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For the relative gene expression in rice and nematode samples, data were analyzed using the MxPro software package to obtain the relative expression levels of rice genes.
Mineralogical analysis of the coal samples were performed by means of X-ray diffraction (XRD) with Ni-filtered CuKα radiation at (10° 70°)/(2θ) at a scan rate of 2°/min (Discoverver Bruker) using High Score Plus software package to obtain quantitative mineral proportion.
Coding sequences were aligned using ClustalW under the Mega3 package to obtain inframe alignment of codons.
Noncompartmental analysis was performed using the PK package to obtain AUC0 ∞ (midazolam) or AUC0 6 (nifedipine).
The 94 network features were combined into SVM using the liblinear package to obtain a ranking model.
The Progenesis analysis results were further processed using the SafeQuant R package to obtain protein relative abundances.
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LINGO, CPLEX and GAMS are the most commonly used software packages to obtain optimal solutions for mathematical programming models (Agrawal et al. 2015; Esmailnezhad et al. 2015; Anbumalar and Raja Chandra Sekar 2015; Pinheiro et al. 2016; Azadeh et al. 2015; Kasimbeyli et al. 2010).
The raw data was then computationally reconstructed using Wiener filter settings 0.002 and channel-specifically measured optical transfer functions (OTFs) using the softWoRx 6.0 software package (Applied Precision) to obtain a super-resolution 3D image stack with a lateral (x-y) resolution of approximately 120 nm and an axial (z) resolution of approximately 300 nm [ 31, 43].
Prior to recruitment of patients, providers in the intervention arm received training on the recognition of depression, the delivery of the manualized intervention package, how to obtain and document support and supervision received from the GP using mobile phones.
We used TreeStat 1.6.1 [ 48] to recover these node ages from the sample of the MCMC search in BEAST and used the "fitdistr" option of the R package MASS to obtain a gamma function adjusting the distribution of sampled ages, thus including uncertainty associated to the age estimations (Table 3).
The choice of the PAML package is to obtain high accuracy of ML branch length and topology estimates, which ensures the effects we study are the product of ML inference and not a quirk of a heuristic and fast tree-search program.
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