The spectra obtained were analyzed in terms of convoluted Lorentzian functions by using a best-fitting routine of GRAMS/AI (2001, Thermo Electron) program, which is based on the Levenberg-Marquardt nonlinear least-square methods.
Positive end-expiratory pressure (PEEP) was determined by using a 'Best-PEEP-Trial' in 50%, empirical means in 46%, or the ARDS-Network table in 36%.
The dataset was constructed by using a best-of-six structural aligner using SSAP (Taylor and Orengo, 1989), STRUCTAL, DALI (Holm and Sander, 1996), LSQMAN (Kleywegt, 1996), CE (Shindyalov and Bourne, 1998) and SSM (Kolodny et al., 2005; Budowski-Tal et al., 2010).
For species where a loss was inferred we manually checked the absence of the particular gene product by using a reciprocal best hit approach against the NCBI non redundant database (nrdb).
Therefore, we examined the consistency of the gene model sequences derived from all three studies by similarity searches, using a best reciprocal hit strategy with a minimum sequence identity of 95%.
Record linkage was carried out by the NSW Centre for Health Record Linkage (CHeReL) [ 30] using a best practice approach in preserving privacy [ 31] and the open source probabilistic record linkage software ChoiceMaker [ 32].
The PCR primer efficiency curve was fit to cycle threshold (Ct) versus log [genomic DNA concentration] by using an r best fit.
We defined the amplitude and phases of SPW1 and SPW2 by using a least squares best fit approach applied in a 3-day window that moved through the time series with steps of 1 day.
For example, a wrapper function is provided to interface between the ITEP database and OrthoMCL, a program that applies a percent identity cutoff between pairs of homologous proteins, identifies likely orthologs by using a modified bidirectional-best-hits approach, and then runs MCL to cluster the smaller subset of nodes and edges into protein families [ 32].
