The mice on the low-carb diet had lipid profiles similar to the mice on the "western" diet, but much worse plaque. So in this study, cholesterol levels were not related to the level of heart disease, at least comparing a western diet with a low-carb diet. The mice on the standard mouse diet had the least plaque, and lower cholesterol.
I don't think I have seen any credible claim that a low-carb diet prevents heart disease.
I agree that a calorie is a calorie, but I find it easier to reduce calories if I cut the carbs - but not too much
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