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Access Microbiology open research platform logo



Aims and scope

Access Microbiology introduces a new Open Access. open research platform to members of our community, allowing the publication of replication studies, negative or null results, research proposals, data management plans, additions to established methods, and interdisciplinary work. 

We believe that too many of these valuable research outputs have been lost because they are not seen as ‘high impact’, creating a situation in which research is re-done in multiple labs for no gain. Access Microbiology aims to reduce this kind of research waste, so our publication criteria are based on methodological rigor rather than novelty. 

To further support this goal, the platform has an Open Data policy and so authors are required to make their supporting data publicly available through initiatives such as Figshare.  

The platform's scope covers:

  • The full spectrum of microscopic life forms, from bacteria and viruses to fungi, protists, archaea, and algae.
  • All approaches, from computational, biotechnology, and laboratory work, to environmental, clinical, and veterinary studies.
  • In response to community requests, we will also publish pedagogy papers on microbiology education.
  • Article types include Research Articles, Short Communications, Methods, Pedagogy articles, Study Protocols, Data Notes, Software Articles, and Case Reports.

During the conception and development of the platform, we engaged with our authors, members, Editors, preprint users, and early career researchers through focus groups and a community survey, to ensure the platform meets the needs of our community. The platform will continue to evolve and innovate, and we welcome feedback or suggestions on how it can be improved.

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How does it work?

Unlike traditional journal publishing, the peer review process of Access Microbiology has been completely turned inside out, so that the entire lifecycle of the article is posted publicly on the platform for all to see. This includes posting all versions of the article as a preprint, and posting the peer reviews and the Editor’s decision alongside these, thereby increasing the transparency of the peer review process. The platform has a mandatory Open Data policy and incorporates various manuscript Review Tools during the submission process, allowing authors to improve their article right from the very beginning of the peer review process. 

  1. Submission: authors are directed to run their article through the manuscript Review Tool, Penelope.ai to check it complies with the platform's article, editorial and ethical polices. Once they have made the necessary changes, they submit the article to our peer review system. Authors select which Creative Commons license their preprints should be posted under and indicate whether they want their article returned to them to correct based on the Review Tool reports, or if they would like their preprint to be posted online immediately.
  2. Review Tools scan article: SciScore and iThenticate reports are generated and the Editorial Office performs the standard ethical and editorial compliance checks. 
  3. (Optional) Revision: if requested by the authors during submission, the Editorial Office returns the article to the authors to improve using the reports of SciScore and iThenticate. Authors then resubmit the article and SciScore and iThenticate are re-run to generate new reports.
  4. Preprint and Review Tool reports posted online: the article is posted publicly online as a preprint in PDF format with a citable DOI, meaning authors can gain credit for their work and start receiving community feedback. The most recent reports from the manuscript Review Tools are also posted alongside the preprint. The preprint is indexed in Europe PMC and Google Scholar to increase discoverability.
  5. Peer review: the preprint is assigned to an Editor and it undergoes transparent peer review. If necessary, the Editor may request that the authors revise their article before sending it to reviewers.
  6. Editor decision and review reports posted online: once the Editor makes their recommendation, the reviewer reports and Editor’s decision and comments are posted online with their own DOIs. Whilst all reviews are posted alongside the article, reviewers can choose to remain anonymous if they wish. Editorial decisions can be Minor AmendmentMajor Revision, or in rare circumstances, No Longer Under Review.
  7. Revision: the authors revise their article and re-submit to the peer review system. If the authors did not correct their article based on the Review Tool reports during the initial submission, SciScore and iThenticate are run again. The revision and author response to reviewer is posted as a new preprint, along with the new Review Tool report, if run again at this stage. The Editor assesses the new version for improvements, and can make a final decision or send out for re-review, if necessary.
  8. Accepted: once the Editor considers the article to be significantly improved and it is scientifically sound, they will recommend an Accept decision.
  9. Version of Record published and indexed: the article is fully copyedited and typeset in our platform style and branding, published on the platform in full-text HTML and a PDF, and deposited in PubMed, PubMed Central, and other indexing services.

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What should I know before submitting?

