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could that be interpreted as the ones with trash balls (NFTs) might actually be the ones handling it 'better'?

You mean like the NFTs are somehow protective against the Prion forms? That is a possible interpretation that this study does not directly disambiguate.

Could just be an innocuous buildup with no effects either way, that just results from having the disease a long time. I doubt it's a direct result of handling the disease well but I don't know anything about what defenses our brains have against prions

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