagiarism, data or figure manipulation, knowingly providing incorrect information, copyright infringement, inaccurate author attributions, attempts to inappropriately manipulate the peer review process, failures to declare conflicts of interest, fraud, and libel. This list is not exhaustive - if there is uncertainty of what constitutes such actions, then more resources may be found at the World Association of Medical Editors (WAME), the Committee on Publication Ethics (COPE) or the International Committee of Medical Journal Editors (ICMJE).
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PeerJ will rigorously enforce our standards, and follow up on any transgressions. In extreme cases, this may call for individuals to be reported to their institutions and/or for manuscripts to be retracted. Any complaints should be directed to editorial.support@peerj.com

Committee on Publication Ethics (COPE)

PeerJ adheres to the COPE Code of Conduct and Best Practice Guidelines. We follow recommended COPE procedures whenever we are alerted to an issue which requires investigation.

Competing Interests

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PeerJ requires that all parties involved in a publication (i.e. the authors, reviewers and academic editors) should transparently declare any potential Competing Interests (also known as Conflicts of Interest). The disclosure of a Competing Interest does not necessarily mean that there is an issue to be addressed; it simply ensures that all parties are appropriately informed of any relevant considerations while they work on the submission.
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Authors are asked to declare all competing interests upon submission. Reviewers are expected to consider any competing interests before agreeing to review, and to confirm that they have no competing interests before submitting their review. Academic Editors are expected to recuse themselves from handling a manuscript if they feel they have a competing interest.
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Potential competing interests should be declared even if the individual in question feels that these interests do not represent an actual conflict. Examples of Competing Interests include, but are not limited to: possible financial benefits if the manuscript is published; prior working, or personal, relationships with any of the authors; patent activity on the results; consultancy activity around the results; personal material or financial gain (such as free travel, gifts, etc.) relating to the work; personal convictions (religious, political, etc.) which may have a bearing on the work, and so on.
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While possible financial benefits should appear here, actual funding sources (institutional, corporate, grants, etc.) should be detailed in the funding disclosure statement.

Funding Disclosure

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Separately from declaring Competing Interests, PeerJ also requires that authors disclose the financing which made their work possible.
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The Funding statement is published in the final article. This disclosure provides added transparency.

Ethics Statement

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Where applicable, PeerJ requires that authors provide an Ethics statement which details the relevant ethical standards which were met when conducting the research.
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Ethics statements are required whenever research is conducted on humans or human tissue; on animals or animal tissue; when conducting field studies; or whenever the approval of an Institutional Review Board (IRB) was required.
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In addition to providing an Ethics statement upon submission (for review purposes), this same statement should also be provided in the Materials and Methods section of the manuscript.
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Where IRB approval was required, the IRB that granted the approval should be named in the article.

Dual Use Research of Concern

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'Dual Use Research of Concern' is defined by the National Science Advisory Board for Biosecurity (NSABB) as any "biological research with legitimate scientific purpose that may be misused to pose a biologic threat to public health and/or national security."
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On a case by case basis, PeerJ reserves the right to consider whether or not a submission could be considered as sensitive in this context.
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If an author, editor or reviewer feels that a submission may be subject to concerns surrounding dual use then it is incumbent on them to report this concern to staff.

Data and Materials Sharing

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PeerJ is committed to improving scholarly communications and as part of this commitment, all authors are responsible for making materials, data and associated protocols available to readers without delay. The preferred way to meet this requirement is to publicly deposit as noted below. Cases of non-compliance will be investigated by PeerJ, which reserves the right to act on the results of the investigation.

- FORCE11 has developed a useful overview for reporting in the life sciences. Please review these recommendations before submitting. Recommendations cover the following areas: Sequence Molecule Identification, Reporting of Antibodies, Reporting of Model Organisms, Reporting of Cell Lines, Constructs, and Reporting of Knockdown Reagents.

- Large domain-specific datasets should be deposited in a public repository (e.g. GenBank, INSDC, Protein Data Bank, UK Stem Cell Bank, Addgene, RIKEN Bioresource Centre) and an accession number or access address provided in the published article. Additional databases may be found by consulting the BioSharing database, re3data.org, or the NIH Data Sharing Repositories list.

- Where suitable domain-specific repositories do not exist, authors may deposit in either Dryad or an institutional repository and provide the access information with the manuscript. Alternately, authors may choose to deposit non-standard data (including figures, posters, rich media) on Figshare or PeerJ PrePrints, for example. In all cases, the DOI reference (where applicable) should be provided in the article.

