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The run time of the phrap step is strongly influenced by the amount and pattern of redundancy within the dataset.
The same pattern of redundancy variation was found in both Copia and Gypsy superfamilies, that is, wild accessions generally showed lower levels of LTR-RT redundancy compared with cultivars.
Whereas a linear but only slightly increasing relationship between SR and FD shows a continuous pattern of redundancy, the curvilinear shape observed for tadpole communities shows that functional redundancy depends on the level of SR, with the highest functional redundancy assigned to species-rich communities in large streams.
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Patterns of redundancy have been reported when using functional groups e.g. for bat [ 48], plant [ 49- 51], bacterial soil communities [ 52], and coastal marine assemblages [ 53].
Facing adult frog plus tadpole traits and using about twice the number of species as in the present study (up to 39 per site and 55 in total) showed quite clear patterns of redundancy in West Africa [ 15].
These two genes are also required for zonula adherens (ZA) assembly but display an unusual pattern of cellular redundancy for this function, as each gene is required in only one of two adjoining cells.
Interestingly, not only are group members co-expressed, in many cases they show a pattern of phenotypic redundancy where severe developmental defects are only observed when multiple members of the same group are removed [ 27, 37- 43].
A pattern of functional redundancy and specificity among Ssa proteins has previously been observed for both yeast prion propagation and protein folding activities (Sharma et al., 2009; Sharma and Masison, 2011).
Patterns of functional redundancy were identified using FD in mammal, bird [ 14], and amphibian communities [ 15, 16].
We applied polynomial regression of observed FD values as response and SR as independent variable to test for coherency and patterns of species redundancy (non linearity).
As focusing on few traits likely leads to findings of patterns of functional redundancy [ 9, 49], we used a continuous measure using 18 morphological traits relating differently to habitat use and feeding ecology (Table 1) to include a wide range of species functions that can influence stream ecosystem structure and function.
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