  • If the work is sound and ethical, it can be published: the sound science nature of the platform provides microbiologists with a place to publish all their work, as long as it is related to microbiology, the work is sound and it complies with our policies. We welcome any original research (including null, negative and replication studies), descriptions of large datasets, case reports, a new tool or code used to help researchers in their research, or even the description of a useful technique used in microbiology teaching or outreach.
  • It is currently free to submit and publish: if accepted for publication, the cost will be covered in one of the following ways:
    • If you are affiliated with an institution that has signed a Publish and Read deal with the Society (see here) your OA publication charge will be covered under the agreement.
    • Thanks to funding from Wellcome Trust and the Howard Hughes Medical Institute, the Society is able to offer authors not covered by Publish and Read a subsidy to cover their APC during the first year of launch of the platform. We encourage early submission to take advantage of this.
  • Open Data policy: authors are asked to deposit all supporting data necessary to replicate their study’s findings and make it publicly available without restriction at the point of submission Please refer to our Open Data page for the minimum data requirement and recommended repositories.
  • All article versions are posted as preprints: preprints cannot be removed from the platform so all co-authors must have therefore been consulted and agree to this before submission begins.
  • The platform is not a preprint server: once a preprint is posted online, it is assigned to an Editor and is considered under peer review. Authors cannot choose to post a preprint and opt-out of peer review.
  • Articles are posted online exactly as you submit it: we do not copyedit or typeset our preprints, so authors should submit their manuscript exactly how they wish it to be read online, such as including high quality figures within the main body of the article. Articles will have a 'Preprint' watermark, the DOI, date of posting and license statement added before they are posted on the platform.
  • Preprints are posted under a Creative Commons license: all versions will be hosted and published as Open Access under a Creative Commons license. Authors can choose a Creative Commons license of their choice during submission. If the article is accepted for publication, we will then ask the authors to sign a separate license for the Version of Record.

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Article types

The open research platform publishes a wide range of article types, including Research Articles, Short Communications, Methods, Pedagogy articles, Study Protocols, Data Notes, Software Articles, Case Reports (and Case Series), Personal Views, Insight Reviews, Editorials and Letters. For authors who wish to publish replication studies, or negative or null results, we recommend submitting this as either a Research Article or Short Communication article type, depending on the length.

In the near future, we also hope to offer Registered Reports as an additional article type. These will allow authors to publish their methods and proposed analyses before undertaking the research, thereby improving the study design, reducing researcher bias, and improving the rigour of their research.

If you are unsure which article type to use, or if your research is within scope, please contact the Editorial Office who will support you.

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Review Tools: Penelope.ai, SciScore and iThenticate

Designed to give submitting authors immediate feedback, these easy Review Tools used during the submission process will help authors in helping them improve their article right from the beginning of the submission process. This includes navigating publication requirements and policies, increasing the rigour and reproducibility of their research, and improving the chances of quicker review and publication of the article. The corresponding reports of SciScore and iThenticate will be also posted on the platform alongside the preprint, allowing readers to assess the preprints themselves, providing an additional safeguard and data integrity check on the manuscript.

However, we recognise that, as with any software, the results of these should only be used as a guide, within the overall context of the article itself, and should never replace full peer review. Therefore, all posted reports will include a statement encouraging readers to use the report appropriately and provide links to documentation on how to interpret and contextualise the results. We also work closely with the developers of the tools to help improve their functionality and enhance our authors’ experience. If you have any feedback or problems about these tools, please contact us at [email protected].

Penelope.ai

What does Penelope.ai do?

Penelope.ai is a quick web-based tool that scans the article for compliance with the platform’s editorial and ethical requirements. Useful features include scanning for the presence of funding, conflict of interest and data summary statements, the presence of an ethical statement (if required), a title page, abstract, if a cited figure or table is missing, or whether any references have been accidentally omitted. The tool presents these results using clear point-by-point responses and a traffic light colour system – crucial changes are indicated in red, items to be double-checked in yellow, and items that passed the checks in green.

How does it work on the platform?

