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The phrase "a subtle negative effect" is correct and usable in written English.
It can be used when discussing the impact of something that is not immediately obvious but still has a detrimental influence.
Example: "The new policy may have a subtle negative effect on employee morale over time."
Alternatives: "a slight adverse impact" or "a minor detrimental effect".
Exact(2)
But over time this has had a subtle, negative effect.
The main effect size of income is −0.01 (p < 0.1), which reveals that income has a subtle negative effect on females' remarriage.
Similar(58)
Many studies -- though not all -- have concluded that low levels can have subtle negative effects as well if certain fish are a major part of the diet.
Despite this, subtle negative effects on primary production were detected using a modelling approach, being the impact lower on phytoplankton communities dominated by diatoms.
Some researchers now wonder whether Zetia may have subtle, negative effects that counteract its LDL-lowering ability.
Our findings suggest that the amphibian pheromonal system is one of the systems subject to subtle negative effects of environmental chemicals.
The conclusions of Boersma and Lanting were: "These data give evidence that prenatal exposure to PCBs do have subtle negative effects on neurological and cognitive development of the child up to school-age.
Moving to a larger class had a negative effect.
A cliff edge could have a sharp, negative effect.
THE EFFECT ON HIS FAMILY It had a very negative effect on my family.
This has a broadly negative effect on our health.
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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