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Consistently, the resulting recombinant genome was found in the same host species than at least one of its parental in 21/22 cases, representing strain AJ810418 a particular case, since its region 2862 3491 came from viruses isolated from wheat and oat.
A KP-M1 (serotype K1) strain was isolated from an enrolled patient with invasive syndrome presenting as liver abscess and endophthalmitis and was used as the representing strain in the following experiments.
We used the limma package in R to model the expression of each gene with coefficients representing strain replicates and susceptibility status [ 53, 54] and the false discovery rate (FDR) was estimated using q-value [ 55].
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Representing strains coordinates along these components showed that there was no obvious subgroup of strains with specific phenotypic noise values.
The multiple-biomarker tensor is constructed this way, with one of the modes representing strains and other modes representing biomarkers.
To date, four major genotypes of DENV-4 have been described [ 17]: genotype I, representing strains from Thailand, the Philippines, Sri Lanka and Japan; genotype II, representing strains from Indonesia, Malaysia, Tahiti, the Caribbean and the Americas; genotype III, representing Thai strains that are distinct from other Thai isolates; and genotype IV, representing sylvatic strains from Malaysia.
In our experiments, we use this multidimensional array or tensor with three modes representing strains, spoligotype deletions, and MIRU patterns.
In our case, three of the strains, namely, SP73, SP75, and SP93 have been clustered together with known Geobacillus kaustophilus strains most probably representing strains of this species.
When representing strains from classes I, II and III on the tree of genetic distances, we observed that class I strains were genetically close.
The Y-axis represents strain.
Black lines represent strain time-series after tidal components are removed, with gray lines representing the original time series.
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