The empirical covariance estimates were regularized via the "shrunk" method, as recommended by Engemann and Gramfort65.
In [17], the calibration results for large-scale parameter statistics are based on the angular parameters, which are generated in Step 4. In this contribution, we provide the calibration results for large scale parameter statistics, using the circular angle spread method, as recommended in [25].
CRP was assayed in serum by using a specific ELISA method, as recommended by the provider (ALPCO).
MICs of thymol for S. aureus were evaluated in triplicate by a broth microdilution method as recommended by the Clinical and Laboratory Standards Institute [35].
The relative amount of mRNA was calculated using the comparative threshold cycle (ΔΔCT) method as recommended by the manufacturer in the Applied Biosystems protocols.
Individual MICs and MFCs were determined following the broth microdilution method as recommended by the NCCLS, following the approved standard M38-A (NCCLS, 2002) as modified [27] [29].
Minimal inhibitory concentrations (MICs) of fosfomycin, tobramycin and imipenem were determined for the PA14 strain and its derivative mutants mutS::MAR2xT7 and glpT::MAR2xT7 by the broth microdilution method, as recommended by the CLSI [39].
Furthermore, because of the highly congruent branch pattern from these two runs, the bootstrap analysis was done with the most efficient PROTCAT method (as recommended recently [36]) and rtREV+F on 100 pseudoreplicates and one random starting tree for each replicate.
Total RNA was extracted from cells using the Trizol method as recommended by the manufacturer (Invitrogen).
Sensitivity testing for non enterobacteriaceae was done using agar dilution method as recommended by CLSI [ 13].
Attributes were selected using a rigorous qualitative method as recommended in good practice guidelines [ 1, 13].