- Any supporting data sets for which there are no suitable repositories must be made available as publishable Supplemental Information files by PeerJ.

- Where appropriate, physical materials (for example mutant seed stock, or paleontological specimens), should be deposited in recognized centers (for example seed stock centers for the former, or recognized museums or institutions for the latter).

- A non exhaustive list of repositories for physical materials such as cell lines or mutant strains includes the RIKEN Bioresource Centre; the Jackson Laboratory; the European Mouse Mutant Archive; the European Conditional Mouse Mutagenesis Program; the American Type Culture Collection; the Knockout Mouse Project; Addgene; the Mutant Mouse Regional Resource Centers.

- Where novel research compounds are used, their chemical identity must be disclosed.

- Publications using commercial antibodies should report the supplying company and code number for all antibodies used. We recommend reporting using the following format:

The following antibodies were used: Mouse anti-protein A monoclonal antibody (company E, catalogue number #1000) was used for Western blotting with human cells, as validated in (figure X or reference Y or validation profile Z).

- In accordance with the principles in Sharing Publication-Related Data and Materials (National Academies Press, 2003), research using proprietary data must also evaluate a piece of comparable public data if the authors cannot or do not make the proprietary data available.

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In all cases, accession / deposition reference numbers must be provided in the manuscript.
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Some repositories offer authors the option to host data associated with a manuscript confidentially, and provide anonymous access to PeerJ for reviewing purposes. Therefore, if allowed by the repository, it is the authors' responsibility to coordinate prompt public release of the data with the repository on the publication date if kept confidential during peer review.
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Any potential restrictions on data and materials (for example: proprietary data, material limitations, or information relating to human subjects), including how other researchers might attempt replication without this data, must be disclosed at the time of submission. PeerJ reserves the right to refuse consideration of such articles.

Reporting and Study Guidelines

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We strongly recommend (and in some cases require) that authors adhere to the reporting standards which have been adopted by their field (or which apply to their study design).
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Authors should indicate which standards were followed and should, where appropriate, provide checklists, protocols, flowcharts etc as Supplemental Information as part of their article submission. Where accession or reference numbers have been obtained, these should also be provided in the text.

Discipline Specific Standards

The following is a non-exhaustive list of standards that should be followed depending on the study type:

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Articles which report on protein structures should follow the standards laid out in the Worldwide Protein Data Bank (a general resource listing reporting standards, and worldwide deposition databases for protein information).
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Articles which report on diagnostic accuracy studies (studies which evaluate the ability of a test to differentiate between patients who have the target condition and those who do not have the target condition) should follow the STARD requirements.
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Articles which report on clinical trials must follow the WHO definition of a clinical trial. In accordance with the ICMJE guidelines, all trials initiated from July 1st, 2005 must be registered in an approved registry. Unregistered trials will not be considered. Authors must adhere to CONSORT reporting guidelines and provide all appropriate trial registration documentation with the submission for prospective publication. Specifically, authors must provide a copy of the trial protocol and a completed CONSORT checklist as supplemental information (these documents will also be published with the manuscript, if accepted). The CONSORT flow diagram must also be included, preferably as Figure 1 of the manuscript. The manner of the informed consent should be discussed in the article, and where possible a copy of the patient consent form should be provided as a Supplemental Information file.
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Reports of systematic reviews and meta-analyses must use the PRISMA statement for clinical articles; it may be used for all non-clinical articles. Authors should include a completed PRISMA checklist and flow diagram to accompany their text and should state (within their Methods section) whether a protocol exists for their systematic review (in which case they should provide a copy of the protocol as Supplemental Information). Authors may register their systematic review (e.g. in a registry such as PROSPERO) in which case they should provide the registry number in their manuscript. Systematic reviews or meta-analyses should include those terms in the Title, Abstract and / or full manuscript.
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Reports utilizing quantitative real time PCR should follow the MIQE guidelines (the Minimum Information for Publication of Quantitative Real-Time PCR Experiments) and checklist.
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Articles which report on microarray experiments should conform to the standards published by the Functional Genomics Data Society, the most well known of which are the MIAME guidelines. The MIAME checklist must be provided, and the data from the experiments must be deposited in a publicly accessible database (ArrayExpress or GEO) with the accession numbers provided in the manuscript.
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Articles which report on medical observational/epidemiological studies (specifically cohort, case-control, and cross-sectional studies) should adhere to the STROBE initiative.
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In addition, PeerJ suggests that authors consult the EQUATOR Network (a general resource listing various reporting standards for health research studies); the MIBBI Portal (a listing of Minimum Information guidelines from diverse bioscience communities); or the BioSharing site for additional reporting guidelines or checklists which might apply to their work.
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As a general statement, data should be referred to by the most specific identifier available for the database archive it is submitted to.

