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We performed a genetic study to test the prior hypothesis that host factors influence specifically the risk of developing CM syndrome in the context of severe malaria.
In agreement with the prior hypothesis, the treatment effect was greatest in those with the highest baseline level of tHcy, with a reduction in atrophy rate of 53% in those in the top quartile of tHcy (>13.0 µmol/L).
To avoid multiple testing issues we analysed the data under a dominant model with the prior hypothesis that carriers of rs765250 [A] (A/A+A/G verses G/G) would have higher BP levels and be at increased risk for EH compared to G/G homozygotes, as determined from our primary analysis in the BRIGHT study case-control resource.
We tested for association with BP as a continuous trait and hypertension in all cohorts under a dominant model, with the prior hypothesis that carriers of rs765250 allele A (A/A+A/G verses G/G) would have higher BP levels and be at increased risk for EH compared to G/G homozygotes – as determined from our primary analysis in the BRIGHT study.
This approach is based on the prior hypothesis that such loss-of-function mutations are more likely to cause severe phenotypic effects commonly seen in rare diseases.
As the above enrichment analysis was biased for MAP kinase pathway due to the prior hypothesis regarding its possible involvement, I next examined if evidence for this pathway is further supported in an unbiased analysis.
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Values in bold indicate the relationships mentioned in the prior hypotheses.
We show below how to introduce these prior hypotheses into the linear classification algorithm.
Limitations of the study are the lack of a flavone-specific prior hypothesis, the emergence of findings after undertaking multiple analyses and questions concerning the applicability of US-based flavonoid food composition tables to Greek foods.
The ability to detect such divergence points without the need to specify a prior hypothesis about the location or timing of the divergence point should help scientists identify historically important selection events and decipher mechanisms of evolution.
This is an appropriate test for positive selection when the investigator has a prior hypothesis about the potential influence of natural selection and when there are a small number of candidate loci.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com