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The phrase "significant differences with" is correct and usable in written English.
It can be used when discussing variations or distinctions between two or more subjects, particularly in academic or analytical contexts. Example: "The study revealed significant differences with the control group, indicating a strong effect of the treatment."
Exact(60)
Mr. Bush still has significant differences with the N.A.A.C.P., and not just over the death penalty.
"He can play an important role in helping to resolve our significant differences with Iran peacefully".
There were no significant differences with the lesser concentrations.
We still have significant differences with China, but through engagement we have a better mechanism to resolve them.
Burzynski noticed that cancer patients had significant differences with peptides (amino acid chains) in their blood compared with healthy people.
Ms. Pirro and others in law enforcement say that they still have significant differences with the archdiocese regarding its handling of sexual abuse cases.
But people familiar with his thinking say Mr. Geithner has had significant differences with Mr. Paulson over how the bailout should proceed.
Yet a closer look at the EMI itself suggests some significant differences with the Bundesbank.
There are few significant differences with the iPhone app which we reviewed here.
Significant differences with the NM/TiO2 catalysts are observed.
Some significant differences with previous published models are highlighted.
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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