MSID: 101630 Version: 1 DOI: 10.1101/2024.08.29.609024

[fred-atherden]

MSID: 101630

Version: 1

Preprint DOI: https://doi.org/10.1101/2024.08.29.609024

Step 1. Awaiting reviews

Editorial to post reviews via hypothesis

Useful links:

• DocMap: https://data-hub-api.elifesciences.org/enhanced-preprints/docmaps/v2/by-publisher/elife/get-by-manuscript-id?manuscript_id=101630
• New model tracking: https://docs.google.com/spreadsheets/d/1_fHaoOy7hjyocptKtVJRijeNpUY4hBS7Ck_aVmx6ZJk/
• Reviews on sciety: https://sciety.org/articles/activity/10.1101/2024.08.29.609024

For trouble shooting (e.g. no Docmaps available):

• DocMap issue addressing: https://miro.com/app/board/uXjVNCwK6EI=/
• Explore DataHub DocMaps API: https://lookerstudio.google.com/reporting/4c2f0368-babb-4beb-b5b3-497e7e7b0f08/page/ejphD
• Unmatched submissions and preprints: https://lookerstudio.google.com/u/0/reporting/9f86204f-3bf7-477c-9b18-5c5ef141bf69/page/p_gxi57ha93c
• Unmatched manuscripts spreadsheet: https://docs.google.com/spreadsheets/d/15QcK8w-ssB7109RQEDtFpJPZ0J5HTGxoHa_2TtpMBbg/edit#gid=1336081641

Step 2. Preview reviewed preprint

Production QC content ahead of publication

Instructions:

• QC preview: https://prod--epp.elifesciences.org/previews/101630v1
• Update ticket with any problems (add blocked label)
• When QC OK, add QC OK label to ticket and add publication date and time to https://docs.google.com/spreadsheets/d/1amAlKvdLcaDp5W8Z8g77NmkwbMF5n_u89ArSqPMO8jg
• Move card to next column
• (At end of the day post link in #enhanced-preprint and ask for PDF to be generated)

Useful links:

• Preprint DOI : https://doi.org/10.1101/2024.08.29.609024
• Confirm reviews returned by EPP: https://prod--epp.elifesciences.org/api/reviewed-preprints/101630/v1/reviews
• To update the MECA path in the docmap: https://docs.google.com/spreadsheets/d/1mctCQuNFBjSn97Lihy7_vBO6z7-N-oqyLv4clyi6zHg

Step 3: Awaiting search reindex

This step adds the reviewed preprint to the homepage: https://elifesciences.org

The search reindex is triggered once an hour. We need the reviewed preprint to be indexed as the search application serves the journal homepage.

Useful links:

• Jenkins pipeline to reindex search can be triggered sooner or monitored here: https://alfred.elifesciences.org/job/process/job/process-reindex-reviewed-preprints/

Step 4: Published! PDF requested

Waiting for PDF to be generated

Useful links:

• PDF tracking: https://docs.google.com/spreadsheets/d/106_XeDjmuBae7gexOTNzg60lapeqjl2aRn9DzupGyS8/

Step 5: Introduce PDF to data folder and git repo

Upload PDF to relevent folder in git repo https://github.com/elifesciences/enhanced-preprints-data/

Step 6: Done!

• [ ] Kettle is on!

[elife-bot]