Animal Research

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For research conducted on regulated animals (which includes all live vertebrates and/or higher invertebrates), appropriate approval must have been obtained according to either international or local laws and regulations. Before conducting the research, approval must have been obtained from the relevant body (in most cases an Institutional Review Board, or Ethics Committee). The authors must provide an ethics statement as part of their Methods section detailing full information as to their approval (including the name of the granting organization, and the approval reference numbers). Research on non-human primates is subject to specific guidelines from the Weatherall (2006) report (The Use of Non-Human Primates in Research).
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For research conducted on non-regulated animals, a statement should be made as to why ethical approval was not required.
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Experimental animals should have been handled according to the highest standards dictated by the author’s institution.
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We strongly encourage all authors to comply with the 'Animal Research: Reporting In Vivo Experiments' (ARRIVE) guidelines, developed by NC3Rs.
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Articles should be specific in descriptions of the organism(s) used in the study. The description should indicate strain names when known.

Human Subjects Research

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For experiments involving human subjects, appropriate approval must have been obtained from the relevant approval body (in most cases the authors’ Institutional Review Board, or ethics committee). The authors must provide an ethics statement as part of their Materials and Methods section detailing full information regarding their approval (including the name of the granting organization, and the approval reference numbers). Any research must have conformed to the Declaration of Helsinki.
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Authors must include a statement confirming that informed consent was obtained from all subjects. Where possible, a copy of the consent form used should be provided as Supplemental Information. If consent was verbal instead of written, then an explanation should be provided (in the Materials and Methods section), and verbal consent must have been approved by the IRB which gave permission for the study.
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Patient privacy and anonymity must be protected. Identifying information (such as names, photographs, identifying data) should not be included in the manuscript. Exceptions can be made only when evidence is provided that the individuals in question have given explicit approval. More information about patient privacy, anonymity, and informed consent can be found in the ICMJE Privacy and Confidentiality guidelines.

New Species

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New Zoological Taxonomic Names: Electronic publication of new zoological taxonomic names is now permitted by the ICZN with an amendment to the current Code. To name a new zoological species, genus or family, authors must comply with rules of the ICZN that require details of the publication to be entered into the official ICZN registry, Zoobank. Authors are advised to ensure the details of their article are entered in ZooBank and to confirm correct compliance at the time of acceptance. Please note that PeerJ will be archived in PubMed Central and CLOCKSS, and will show up as a known journal during the ZooBank registration process.

- Authors should use the following text in the Methods section:

"The electronic version of this article in Portable Document Format (PDF) will represent a published work according to the International Commission on Zoological Nomenclature (ICZN), and hence the new names contained in the electronic version are effectively published under that Code from the electronic edition alone. This published work and the nomenclatural acts it contains have been registered in ZooBank, the online registration system for the ICZN. The ZooBank LSIDs (Life Science Identifiers) can be resolved and the associated information viewed through any standard web browser by appending the LSID to the prefix "http://zoobank.org/". The LSID for this publication is: [INSERT HERE]. The online version of this work is archived and available from the following digital repositories: PeerJ, PubMed Central and CLOCKSS."
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New Botanical Taxon: To publish the name of a new botanical taxon (or to publish new combinations or replacement names), PeerJ has two requirements that must be met:

- The globally unique identifier, currently a Life Science Identifier (LSID), should be listed under the new taxon name in the Results Section.

  • At acceptance, the International Plant Names Index (IPNI, a database which deals only with seed plants, ferns & lycophytes) will be contacted by PeerJ editorial staff to provide the identifier. It should be noted that obtaining an LSID isn’t a requirement under the ICN, but it is a requirement of PeerJ.

