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Matlab v r2017b

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MATLAB is a high-performance language for technical computing. It integrates computation, visualization, and programming in an easy-to-use environment where problems and solutions are expressed in familiar mathematical notation. MATLAB version R2017b includes enhancements and bug fixes from the previous release.

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Lab products found in correlation

5 protocols using matlab v r2017b

1

Physicochemical Characterization of Incinerated Thermoplastics

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All incinerated virgin and NECs used in this study were provided by Dr. P. Demokritou’s lab at Harvard University following extraction from in-line filters. Generation of incinerated thermoplastic samples using the Harvard INEX system and particle extraction are described elsewhere [94 (link)–96 (link)]. Previous work using these materials fully characterized their physicochemical properties, including CNT loading and signature impurities [29 (link), 42 (link)].
Particle deposition for thermoplastics was modeled using the Harvard Distorted Grid (DG) model as described in GM DeLoid, JM Cohen, G Pyrgiotakis and P Demokritou [97 (link)] to estimate average deposited dose up to 72 h post-treatment. Deposited modeling was conducted using MatLab v. R2017b (MathWorks, Inc., Natick, MA). Except for data derived from dynamic light scattering and deposited modeling, methodological approaches for ascertaining medium density, viscosity, and refractive index may be found within Table S1 and Supplemental Methods.
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2

In silico Prediction of Xylose and Glucose Consumption

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The Yeast v7.6 consensus metabolic model (Aung, Henry and Walker 2013 ) was used for in silico prediction of relative xylose and glucose consumption rates in aerobic bioreactor batch cultures of strain IMS0629. The COBRA v2 toolbox (Becker et al.2007 (link)) was used to read the model in MATLAB vR2017b (Mathworks, Natick, MA), supported by the SBML Toolbox v4.1 and the libSBML v5.12 (Hucka et al.2003 (link)). The Gurobi v6.5 linear programming solver (Gurobi Optimization Inc, Houston, TX) was installed and used according to the manual provided. The MATLAB script is provided in Additional File 4.
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3

NMR Data Processing and Analysis Protocol

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NMR spectra were imported into MatLab v.R2017b (Mathworks, Natick, WA, USA) using the ProMetab v.1.1 script [53 (link)]. Each raw spectrum consisted of 31,313 data points between −0.60 and 10.00 ppm.
Statistical analyses were performed in MatLab utilizing the PLS Toolbox v. 8.5.2 (Eigenvector Research Inc., Manson, WA, USA). The spectral region containing the residual water peak (δ 4.68–5.00) was removed. Spectra were aligned using the correlation optimized warping algorithm [54 (link)] to account for chemical shift drift, then normalized to total signal area to account for inherent concentration differences between samples. After normalization, spectral regions containing methanol (δ 3.32–3.36) and DSS-d6 (δ 0.4–−0.60) peaks, and the non-informative region beyond 9.00 ppm were removed. Finally, spectra were baseline corrected using automatic weighted least squares, and scaled by mean centering. After editing, a total of 24,349 chemical shift datapoints were included in subsequent statistical analyses.
For multivariate analyses, unsupervised principal component analysis (PCA) was used. Peaks of interest were identified using the Chenomx NMR suite software v.8.4 (Chenomx Inc., Edmonton, AB, Canada), comparison to the literature, and 2D NMR analysis.
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4

Metanephros Branching Analysis

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The longitudinal metanephros length (mm) and the volumes of the UCS and the whole metanephros (mm3) were calculated with Amira v. 5.5.0 (Visage Imaging GmbH, Berlin, Germany). The UCS volume was that of the segment between the zeroth- and fifth metanephros branching generations. The 3-D coordinates of all branching points were acquired using Amira 5.5.0 (Visage Imaging GmbH, Berlin, Germany). The coordinates were analyzed with Matlab v. R2017b (MathWorks, Inc., Natick, MA, USA) to calculate the generation of all branches. The following parameters were calculated according to each CS: (a) average UCS end-branching generation; (b) total amount of UCS end-branching; and (c) maximum UCS end-branching generation. The four lobes were defined as upper-polar, upper-interpolar, lower-interpolar, and lower-interpolar according to the second UCS branching generation. The polar lobe (PL) group included the upper- and lower-polar lobes whereas the interpolar lobe (IL) group included the upper- and lower-interpolar lobes. Deviations of the end-branching between the PL- and IL groups were statistically analyzed.
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5

Manual Delineation of Tree Crowns

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The manual delineation dataset was obtained by manually drawing outlines of the 12 crowns from the RGB orthomosaic of September 2016 in Adobe Photoshop software (Adobe Systems Incorporated, USA) and then calculating the two orthogonal crown widths and the CPA based on the drawn crowns and ground resolution in Matlab v. R2017b software (MathWorks Inc., USA).
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