- error: [aff-multiple-ids] Affiliation contains more than one institution-id element: https://ror.org/041rsh762; https://ror.org/050jn9y42; https://ror.org/04xaa4j22 in 3 https://ror.org/041rsh762 https://ror.org/050jn9y42 https://ror.org/04xaa4j22 Institut National des Sciences Appliquées (INSA), Lyon, France
- error: [aff-multiple-ids] Affiliation contains more than one institution-id element: https://ror.org/01a6zh966; https://ror.org/057qpr032; https://ror.org/03pbgwk21 in 4 https://ror.org/01a6zh966 https://ror.org/057qpr032 https://ror.org/03pbgwk21 Institut de Neurosciences Cognitives et Intégratives d’Aquitaine, CNRS UMR 5287, Université de Bordeaux, Bordeaux, France
- error: [aff-multiple-ids] Affiliation contains more than one institution-id element: https://ror.org/029brtt94; https://ror.org/03bbjky47; https://ror.org/048r71s66 in 5 https://ror.org/029brtt94 https://ror.org/03bbjky47 https://ror.org/048r71s66 CarMeN Laboratory, INRAE U1397, INSERM U1060, Claude Bernard Lyon 1 University, Lyon, France
- error: [aff-multiple-ids] Affiliation contains more than one institution-id element: https://ror.org/02en5vm52; https://ror.org/02feahw73; https://ror.org/02mh9a093 in 7 https://ror.org/02en5vm52 https://ror.org/02feahw73 https://ror.org/02mh9a093 Sorbonne Université, Institut du Cerveau – Paris Brain Institute – ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
- error: [aff-institution-wrap-test-3] institution-wrap cannot contain text. It can only contain elements.
- error: [aff-institution-wrap-test-3] institution-wrap cannot contain text. It can only contain elements.
- error: [aff-institution-wrap-test-3] institution-wrap cannot contain text. It can only contain elements.
- error: [journal-ref-article-title] This journal reference (id c26) has no article-title element.
- error: [junk-character-presence-3] p element contains a junk character '□' which should be replaced or deleted.
- error: [junk-character-presence-3] p element contains a junk character '□' which should be replaced or deleted.
- error: [junk-character-presence-3] p element contains a junk character '□' which should be replaced or deleted.
! warning: [given-names-test-10] given-names ends with de, der, or den - should this be captured as the beginning of the surname instead? - 'Priscille De'.
! warning: [given-names-test-10] given-names ends with de, der, or den - should this be captured as the beginning of the surname instead? - 'Priscille De'.
! warning: [aff-no-wrap] Affiliation doesn't have an institution-wrap element (the container for institution name and id). Is that correct?
! warning: [aff-no-country] Affiliation does not contain a country element: 8French Reference Center on Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon
! warning: [aff-no-wrap] Affiliation doesn't have an institution-wrap element (the container for institution name and id). Is that correct?
! warning: [mixed-citation-other-publication-flag] mixed-citation in reference (id=c1) has a publication-type='other'. Is that correct?
! warning: [mixed-citation-other-publication-flag] mixed-citation in reference (id=c35) has a publication-type='other'. Is that correct?
! warning: [mixed-citation-other-publication-flag] mixed-citation in reference (id=c37) has a publication-type='other'. Is that correct?
! warning: [title-lower-case] Content of <title> element is entirely in lower-case case: Is that correct? 'k-means clustering identifies highly different populations contralaterally vs ipsilaterally in an ischemic stroke model but offers a heterogeneous cluster composition.'
! warning: [p-all-bold] Content of p element is entirely in bold - 'Supplemental figure 1: Parameters ranked according to their normalized projection onto PC1 for the 5 tested datasets.'. Is this correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Supplemental table 1: Identification of the optimal threshold.'. Is this correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Supplemental figure 2: Andrews plots at a 0.8 threshold.'. Is this correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Supplemental figure 3: MorphoCellSorter rankings generated for the 5 datasets at a 0.8 threshold.'. Is this correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Supplemental figure 4: Elaboration of MorphoCellSorter ranking for the AD dataset.'. Is this correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Supplemental figure 5: Elaboration of MorphoCellSorter ranking for the CCHS dataset.'. Is this correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Supplemental figure 6: MorphoCellSorter automated ranking of the CCHS dataset.'. Is this correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Supplemental figure 7: Pre-processing and segmentation procedure for all used datasets.'. Is this correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Supplemental figure 8: Illustration of the 20 morphological indexes automatically computed.'. Is this correct?
+ info: [article-version-flag] This is preprint version 1.1.
+ info: [permissions-info] This article is licensed under a CC BY 4.0 license. http://creativecommons.org/licenses/by/4.0/ https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#permissions-info