Although optional, prior to submitting, authors are encouraged to run their manuscript through the tool. Within just a few minutes, authors can act on any items flagged by the tool, before continuing their submission. This means that authors will be much less likely to have their article returned to them, reducing the time taken for their article to be posted on the platform. As an example, authors who submit Case Reports may find this tool particularly useful for reminding them to include the all-important ‘Consent to publish’ statement required for this article type. Authors will also benefit from reminders to include e.g., a conflict of interest or funding statement, which they will be able to immediately add without having their article returned to them by the Editorial Office.

SciScore

What does SciScore do?

SciScore assesses the methodology, data availability and ethics information in manuscript to evaluate whether the authors have included important scientific rigour criteria such as blinding, sex, randomisation of subjects into groups, power analysis, and replication. It also scans the text for key biological resources and their associated Research Resource Identifiers (RRIDs) like antibodies, cell lines, plasmids and tools, and highlights if these are accessible or have problems associated. Using a ‘scored’ approach, this tool has been designed to highlight when the article has insufficient information that would allow others to replicate their work, thereby improving the rigour and reproducibility of their research. We hope that by offering this tool, it will educate and encourage better practice for our author's future research.

How does it work on the platform?

Authors simply provide the text of their methods, data summary and ethics sections (and any other required information) during submission, and the integrated tool then scans this text when the article is submitted, generating the reports. When the article is posted on the platform, the SciScore MDAR and Core report are posted alongside the article with a citable DOI, helping readers to assess the work prior to completion of peer review. 

During the submission process authors indicate if they would like the article returned to them to improve based on the results, or if they would like the article and reports posted immediately. Authors who choose to correct their article will have the Review Tools run a second time on the corrected version and the newest reports are posted with the preprint. Authors who choose to post their article immediately will have the Review Tools run the second time on the revised article after peer review and these reports are posted alongside the revised version.

Unless clear ethical concerns are highlighted by the reports, the Editorial Office will not use these when checking an article, however reviewers and Editors are encouraged to use these to support their assessment. 

For tips on how to improve your score, please see SciScore's MDAR and Core report pages.

iThenticate

What does iThenticate do?

iThenticate has a comprehensive database of over 91 billion articles from the internet and over 82 million scholarly publications. This tool checks the submitted article against this database and highlights where similar sentences or phrases have been used previously, including in their own published work. Each individual match is given a percentage score based on how much it overlaps with the previously existing work, and an overall similarity score is given. During our testing we noticed that a surprising number of authors accidentally and unknowingly reuse text from previously published work, so we envisage many of our authors choosing to use this report to correct their article, thereby increasing the originality and improving the scholarship of the work. 

How does it work on the platform?

Authors are not required to do anything during the submission process. iThenticate is integrated within Editorial Manager and the report is automatically generated after completing the submission. As with SciScore, authors indicate if they would like the article returned to them to improve based on the results, or if they would like the article and reports posted immediately. Authors who choose to correct their article will have the Review Tools run a second time on the corrected version and the newest reports are posted with the preprint. Authors who choose to post their article immediately will have the Review Tools run the second time on the revised article after peer review and these reports are posted alongside the revised version.

Unless plagiarism is clearly detected, the Editorial Office will not use this report to assess an article, however reviewers and Editors are encouraged to use these to support their assessment.

For help on how to interpret the report and use the interface, see iThenticate's Resources page and user page

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Platform policies

The polices outlined in our Prepare an article and Ethics policies pages also apply to the platform, as well as the platform-specific polices described here.

Our responsibility as a Society publisher is not just to the scientific record, but to the microbiological community and our membership. As such, our policies regarding preprints may differ from other publishers and preprint servers. To be as transparent as possible, we have outlined below our policies for the platform and the steps we might take in some circumstances. The Microbiology Society is a member of the Committee on Publication Ethics (COPE), and we will consult with the rest of the membership on cases that have not yet received formalised guidance to develop future policies that will safeguard the scientific record. 

