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Therefore, hydrogen-consuming pathways were likely to occur either through homoacetogenesis (low butyric/acetic acid ratio, equation 4) or the propionic acid-producing pathway (equation 5) [ 17].
As illustrated with a simple linear metabolic pathway (equation 3), different temperature dependencies of enzyme reactions inevitably result in (large) changes in concentrations of pathway metabolites.
The recall rate is defined as the fraction of PPIs/proteins in the reference pathway that are inferred (Equation 2) and the precision rate is defined as the fraction of inferred PPIs/proteins that are contained in the reference pathway (Equation 3).
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In Additional File 1 we further show that noise terms are indeed sufficiently small that linearisation of the pathway equations is justified.
After fitting Equations 1 and 2 to the data, we found substantial statistical evidence (AIC difference = 5.473) favoring the model with two metabolic pathways (Equation 2).
Because the thermodynamics is independent of the reaction pathway, the equation β2 = KI × KII,I = KII × KI,II is upheld where KI,II is intrinsic Ca2+ binding constant for EF1 in the presence of Ca2+-bound EF2.
It was interesting to note that the sensitivity as Hills coefficient was same as obtained with respect to adenylate cyclase of cAMP-PKA pathway (see Equation 3).
Edges were created using the Jaccard similarity coefficient to measure proportional overlap between pairs of pathway annotations (Equation 1).
Because the AIC values were –313.755 for the one-pathway model (Equation 1) and −319.320 for the two-pathway model (Equation 2), resulting in a difference of −313.755 − (−319.320) = 5.473, we conclude that the two-pathway model provides a much better fit to the data.
This second regime is determined by the existence of a limited cytoplasmic solvent capacity for allocating the components of the ATP generating pathways (see equation (6)).
Under the one-pathway model (Equation 1), this exposure-specific metabolite level would be Ymax/ X50 = 68.6 μM/ppm, whereas under the two-pathway model (Equation 2) it would be the sum Ymax,1/ X50,1 = 48.7 μM/ppm plus Ymax,2/ X50,2 = 135 μM/ppm, or 184 μM/ppm (Table 2).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com