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For STRUCTURE, we explored a range of clusters (from K = 1 to K = 10).
DNA strands can produce a range of clusters, but this violet species emerges over alternate clusters by using relatively low Ag+/DNA concentrations, low ionic strength buffers, and high O2 concentrations.
We have investigated a range of clusters from 2 to 12 in number and evaluated the quality of the clustering results using a Computational Negative Control (CNC) approach [ 57, 58].
Given a range of clusters, clvalid computes the connectivity (Handl et al., 2005), Dunn Dunnn, 1974) and Silhouette (Rousseeuw, 1987) indexes for various clustering algorithms (hierarchical, k-means, SOM and other) and suggests the optimal algorithm and clusters for the dataset.
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The heterogeneity analysis of a range of cluster solutions again points to a solution with nine clusters.
Detailed APT studies showed Cr shells around oxide particles of all sizes in the Fe Cr Ti Y2O3 alloy, that a range of cluster compositions are present and that the particle chemistry varies with cluster size.
On the one hand, hierarchical clustering algorithms have the advantage of being independent of initial parameters (the number of clusters and their initial centers), and these algorithms allow the analyst to investigate a range of clustering solutions produced through iterative optimal cluster joining or splitting.
Actin ultrastructural analysis in dorsal root ganglion neurons grown on laminin-coated substrata patterned with aggrecan cluster arrays revealed filopodial and lamellapodial edge contact avoidance of individual clusters, while growth cone lamellapodia and central domains were able to span multiple clusters over a range of cluster densities.
Numerous theoretical studies of (ZnO) n clusters have explored optimized geometries for a range of cluster sizes, and a prevalent theoretical observation shows that a fullerene-like structures are more stable in the case for smaller-sized clusters, while a wurtzite-like structure shows increased stability for larger clusters [9].
It is worth noting here that a range of other approaches have been used, especially in drug discovery, such as self-organising/Kohonen maps (SOM), generative topographic maps (GTM) and a range of clustering approaches, and these have recently been reviewed [20].
Several standard clustering methods were evaluated using a range of cluster numbers from 25 to 500 including the expression values calculated from all MG1655 specific probe sets.
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