  1. Access Microbiology has a mandatory Open Data policy, and requires that authors deposit all supporting data necessary to replicate their study’s findings and make it publicly available without restriction at the point of submission.
  2. Authors must not contact any reviewers directly during the peer review process, and any communication with them once peer review has completed must be conducted with respect and professionalism.
  3. Whilst we strive to ensure all preprints posted on the platform are appropriate, safe and not libellous, the content of a posted preprint is wholly the responsibility of the author, not the Microbiology Society as a publisher.
  4. The Microbiology Society reserves the right to withhold from posting a preprint or peer review report for any reason. In such cases, the authors of the content will always be made aware of the reason.
  5. Posted preprints or peer review reports will not be removed from the platform, unless valid concerns are raised about their damage to wider society or if they have legal implications, in which case 6.2 below may be applied after investigation.
  6. If a posted preprint is deemed to contain potentially damaging content, an investigation will take place over the fidelity of the paper and the potential damage to the wider community:
    1. Where the preprint has ethical concerns but is not deemed damaging to wider society, it will still go through full peer review. If found to be ethically compromised after review, the article will be labelled as 'No Longer Under Review' and the Editor's and reviewers' reasons will be available for readers. The Society may also add an additional note to highlight the concerns.
    2. In very rare circumstances where a preprint or peer review report is deemed to be potentially harmful or has legal implications, the respective posted content will be removed from the platform and a note added alerting readers to highlight the concerns and why it was removed. The DOI will remain resolvable and the key article metadata be available to maintain the integrity of the academic record (e.g. author names, affiliations, title).

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Glossary

  • Accept: the final editorial status of an article which has completed peer review. 
  • Author-accepted manuscript: the version of a scientific manuscript that has been posted online, that has been editorially accepted and completed the formal peer review process, but has not been fully formatted and published.
  • Major Revision: a recommendation or decision made on a preprint that is Under Review. It indicates that the article must be substantially improved before it can be accepted.
  • Minor Amendment: a recommendation or decision made on a preprint that is Under Review. It indicates that the content of the article is sufficient but minor changes are needed before acceptance.
  • Posted: the action of putting either a preprint, peer review or Editor decision publicly on the platform.
  • Preprint: the version of a scientific manuscript that has been posted online and that has not completed the formal peer review process, i.e., it has not been editorially accepted for publication. They should not be reported in the media as conclusive or as fact, and should not be used to inform clinical or health-related behaviour or policy.  
  • Published: used to describe the action of making something public on the platform, and it is the Version of Record.
  • No Longer Under Review: the final editorial status of a posted preprint which is no longer being considered for publication on the platform. This can be either because it is found to be inappropriate for the platform after consideration by an Editor, or the author no longer wishes to continue with the peer review process. The reason is indicated on each article. The authors are free to submit their article to another journal or platform.
  • Review Tool: an automated tool that is run either just before or during the submission process on the manuscript and which is used to improve the submitted manuscript and/or support the assessment of a preprint. The three Review Tools are Penelope.ai, SciScore and iThenticate
  • Review Tool report: the results of SciScore (MDAR and Core) and iThenticate Review Tools which are combined into a single PDF and posted publicly on the platform. 
  • Transparent peer review: the contents of the Editor and reviewers' comments are posted publicly online, as well as the author's response to reviewers. However, reviewers can choose to remain anonymous on their review reports, if they wish.
  • Under Review: the editorial status of a preprint that has not completed peer review on the platform. The preprint can either be with the Editor for assessment, under active peer review or with the author for revision. 
  • Version of Record: the peer reviewed, fully formatted, final version of the article that has been published online. Suitable for reporting to a lay audience with a high level of confidence that the results have been thoroughly scrutinized, and the conclusions stated in the manuscript are true to the underlying data.

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FAQs

Why has the Society converted Access Microbiology into an open research platform?

Converting Access Microbiology into an open research platform means we are able to offer a new publishing model to the microbiology community that delivers greater peer-review transparency and which can help fast-track the communication of valuable research, thereby maximizing its potential for impact and influence. Versioning of preprints, including the reviewer reports and responses to authors, makes the entire publication process more transparent. We believe this helps lay audiences better understand the status of the research, as well as helping early career researchers (ECRs) to better understand the process and thereby improve their work and their peer-review skills. Using manuscript review tools as part of the platform for preprints not only helps authors improve their work before posting the first preprint, but posting these reports publicly also highlights potential flaws in the work, giving readers a ‘health warning’ about its reliability.

What is an open research platform?

