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In brief, samples (n = 4 scaffolds, for each scaffold) were digested by trypsin, and the resulting peptides were analyzed by LC-MS/MS.
Cell morphology, viability and alkaline phosphatase (ALP) activity on each scaffold were examined at different time points.
The GFF3 file and a FASTA format file of each scaffold were converted to a GENBANK format file using EMBOSS Seqret75 program (ver. 6.6.0.0) with the options "-fformat gff -osformat genbank".
Next, rMSCs in each scaffold were preconditioned with chondrogenic media in vitro for 1 week and implanted in the backs of nude mice for 6 weeks.
Six samples for each scaffold were prepared.
Both the height and diameter of each scaffold were measured using a digital micrometer (with accuracy of 0.01 mm) after putting the sample between glass slides in un-deformed state (before testing).
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Each scaffold was seeded with 1 million human stem cells.
The number of molecular markers (SSR or ILP) was counted using a Perl script and the molecular density (per Mb) of each scaffold was calculated.
Strut diameter for the 17 sections of each scaffold was optimized independently in order to match the biomechanical stability of intact bone.
Each scaffold was scanned with a 20-kb window to ensure that the number of distinct clusters that covered the entire window (indicating support for this 20-kb connection by several long molecules) was statistically significant with respect to the number of clusters that spanned the left and right edges of the window.
Then the molecules with each scaffold are counted.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com