-Assuming an LSID is obtained, authors will be made aware of them by PeerJ staff and should use the following text in the Methods section:

"The electronic version of this article in Portable Document Format (PDF) will represent a published work according to the International Code of Nomenclature for algae, fungi, and plants (ICN), and hence the new names contained in the electronic version are effectively published under that Code from the electronic edition alone. In addition, new names contained in this work which have been issued with identifiers by IPNI will eventually be made available to the Global Names Index. The IPNI LSIDs can be resolved and the associated information viewed through any standard web browser by appending the LSID contained in this publication to the prefix "http://ipni.org/". The online version of this work is archived and available from the following digital repositories: PeerJ, PubMed Central, and CLOCKSS".
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New Fungal Taxon: As of Jan 2012 the ICN accepts electronic PDFs as publications of record establishing new scientific names for algae, fungi, and plants.

- An additional ICN publication requirement effective January 1, 2013: all manuscripts naming fungi must obtain the citation of an identifier issued by a recognized repository such as MycoBank or Index Fungorum and include it in the protologue (everything associated with a name at its valid publication). Life Science Identifiers (LSIDs) or Globally Unique Identifier are only required for fungi. - In the Methods section, authors should include a sub-section called "Nomenclature" using the following wording (this example is for taxon names submitted to MycoBank; please substitute appropriately if the name was submitted to Index Fungorum):

"The electronic version of this article in Portable Document Format (PDF) will represent a published work according to the International Code of Nomenclature for algae, fungi, and plants, and hence the new names contained in the electronic version are effectively published under that Code from the electronic edition alone. In addition, new names contained in this work have been submitted to MycoBank from where they will be made available to the Global Names Index. The unique MycoBank number can be resolved and the associated information viewed through any standard web browser by appending the MycoBank number contained in this publication to the prefix "http://www.mycobank.org/MycoTaxo.aspx?Link=T&Rec=". The online version of this work is archived and available from the following digital repositories: PeerJ, PubMed Central, and CLOCKSS."

Procedures


Reviewer and Editor Blinding

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Authors may request that specific individuals be prevented from seeing their submission (a practice known as 'blinding').
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Requests to blind individuals should be limited in nature, should refer to specific individuals (not broad lists or categories of people), and should be made only with good reason.
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While we will attempt to honor these requests, we cannot guarantee that all requests will be honored.

Appeals

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If an author feels strongly that an inappropriate decision has been made on their decision, then PeerJ allows them to make a single Appeal.
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Appeals must be submitted with detailed information as to why the original decision was in error.
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We will first approach the original academic editor and determine whether, in light of this feedback, they now wish to change their mind. If they do not, then a second Academic Editor (or in some cases a committee of Academic Editors) will be asked to make an adjudication. In some cases this may involve re-review of the article.
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The new decision is considered final.
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Authors should be aware that Appeals often take some time to be resolved.

Blogs, Embargoes, and the Media

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PeerJ does not consider articles which have previously appeared in a recognized peer reviewed journal (as this represents dual publication).
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PeerJ accepts submissions which have previously appeared on preprint servers (including PeerJ PrePrints and arXiv); have previously been presented at conferences; or have previously appeared in other ‘non journal’ venues (for example: blogs or posters).
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We encourage authors to discuss and disseminate their findings as they wish. If they are discussing submissions which have not yet been formally accepted, then they should state this fact. If they are discussing with journalists, they should inform the editorial office so that we are aware of potential news deadlines.
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When an article is selected to be Press Released, PeerJ will set an embargo on news coverage corresponding to the publication date of the article. Once it is set, we request that news media do not publish stories ahead of this embargo (primarily as the final article itself will not be available until that date).
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Once accepted and press released, authors may not prevent journalists from discussing an embargoed article with other researchers (for example by requiring an NDA to be signed).

Commenting Policies

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PeerJ requires that all public comments follow the normal standards of professional discourse.
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All commenters are named, & their comments are associated to their PeerJ profile.
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PeerJ does not allow anonymous or pseudonymous commenting or user profiles.
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PeerJ does not tolerate language that is insulting, inflammatory, obscene, or libelous.
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Any comments which do not meet our standards will be removed. Repeat offenders will have commenting rights removed. PeerJ is the final arbiter as to the suitability of any comments.
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PeerJ publishes accepted manuscripts under a CC-BY license.
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It is the author’s responsibility to obtain the appropriate permissions from the original publisher to republish any previously published text, figures, tables, Supplementary Information, etc., in an Open Access journal under a CC-BY license.

Retraction Policy

PeerJ reserves the right to retract articles which are found to be fraudulent (for example subject to deception such as data manipulation) or in serious breach of one of our policies.