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For three decades mammalian mtDNA has generally been considered to replicate via a characteristic DNA replication mechanism, a strand-displacement model which entails continuous synthesis of both strands of DNA, without the synthesis of short lagging strand fragments, known as Okazaki fragments [1,2].
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It is not obvious what kind of advantage may obtain the mobile elements involved, and therefore those non-autonomous sequences are considered to replicate parasitically.
In GWA studies, a finding is considered to be "replicated" if and only if there is an initial finding which did appropriately control for multiple testing with strong control of the family-wise type I error rate (FWER) and in a second independent sample this finding is re-detected in a confirmatory hypothesis testing setting [2].
Only mutations in the longest isoform were considered to avoid replicating individual mutations in the DNA across multiple proteins.
Each run of the experiment produced a single value and was considered to be a replicate, giving n = 4 for each test.
Equilibrium was considered to be attained when replicate scans separated by 6 h were indistinguishable.
Samples with identical treatments were considered to be biological replicates.
In the field a common practice is that a significant GWA finding is considered to be "true" if replicated by several subsequent studies (not necessarily all).
Qualitative analyses of gene expression were conducted for both B. napus 1 and B. napus 2. Unigenes were called as expressed if they had one or more reads aligning in all four replicates and were called as non-expressed if they had zero counts in all four replicates (the remaining unigenes were considered to be inconsistent between replicates).
Each plate was considered to be a biological replicate.
Due to possible within pot effects, such as competition for resources, each pot was considered to be a single replicate with the four seedlings' measurements being combined for determining the growth and water use.
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