An open research platform is an evolution of the academic publishing process. It combines elements of a preprint server, and all the elements of an open access journal like Access Microbiology into a single, unified, and transparent service. Authors can submit a manuscript, and pending checks from our Editorial Office for the crucial components of a manuscript, as well as some potential improvements from manuscript review tools, their article is then posted online as a preprint. The article then enters transparent peer review, which may lead to the article being eventually published. The entire review process is made as open as possible, including posting all versions of the article, the peer reviews, manuscript review tool reports and the Editor’s decision.

Is Access Microbiology a journal

No. Since XXX it has been an open research platform. The open research platform contains everything found in the previous journal format, with the addition of this preprint capability, manuscript Review Tools to assist authors in improving their work, and a transparent review process.

How is an open research platform different to a journal?

With journals, the peer review process is often only visible to the Editor, review and authors, and the only version of an article that is publicly available is the published Version of Record at the end of the peer review process. With an open research platform, the entire review process is made as open as possible in an effort to increase transparency, rigour and reproducibility. This means posting all versions of the article, the peer reviews and the Editor’s decision onto the platform for everyone to read. Moreover, once an article passes peer review it is published as the Version of Record and can be cited as such. Before acceptance, whilst it does not count towards an author’s publications, it can still be cited as a preprint.

What does this platform offer that submitting to a preprint server and then a journal separately doesn’t already?

A unified platform means the DOI from the first posted preprint to the final, published Version of Record article are connected, and therefore you can begin accruing citations from the initial posting and all your article versions are kept together in one location. Additionally, upon submitting to our platform, authors can choose to improve their work immediately via feedback from various manuscript review tools (Penelope, SciScore and iThenticate), which have been tested for use by focus groups in improving a submitted article. Submitting to a Microbiology Society-owned platform also means you are directly supporting the grants and prizes, outreach, policy work and many events that the Society can provide to its members and the microbiology community every year.

What is the difference between a preprint and a publication?

A preprint is any version of an article that is posted on our platform, and assigned a DOI, but it has not completed the peer review process and been accepted. Once an article has been accepted and has been formatted in our platform branding, it is then formally published in Access Microbiology as the published Version of Record. A published article will be sent to the various indices which collate Access Microbiology content.

What kind of data do I need to provide at submission?

You will need to provide all data necessary to replicate the study’s findings, in line with the platform's Open Data policy. For more information on how to prepare data, minimimum requirements and our recommended repositories, see our Open Data policy page.

Can I opt-out of using the Review Tools during submission and/or having their reports posted online?

You can choose to opt-out of using Penelope during submission, although we strongly encourage authors to use it as authors are far less likely to miss key requirements and have their article returned to them at the very first hurdle. We do not post the report produced by Penelope. However, all peer reviewed articles have the SciScore and iThenticate tools run on their first submitted article and these are always posted on the platform. This is to ensure complete transparency, and to support readers in assessing the work and its reliability themselves prior to completion of peer review.

How long will it take for my preprint to be posted?

During the submission process, authors are asked if they would like to have their article returned to them to improve based on reports from the Review Tools, and may be asked to correct any in-house Editorial Office checks. As soon as we receive the corrected version, we aim to post the article on the platform within days, along with the manuscript Review Tool report.

Can I post in bioRxiv or another preprint server at the same time as submitting to Access Microbiology?

Authors may post their preprint on other preprint servers if they wish, however this increases the chance of splitting their citations and may frustrate readers to find the same article in multiple locations. The Microbiology Society encourages authors to therefore to only submit to Access Microbiology and to use this preprint to receive community feedback on.

What type of checks occur on a preprint before it is posted?

The Editorial Office staff will perform a series of checks to ensure the article complies with the platform's editorial and ethical policies. This will include checking that all supporting data has been deposited and is accessible, that there are declarations over conflicts of interest, funding sources, author contributions, and any ethical approval statements and documents, if required (such as patient consent forms). They will also check that the work is in scope (i.e. the research relates to microbiology?) and for any potentially libellous, dangerous or inflammatory content. Articles of concern will be flagged to our Editors-in-Chief for a further assessment. The Microbiology Society retains the right not to post any article.

