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Subjects compared were those presenting acutely and excluded those with underlying immunosuppression or severe underlying disease (see Methods for criteria to assign disease categories).
CMP-regulated proteins were clustered (see Materials and Methods for criteria) into gene ontology (GO) groups (Table 6) and KEGG (Kyoto Encyclopedia of Genes and Genomes) signaling pathways (Table 7) using parametric gene set enrichment analysis (WebGestalt).
To detect differences in the proportion of nicotinic receptor-expressing cells in layer VI, we compared the number of cells expressing α4YFP to neuronal nuclei labeled by DAPI (shown in green, see Methods for criteria to determine neurons labeled by DAPI and Figure S1 for staining with DAPI and NeuroTrace).
First, the DLRP-rev1 gene list was used to extract all the L/R pairs significantly correlated in normal controlateral or in PTC samples Subsequently, a paired t-test was used to identify significantly regulated Ligands and Receptors in PTCs, relative to their normal counterparts (see Materials and Methods for criteria of selection).
See materials and methods for criteria.
However, 16 of the viridans group strains (4%) had alleles that were considered to be foreign (see Methods for criteria used to assign alleles as foreign).
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Our results are based upon 431 species for which useful models could be fitted (from a total of 496 species whose European breeding distributions have been mapped [6]; see Supplementary Material (Table S1) for a list of the 431 species included in the synthesis, and Materials and Methods for the criteria for selection of these species).
See online Supplementary Methods for exclusion criteria.
Please see Supplemental Methods for assessment criteria.
catarrhalis genomes (Table 1 and Additional file 1: Figure S1.; see methods for classification criteria).
* See methods for the criteria used to define of each pattern.
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