RUP wiki - Notes and How to

Notes and How to

Notes:

File sizes

JPS: JPS imposes a file size limit of 500 MB per file. No max for article package.
Nimble: Figures that are too large will cause the article to fail. The maximum pixel dimensions allowed are a width of ~6,400 and height of ~7,685. Note that this is different than the dpi - the dpi could be 300 but the pixels could still be too high. The dpi of a figure shouldn't be over 1,200. There is no official article package limit for Nimble, but packages over 500 MB caused Nimble to stall at every step in the workflow.
Zipline: There is a 1-GB package limit on Zipline.

You can try to reduce the size of source data files if the combined article package is too big. Open the PDF in Acrobat and go to Tools/Optimize PDF. Click Advanced Optimization, and then in the upper right corner, click Audit Space Usage. If “Document Overhead” is huge, using the Optimizer, uncheck all of the options in the left column. Check only “Discard User Data” and to the right, “Discard private data of other applications.” See the screenshot below. Make sure to visually compare the two file versions to make sure they look the same - it's very important not to alter how source data look.

Extracting images from Word file

1) Make a copy of the .docx file. Then rename the copy, changing the file extension from .docx to .zip.

2) Unzip the package. Image files will be found in word/media.

3) Open the .emf files in Illustrator. Export to create a .tif file, choosing grayscale as the color model if there is no color in the image. Anti-aliasing: None. Check off LZW Compression. If the image is RGB, check off Embed Profile.

Adding authors after article acceptance

The scientific editor must approve the change.

The manuscript editor then needs to

- send a new copyright form to the corresponding author
- send disclosure forms to the new authors
- notify all authors of the change; the email to all authors listing everyone's Credits should be resent

You:

- create author profiles in JPS and update the article record
- make sure the managing editor sends the updated forms to JPS
- add author Credits, any certified ORCIDs, and any funding information to the article metadata
- add affiliations if necessary
- update the Acknowledgment and disclosure statement
- update the OAS record

MliFlow How to:

Handle text boxes in board member Editorials

Click here for a sample of how to structure the editorial board member text boxes, such as that in https://doi.org/10.1083/jcb.202203028. An example is given of the Word file and its resulting XML.

JPS/Proof Central How to:

Replace, add, and remove files while the article is in Proof Central

- You cannot easily replace a file with a different file type (e.g., replace TableS1.doc with TableS1.pdf); Nimble will see it as an additional file, not a replacement, and will fail. TnQ will have to manually intervene. Before exporting the new file, open a ticket and attach the new file, and wait for a response before proceeding.
- If you need to remove a file (e.g., the author merged Tables S4 and S5 and you need to delete S5), manual intervention is needed. Open a ticket before proceeding. TnQ will have to delete Table S5 from their ms files first.
- If you need to introduce a new file, you should be able to do so without intervention. Annotate a figure file in the usual interface before editing the XML (see instructions below for how to add external supplements). Upload the new file, naming appropriately for the stage you're in (without the R pre-author proof, with the R otherwise). You must send a fake figure reshoot file along with it. At the ArticleExpress Review step, the version of the new file will be "New." At any step, the status must say "Send to Vendor."
- Boxed figures: These are treated differently by PFX because they are inline graphics. There is no "Annotate" button on these. If you have a paper with only boxed figures, there is no way to indicate that a graphics change is needed within the usual interface. Opening the XML Editor and choosing graphics change from there does not work. So, if you only have boxed figures, you must open a ticket.

Add external supplemental files mid-workflow

If supplemental tables and datasets need to be added when the article is already in PFX, XML tagging needs to be added. If you add the supplement citations and upload the new files without editing the XML, it will cause a problem.

A link to the external file needs to be inserted. The existence of the link is what makes the external file appear in the Supplements widget in the online article.

The XML below is what links Table S1 and Table S2 to the article. It should be inserted directly above the <history>. You can find an example XML file here.

<supplementary-material id="sup1" content-type="data-supplement"

xlink:href="JCB_201908097_TableS1">

<label>Table S1</label>

<p>lists datasets used in the bioinformatic analysis.</p>

</caption>

</supplementary-material>

<supplementary-material id="sup2" content-type="data-supplement"

xlink:href="JCB_201908097_TableS2">

<label>Table S2</label>

<p>lists the oligonucleotides used in this study.</p>

</caption>

</supplementary-material>

In Proof Central, submit with a graphics change. Even though this is the first version of the file, place the "R" in the file name if the article is past the author proof step. Upload a fake revised figure along with the supplemental file.

JPS How to:

Resend the release signal

Only do when the article is at the Awaiting Final XML step and you're certain that the release signal was not sent successfully/not received.

Go to Advanced Manuscript Tasks from the 'Tasks' tab.
Click into Move Content/Reset Status.
Click the 'Open' checkbox for Queue for Release.
Go back to the tasks tab once that task is reopened and click the 'Retry Release' link.
Click the 'Complete Task' link.

Delay the author proof chaser email

Chaser emails are automatically sent to the author three business days after the proof is sent out. If the author tells you they will need more time, you can delay sending of the second and subsequent emails. You can’t cancel chaser emails or delay sending of the first one. You can only push out future emails a large number of days so as to prevent them from being sent.

Go to Advanced Tasks from the JPS home page.
Under the Advanced Manuscript Tasks section, click Select Manuscript and enter the manuscript number.
Click on the Modify Task and Query Durations link below.
Increase the number in the Queries Duration field and click the Update Durations button. Note that nothing will populate in the Pending Queries field until a chaser email has already been sent out.

You can also look at an overall list of open chasers by journal. Click on Chasers from the home page, and there is an edit link under the Next Chase Date column.

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