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After parameter fitting (standard or iterative approach), the areas under the time-activity curves were determined and subsequently, the time-integrated activity coefficients were calculated.
Blank absorbance was subtracted and a 4-parameter logistic fitting standard curve was plotted.
Photosynthetic parameters (Fv/Fm and σPSII) were estimated by fitting standard models to data to determine values of Fo (initial fluorescence), Fm (maximal fluorescence), Fv (Fm-Fo), σPSII (functional cross-sectional area of PSII) and p (PSII connectivity parameter) [107].
These associations have been reported on the basis of fitting standard regression models to large data sets.
Note that proper inference and testing after model selection is an incredibly challenging problem, and fitting standard models to yield measures of significance post-model selection obviously leads to inflated Type 1 error rates and overly optimistic results.
This analysis can be performed using output from fitting standard weighted linear regression models, whilst ensuring that the reported standard errors are adjusted, as explained by Sharp and Thompson [ 2].
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For determining the most adequate model, we first selected the best-fitting standard DNA model for the unpaired loop partition, which we subsequently kept fixed in likelihood estimations, varying only the model for the stem partition [see Additional file 1].
This is perhaps unsurprising as our data departed in several ways from the ideal conditions for the fitting of standard factor models with maximum likelihood.
The three model specifications were tested for over-fitting using standard goodness-of-fit criteria such as the deviance and the AIC (Akaike information criteria).
These weighted exposure metrics were evaluated via fittings of standard log-linear models as well as via fittings of linear relative rate models [the latter being the model form implied by the work of Whittemore (1977), whereas the former approach was consistent with the model form used in the exposure time window analyses].
Curve fitting of standards and calculation of sample concentrations was done with SoftMax Pro software (Molecular Devices).
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