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The internal/external stimuli that activate Muse cells (prolonged treatment with proteolytic enzymes, lack of nutrients, low temperatures, hypoxia) are entirely different than those that activate cancer stem cells (ionizing radiation, ultraviolet radiation, chemical compounds, reactive oxygen species, error prone DNA repair, among others).
We note that because the test we developed is exact, meaning by that we know the probability of the first species error and the potency of the test, the number of false positives does not increase with the continued use of the test.
***p<0.001; **p<0.01 (Mann Whitney non-parametric t test), compared to no obstacle scenario for the same parameter and same RNA species; error bars represent SEM.
In general, the assay is more accurate for rare and intermediate species (error in α within 3% over the entire range of kf-bound tested) as compared to abundant species and for lower differential expression ratios compared to higher ratios.
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On simulated Sanger sequencing reads, MetaGene and MetaGeneAnnotator show the highest gene prediction sensitivities (~94% over all species on error free reads and ~80% on reads with the highest error rate) while Orphelia has the best specificity values with ~96% on error free reads and ~92% on reads with the highest error rate (compare Table 2).
Some observed trends were expected: all summary methods gave improved accuracy as the sequence length in each gene increased from 500 to 1000 bp; using true gene trees gave the best results (Fig. 2a); species tree error rates generally reduced as the number of genes increased (Fig. 2b); and species tree error rates increased as ILS levels increased (Fig. 2c).
With even sampling, using five reference sequences for each species, cumulative error is minimized at 31% at DK2P = 0.065.
Considering a total of 260 identified Australian species, the error rate through due to species para- or polyphyly was 6.9%, even after morphological re-evaluation of non-monophyletic taxa (i.e., after the improvement of a previously imperfect taxonomy, or reciprocal illumination [51], [54]).
It has already been demonstrated that increased within-species sampling reduces species determination error [ 60].
As in the previous model for all six tree species, an error autoregressive correlation structure of order one provided the most-parsimonious fit.
Under an assumption of independence of model errors across species, the model error variance for a group or all species combined are computed as the sum of the variances of individual species.
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