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Using Clumpp, collated results were used to generate a mean and close match of permuted matrices across all replicates under the same cluster (Jakobsson and Rosenberg [2007]) and these results were visualized in distruct (Rosenberg [2004]).
Although the recovery of NIBSC IL-6 was lower in PBS and saline as compared to serum and the defined vaginal simulant, assay calibrators were equally recoverable from all matrices across all assays.
These masks were then used to threshold individual connectivity matrices across all groups, consistent with thresholding strategies in the seminal rich club paper (van den Heuvel and Sporns, 2011).
We used Mantel tests of matrix correspondence following the methods of Smouse et al. [ 16] to test for isolation by distance by comparing the pairwise geographic and total genetic distance matrices across all samples, and within clades, with tests of significance by 9,999 permutations.
Given the similarity of correlation matrices across all three conditions, this widespread eccentricity-based correlation pattern appears to reflect an eccentricity bias that is inherent to the organization of the visual system (i.e., stable during rest) and may support processing during active perception of the visual environment (e.g., during movie viewing).
Next, a group-averaged FC matrix was created by averaging the individual FC matrices across all individuals, and the formation of functional communities -also referred to as resting-state networks- was examined by means of modular decomposition of this group-averaged FC matrix (Rubinov and Sporns 2010, 2011).
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Our solution to preserve stability of the LPC synthesis filters is to put all five generated codewords into a matrix and then sort each column of not yet ascended order columns of the reproduced spectral parameters matrix across all 5 codewords in ascending order.
We then used each method to search the entire set of probes for TFBSs corresponding to each matrix, across all positions in the probe.
Our cubic B-spline methods used to model the cell cycle time courses, together with PCA and SVD analyses of the mRNA data matrix across all genes and time points, provided objective criteria for identifying cyclic mRNA patterns and the natural grouping of genes into two predominant subtranscriptomes.
To measure this coherence, we computed a correlation matrix across all channels of the spectrogram.
A is a numerator relationship matrix across all animals inferred from the pedigree (n = 3 360), and I is an identity matrix with an order equal to the number of observations in y.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com