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Objects representing individual organisms were defined, each with a unique genotype composed of gene objects.
Proteins between different organisms were defined as orthologs when (i) they displayed a minimal percentage sequence identity of 35%; (ii) they are each other's reciprocal best BLAST hit; and, (iii) the sequence identity was measured over at least 80% of the smallest protein.
ESBL organisms were defined as E. 3coli and K. pneumoniae resistant to a third-generation cephalosporin.
One-third (31%) of organisms were defined as clinically important pathogens, while two-thirds (69%) were contaminants.
Multiresistant Gram-negative organisms were defined according to the guidelines of KRINKO (German commission for hospital hygiene and infection protection) for MRGN [ 21].
Organisms were defined as multidrug-resistant if they exhibited resistance to at least three of the major antibiotic classes (aminoglycosides, β-lactams, carbapenems, and fluoroquinolones) or produced either extended spectrum β-lactamases or K. pneumoniae carbapenemases [ 33].
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As the distance measurement of two gene networks from organisms was defined, a distance matrix can be obtained by comparing each species against all the others.
Cellular identities in multicellular organisms are defined by their individual gene expression programs.
Emergence of MDR organisms was defined as newly isolated MDR organisms during therapy, after excluding patients with MDR organisms isolated from initial cultures.
However, LGT enables a different view of communities, where interactions between organisms are defined strictly on the basis of gene exchange (Jain et al., 2003; Skippington & Ragan, 2011).
Multi-drug resistant organisms are defined as resistant to three or more antimicrobial classes normally used for the treatment of infections [ 8].
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