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The raw Orbitrap™ files conversion to mzXML formatted files was tested with Readw.exe version 4.3.1.
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The files were tested using the default parameters.
The two gene set files were tested on both the original training dataset and a newly generated validation dataset.
Thirteen ProTaper Dentsply/Maillefer sets used clinically on patients and a new reference set, in total a number of 84 files, were tested [ 3].
Pre-acute lung injury (ALI) (Table S1 in additional data file) was tested only against baseline ALI (BL-ALI).
The primers are listed in Additional data file 2. In addition, the expression of 180 adhesion, migration and cytoskeleton genes (see Additional data file 3) was tested from 1 μg cDNA using SYBR Green reagent on an ABI7700 system (Applied Biosystems, Foster City, CA, USA).
Pre-acute lung injury (ALI) (Table S2 in additional data file 1) was tested only against baseline ALI.
The modified questionnaire (Additional file 1) was tested on fifteen (15) pre-surgical patients to ensure it was easy to understand.
The 3-page questionnaire (see Additional File 1) was tested on 12 family caregivers for comprehensibility and acceptability in a pilot phase.
The final version of the VISA-A-S (Additional file 1) was tested on both healthy individuals and patients with a diagnosis of Achilles tendinopathy.
I believe the problem is in the way KEGGTranslator is called in that lacks the --format option (I found the call to KEGGTranslator in the parsing.log file; this was tested on OS X 10.8.5).
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com