In a second step, we asked if, besides the already incorporated (conservative) constraints, the network topology also fulfils the constraints related to the less conservative interpretation of the basal expression phenotype, as e.g. observed in the mutant strain with a yegE-knockout (Fig. 1 a, see " Methods" for a description of model constraints).
Nikitidis et al. incorporated discriminant constraints to build the supervised NMF learning method [23, 24].
To guarantee model consistency across the genotype space, we explicitly incorporated biochemical constraints that underly observed phenotypic trade-offs.
To obtain a stable inversion solution, we used the data covariance matrix from the observation and modeling errors, incorporated smoothing constraints and determined their optimal values by using the Akaike Bayesian Information Criterion ABICC).
Additionally, it is unclear whether teachers incorporated developmental constraints, or other lesser-known non-adaptive factors (see Gould 2002), into their teaching in all the biology classes or if it was only found in the evolution course.
We incorporated such constraints into our PBTK model and revised our calculation of Kp for naphthalene.
The design also incorporated practical constraints, inexpensive materials, easy visibility in the lecture hall, and a restricted time allotment of 10 min to collect and analyze the experimental data with the students.
A binary variable y j is associated with each reaction with '1' indicating the presence/activation of the reaction and '0' its absence/deactivation. Cellular objectives are incorporated as constraints, for example, the objective in Eq. (2) is to produce at least ν max biomass biomass.
We also incorporated simple constraints to ensure that the viability weight was nonnegative, the viability weight at any gestation was lower than the low optimal weight at that gestation, the slope B1 was negative, and the slope B2 was positive; 95% confidence intervals based on the asymptotic distribution were estimated around these birth weights.
To ensure that this does not result in model configurations that produce unrealistic values for total lung resistance, we incorporated a constraint function into the optimization algorithm that limits the increase in the total lung inflow resistance to ten times its basic (healthy) value, as expected in patients with COPD [22].