Will my article be peer reviewed?

If your article passes the basic checks by our Editorial Office to ensure it complies with our editorial and ethical policies, it is within scope, and it is not considered potentially harmful to the public, it can be posted online. At this point an Editor will make an initial assessment as to whether it should be sent out to review immediately, or if there are revisions they would like the authors to make before this happens. In rare circumstances, if the Editor, with the input from another Editorial Board Member, considers the work to be fundamentally unsound beyond improvement or is ethically compromised, they may also decide at this point that the article will no longer be considered for publication.

How will peer review be different to a journal?

Access Microbiology is a sound science platform, and therefore already works slightly differently. Reviewers are asked to assess the validity and soundness of the article, rather than on novelty or positive results. Authors on the open research platform will also be given multiple opportunities to improve their manuscript, and should only receive notification that the platform is no longer considering their article for publication if they have repeatedly not addressed the feedback provided, or the work is fundamentally not sound or is incomplete. Reviews, the Editor decision, the author response to reviewers and the manuscript Review Tool reports will also be posted publicly alongside the version of the article, to enhance the transparency of the peer review process.

Will peer reviews be made publicly available?

Yes, every review will be posted alongside each version of the article. However, reviewers can choose of remain anonymous or sign their name to their review, known as transparent peer review. During the platform’s development we consulted with our community to determine whether reviewers’ names should also be required (open review), or whether reviewers should have the option to opt-out of providing their name. (transparent review). The vast majority of the surveyed community indicated they would sometimes wish to remain anonymous.

How can my article be accepted?

Following a round of review on the platform, the Editor will make an assessment as to whether the authors have sufficiently addressed the reviews in their revised version. If they have, and the article is sound and rigorous, it can be accepted for publication.

Can my article be rejected?

Since the scope of the platform is based on sound science, we expect that the overwhelming majority of articles will undergo revisions and eventually be accepted for publication. However, in cases where serious misconduct or ethical concerns are raised, where authors continually neglect to respond to the feedback from Editors and reviewers requiring improvements to validate the science, or where reviewers are unable to judge validity, we will have an option to cease considering the article for publication. The status of an article removed from the review cycle will be updated to clearly indicate that it is no longer under consideration for publication (labelled as ‘No Longer Under Review’), and the preprint will remain on the platform as such.

How do I submit a revised article?

If the Editor has made a Minor Amendment or Major Revision decision, once you have revised your article you can simply resubmit your revised article through Editorial Manager, as before. In Editorial Manager, you enter the 'Submissions Needing Revision' folder, there you can find your previous submission and select 'Revise Submission'.Please ensure you provide all the required documents and formatting, as outlined in the Revision checklist in the Prepare an article page.

How do I know if a preprint has been revised or not?

All preprints have a green 'Version' label infront of the title. The first, un-revised version is always 'Version 1', so any revisions will have a 'Version' number higher than 1.

Where will my article be indexed?

Posted preprints will be indexed in Europe PMC and Google Scholar, whilst published Version of Record articles will be indexed in PubMed, PubMed Central, Google Scholar and CAB Abstracts. We will submit it to further indices at the appropriate point of the platform’s life cycle.

I published in Access Microbiology before it became an open research platform. What will happen to my article now?

Your article will be unaffected by this change. It will remain a fully published and indexed article on the platform.

I submitted to Access Microbiology before it changed to an open research platform and it is still under review. What happens happen to my article now?

Your article will be unaffected by this change. It will undergo peer review using the previous, single-blind journal workflow. This means that only the final, Version of Record will be made publicly available on the platform, and no article versions, peer reviews or Editor decisions will be posted publicly. If you have any concerns at all or would like more information, we would be happy to discuss it with you further, please contact the Editorial Office.

I have been asked to review an article that was submitted before the change to an open research platform. What will happen to my review if I submit one?

Your review will be treated usig the previous single-blind, journal workflow. This means that your review will remain anonymous to author throughout the peer review process, and it will not be posted publicly at any point. If you have any concerns at all or would like more information, we would be happy to discuss it with you further, please contact the Editorial Office.

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Contact us

Email the journal Editorial Office at [email protected]

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